From noreply at release.debian.org Sun May 1 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sun, 01 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] staden is marked for autoremoval from testing Message-ID: staden 2.0.0+b10-4 is marked for autoremoval from testing on 2016-06-06 It (build-)depends on packages with these RC bugs: 822293: tcllib: uuid broken in tcllib when /sbin not in PATH From noreply at release.debian.org Sun May 1 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sun, 01 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] biomaj-watcher is marked for autoremoval from testing Message-ID: biomaj-watcher 1.2.2-2 is marked for autoremoval from testing on 2016-05-31 It (build-)depends on packages with these RC bugs: 800767: biomaj: depends on obsolete libcommons-net2-java library From noreply at release.debian.org Sun May 1 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sun, 01 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] biomaj is marked for autoremoval from testing Message-ID: biomaj 1.2.3-6 is marked for autoremoval from testing on 2016-05-31 It is affected by these RC bugs: 800767: biomaj: depends on obsolete libcommons-net2-java library From adconrad at debian.org Sun May 1 04:26:43 2016 From: adconrad at debian.org (Adam Conrad) Date: Sat, 30 Apr 2016 22:26:43 -0600 Subject: [Debian-med-packaging] Bug#813065: mgltools-gle: FTBFS in sid: Error: Unknown SWIG preprocessor directive: typemaps Message-ID: <146207680372.11722.13006598974577500693.reportbug@nosferatu> Package: mgltools-gle Version: 1.5.7~rc1+cvs.20140424-1 Followup-For: Bug #813065 User: ubuntu-devel at lists.ubuntu.com Usertags: origin-ubuntu yakkety ubuntu-patch In Ubuntu, the attached patch was applied to achieve the following: * typemap-comments.patch: Fix FTBFS with stricter new swig (LP: #1562470) Turns out the FTBFS was just a result of using an incorrect comment style in the code which the newer swig is stricter about. This patch fixes that. ... Adam -- System Information: Debian Release: stretch/sid APT prefers yakkety APT policy: (500, 'yakkety') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.4.0-21-lowlatency (SMP w/4 CPU cores; PREEMPT) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) -------------- next part -------------- A non-text attachment was scrubbed... Name: mgltools-gle_1.5.7~rc1+cvs.20140424-1ubuntu1.debdiff Type: text/x-diff Size: 2655 bytes Desc: not available URL: From ftpmaster at ftp-master.debian.org Sun May 1 05:28:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 01 May 2016 05:28:01 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-genomeinfodb_1.6.3-1_source.changes Message-ID: r-bioc-genomeinfodb_1.6.3-1_source.changes uploaded successfully to localhost along with the files: r-bioc-genomeinfodb_1.6.3-1.dsc r-bioc-genomeinfodb_1.6.3.orig.tar.gz r-bioc-genomeinfodb_1.6.3-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 1 05:34:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 01 May 2016 05:34:11 +0000 Subject: [Debian-med-packaging] r-bioc-genomeinfodb_1.6.3-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 01 May 2016 07:14:36 +0200 Source: r-bioc-genomeinfodb Binary: r-bioc-genomeinfodb Architecture: source Version: 1.6.3-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-genomeinfodb - BioConductor utilities for manipulating chromosome identifiers Changes: r-bioc-genomeinfodb (1.6.3-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: de6c2a187404c84a75a65ad2b2f2f649ea96fe3d 2195 r-bioc-genomeinfodb_1.6.3-1.dsc 29bd641c2c322950d3c8d8ab70384a102c5f81a8 19364480 r-bioc-genomeinfodb_1.6.3.orig.tar.gz 23a429fe4418b285308ae3aa954592a492d58815 3740 r-bioc-genomeinfodb_1.6.3-1.debian.tar.xz Checksums-Sha256: 0f008c5e6027e2d8d8f5aa3e2a918d82d70b95ea42cbf3f2349ceaa3f3ef3cc2 2195 r-bioc-genomeinfodb_1.6.3-1.dsc c33492e2ca853cee4cb3b04116b22788b44c7c49f6d30840539366610b00f7bd 19364480 r-bioc-genomeinfodb_1.6.3.orig.tar.gz fb6ff9170bcd8d511f220699ef2eed5be5cc982e411b5d9c7d6fccebfcc12d4f 3740 r-bioc-genomeinfodb_1.6.3-1.debian.tar.xz Files: aed35cf70150ba8414a60b419f6dc5c8 2195 gnu-r optional r-bioc-genomeinfodb_1.6.3-1.dsc aaec18652bbbe80c76bb0c2cde51eff6 19364480 gnu-r optional r-bioc-genomeinfodb_1.6.3.orig.tar.gz ce25c30a1a91217bcf4a9b02ff0077bf 3740 gnu-r optional r-bioc-genomeinfodb_1.6.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXJZILAAoJEFeKBJTRxkbRNTUP/jl/B0z8qGnt55FCLeCFgxvD kbM+o3eFKv4JvFdVWwXTFlVcWNEnrAI4zpZ3YBz98GD2Is9ZlznwFTzEvBD3FtdG Yltzlrfth6ZWSj59/UzJyf8cucjZXVOohRZTnZVCM97RJ51cD6RjrmD7KmB7c7dF ntvzbTH0w3OvhkS91DsWUUBM8M1/RQvHsSn5IUcKy5/GH4c9DjfKXExnnYc/IUzs 555ofJ57C6YVw58GGRfnMnlSjoyTNUF2L3JKQUzVEyPFJ3+Wy6OmifvQoIPIkIlS IZjhfkUeKGe4VcIgS6e4H7kG43j9nQAU8GLLueEUAEbfnkn+YfkGLQ9RqpR2ghRj AJinwIV8kBSYK6CNj3vRkhNC/e463CCieM44lM2TS+ulb9hWKyc/2JXMTmKZDTNK ruCc/BE4P2/iAgSN24079oOCQuzTty4TJ9UgNcWrIjBZzuE33qSwI2bhD/WoR0il Wr92+7UbuzyxxiuOtVHKkT/Y8BW7bpGHgB2ua0nPk7n9K0/2NNDHsrrSpPYcJfpD NRyWV7mO7Ps6zpZr+VIMiGxyayhG0ndRdnVU1V3BKERiRrSfdU2zsJCUV3BzR3yS hPXrbEetyJtV+uVY6FPclI4Z0u1J2njXJurFMcgSyyihG5THPKHScaUG+xumfgLp GAsFgA9wmjSumcQ8bKwp =qR3G -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 1 06:58:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 01 May 2016 06:58:04 +0000 Subject: [Debian-med-packaging] Processing of mgltools-gle_1.5.7~rc1+cvs.20140424-2_source.changes Message-ID: mgltools-gle_1.5.7~rc1+cvs.20140424-2_source.changes uploaded successfully to localhost along with the files: mgltools-gle_1.5.7~rc1+cvs.20140424-2.dsc mgltools-gle_1.5.7~rc1+cvs.20140424-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 1 07:06:52 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 01 May 2016 07:06:52 +0000 Subject: [Debian-med-packaging] mgltools-gle_1.5.7~rc1+cvs.20140424-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 01 May 2016 08:50:14 +0200 Source: mgltools-gle Binary: mgltools-gle Architecture: source Version: 1.5.7~rc1+cvs.20140424-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: mgltools-gle - GLE library Python extension Closes: 813065 Changes: mgltools-gle (1.5.7~rc1+cvs.20140424-2) unstable; urgency=medium . * Fix FTBFS with stricter new swig (Thanks for the patch to Adam Conrad) Closes: #813065 (LP: #1562470) * cme fix dpkg-control * debhelper 9 * DEP5 * remove obsolete debian/pycompat Checksums-Sha1: 5a9d318b47f1a6611249cd7f77bc68a32a738810 2306 mgltools-gle_1.5.7~rc1+cvs.20140424-2.dsc 3730fbbd80259bcbd8ca8b33dce419b64eca9e48 8248 mgltools-gle_1.5.7~rc1+cvs.20140424-2.debian.tar.xz Checksums-Sha256: 6f44e411f4414ca5933fc4cc1cb7589a6a738ec2f75c02cf4c6bcf8401f8a39a 2306 mgltools-gle_1.5.7~rc1+cvs.20140424-2.dsc ebd00af705880ff5543b545f058f6a6a6d276d658e1fc37b50113802d81f848a 8248 mgltools-gle_1.5.7~rc1+cvs.20140424-2.debian.tar.xz Files: 02a88b970e0eff19bd25031287b5fd84 2306 non-free/libs optional mgltools-gle_1.5.7~rc1+cvs.20140424-2.dsc e9be036d38310463609a81334e036934 8248 non-free/libs optional mgltools-gle_1.5.7~rc1+cvs.20140424-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXJaigAAoJEFeKBJTRxkbRwi8P/2VSBiw6+91j7Mz1srrTruSa Bdb17osoWPHnSf+++Gp2wAZBgiszSXNbHbkkbp7qHckT2IeFFcQcG2reM8OkrVr6 9JC9sTVu7uP7n0YZDZ42D7fbyKapFr0hsFW7s7P1qa1oRd55jouViDVIkT03MaZz TLfgNiVfIPIXCxK4TIXNWb72X0Lj/R5Jpz6w+kXw57JZFTQMgBUaxq56QLWvnCkn prunO88CLJe6UDl2MQnDMDyx1WPEGgE0EBD+NB7scv77vxPY3KOhUqZPf+LfYqRW FgQjcc4t/LK6SNzoQGNj0twkThiZeUbScu82pwAlpt8Qrxm8m/ifub5GsZi7z0Fx knEQQD0Hp7AYFA0iQKFw9e+xnAaOe2vlnAXfdCS6r31Ow+nbhTYBdenLHJL7QNjU 1WnQFXqvcEoLMAGeA4eKaHxmczuASb69+rGncYBIoJUrQ3m60OVo3SWZR487pFIq /S0b/exhDtShYCudg2C4lt8tTRe6/vbGvAcoCY8s7pzd1ytEcObHtmkC2IXgfo+h h5cr0pIxY+c+I5Cbmby/v3K6LNSddd1FS5NXzHThEk0I8jtCek5xehoLsxv9MIvF tFheCqUc5oYWe08h/bXB69tCdwMqlbPPIQ9JXCZ1wssXHLGBeoHrGn88blr6HTnk oFoHKVPjVJ0G/MgS8lgS =PLPj -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Sun May 1 07:09:06 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sun, 01 May 2016 07:09:06 +0000 Subject: [Debian-med-packaging] Bug#813065: marked as done (mgltools-gle: FTBFS in sid: Error: Unknown SWIG preprocessor directive: typemaps) References: <20160129000807.11499.74725.reportbug@zam581.zam.kfa-juelich.de> Message-ID: Your message dated Sun, 01 May 2016 07:06:52 +0000 with message-id and subject line Bug#813065: fixed in mgltools-gle 1.5.7~rc1+cvs.20140424-2 has caused the Debian Bug report #813065, regarding mgltools-gle: FTBFS in sid: Error: Unknown SWIG preprocessor directive: typemaps to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 813065: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=813065 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Andreas Beckmann Subject: mgltools-gle: FTBFS in sid: Error: Unknown SWIG preprocessor directive: typemaps Date: Fri, 29 Jan 2016 01:08:07 +0100 Size: 3026 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#813065: fixed in mgltools-gle 1.5.7~rc1+cvs.20140424-2 Date: Sun, 01 May 2016 07:06:52 +0000 Size: 5206 URL: From erik.sjolund at gmail.com Sun May 1 08:10:42 2016 From: erik.sjolund at gmail.com (Erik =?UTF-8?Q?Sj=C3=B6lund?=) Date: Sun, 1 May 2016 10:10:42 +0200 Subject: [Debian-med-packaging] Bug#812031: prime-phylo: FTBFS with GCC 6: needed for in-class initialization In-Reply-To: <20160426131748.GH32498@an3as.eu> References: <20160119092023.16EB32819B4@dl580gen9-02.hlinux> <20160120044057.GH4951@jirafa.cyrius.com> <20160426131748.GH32498@an3as.eu> Message-ID: Hi Andreas, I did the debian packaging as part of a job project with Lars Arvestad, who is one of the main authors of prime-phylo. Since then I've switched working group so I am not so up-to-date about the status of the prime-phylo development. The best thing would be if we could involve Lars more in the loop too so I CC:ed him to this email. Lars, could you give us a brief update about the development of prime-phylo? I heard there is now also a java implementation called jprime. Lars, maybe it is a good idea to set up a Githup repo for the prime-phylo source code? I see you already have a number of repositories: https://github.com/arvestad Regarding the compile errors in this specific bug, it seems they are caused by the fact that gcc now by default compiles for a newer C++ standard. A quote from: https://gcc.gnu.org/gcc-6/changes.html "The default mode for C++ is now -std=gnu++14 instead of -std=gnu++98." I guess the easiest solution would be to use https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html#variable:CMAKE_CXX_STANDARD and add the line set(CMAKE_CXX_STANDARD 98) as in the untested attached patch. regards, Erik On Tue, Apr 26, 2016 at 3:17 PM, Andreas Tille wrote: > Hi Erik, > > there is a bug in the Debian bug tracking system for prime-phylo. Could > you please have a look? > > Thanks > > Andreas. > > On Tue, Jan 19, 2016 at 08:40:57PM -0800, Martin Michlmayr wrote: >> Package: prime-phylo >> Version: 1.0.11-2 >> Severity: important >> User: debian-gcc at lists.debian.org >> Usertags: ftbfs-gcc-6 >> >> This package fails to build with GCC 6. GCC 6 has not been released >> yet, but it's expected that GCC 6 will become the default compiler for >> stretch. >> >> Note that only the first error is reported; there might be more. You >> can find a snapshot of GCC 6 in experimental. To build with GCC 6, >> you can set CC=gcc-6 CXX=g++-6 explicitly. >> >> You may be able to find out more about this issue at >> https://gcc.gnu.org/gcc-6/changes.html >> >> > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux >> ... >> > cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /<>/src/cxx/libraries/prime/TreePerturbationEvent.cc >> > In file included from /<>/src/cxx/libraries/prime/ODESolver.cc:4:0: >> > /<>/src/cxx/libraries/prime/ODESolver.hh:359:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C2' of non-integral type [-fpermissive] >> > static const Real C2 = 1.0 / 5.0; >> > ^~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:360:41: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C3' of non-integral type [-fpermissive] >> > static const Real C3 = 3.0 / 10.0; >> > ^~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:361:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C4' of non-integral type [-fpermissive] >> > static const Real C4 = 4.0 / 5.0; >> > ^~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:362:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C5' of non-integral type [-fpermissive] >> > static const Real C5 = 8.0 / 9.0; >> > ^~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:363:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A21' of non-integral type [-fpermissive] >> > static const Real A21 = 1.0 / 5.0; >> > ^~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:364:41: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A31' of non-integral type [-fpermissive] >> > static const Real A31 = 3.0 / 40.0; >> > ^~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:365:41: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A32' of non-integral type [-fpermissive] >> > static const Real A32 = 9.0 / 40.0; >> > ^~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:366:41: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A41' of non-integral type [-fpermissive] >> > static const Real A41 = 44.0 / 45.0; >> > ^~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:367:41: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A42' of non-integral type [-fpermissive] >> > static const Real A42 = -56.0 / 15.0; >> > ^~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:368:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A43' of non-integral type [-fpermissive] >> > static const Real A43 = 32.0 / 9.0; >> > ^~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:369:39: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A51' of non-integral type [-fpermissive] >> > static const Real A51 = 19372.0 / 6561.0; >> > ^~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:370:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A52' of non-integral type [-fpermissive] >> > static const Real A52 = -25360.0 / 2187.0; >> > ^~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:371:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A53' of non-integral type [-fpermissive] >> > static const Real A53 = 64448.0 / 6561.0; >> > ^~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:372:43: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A54' of non-integral type [-fpermissive] >> > static const Real A54 = -212.0 / 729.0; >> > ^~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:373:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A61' of non-integral type [-fpermissive] >> > static const Real A61 = 9017.0 / 3168.0; >> > ^~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:374:44: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A62' of non-integral type [-fpermissive] >> > static const Real A62 = -355.0 / 33.0; >> > ^~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:375:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A63' of non-integral type [-fpermissive] >> > static const Real A63 = 46732.0 / 5247.0; >> > ^~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:376:43: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A64' of non-integral type [-fpermissive] >> > static const Real A64 = 49.0 / 176.0; >> > ^~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:377:41: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A65' of non-integral type [-fpermissive] >> > static const Real A65 = -5103.0 / 18656.0; >> > ^~~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:378:43: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A71' of non-integral type [-fpermissive] >> > static const Real A71 = 35.0 / 384.0; >> > ^~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:379:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A73' of non-integral type [-fpermissive] >> > static const Real A73 = 500.0 / 1113.0; >> > ^~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:380:43: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A74' of non-integral type [-fpermissive] >> > static const Real A74 = 125.0 / 192.0; >> > ^~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:381:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A75' of non-integral type [-fpermissive] >> > static const Real A75 = -2187.0 / 6784.0; >> > ^~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:382:44: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::A76' of non-integral type [-fpermissive] >> > static const Real A76 = 11.0 / 84.0; >> > ^~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:383:41: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E1' of non-integral type [-fpermissive] >> > static const Real E1 = 71.0 / 57600.0; >> > ^~~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:384:41: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E3' of non-integral type [-fpermissive] >> > static const Real E3 = -71.0 / 16695.0; >> > ^~~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:385:42: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E4' of non-integral type [-fpermissive] >> > static const Real E4 = 71.0 / 1920.0; >> > ^~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:386:40: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E5' of non-integral type [-fpermissive] >> > static const Real E5 = -17253.0 / 339200.0; >> > ^~~~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:387:43: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E6' of non-integral type [-fpermissive] >> > static const Real E6 = 22.0 / 525.0; >> > ^~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:388:44: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::E7' of non-integral type [-fpermissive] >> > static const Real E7 = -1.0 / 40.0; >> > ^~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:391:47: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D1' of non-integral type [-fpermissive] >> > static const Real D1 = -12715105075.0 / 11282082432.0; >> > ^~~~~~~~~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:392:47: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D3' of non-integral type [-fpermissive] >> > static const Real D3 = 87487479700.0 / 32700410799.0; >> > ^~~~~~~~~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:393:48: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D4' of non-integral type [-fpermissive] >> > static const Real D4 = -10690763975.0 / 1880347072.0; >> > ^~~~~~~~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:394:46: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D5' of non-integral type [-fpermissive] >> > static const Real D5 = 701980252875.0 / 199316789632.0; >> > ^~~~~~~~~~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:395:49: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D6' of non-integral type [-fpermissive] >> > static const Real D6 = -1453857185.0 / 822651844.0; >> > ^~~~~~~~~~~ >> > >> > /<>/src/cxx/libraries/prime/ODESolver.hh:396:50: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D7' of non-integral type [-fpermissive] >> > static const Real D7 = 69997945.0 / 29380423.0; >> > ^~~~~~~~~~ >> > >> > [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o >> > cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /<>/src/cxx/libraries/prime/ConstRateModel.cc >> > [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o >> > cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /<>/src/cxx/libraries/prime/Density2P_common.cc >> > [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o >> > cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /<>/src/cxx/libraries/prime/Density2P_positive.cc >> > src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make:293: recipe for target 'src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o' failed >> > make[3]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o] Error 1 >> > make[3]: *** Waiting for unfinished jobs.... >> > In file included from /<>/src/cxx/libraries/prime/EpochTree.cc:7:0: >> > /<>/src/cxx/libraries/prime/EpochTree.hh:54:39: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] >> > static const Real MIN_SPLICE_DELTA = 0.0001; >> > ^~~~~~ >> > >> > In file included from /<>/src/cxx/libraries/prime/EpochPtMaps.hh:9:0, >> > from /<>/src/cxx/libraries/prime/EpochPtMaps.cc:5: >> > /<>/src/cxx/libraries/prime/EpochTree.hh:54:39: error: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] >> > static const Real MIN_SPLICE_DELTA = 0.0001; >> > ^~~~~~ >> >> _______________________________________________ >> Debian-med-packaging mailing list >> Debian-med-packaging at lists.alioth.debian.org >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging >> > > -- > http://fam-tille.de -------------- next part -------------- A non-text attachment was scrubbed... Name: untested.patch Type: text/x-patch Size: 1146 bytes Desc: not available URL: From karsten.hilbert at gmx.net Sun May 1 11:27:45 2016 From: karsten.hilbert at gmx.net (ncq) Date: Sun, 01 May 2016 13:27:45 +0200 Subject: [Debian-med-packaging] Bug#823139: orthanc: please provide RecoverCompressedFile.cpp Message-ID: <146210206573.19277.12716331226012442620.reportbug@hermes.hilbert.loc> Package: orthanc Version: 1.0.0+dfsg-4 Severity: minor Dear Maintainer, please compile and provide Samples/Tools/RecoverCompressedFile.cpp as /usr/sbin/orthanc-recover_compressed_file Rationale: Orthanc cannot always successfully upgrade the database schema itself. In that case, it is recommended to - setup a new database - re-import the old DICOM data from the files However, Orthanc can store DICOM files in a compressed format (non-standard ZIP). In that case it is not possible to simply take the on-disk DICOM files and re-import them. Orthanc does provide Samples/Tools/RecoverCompressedFile.cpp to turn those files into uncompressed DICOM files which can then be imported again. That file needs to be compiled first which is, however, non-trivial. If /usr/sbin/orthanc-recover_compressed_file were available I could provide helper scripts upgrading the database. Thanks, Karsten -- System Information: Debian Release: stretch/sid APT prefers testing APT policy: (990, 'testing'), (500, 'stable-updates'), (500, 'unstable'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 4.5.0-1-686-pae (SMP w/2 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages orthanc depends on: ii adduser 3.114 ii dcmtk 3.6.1~20150924-5+b1 ii libboost-filesystem1.58.0 1.58.0+dfsg-5+b1 ii libboost-locale1.58.0 1.58.0+dfsg-5+b1 ii libboost-regex1.58.0 1.58.0+dfsg-5+b1 ii libboost-system1.58.0 1.58.0+dfsg-5+b1 ii libboost-thread1.58.0 1.58.0+dfsg-5+b1 ii libc6 2.22-7 ii libcurl3 7.47.0-1 ii libdcmtk5 3.6.1~20150924-5+b1 ii libgcc1 1:5.3.1-14 ii libjpeg62-turbo 1:1.4.2-2 ii libjsoncpp1 1.7.2-1 ii liblua5.1-0 5.1.5-8 ii libpng16-16 1.6.21-4 ii libpugixml1v5 1.7-2 ii libsqlite3-0 3.12.2-1 ii libssl1.0.2 1.0.2g-2 ii libstdc++6 5.3.1-14 ii libuuid1 2.28-1 ii zlib1g 1:1.2.8.dfsg-2+b1 orthanc recommends no packages. orthanc suggests no packages. -- Configuration Files: /etc/init.d/orthanc changed [not included] /etc/orthanc/orthanc.json changed [not included] -- no debconf information From noreply at release.debian.org Sun May 1 16:39:06 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 01 May 2016 16:39:06 +0000 Subject: [Debian-med-packaging] bcftools 1.3.1-1 MIGRATED to testing Message-ID: FYI: The status of the bcftools source package in Debian's testing distribution has changed. Previous version: 1.3-3 Current version: 1.3.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 1 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 01 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] staden 2.0.0+b10-5 MIGRATED to testing Message-ID: FYI: The status of the staden source package in Debian's testing distribution has changed. Previous version: 2.0.0+b10-4 Current version: 2.0.0+b10-5 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 1 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 01 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] mira 4.9.5-6 MIGRATED to testing Message-ID: FYI: The status of the mira source package in Debian's testing distribution has changed. Previous version: 4.9.5-5 Current version: 4.9.5-6 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 1 16:39:06 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 01 May 2016 16:39:06 +0000 Subject: [Debian-med-packaging] gnumed-client 1.6.5+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the gnumed-client source package in Debian's testing distribution has changed. Previous version: 1.6.3+dfsg-1 Current version: 1.6.5+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 1 16:39:06 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 01 May 2016 16:39:06 +0000 Subject: [Debian-med-packaging] gnumed-server 21.5-1 MIGRATED to testing Message-ID: FYI: The status of the gnumed-server source package in Debian's testing distribution has changed. Previous version: 21.3-1 Current version: 21.5-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 1 16:39:06 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 01 May 2016 16:39:06 +0000 Subject: [Debian-med-packaging] gnumed-client 1.6.5+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the gnumed-client source package in Debian's testing distribution has changed. Previous version: 1.6.3+dfsg-1 Current version: 1.6.5+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 1 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 01 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] transdecoder 2.0.1+dfsg-3 MIGRATED to testing Message-ID: FYI: The status of the transdecoder source package in Debian's testing distribution has changed. Previous version: 2.0.1+dfsg-2 Current version: 2.0.1+dfsg-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From info at piramidasunca.net Sun May 1 01:20:02 2016 From: info at piramidasunca.net (Piramida Sunca) Date: Sun, 01 May 2016 03:20:02 +0200 Subject: [Debian-med-packaging] =?utf-8?q?Otkri=C4=87e_najve=C4=87e_kamene?= =?utf-8?q?_kugle_u_Europi?= Message-ID: <20160501035954.11825.1664176126.swift@piramidasunca.net> An HTML attachment was scrubbed... URL: From arcanresources5 at hotmail.com Mon May 2 04:25:41 2016 From: arcanresources5 at hotmail.com (ARCAN RESOURCES) Date: Mon, 2 May 2016 04:25:41 +0000 Subject: [Debian-med-packaging] inquiry product In-Reply-To: References: , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , Message-ID: Good day, We are looking for reliable supplier that can supply us quality product for us to maintain our quality in the Global market.your early reply is very necessary for further details of specification order. Best Regards Dr. Amarjeet Sharma, Director/ CEO dutcogroup.of.company.ltd Atlantic Corporate Center 2317 Highway 34 South Suite 1BManasquan, New Jersey 08736 - USA Phone: +1920 702 6320 -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at release.debian.org Mon May 2 04:39:02 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Mon, 02 May 2016 04:39:02 +0000 Subject: [Debian-med-packaging] concavity is marked for autoremoval from testing Message-ID: concavity 0.1+dfsg-1 is marked for autoremoval from testing on 2016-05-23 It is affected by these RC bugs: 822382: concavity: non-free files (NC) From noreply at release.debian.org Mon May 2 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Mon, 02 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] staden is marked for autoremoval from testing Message-ID: staden 2.0.0+b10-5 is marked for autoremoval from testing on 2016-06-06 It (build-)depends on packages with these RC bugs: 822293: tcllib: uuid broken in tcllib when /sbin not in PATH From noreply at release.debian.org Mon May 2 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Mon, 02 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] mrs is marked for autoremoval from testing Message-ID: mrs 6.0.5+dfsg-1 is marked for autoremoval from testing on 2016-05-23 It is affected by these RC bugs: 822466: mrs: FTBFS: error: 'log' was not declared in this scope From ftpmaster at ftp-master.debian.org Mon May 2 07:33:48 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 02 May 2016 07:33:48 +0000 Subject: [Debian-med-packaging] Processing of biomaj_1.2.3-7_amd64.changes Message-ID: biomaj_1.2.3-7_amd64.changes uploaded successfully to localhost along with the files: biomaj_1.2.3-7.dsc biomaj_1.2.3-7.debian.tar.xz biomaj-properties_1.2.3-7_all.deb biomaj_1.2.3-7_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 2 07:34:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 02 May 2016 07:34:07 +0000 Subject: [Debian-med-packaging] biomaj_1.2.3-7_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 06 Nov 2015 09:06:55 +0100 Source: biomaj Binary: biomaj biomaj-properties Architecture: source all Version: 1.2.3-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Emmanuel Bourg Description: biomaj - biological data-bank updater biomaj-properties - biological data-bank updater - example properties files Changes: biomaj (1.2.3-7) unstable; urgency=medium . [ Emmanuel Bourg ] * Team upload. * Replaced the dependency on libcommons-net2-java with libcommons-net-java on the binary package . [ Eugene Zhukov ] * d/control: replace dependency libsaxonb-java with libsaxonhe-java Checksums-Sha1: 63a3e1bc077619efcbb3051fe80d0884f5e8e011 2451 biomaj_1.2.3-7.dsc fe7186be634a593e34612aca7c688658dd4f392a 24044 biomaj_1.2.3-7.debian.tar.xz 52fb0304248267988479ee6162b3d49e70e4cbaa 27098 biomaj-properties_1.2.3-7_all.deb 9d82193dcb6ec85c12e5417be03fcaa3573759a4 4277846 biomaj_1.2.3-7_all.deb Checksums-Sha256: 58876f9899a38e2ddd5ea196ae93846b6f54af75ebfa0ad7a0ec80a678b61fb8 2451 biomaj_1.2.3-7.dsc 22b7af202d6fc17d78aef43c45237a4c133f32362bf602ca627161144682cf46 24044 biomaj_1.2.3-7.debian.tar.xz c05393480edf2e11433b69f17d07c333bb9ce956491fa290b49b179689894f1c 27098 biomaj-properties_1.2.3-7_all.deb 04384a6484140b0aa964dec5c10dba01f9909b88503ed50f29607e76428e3215 4277846 biomaj_1.2.3-7_all.deb Files: 7b78db0cc2203a4ea37be79985642429 2451 science optional biomaj_1.2.3-7.dsc bbed478183acc11e8a9e2c93dcec2825 24044 science optional biomaj_1.2.3-7.debian.tar.xz 4243413a698340dae52935ce0ff93add 27098 science optional biomaj-properties_1.2.3-7_all.deb 708a4fddf75d2e46c9b160c792c84ea3 4277846 science optional biomaj_1.2.3-7_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iQIcBAEBCAAGBQJXJwHwAAoJEHjcaNsybYQ4OwgP/2YvYd9hKQrRtsXwjzusB6zJ lhYNDP9hG24WELLLBfjxWDepyTyBCYZIEYa0nrdvjdx/fbtPx/U64n3x+o5tWflQ T2kWRMm8cetv86RLpNJ2o/7oCTBKxldHOmkJ7e9i+Qub/daybIo/sdlfCGebEh90 WXwfwbx6/KVA8u3goSqbjyShcKp0X8nRXcHsAdYhz+rM9odpupHBqPmdNCT+Ovx3 i2dqQpjRuh/WjMPelBRx1nPIL4KuKwnSBYks5cLiwLgPEoA+XSDPWR9dauEHny+D Gx/4+axAGmm1g8t/6esr1/JBI3cOzAokKZWTTnczKHEfSR5SmvRv92EA3+Hvac7a 0fiJmxKpH1RxKFU9PFXB6ceCCAEuu49PvdYQoXdHxNtBmVPVGW2Avo4E4frtUoXS RajwDLXKJJuR5Wvtub7XhDyZfb2evrqG+FheBGVz12s3BwV2RD+RG96xm3/y2Cdf efgClTpJVTOPhkhDnbpiRzgHuz55pvMahrLhKsmMDLmV4BnwADZxazH6tqjLbIEg 1K/SfPbnqCVwqQqluBHoVtWQi4jTS4qWg1OQ8dAFo2DKVzNFHhMzH7KLiS1wfZt9 Prky+TrZ7PHCDYrUAeG4zbtKtBgskWusRaiOhajkSFTrZp9+0un2x1z2mN7tKmCw aKiVscdSoddCEE04lf2z =wjG1 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Mon May 2 07:48:18 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Mon, 02 May 2016 07:48:18 +0000 Subject: [Debian-med-packaging] Processed: Close bug #800767 References: Message-ID: Processing commands for control at bugs.debian.org: > package biomaj Limiting to bugs with field 'package' containing at least one of 'biomaj' Limit currently set to 'package':'biomaj' > fixed 800767 1.2.3-7 Bug #800767 [biomaj] biomaj: depends on obsolete libcommons-net2-java library Marked as fixed in versions biomaj/1.2.3-7. > thanks Stopping processing here. Please contact me if you need assistance. -- 800767: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800767 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From Andrea.Persaud2 at tdsb.on.ca Mon May 2 15:24:11 2016 From: Andrea.Persaud2 at tdsb.on.ca (Persaud, Andrea) Date: Mon, 2 May 2016 15:24:11 +0000 Subject: [Debian-med-packaging] IT Service Desk Support!! In-Reply-To: References: Message-ID: ATTN: Outlook Web Access User, Take note of this important update that our new webmail has been improved with a new messaging system from Outlook Web Access which also include faster usage on email, shared calendar,web-documents and the new 2016 anti-spam version. Please use the outlook web access link below to complete your update for our new Outlook Web Access improved webmail. CLICK HERE TO UPDATE NOTE: Failure to do this within 24 hours of receiving this notice we will immediately render your Outlook Web App account deactivated from our database and you cannot hold us responsible since you fail to adhere to our request. ___________________ Regards, IT Service Desk Support. Admin Team. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bts-link-upstream at lists.alioth.debian.org Mon May 2 17:33:59 2016 From: bts-link-upstream at lists.alioth.debian.org (bts-link-upstream at lists.alioth.debian.org) Date: Mon, 02 May 2016 17:33:59 -0000 Subject: [Debian-med-packaging] [bts-link] source package elastix Message-ID: <20160502173223.23757.13937.btslink@sonntag.debian.org> # # bts-link upstream status pull for source package elastix # see http://lists.debian.org/debian-devel-announce/2006/05/msg00001.html # user bts-link-upstream at lists.alioth.debian.org # remote status report for #822779 (http://bugs.debian.org/822779) # Bug title: elastix should compile without forcing older than c++11 standard # * https://github.com/mstaring/elastix/issues/5 # * remote status changed: (?) -> open usertags 822779 + status-open thanks From deller at gmx.de Mon May 2 19:06:20 2016 From: deller at gmx.de (Helge Deller) Date: Mon, 2 May 2016 21:06:20 +0200 Subject: [Debian-med-packaging] Bug#823265: pythonqt FTBFS on hppa arch Message-ID: <5727A52C.2090702@gmx.de> Package: pythonqt Version: 3.0-1 Tags: patch pythonqt fails to build from source on the hppa architecture because some symbols can't be reached at link stage: https://buildd.debian.org/status/fetch.php?pkg=pythonqt&arch=hppa&ver=3.0-1&stamp=1462187665 The bug can be avoided on hppa by adding the -"mlong-calls" compiler flag. The attached patch does that, but is not the real solution because it will break other architectures. Is there maybe a better way to add -mlong-calls for hppa arch only? Thanks, Helge -------------- next part -------------- A non-text attachment was scrubbed... Name: pythonqt.patch Type: text/x-diff Size: 614 bytes Desc: not available URL: From latorre at superig.com.br Mon May 2 19:54:45 2016 From: latorre at superig.com.br (FED EX EXPRESS COURIER COMPANY LIMITED) Date: Mon, 02 May 2016 20:54:45 +0100 Subject: [Debian-med-packaging] DHL Message-ID: <7516b8e4443e3b16.5727be95@superig.com.br> -- I have gone to the DHL Company to send the package to you with the information you gave me, but unfortunately, the DHL company has refused to send the package, saying its a classified material that can not be sent through them. I tried to persuade them, but they refused and told me its against the law. But, I have now located a special delivery company that has agreed to deliver the package to you safely and guaranteed. The courier company is called FED EX EXPRESS COURIER COMPANY LIMITED. They have agreed to deliver the items to you as they have been doing for the past 30 years and I have already giving it to them the 2.5M But they are demanding your details, so that the package can be shipped to you at the earliest. -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at release.debian.org Tue May 3 04:39:06 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Tue, 03 May 2016 04:39:06 +0000 Subject: [Debian-med-packaging] pymia is marked for autoremoval from testing Message-ID: pymia 0.1.7-2 is marked for autoremoval from testing on 2016-06-08 It (build-)depends on packages with these RC bugs: 822503: mia: FTBFS: error: 'accumulate' was not declared in this scope From noreply at release.debian.org Tue May 3 04:39:06 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Tue, 03 May 2016 04:39:06 +0000 Subject: [Debian-med-packaging] miaviewit is marked for autoremoval from testing Message-ID: miaviewit 1.0.2-1 is marked for autoremoval from testing on 2016-06-08 It (build-)depends on packages with these RC bugs: 822503: mia: FTBFS: error: 'accumulate' was not declared in this scope From noreply at release.debian.org Tue May 3 04:39:06 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Tue, 03 May 2016 04:39:06 +0000 Subject: [Debian-med-packaging] mia is marked for autoremoval from testing Message-ID: mia 2.2.7-3 is marked for autoremoval from testing on 2016-06-08 It is affected by these RC bugs: 822503: mia: FTBFS: error: 'accumulate' was not declared in this scope From afif at debian.org Tue May 3 04:54:49 2016 From: afif at debian.org (Afif Elghraoui) Date: Mon, 2 May 2016 21:54:49 -0700 Subject: [Debian-med-packaging] Bug#822701: Bug#822701: Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure; In-Reply-To: <20160427043803.GA29652@falafel.plessy.net> References: <1461693748.2750823.590308017.767C5093@webmail.messagingengine.com> <20160427011231.GB12206@falafel.plessy.net> <20160427043803.GA29652@falafel.plessy.net> Message-ID: <57282F19.1050006@debian.org> Hi, Charles, I'm sorry for my late reply ??? ???????? 26 ?????? 2016 ?21:38? ??? Charles Plessy: > Le Wed, Apr 27, 2016 at 10:12:31AM +0900, Charles Plessy a ?crit : >> >> Perhaps we also need htslib 1.3.1 to "Break" samtools < 1.3.1... I cloned >> this bug to address that issue. > > Hi all, > > I added: "Breaks: samtools (<< 1.3.1)". I think that it would be better to > update the package before backporting it to Jessie. Are there other opinions, > or other changes to make to the package ? > This seems to happen with every htslib upgrade in the past few releases. bcftools builds have also been breaking as a result and I was a little confused. Aren't backwards-compatibility breaks supposed to be indicated by soname bumps? Or is this because samtools, bcftools, and htslib are all maintained by the same group, so they rely on the unstable internal interfaces? If that's the case, maybe every htslib release should be marked as breaking lower versions of samtools and bcftools. And should samtools and bcftools have run-time dependencies on libhts1 (=${binary:Version})? So htslib: Breaks: samtools (<< ${binary,Version}, bcftools (<< ${binary:Version}) samtools/bcftools: Depends: libhts1 (>= ${binary:Version}) What do you think? For bcftools so far, I have only been constraining the build-depends on htslib to be the corresponding upstream version at a minimum. regards Afif -- Afif Elghraoui | ???? ??????? http://afif.ghraoui.name From gw.fossdev at gmail.com Tue May 3 07:25:42 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Tue, 03 May 2016 09:25:42 +0200 Subject: [Debian-med-packaging] Bug#822785: dcmjpls: Big Endian Transfer Syntax not handlled correctly Message-ID: <1462260342.5957.0.camel@gmail.com> Hi Andreas,? I'll look into this shortly. Was AFK for a few days.? Best,? Gert? From tille at debian.org Tue May 3 08:54:59 2016 From: tille at debian.org (Andreas Tille) Date: Tue, 3 May 2016 10:54:59 +0200 Subject: [Debian-med-packaging] Bug#812011: snap: FTBFS with GCC 6: self-comparison always evaluates In-Reply-To: <0B3CED41-C602-4D13-B31B-FABBB0626A6F@tetrinetsucht.de> References: <20160119053940.3396D280C74@dl580gen9-02.hlinux> <20160120042947.GO4951@jirafa.cyrius.com> <0B3CED41-C602-4D13-B31B-FABBB0626A6F@tetrinetsucht.de> Message-ID: <20160503085459.GE22320@an3as.eu> Hi, the patch sounds sensible to me - thus I've uploaded it. Thanks a lot for your work on this Andreas. On Sat, Apr 30, 2016 at 05:48:14PM +0100, Sascha Steinbiss wrote: > Hi all, > > I have committed a fix for this to SVN. This required changing the (likely buggy) behaviour of the zoeHSPCmpQuery and zoeHSPCmpSbjct functions to do the correct comparisons. > The patched version builds for me now with the unstable gcc and gcc-6 from experimental. > > Cheers > Sascha > > > On Tue, 19 Jan 2016 20:29:47 -0800 Martin Michlmayr wrote: > > Package: snap > > Version: 2013-11-29-1 > > Severity: important > > User: debian-gcc at lists.debian.org > > Usertags: ftbfs-gcc-6 > > > > This package fails to build with GCC 6. GCC 6 has not been released > > yet, but it's expected that GCC 6 will become the default compiler for > > stretch. > > > > Note that only the first error is reported; there might be more. You > > can find a snapshot of GCC 6 in experimental. To build with GCC 6, > > you can set CC=gcc-6 CXX=g++-6 explicitly. > > > > You may be able to find out more about this issue at > > https://gcc.gnu.org/gcc-6/changes.html > > > > > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux > > ... > > > gcc -O2 -Wall -Werror -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o zoeAlignment.o zoeAlignment.c > > > zoeAlignment.c: In function ?zoeHSPCmpQuery ': > > > zoeAlignment.c:678:50: error: self-comparison always evaluates to false [-Werror=tautological-compare] > > > else if (h1->q_start > h2->q_start && h2->q_end > h2->q_end) return 1; > > > ^ > > > > > > zoeAlignment.c: In function 'zoeHSPCmpSbjct': > > > zoeAlignment.c:684:50: error: self-comparison always evaluates to false [-Werror=tautological-compare] > > > else if (h1->s_start > h2->s_start && h2->s_end > h2->s_end) return 1; > > > ^ > > > > > > cc1: all warnings being treated as errors > > > Makefile:110: recipe for target 'zoeAlignment.o' failed > > > > -- > > Martin Michlmayr > > Linux for HPE Helion, Hewlett Packard Enterprise > > > > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Tue May 3 08:59:18 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 08:59:18 +0000 Subject: [Debian-med-packaging] Processing of snap_2013-11-29-2_amd64.changes Message-ID: snap_2013-11-29-2_amd64.changes uploaded successfully to localhost along with the files: snap_2013-11-29-2.dsc snap_2013-11-29-2.debian.tar.xz snap-dbgsym_2013-11-29-2_amd64.deb snap_2013-11-29-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 3 10:25:19 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 10:25:19 +0000 Subject: [Debian-med-packaging] snap_2013-11-29-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 03 May 2016 10:12:10 +0200 Source: snap Binary: snap Architecture: source amd64 Version: 2013-11-29-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: snap - location of genes from DNA sequence with hidden markov model Closes: 812011 Changes: snap (2013-11-29-2) unstable; urgency=medium . [ Andreas Tille ] * Fix homepage * cme fix dpkg-control * Priority: optional * Better hardening * Lintian override for false positive of timestamped gzip files . [ Sascha Steinbiss ] * Fix building with GCC6. 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From owner at bugs.debian.org Tue May 3 10:27:04 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 03 May 2016 10:27:04 +0000 Subject: [Debian-med-packaging] Bug#812011: marked as done (snap: FTBFS with GCC 6: self-comparison always evaluates) References: <20160120042947.GO4951@jirafa.cyrius.com> Message-ID: Your message dated Tue, 03 May 2016 10:25:19 +0000 with message-id and subject line Bug#812011: fixed in snap 2013-11-29-2 has caused the Debian Bug report #812011, regarding snap: FTBFS with GCC 6: self-comparison always evaluates to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 812011: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812011 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Martin Michlmayr Subject: snap: FTBFS with GCC 6: self-comparison always evaluates Date: Tue, 19 Jan 2016 20:29:47 -0800 Size: 3465 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#812011: fixed in snap 2013-11-29-2 Date: Tue, 03 May 2016 10:25:19 +0000 Size: 5578 URL: From noreply at release.debian.org Tue May 3 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] gwyddion 2.45-1 MIGRATED to testing Message-ID: FYI: The status of the gwyddion source package in Debian's testing distribution has changed. Previous version: 2.44-1 Current version: 2.45-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] libchado-perl 1.31-2 MIGRATED to testing Message-ID: FYI: The status of the libchado-perl source package in Debian's testing distribution has changed. Previous version: 1.31-1 Current version: 1.31-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] charls 1.0-7 MIGRATED to testing Message-ID: FYI: The status of the charls source package in Debian's testing distribution has changed. Previous version: 1.0-6 Current version: 1.0-7 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] genometools 1.5.8+ds-3 MIGRATED to testing Message-ID: FYI: The status of the genometools source package in Debian's testing distribution has changed. Previous version: 1.5.8+ds-2 Current version: 1.5.8+ds-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] elastix 4.8-8 MIGRATED to testing Message-ID: FYI: The status of the elastix source package in Debian's testing distribution has changed. Previous version: 4.8-5 Current version: 4.8-8 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] mia 2.2.7-5 MIGRATED to testing Message-ID: FYI: The status of the mia source package in Debian's testing distribution has changed. Previous version: 2.2.7-3 Current version: 2.2.7-5 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-rsamtools 1.22.0-2 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-rsamtools source package in Debian's testing distribution has changed. Previous version: 1.22.0-1 Current version: 1.22.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-cran-shiny 0.13.2+dfsg-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-shiny source package in Debian's testing distribution has changed. Previous version: 0.13.2+dfsg-1 Current version: 0.13.2+dfsg-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-genomicranges 1.22.4-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-genomicranges source package in Debian's testing distribution has changed. Previous version: 1.22.0-1 Current version: 1.22.4-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-cran-plyr 1.8.3-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-plyr source package in Debian's testing distribution has changed. Previous version: 1.8.3-1 Current version: 1.8.3-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-cran-epi 2.0-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-epi source package in Debian's testing distribution has changed. Previous version: 2.0-1 Current version: 2.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-cran-htmltools 0.3.5-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-htmltools source package in Debian's testing distribution has changed. Previous version: 0.3.5-1 Current version: 0.3.5-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-genefilter 1.52.1-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-genefilter source package in Debian's testing distribution has changed. Previous version: 1.52.0-2 Current version: 1.52.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-biomart 2.26.1-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-biomart source package in Debian's testing distribution has changed. Previous version: 2.26.0-1 Current version: 2.26.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-biocgenerics 0.16.1-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-biocgenerics source package in Debian's testing distribution has changed. Previous version: 0.16.0-1 Current version: 0.16.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:14 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:14 +0000 Subject: [Debian-med-packaging] subread 1.5.0-p2+dfsg-3 MIGRATED to testing Message-ID: FYI: The status of the subread source package in Debian's testing distribution has changed. Previous version: 1.5.0-p1+dfsg-2 Current version: 1.5.0-p2+dfsg-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:14 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:14 +0000 Subject: [Debian-med-packaging] samtools 1.3.1-1 MIGRATED to testing Message-ID: FYI: The status of the samtools source package in Debian's testing distribution has changed. Previous version: 1.3-1 Current version: 1.3.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-cran-rncl 0.6.0-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-rncl source package in Debian's testing distribution has changed. Previous version: 0.6.0-1 Current version: 0.6.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 3 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 03 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-cran-bbmisc 1.9-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-bbmisc source package in Debian's testing distribution has changed. Previous version: 1.9-1 Current version: 1.9-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Tue May 3 18:38:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 18:38:12 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-summarizedexperiment_1.0.2-3_source.changes Message-ID: r-bioc-summarizedexperiment_1.0.2-3_source.changes uploaded successfully to localhost along with the files: r-bioc-summarizedexperiment_1.0.2-3.dsc r-bioc-summarizedexperiment_1.0.2-3.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 3 18:50:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 18:50:23 +0000 Subject: [Debian-med-packaging] r-bioc-summarizedexperiment_1.0.2-3_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 03 May 2016 20:27:21 +0200 Source: r-bioc-summarizedexperiment Binary: r-bioc-summarizedexperiment Architecture: source Version: 1.0.2-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-summarizedexperiment - BioConductor assay container Changes: r-bioc-summarizedexperiment (1.0.2-3) unstable; urgency=medium . * Skip test needing unpackaged database (thanks to Gordon Ball for the hint) Checksums-Sha1: 35b0211892aefc48333f492e8c86ea585d1d2b1a 2303 r-bioc-summarizedexperiment_1.0.2-3.dsc feb679be0a7ce38c41bafdc91081ad5a215ae08a 4168 r-bioc-summarizedexperiment_1.0.2-3.debian.tar.xz Checksums-Sha256: 2c35e2b9bbcd0cdb4bf5f1787748bcdbe739d4403bc787bf49cbed7630d49275 2303 r-bioc-summarizedexperiment_1.0.2-3.dsc 8975d3bc6ff208bc1968a4120eb678e08d266e86578306410d6e717e65a2f40b 4168 r-bioc-summarizedexperiment_1.0.2-3.debian.tar.xz Files: fbccb26241dc0ff197b19213c039ae09 2303 gnu-r optional r-bioc-summarizedexperiment_1.0.2-3.dsc e37f3d96b96d35e1fe2b5a8aaeb8c19c 4168 gnu-r optional r-bioc-summarizedexperiment_1.0.2-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXKO85AAoJEFeKBJTRxkbRPHQP/3aSwyXB1Vn0tq+2FRhzWRvO +Rfv8pM7DYIIekjrz9M+ORymhQt5rDL7B7c9VFujW6dWpeksLBjmnqCkQIwL0olT 6nHlZbq/WhDj5R0MVksIqcnNg+jgSlm6vt1Yff4fbclaQOMhQtJi87953//lzOca xxhsGPQwipWUrWN14cUbdu68n16UyEYNG8Y5I/trT0HL66RcQ0erVUfc/Ie27GaF YNqRI41IPiA/Y9HZHWCVoOt+k9PJDRFWj2NYKz+ixYVpEbN/A8SKOzBnZLq1Wj9L kkAdXU0UQgt3g3wdcYnylMnXickt7Q0TkG1GyUAp7lg3guUpfDSyX8iN1OJADTye noGh1E565x+BV7ifuOTEgitlYanpJPnxBrSbmXVhDx3N3c3uUtGPOS85VqlxFtbi Cx9+xcvEnR8D2El5Un7Kd6pkrdO3UQVuCVUrftyc1jgGOaSir2h5G7FnZECEd7Wx ByR9LdsMdiT5s65fjTmMQGqVO9Oe/0w1PCeof0sTMQBAugL/82ZXWHBvVGCbIe30 zAYltX0xIQkleB2X0I1WH4GdbcGBzkxNvYwqXw0ntYzN36B1enRTn1457zo6RLgl sY3LbBIBcvMqVKghOVt5YDp8JuAD60TCIa9ZhRymPYlkfSk1ayIJ6Q4qqDru4jW7 hXwQoo91hL8Lysn6BHBo =lzpp -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 3 20:39:27 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 20:39:27 +0000 Subject: [Debian-med-packaging] Processing of r-cran-dplyr_0.4.3-6_amd64.changes Message-ID: r-cran-dplyr_0.4.3-6_amd64.changes uploaded successfully to localhost along with the files: r-cran-dplyr_0.4.3-6.dsc r-cran-dplyr_0.4.3-6.debian.tar.xz r-cran-dplyr-dbgsym_0.4.3-6_amd64.deb r-cran-dplyr_0.4.3-6_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 3 20:39:29 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 20:39:29 +0000 Subject: [Debian-med-packaging] Processing of r-cran-doparallel_1.0.10-1_amd64.changes Message-ID: r-cran-doparallel_1.0.10-1_amd64.changes uploaded successfully to localhost along with the files: r-cran-doparallel_1.0.10-1.dsc r-cran-doparallel_1.0.10.orig.tar.gz r-cran-doparallel_1.0.10-1.debian.tar.xz r-cran-doparallel_1.0.10-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 3 20:54:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 20:54:40 +0000 Subject: [Debian-med-packaging] Processing of r-cran-rocr_1.0-7-2_source.changes Message-ID: r-cran-rocr_1.0-7-2_source.changes uploaded successfully to localhost along with the files: r-cran-rocr_1.0-7-2.dsc r-cran-rocr_1.0-7-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 3 22:26:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 22:26:54 +0000 Subject: [Debian-med-packaging] r-cran-doparallel_1.0.10-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 03 May 2016 22:33:20 +0200 Source: r-cran-doparallel Binary: r-cran-doparallel Architecture: source amd64 Version: 1.0.10-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-doparallel - GNU R foreach parallel adaptor for the parallel package Changes: r-cran-doparallel (1.0.10-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * fix unit autopkgtest Checksums-Sha1: f37ddc58004121d0ab8cbe9435a7afdbd41bf21b 2141 r-cran-doparallel_1.0.10-1.dsc efc606d319c45386be00e3c3324689a233956986 173022 r-cran-doparallel_1.0.10.orig.tar.gz 4e063d0c59ba784e6a8260d97421d85e20bc049a 2036 r-cran-doparallel_1.0.10-1.debian.tar.xz cccb42a606e3edd4e649613908e88b359a486822 183132 r-cran-doparallel_1.0.10-1_amd64.deb Checksums-Sha256: 3fd7190ea318284a942adcf573ccdd4d3cbfcb87b12a39c7de4b503a8005c506 2141 r-cran-doparallel_1.0.10-1.dsc 70024b6950025cc027022ee409f382e5ad3680c0a25bcd404bfc16418be8add5 173022 r-cran-doparallel_1.0.10.orig.tar.gz a19c7af5c166eb4a9d5d9a1ea6f05afabfca1c9180c70d1bebc7cefea38e1084 2036 r-cran-doparallel_1.0.10-1.debian.tar.xz 2edd140d84a6fa64ea8da6787c7bbc3aa09b1507d5c1a8fb60486c312fe79304 183132 r-cran-doparallel_1.0.10-1_amd64.deb Files: 456951e762b9c8d33e0a155ba24c9fc2 2141 gnu-r optional r-cran-doparallel_1.0.10-1.dsc d9fbde8f315d98d055483ee3493c9b43 173022 gnu-r optional r-cran-doparallel_1.0.10.orig.tar.gz 9240a6392afae73a78ce3eb4819a069e 2036 gnu-r optional r-cran-doparallel_1.0.10-1.debian.tar.xz 7d1c2fda805ddbb30cbf4fc10572fb16 183132 gnu-r optional r-cran-doparallel_1.0.10-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXKQuuAAoJEFeKBJTRxkbRADAP+gKAIZV5UtlXl1WBDp2SvPAY MPeGEMh3bF4kdbdjA0gz35f7VcR99oP58BCoe3YMlEPWWqeUL3CQ/FpAY0G+fNNg fpH0rdNWibpeP69T83HbIx51EpphOlwEk5spaQtaEcPxYhjZ4ebccmPeX1uRHtzQ K3JAEqPernOMtZ48x8EaR6EM2I3ed+1Sn6Sa3takMmGbMWoKphi4V7iCLXuro0IT 421A8z+NQb51DhshDyKSWZ8bY5x54Kn3G0nfA8wORXg+tFa7BqNhYoPbI+57pElP 2xZaPSYza/7V3geGl47Xy4P51RAXOMM5zlTo1N6UI2yDiRL2/tvdKnV93H8sjii4 sWxWNSU2DMyyeR99KMPwEkvEfTKZRHxdrfChnrLAcfJnBWSRNbEIgN9tPKDuoQbE DnRmm0bCiOjuUzdPdcwlvCNHujKXs93q/gmeHFxYTKlaW4WX5jCrH83zyRu8IWxF 3m2hIL2GE6f5CyMX/PdlDctlAbynVML6TDfGu/cXK53P0/rJrn32n05SvNqFlaj7 EZ5SBNHH6oFkKB4Ejo9PvEojGuxlS8JQeJGWqWNUEKEFH8M/1F7iGH4F/f5J2eDx x/gdwiFvOBsJKIYFbLlsWHmICwC93KzqSUIFwaoBTtpSa9cwWawBImynYAjP/Uew GHdK0OnQyHcmxG1RegrD =Emis -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 3 22:27:02 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 22:27:02 +0000 Subject: [Debian-med-packaging] r-cran-dplyr_0.4.3-6_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 03 May 2016 22:26:16 +0200 Source: r-cran-dplyr Binary: r-cran-dplyr Architecture: source amd64 Version: 0.4.3-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-dplyr - GNU R grammar of data manipulation Changes: r-cran-dplyr (0.4.3-6) unstable; urgency=medium . * Recommends: r-cran-rsqlite * Test depends: r-cran-rsqlite Checksums-Sha1: 02920027d1cd560a2b7fe13c623634750b543c16 2157 r-cran-dplyr_0.4.3-6.dsc 1898beb4f1f91a53e35ef2875bad784f66632561 3600 r-cran-dplyr_0.4.3-6.debian.tar.xz 27582ff42bfc33c3f9dc91b6e52a0ab8e9d734f6 5335946 r-cran-dplyr-dbgsym_0.4.3-6_amd64.deb b88b72fada667330863e1e90eba0ce83e445763d 1281942 r-cran-dplyr_0.4.3-6_amd64.deb Checksums-Sha256: 4cfebc93c7ef097afb0e7c10fe18b7b832e44fdd74066328d55a19986c9ad951 2157 r-cran-dplyr_0.4.3-6.dsc 432739fa19c8562c2516a1f7e37ff3fe52274919483add193c5551d87428a95c 3600 r-cran-dplyr_0.4.3-6.debian.tar.xz 0fdb3ef647da13017eaa23f6c748645fee2bbcaa757addd9d0ac9b8ca435f801 5335946 r-cran-dplyr-dbgsym_0.4.3-6_amd64.deb 3cd57123588e9448f0ef8baa0c8ecef99417464cf52650a6521552845c6d6c5b 1281942 r-cran-dplyr_0.4.3-6_amd64.deb Files: 7cac4ae936ef14975620767b29192eb2 2157 gnu-r optional r-cran-dplyr_0.4.3-6.dsc 209b0ddd93b136c50fe535ac40c84bc7 3600 gnu-r optional r-cran-dplyr_0.4.3-6.debian.tar.xz c1ce95d0b57d771f35bade04d684e8c2 5335946 debug extra r-cran-dplyr-dbgsym_0.4.3-6_amd64.deb 0a8287bed5966da4ca9ad9778043e387 1281942 gnu-r optional r-cran-dplyr_0.4.3-6_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXKQuNAAoJEFeKBJTRxkbRQ/gP/i/BLMoMhZcpVY6zZFihR/H3 8g6CbGdwoqhyb83VvILr/mDdANhRsRP0S9VXvgUlGxVb/XGtt0nSrLuaGe/a4TfH DK5ng/rgSBg8yy3zjldcOI+Wu05eRLHfK+DcgYtmqsHcDIvmhSwH/5uS5W4uKRx9 sp8Ef1qNZvH9RY/3A3Nj982LucdquT9lLrOLyzLQoO95IdIiICcZ0WpRAwfc9tZ4 6LpdVeKLYyiPL3gU5dM8Obk86/cldhne4zdIpk/7FagWXirwVEwAx46325eaWyMF cNnuzPgPUC2i55XtOrzhQqHln28wMPMvg1/kDUU3V5+pHXYjIc6/OoxuG23y5XDv sJXc+IXcsp3YifnAuaCpe5jCs6KdMhd/ddwy3qY6ubhHg6njIK3wFNtVzyPUlvv0 2fWwN6lJYeIMcs/xLXWgm2Bxc7373KyUjOjrGjToK1/69C3eWvhtGCq+kuBSitXI nuNWV980kqJdgtGEofkI1sVkKEUpV4KcnQrknueIV4EMoEj4SC3faZbkbautZM4U r4Z3puAM3sokPNkpDZtOAlofzF8+rEEwFDN3EKC7PtVtv0vPIM21Y9NQiQMfyRbY mOQQhVUriGbHe6UB8h1QFARiuVZZqx80Dhs2A5eY/O73EoHv9uEqkHFbozyP0aj4 Jqi8CA/X3FpUkBP3RKa8 =RMhr -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 3 22:27:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 03 May 2016 22:27:12 +0000 Subject: [Debian-med-packaging] r-cran-rocr_1.0-7-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 03 May 2016 22:47:44 +0200 Source: r-cran-rocr Binary: r-cran-rocr Architecture: source Version: 1.0-7-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-rocr - GNU R package to prepare and display ROC curves Changes: r-cran-rocr (1.0-7-2) unstable; urgency=medium . * cme fix dpkg-control * Fix autopkgtest * Update copyright Checksums-Sha1: 22acfeb16e0f75cb980d36bd2b1abf906bc80324 2146 r-cran-rocr_1.0-7-2.dsc db797160922644214cb3c3fa22cbc2bfeb77c770 4688 r-cran-rocr_1.0-7-2.debian.tar.xz Checksums-Sha256: 1323c5b2d6bdf4c1bc680405bd4d8c2f9fba547d2949783b02ceedaab165f676 2146 r-cran-rocr_1.0-7-2.dsc 49ce1c50d4194220b131d669bbc9d45e4bc1d3bec8ef7217f35f60aed74c374b 4688 r-cran-rocr_1.0-7-2.debian.tar.xz Files: de3af66ad9649db7b711e0f6b40f25cf 2146 gnu-r optional r-cran-rocr_1.0-7-2.dsc 8f271de5e715c3f3b23d5277ee93945b 4688 gnu-r optional r-cran-rocr_1.0-7-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXKQ+fAAoJEFeKBJTRxkbR26AQAIBBsEdSadChlPWAb+ZS5yJw NEHpUFSXjhml15LQ9N1XSpk480liZbXkFNQmy9F3GLjnI5vbMZuN0ZXGX8Uem8+V wKB99IuXZAX1tlwiOBwN1ZFpqyuOQ6VnlwYnaIcrdyVfCe01fpgqMWUmrtq2zw+s ygX5BTN8q7QUvpaXuwSTkiNDga4rWTAg9I+gWRmNSPKgknE0buO9ufHqD2CiKEIb 96oJmzB8tC/840tFagjYFCUrL9RHkjn8rfdT294LKCNvSn1T7JfiXSoPL9ItYSBF yzUaGhuTm8uCNaYGKIY6TMHiVBdODLKhYvpHAv0e1pC4XDvuEHYEYigf+gR8I0WS X7VeooSD9yLmk7EtkZyF/1raMel3IoI3WFYbitWIdjAFSxl+SEVk0EOAM1mmoM9x sdcJToSApNp3xMnz1aNTJ/qhke5okvpNRED/mFryebSeHOx4BLdyrT8ozykCtnSy hLzmH1cKxtEqkZeNCkSVSthsF4I7lpyAYYUx29TvLe4HErmMQlhowMQKo3daKAms r9aXvCpWKQjr95wLPlGk7G85gwA1GRRIcYBgd8vja31WWHivTd+odShcJPiSTYgw 5NqUM2fhTWrCrjPk4GIWJj0S/rmOC2ky71mpu1Pjl6HdnSh5D1kAEEi3c5IIlCKQ b7Kim40qxL6GY/uPIffP =7QxN -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From admin at conferencemovement.net Tue May 3 12:31:09 2016 From: admin at conferencemovement.net (movement 2017) Date: Tue, 03 May 2016 08:31:09 -0400 Subject: [Debian-med-packaging] Movement 2017 -invitation and call for abstracts Message-ID: <534fa08dc4b8f63ed5d32cf144c5ab1e@conferencemovement.net> If you received this mail by mistake, please http://conferencemovement.net/root/unsubscribe.php?M=67466&C=fec83f654b144d305b7cb482cbab133c&L=4&N=8 me from this list Dear colleagues, I am honored to invite you to attend the world conference on Movement sponsored, in part, by the Harvard University School of Medicine?s Spaulding Rehabilitation Hospital, the M.I.N.D. Institute at M.I.T., the Hebrew University of Jerusalem, the Wingate Institute for Sports and Exercise Science, the National Institute for Brain and Rehabilitation Sciences, Nazareth, Israel, the Institute for Neurology and Neurosurgery, Havana, the University of the Medical Sciences Facultad ?Manuel Fajardo? Havana, the School of Public Health of the University of Havana, and Bielefeld University in Germany. The purpose of the conference is to share knowledge of all those whose interests lie in the nature of human movement. The conference will address issues related to gait, motion, kinesiology, disorders of movement, movement rehabilitation, motion and balance, movement and cognition, human factors and ergonomics, as well as optimized movement in elite athletes, developmental issues of movement and coordination. Workshops on physiotherapy of movement impairment will also be provided. The abstracts of the conference as well as selected principal papers will be proceedings and will be published in the journal Functional Neurology, Rehabilitation, and Ergonomics published by Nova Scientific publishers. We welcome your participation in this event that addresses the relationship between movement and cognition and I personally welcome your enquiries and suggestions. In the meantime, please check out our website at: www.movementis.net (Our mail: office at movementis.com) Should you have any questions about the nature and form of the abstracts or ertaining to the larger papers, please connect with me at: g.leisman at alumni.manchester.ac.uk I hope to meet each of you at Oxford University in July 2017 Wish very best wishes, Gerry Leisman Chair Scientific Committee, MOVEMENT 2017 Director, The National Institute for Brain and Rehabilitation Sciences, Nazareth, Israel Professor, Human Factors and Rehabilitation Sciences O.R.T.-Braude College of Engineering, Karmiel, Israel Profesor de Neurolog?a restaurativa Universidad de Ciencias M?dicas de la Habana Facultad Manuel Fajardo, Havana, Cuba -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] roary is marked for autoremoval from testing Message-ID: roary 3.6.1+dfsg-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] bedtools is marked for autoremoval from testing Message-ID: bedtools 2.25.0-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] circlator is marked for autoremoval from testing Message-ID: circlator 1.2.0-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] reapr is marked for autoremoval from testing Message-ID: reapr 1.0.18+dfsg-2 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] python-pbcore is marked for autoremoval from testing Message-ID: python-pbcore 1.2.9+dfsg-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] smalt is marked for autoremoval from testing Message-ID: smalt 0.7.6-4 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] spades is marked for autoremoval from testing Message-ID: spades 3.7.1+dfsg-3 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] fitgcp is marked for autoremoval from testing Message-ID: fitgcp 0.0.20130418-2 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] pbalign is marked for autoremoval from testing Message-ID: pbalign 0.2.0-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] pbbam is marked for autoremoval from testing Message-ID: pbbam 0.1.0~20150813+git4e9e417+dfsg-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] stacks is marked for autoremoval from testing Message-ID: stacks 1.37-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] pbsuite is marked for autoremoval from testing Message-ID: pbsuite 15.8.24+dfsg-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] python-pbcommand is marked for autoremoval from testing Message-ID: python-pbcommand 0.3.22-2 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] pbgenomicconsensus is marked for autoremoval from testing Message-ID: pbgenomicconsensus 2.0.0+20151210-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] fastaq is marked for autoremoval from testing Message-ID: fastaq 3.12.1-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] pbbarcode is marked for autoremoval from testing Message-ID: pbbarcode 0.8.0-2 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] samtools is marked for autoremoval from testing Message-ID: samtools 1.3.1-1 is marked for autoremoval from testing on 2016-06-09 It is affected by these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:02 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:02 +0000 Subject: [Debian-med-packaging] python-pysam is marked for autoremoval from testing Message-ID: python-pysam 0.9.0+ds-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] falconkit is marked for autoremoval from testing Message-ID: falconkit 0.1.3+20140820-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] python-pymummer is marked for autoremoval from testing Message-ID: python-pymummer 0.7.0-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] python-pbh5tools is marked for autoremoval from testing Message-ID: python-pbh5tools 0.8.0+dfsg-4 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] trinityrnaseq is marked for autoremoval from testing Message-ID: trinityrnaseq 2.1.1+dfsg2-1 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From noreply at release.debian.org Wed May 4 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Wed, 04 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] gasic is marked for autoremoval from testing Message-ID: gasic 0.0.r18-3 is marked for autoremoval from testing on 2016-06-09 It (build-)depends on packages with these RC bugs: 822701: samtools: samtools 1.3 fails to build against htslib 1.3.1. From ftpmaster at ftp-master.debian.org Wed May 4 08:01:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 08:01:28 +0000 Subject: [Debian-med-packaging] htsjdk_2.1.1+dfsg.1-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 10 Apr 2016 08:10:57 +0200 Source: htsjdk Binary: libhtsjdk-java libhtsjdk-java-doc Architecture: source all Version: 2.1.1+dfsg.1-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libhtsjdk-java - Java API for high-throughput sequencing data (HTS) formats libhtsjdk-java-doc - Documentation for the java HTSJDK library Changes: htsjdk (2.1.1+dfsg.1-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Wed May 4 08:01:31 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 08:01:31 +0000 Subject: [Debian-med-packaging] libbpp-core_2.2.0-2~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 28 Apr 2016 18:51:13 +0200 Source: libbpp-core Binary: libbpp-core-dev libbpp-core2 Architecture: source amd64 Version: 2.2.0-2~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-core-dev - Bio++ Core library development files libbpp-core2 - Bio++ Core library Changes: libbpp-core (2.2.0-2~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Revert v5 name change Checksums-Sha1: e047cb275454eda390eb6618ea37b62905d332fb 2119 libbpp-core_2.2.0-2~bpo8+1.dsc 2abb64d52fb1cad11a24aa43c1d393463c03611e 4284 libbpp-core_2.2.0-2~bpo8+1.debian.tar.xz 8b567828726d109c37eab95ab1b3346924622451 1167056 libbpp-core-dev_2.2.0-2~bpo8+1_amd64.deb 249a9a591abfabe67cf810afe2a2b5a42667514b 516248 libbpp-core2_2.2.0-2~bpo8+1_amd64.deb Checksums-Sha256: a61ae92e413a0a3be105a91ab579aac3167729675b018b4dbb13f59932c2abdd 2119 libbpp-core_2.2.0-2~bpo8+1.dsc dc0da49dc2742cd8e2d1d6fe6ac3cbb38dce25f88d624f31c1aab1fc9c444508 4284 libbpp-core_2.2.0-2~bpo8+1.debian.tar.xz 5470cde10320e71a1661e209f214553725bb9285f44e6de8904ba2008d7c9dd1 1167056 libbpp-core-dev_2.2.0-2~bpo8+1_amd64.deb ea3adff3687d2ed13d55cc7ddc780d4a4b5dceb219a6e4fede9b29e591699912 516248 libbpp-core2_2.2.0-2~bpo8+1_amd64.deb Files: 8f7c123313e80c2178bd965f348e788d 2119 science optional libbpp-core_2.2.0-2~bpo8+1.dsc 1b98d8aeece35431b3338b33d54c54ff 4284 science optional libbpp-core_2.2.0-2~bpo8+1.debian.tar.xz a14c24946a3a650b36e08bb2db883a0b 1167056 libdevel optional libbpp-core-dev_2.2.0-2~bpo8+1_amd64.deb 8d89cf9679a46e4e9c048aaeaee37118 516248 libs optional libbpp-core2_2.2.0-2~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXIkOpAAoJEFeKBJTRxkbRSRwP/iQFPBvSb6jEuvBS41gD2Qgg H1RWDpXKolxDjY/OcFHt84Ds+u8aULOjTWYO9DNnI657bWz5ANq2GHdZIN6/45N7 o26arjWz3OtbMv+EdhM0S85fDrvl+m+6WHjnBwWm7yidO0ljs8oxMe23FODdTkca 6swIss9wtyeRmmhicaRaJkGNaZQD5SpyNS4PJdW9ulpR1jDkEXRQO89SL9Rjv6Np 55Gu4Xi+3rxf5c9iChYQhqg5h/vZjvf2g2nUZhvSY0rmAyoiraE2wnt8VABx21gB I2tfqdwbQPIooHS5iPX8l27jHyyMb/P2H2/evYojnj3lA1yhbFbTz8G9q8Q63xne TEC747o9SEqIZcxMPdIVmJv0YU05XQQx9V5uAYsNhxy51D7ayNQVdo8UIvgaJLfg BLB2TC+LGW4CpxqquMjEC1/LLpEChNsV5bk30jAnjxKNhIoR22UMTEKqzVOjQeFS JHmRWx++rl5GXm5m1fs5YNxz5RIvGQOAxPaDyFyvFdUeebbbKqauTWrMP1KazgtV z93KtqKcKNPh2cADHiFmQn40tabD4do1gUTCOy7B37Z4dnaq/DaTWSmy1J/z2lFM yF60MFx/E20a3Svl/GEXpvgVx6wkRFNYlK/XSvemgrFfiCX6d9IW99XMYFSyDcTc Dsn5diFkRvcEFAOiiOMI =mbQS -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 4 08:01:47 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 08:01:47 +0000 Subject: [Debian-med-packaging] phyml_3.2.0+dfsg-2~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 22 Apr 2016 21:38:01 +0200 Source: phyml Binary: phyml Architecture: source amd64 Version: 3:3.2.0+dfsg-2~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: phyml - Phylogenetic estimation using Maximum Likelihood Changes: phyml (3:3.2.0+dfsg-2~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Wed May 4 08:12:36 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 08:12:36 +0000 Subject: [Debian-med-packaging] Processing of paml_4.91+dfsg-1_amd64.changes Message-ID: paml_4.91+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: paml_4.91+dfsg-1.dsc paml_4.91+dfsg.orig.tar.xz paml_4.91+dfsg-1.debian.tar.xz paml-dbgsym_4.91+dfsg-1_amd64.deb paml-doc_4.91+dfsg-1_all.deb paml_4.91+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From tille at debian.org Wed May 4 09:19:54 2016 From: tille at debian.org (Andreas Tille) Date: Wed, 04 May 2016 11:19:54 +0200 Subject: [Debian-med-packaging] Bug#823396: ITP: beast2-mcmc -- Bayesian MCMC phylogenetic inference Message-ID: <20160504091954.16051.97716.reportbug@mail.an3as.eu> Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name : beast2-mcmc Version : 2.4.1 Upstream Author : Alexei Drummond , Andrew Rambaut * URL : https://github.com/CompEvol/beast2 * License : LGPL Programming Lang: Java Description : Bayesian MCMC phylogenetic inference BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. . This is no new upstream version of beast-mcmc (1.x) but rather a rewritten version. Remark: This package will be maintained by the Debian Med team at https://anonscm.debian.org/git/debian-med/beast2-mcmc.git From ftpmaster at ftp-master.debian.org Wed May 4 10:26:10 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 10:26:10 +0000 Subject: [Debian-med-packaging] paml_4.91+dfsg-1_amd64.changes is NEW Message-ID: binary:paml is NEW. binary:paml-doc is NEW. source:paml is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From georg795 at gmail.com Wed May 4 11:31:41 2016 From: georg795 at gmail.com (SYNERGY JEWELLERY) Date: Wed, 4 May 2016 12:31:41 +0100 Subject: [Debian-med-packaging] Inquiry Message-ID: Dear Sir, There is a product my company needs from DUBAI (U.A.E) but we are having problem from the owner of the product due to language barrier. Our company deals on costumes such as DIAMOND POLISHER. We have been purchasing the product from SAUDI ARABIA but it is very scarce now and we got information that somebody has the product in stock in DUBAI-U.A.E. We contacted the owner of the product through his telephone number but could not understand his language as he speaks Arabic only, This is why we need a reliable company/individual that will help us link with the man. His name is HASSAN MOHAMMED, Please if this proposal interests you, do get back to us for modalities and we will also give you the telephone number of HASSAN MOHAMMED for you to call and confirm if he has the product we need, the price and the name of the product because the one we want is WHITE DIAMOND POLISHER and GREEN DIAMOND POLISHER, we use to buy from SAUDI ARABIA before at the rate of $490 per gram and we need about 4kilos. Assist us to know if the man has in stock up to 4Kilos and each gram that we are buying, we are adding some commission for your assistance. Please immediately you confirm reply only through my private email: palnderson01 at gmail.com so as to enable us arrange for our representative that will come to Dubai for the purchase of the material. Sir, we are seriously in need of the product because of lack of materials in our company. Once you confirm, we will be coming twice monthly. Please co-operate with us because this is a life time transaction. Regards, Paul Anderson. Email: palnderson01 at gmail.com United Kingdom. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Wed May 4 11:34:15 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 11:34:15 +0000 Subject: [Debian-med-packaging] Processing of beast2-mcmc_2.4.1+dfsg-1_amd64.changes Message-ID: beast2-mcmc_2.4.1+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: beast2-mcmc_2.4.1+dfsg-1.dsc beast2-mcmc_2.4.1+dfsg.orig.tar.xz beast2-mcmc_2.4.1+dfsg-1.debian.tar.xz beast2-mcmc-doc_2.4.1+dfsg-1_all.deb beast2-mcmc-examples_2.4.1+dfsg-1_all.deb beast2-mcmc_2.4.1+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 4 11:49:10 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 11:49:10 +0000 Subject: [Debian-med-packaging] beast2-mcmc_2.4.1+dfsg-1_amd64.changes is NEW Message-ID: binary:beast2-mcmc is NEW. binary:beast2-mcmc-doc is NEW. binary:beast2-mcmc-examples is NEW. source:beast2-mcmc is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From andreas at an3as.eu Wed May 4 11:49:13 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 4 May 2016 13:49:13 +0200 Subject: [Debian-med-packaging] Bug#767144: That long-standing nasty Tcl/Tk-bug with autodocktools (Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI)) In-Reply-To: <20160210140049.GA11464@an3as.eu> References: <20151229074001.GG2138@an3as.eu> <56824A87.2070601@gmx.de> <9B9F464463CB36488E8904CF8336917F01F52F75C036@EXCH-CCR01.lj.ad.scripps.edu> <5682DCF4.3060503@scripps.edu> <20151229202959.GF30126@an3as.eu> <56832CC4.6080800@gmx.de> <56BA80D3.2060008@scripps.edu> <20160210140049.GA11464@an3as.eu> Message-ID: <20160504114913.GD20381@an3as.eu> Hi Steffen, any progress with this issue? I'm tempted to remove non-functional software from the Debian archive. It would be really great if you could put some effort into this. Kind regards Andreas. On Wed, Feb 10, 2016 at 03:00:49PM +0100, Andreas Tille wrote: > Hi Steffen, > > On Wed, Feb 10, 2016 at 02:08:48PM +0100, "Steffen M?ller" wrote: > > Hello Michel, > > > > > Gesendet: Mittwoch, 10. Februar 2016 um 01:14 Uhr > > > Von: "Michel Sanner" > > > An: "Steffen M?ller" , "Andreas Tille" > > > Cc: "Stefano Forli" > > > Betreff: Re: That long-standing nasty Tcl/Tk-bug with autodocktools Re: Bitte weiterleiten (Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI)) > > > > > > Hello Steffen > > > > > > Sorry for dropping the ball on this. I am a bit confused why this > > > happens as we ship MGLTools with the Tcl/Tk > > > libraries provided and 1.5.7 rc1 ships with Tcl Tk 8.5 > > > > I admit to be tempted to just tar all you provide up and then redistribute > > just that. Would save us from quite some hassles. > > ... IMHO this will just replace the known hassles by new ones. > > > But we would not have > > identified that bug for you, either :o) From what I had identified about > > half a year ago (two nights or so went into it) I had no idea why 8.5 > > tolerated it. I could well imagine that this fix also helps the overall > > stability of your suite. > > > > The deep theory is that by note having independent (Windows-/Mac-like) > > software installation, i.e. by sharing as much as we all can, any improvemnt > > to any package would have as much of an effect as soon as possible on > > as many as possible other packages. And it should be fun, too. Debian has > > the stable distribution for what works (with Tk 8.5), testing and unstable > > are to get stuff synced up. And, you shall also benefit from 8.6. > > > > https://www.tcl.tk/software/tcltk/8.6.html overview > > http://wiki.tcl.tk/21276 changes > > http://www.tcl.tk/cgi-bin/tct/tip/311 release calendar - 8.6 started 2008 :) > > > > Admittedly, 8.5 is still mainained, also in Debian as it seems > > https://packages.debian.org/search?keywords=tk8.5 > > but the default is 8.6 and all other modules and libraries depending on any > > libtk are rebuilt against the newer version, i.e. any Python module with it, > > https://packages.debian.org/de/sid/python-tk > > I do not think that trying to safe the issue by forcing tk8.5 will be a > sustainable solution. > > > > I suppose you guys rebuild from scratch and do not create an isolated > > > environment for running the Python > > > interpreter that runs AutoDockTools like we do when people install using > > > our installer ? > > > > That is correct. > > > > > I will look if I can find a quick fix as this happens in a gui that is > > > no often made visible > > > > It affects about everything that you can start with AutoDockTools. I will > > not let you alone with it all. I just saw your second email and will address > > that over the weekend the latest. > > As I expressed in my other mail we now have an additional issue with numpy. > > Kind regards > > Andreas. > > > > On 12/29/2015 05:00 PM, Steffen M?ller wrote: > > > > Hello Michel, hello Stefano, > > > > > > > > nice to hear from you, indeed. I happen to be a recent El Capitan user > > > > myself and thus > > > > can help testing on that front, too. > > > > > > > > I was not aware of a release of 1.5.7, which I had seen only as a RC1, > > > > using the > > > > information shown on > > > > http://mgltools.scripps.edu/downloads > > > > The problem should manifest itself on any platform with TclTk 8.6 onwards. > > > > Until a few seconds ago I had truly thought that you were working on > > > > something > > > > completely different already that would be released once it is ready and as > > > > such you did not notice/care about that "works with 8.5" problem. > > > > > > > > How shall we proceed? I propose that we get the code base and tools in sync > > > > and I prepare an update of the Debian packages. Is the CVS repository of > > > > yours > > > > still the place where to look? What version of TclTk do you work with? > > > > Just instruct me. > > > > > > > > Concerning the time line I am swamped till mid January. We have our next > > > > Debian meeting in Copenhagen on the first February weekend. Would be nice to > > > > have the bug fixed till then. > > > > > > > > Best, > > > > > > > > Steffen > > > > > > > > > > > > On 29/12/15 21:29, Andreas Tille wrote: > > > >> Hi Michel, > > > >> > > > >> As far as I know installing Tcl/Tk 8.6 you should be able to reproduce > > > >> the problem. The best resource of information is probably > > > >> > > > >> https://lists.alioth.debian.org/pipermail/pkg-tcltk-devel/2015-December/002938.html > > > >> > > > >> Hope this helps > > > >> > > > >> Andreas. > > > >> > > > >> On Tue, Dec 29, 2015 at 11:20:20AM -0800, Michel Sanner wrote: > > > >>> Happy Holidays all > > > >>> > > > >>> I am not aware of this bug. Could you please let me know how to reproduce it > > > >>> ? and of course > > > >>> if you have a patch I'll be happy to incorporate it. We are working on a bug > > > >>> fix release of MGLTools 1.5.7 > > > >>> > > > >>> This release has been postponed a little as we are trying to address some > > > >>> issues with the newest Mac OS > > > >>> El Capitan. This delay will hopefully gives us time to incorporate a bug fix > > > >>> for this problem as well > > > >>> > > > >>> -Michel > > > >>> > > > >>> On 12/29/15 10:22 AM, Stefano Forli wrote: > > > >>>> Hi Steffen (and Andreas), > > > >>>> I hope you're having happy Holidays yourselves. I'm currently in Italy enjoying some time with family. > > > >>>> No worries about bothering, you're all doing us a huge favor, so we're always in debt. > > > >>>> > > > >>>> I'm CC'ing Michel in the conversation, since he's in charge of the source code. > > > >>>> I got bit by these issues with Tcl with the old Raccoon version you packaged, but I wasn't aware of the problems with the main package AutoDockTools. > > > >>>> If you think it is something that can be solved with a reasonable amount of patches, I believe there's no problem in adding them to our CVS (but I'll let Michel chip in about this). > > > >>>> > > > >>>> I'll be happy to test the patched code, if you have any. > > > >>>> > > > >>>> Thanks! > > > >>>> > > > >>>> S > > > >>>> > > > >>>> > > > >>>> -- > > > >>>> > > > >>>> Stefano Forli, PhD > > > >>>> > > > >>>> Assistant Professor of Integrative > > > >>>> Structural and Computational Biology, > > > >>>> Molecular Graphics Laboratory > > > >>>> > > > >>>> Dept. of Integrative Structural > > > >>>> and Computational Biology, MB-112F > > > >>>> The Scripps Research Institute > > > >>>> 10550 North Torrey Pines Road > > > >>>> La Jolla, CA 92037-1000, USA. > > > >>>> > > > >>>> tel: +1 (858)784-2055 > > > >>>> fax: +1 (858)784-2860 > > > >>>> email: forli at scripps.edu > > > >>>> http://www.scripps.edu/~forli/ > > > >>>> ________________________________________ > > > >>>> From: Steffen M?ller [steffen_moeller at gmx.de] > > > >>>> Sent: Tuesday, December 29, 2015 12:55 AM > > > >>>> To: Andreas Tille; Stefano Forli > > > >>>> Subject: That long-standing nasty Tcl/Tk-bug with autodocktools Re: Bitte weiterleiten (Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI)) > > > >>>> > > > >>>> Hi Stefano, > > > >>>> > > > >>>> some merry Christmas I hope you had and all the best for the New Year, > > > >>>> of course. The inter-annual time (as we say over here) is most likely > > > >>>> the most productive in the Open Source world :) Please forgive me > > > >>>> contacting you during all these festivities. > > > >>>> > > > >>>> I admit to know about this Tcl bug for some time, and I had even kind of > > > >>>> traced it down: the autodocktools do not pack their widgets right, i.e. > > > >>>> they are missing absolute and relative positions. Later versions than > > > >>>> 8.5 are apparently no longer tolerating it, and 8.6 is no longer any > > > >>>> recent version, I am afraid. Andreas is about to remove the package from > > > >>>> the distro as it is unusable as it is. > > > >>>> > > > >>>> How are your feelings about it all? Would you accept patches? Is there > > > >>>> something in your CVS that we should address, instead? > > > >>>> > > > >>>> All the best possible wishes > > > >>>> > > > >>>> Steffen > > > >>>> > > > >>>> On 29/12/15 08:40, Andreas Tille wrote: > > > >>>>> Hi Steffen, > > > >>>>> > > > >>>>> kannst Du das bitte mal an die Autoren weiterleiten (und den Bug in CC > > > >>>>> setzen). Ansonsten lasse ich das Paket entfernen, weil es ja > > > >>>>> offensichtlich zu nichts n?tze ist, wenn es nicht mal startet. > > > >>>>> > > > >>>>> Viele Gr??e > > > >>>>> > > > >>>>> Andreas. > > > >>>>> > > > >>>>> ----- Forwarded message from Sergei Golovan ----- > > > >>>>> > > > >>>>> Date: Thu, 24 Dec 2015 10:52:27 +0300 > > > >>>>> From: Sergei Golovan > > > >>>>> To: Andreas Tille > > > >>>>> Cc: Senthil Kumaran , 767145 at bugs.debian.org, Tcl/Tk Debian Packagers > > > >>>>> Subject: Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI) > > > >>>>> > > > >>>>> Hi Andreas, > > > >>>>> > > > >>>>> On Wed, Dec 23, 2015 at 11:42 PM, Andreas Tille wrote: > > > >>>>>> Hi Tcl/Tk packaging team, > > > >>>>>> > > > >>>>>> unfortunately I got no help on debian-mentors and since we somehow need > > > >>>>>> to tackle bug #767144 I wonder if you Tcl/Tk experts might be able to > > > >>>>>> provide some help. > > > >>>>> As far as I can see, you've stumbled on the change between Tcl/Tk 8.5 > > > >>>>> and 8.6. In Tcl/Tk 8.5 one could mix grid and pack geometry managers > > > >>>>> in one master window. It often works but sometimes leads to > > > >>>>> unpredictable results, sometimes an application which does that just > > > >>>>> hangs. In Tcl/Tk 8.6 this mixing of grid and pack was explicitly > > > >>>>> forbidden, hence this error message. > > > >>>>> > > > >>>>> I don't think that there is an easy way to fix this. You can't just > > > >>>>> revert to using Tcl/Tk 8.5 because Tkinter in Debian is already > > > >>>>> switched to Tk 8.6 (and I guess using custom Tkinter is not an > > > >>>>> option). So, one has to carefully find all mixed up packs and grids > > > >>>>> and make sure that only one of them is used in every particular master > > > >>>>> window. In plain Tcl/Tk I'd override the [pack] and [grid] routines to > > > >>>>> print some debug information (something like > > > >>>>> > > > >>>>> rename pack pack:orig > > > >>>>> proc pack {args} { > > > >>>>> puts stderr "pack: [info level -1] $args" > > > >>>>> pack:orig {*}$args > > > >>>>> } > > > >>>>> > > > >>>>> and similar for grid). This would help to trace where exactly the > > > >>>>> mixed geometry master windows appear. I don't know how you can do > > > >>>>> something similar in Python, but I'm pretty sure it's possible. > > > >>>>> > > > >>>>> Cheers! > > > >>> -- > > > >>> > > > >>> ----------------------------------------------------------------------- > > > >>> o > > > >>> / Michel F. Sanner Ph.D. The Scripps Research Institute > > > >>> o Associate Professor Department of Molecular Biology > > > >>> \ 10550 North Torrey Pines Road > > > >>> o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26 > > > >>> / Fax. (858) 784-2341 > > > >>> o sanner at scripps.edu http://www.scripps.edu/~sanner > > > >>> ----------------------------------------------------------------------- > > > >>> > > > >>> > > > > > > -- > > > > > > ----------------------------------------------------------------------- > > > o > > > / Michel F. Sanner Ph.D. The Scripps Research Institute > > > o Associate Professor Department of Molecular Biology > > > \ 10550 North Torrey Pines Road > > > o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26 > > > / Fax. (858) 784-2341 > > > o sanner at scripps.edu http://www.scripps.edu/~sanner > > > ----------------------------------------------------------------------- > > > > > > > > > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From andreas at an3as.eu Wed May 4 11:49:13 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 4 May 2016 13:49:13 +0200 Subject: [Debian-med-packaging] Bug#783547: Bug#767144: That long-standing nasty Tcl/Tk-bug with autodocktools (Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI)) In-Reply-To: <20160210140049.GA11464@an3as.eu> References: <20151229074001.GG2138@an3as.eu> <56824A87.2070601@gmx.de> <9B9F464463CB36488E8904CF8336917F01F52F75C036@EXCH-CCR01.lj.ad.scripps.edu> <5682DCF4.3060503@scripps.edu> <20151229202959.GF30126@an3as.eu> <56832CC4.6080800@gmx.de> <56BA80D3.2060008@scripps.edu> <20160210140049.GA11464@an3as.eu> Message-ID: <20160504114913.GD20381@an3as.eu> Hi Steffen, any progress with this issue? I'm tempted to remove non-functional software from the Debian archive. It would be really great if you could put some effort into this. Kind regards Andreas. On Wed, Feb 10, 2016 at 03:00:49PM +0100, Andreas Tille wrote: > Hi Steffen, > > On Wed, Feb 10, 2016 at 02:08:48PM +0100, "Steffen M?ller" wrote: > > Hello Michel, > > > > > Gesendet: Mittwoch, 10. Februar 2016 um 01:14 Uhr > > > Von: "Michel Sanner" > > > An: "Steffen M?ller" , "Andreas Tille" > > > Cc: "Stefano Forli" > > > Betreff: Re: That long-standing nasty Tcl/Tk-bug with autodocktools Re: Bitte weiterleiten (Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI)) > > > > > > Hello Steffen > > > > > > Sorry for dropping the ball on this. I am a bit confused why this > > > happens as we ship MGLTools with the Tcl/Tk > > > libraries provided and 1.5.7 rc1 ships with Tcl Tk 8.5 > > > > I admit to be tempted to just tar all you provide up and then redistribute > > just that. Would save us from quite some hassles. > > ... IMHO this will just replace the known hassles by new ones. > > > But we would not have > > identified that bug for you, either :o) From what I had identified about > > half a year ago (two nights or so went into it) I had no idea why 8.5 > > tolerated it. I could well imagine that this fix also helps the overall > > stability of your suite. > > > > The deep theory is that by note having independent (Windows-/Mac-like) > > software installation, i.e. by sharing as much as we all can, any improvemnt > > to any package would have as much of an effect as soon as possible on > > as many as possible other packages. And it should be fun, too. Debian has > > the stable distribution for what works (with Tk 8.5), testing and unstable > > are to get stuff synced up. And, you shall also benefit from 8.6. > > > > https://www.tcl.tk/software/tcltk/8.6.html overview > > http://wiki.tcl.tk/21276 changes > > http://www.tcl.tk/cgi-bin/tct/tip/311 release calendar - 8.6 started 2008 :) > > > > Admittedly, 8.5 is still mainained, also in Debian as it seems > > https://packages.debian.org/search?keywords=tk8.5 > > but the default is 8.6 and all other modules and libraries depending on any > > libtk are rebuilt against the newer version, i.e. any Python module with it, > > https://packages.debian.org/de/sid/python-tk > > I do not think that trying to safe the issue by forcing tk8.5 will be a > sustainable solution. > > > > I suppose you guys rebuild from scratch and do not create an isolated > > > environment for running the Python > > > interpreter that runs AutoDockTools like we do when people install using > > > our installer ? > > > > That is correct. > > > > > I will look if I can find a quick fix as this happens in a gui that is > > > no often made visible > > > > It affects about everything that you can start with AutoDockTools. I will > > not let you alone with it all. I just saw your second email and will address > > that over the weekend the latest. > > As I expressed in my other mail we now have an additional issue with numpy. > > Kind regards > > Andreas. > > > > On 12/29/2015 05:00 PM, Steffen M?ller wrote: > > > > Hello Michel, hello Stefano, > > > > > > > > nice to hear from you, indeed. I happen to be a recent El Capitan user > > > > myself and thus > > > > can help testing on that front, too. > > > > > > > > I was not aware of a release of 1.5.7, which I had seen only as a RC1, > > > > using the > > > > information shown on > > > > http://mgltools.scripps.edu/downloads > > > > The problem should manifest itself on any platform with TclTk 8.6 onwards. > > > > Until a few seconds ago I had truly thought that you were working on > > > > something > > > > completely different already that would be released once it is ready and as > > > > such you did not notice/care about that "works with 8.5" problem. > > > > > > > > How shall we proceed? I propose that we get the code base and tools in sync > > > > and I prepare an update of the Debian packages. Is the CVS repository of > > > > yours > > > > still the place where to look? What version of TclTk do you work with? > > > > Just instruct me. > > > > > > > > Concerning the time line I am swamped till mid January. We have our next > > > > Debian meeting in Copenhagen on the first February weekend. Would be nice to > > > > have the bug fixed till then. > > > > > > > > Best, > > > > > > > > Steffen > > > > > > > > > > > > On 29/12/15 21:29, Andreas Tille wrote: > > > >> Hi Michel, > > > >> > > > >> As far as I know installing Tcl/Tk 8.6 you should be able to reproduce > > > >> the problem. The best resource of information is probably > > > >> > > > >> https://lists.alioth.debian.org/pipermail/pkg-tcltk-devel/2015-December/002938.html > > > >> > > > >> Hope this helps > > > >> > > > >> Andreas. > > > >> > > > >> On Tue, Dec 29, 2015 at 11:20:20AM -0800, Michel Sanner wrote: > > > >>> Happy Holidays all > > > >>> > > > >>> I am not aware of this bug. Could you please let me know how to reproduce it > > > >>> ? and of course > > > >>> if you have a patch I'll be happy to incorporate it. We are working on a bug > > > >>> fix release of MGLTools 1.5.7 > > > >>> > > > >>> This release has been postponed a little as we are trying to address some > > > >>> issues with the newest Mac OS > > > >>> El Capitan. This delay will hopefully gives us time to incorporate a bug fix > > > >>> for this problem as well > > > >>> > > > >>> -Michel > > > >>> > > > >>> On 12/29/15 10:22 AM, Stefano Forli wrote: > > > >>>> Hi Steffen (and Andreas), > > > >>>> I hope you're having happy Holidays yourselves. I'm currently in Italy enjoying some time with family. > > > >>>> No worries about bothering, you're all doing us a huge favor, so we're always in debt. > > > >>>> > > > >>>> I'm CC'ing Michel in the conversation, since he's in charge of the source code. > > > >>>> I got bit by these issues with Tcl with the old Raccoon version you packaged, but I wasn't aware of the problems with the main package AutoDockTools. > > > >>>> If you think it is something that can be solved with a reasonable amount of patches, I believe there's no problem in adding them to our CVS (but I'll let Michel chip in about this). > > > >>>> > > > >>>> I'll be happy to test the patched code, if you have any. > > > >>>> > > > >>>> Thanks! > > > >>>> > > > >>>> S > > > >>>> > > > >>>> > > > >>>> -- > > > >>>> > > > >>>> Stefano Forli, PhD > > > >>>> > > > >>>> Assistant Professor of Integrative > > > >>>> Structural and Computational Biology, > > > >>>> Molecular Graphics Laboratory > > > >>>> > > > >>>> Dept. of Integrative Structural > > > >>>> and Computational Biology, MB-112F > > > >>>> The Scripps Research Institute > > > >>>> 10550 North Torrey Pines Road > > > >>>> La Jolla, CA 92037-1000, USA. > > > >>>> > > > >>>> tel: +1 (858)784-2055 > > > >>>> fax: +1 (858)784-2860 > > > >>>> email: forli at scripps.edu > > > >>>> http://www.scripps.edu/~forli/ > > > >>>> ________________________________________ > > > >>>> From: Steffen M?ller [steffen_moeller at gmx.de] > > > >>>> Sent: Tuesday, December 29, 2015 12:55 AM > > > >>>> To: Andreas Tille; Stefano Forli > > > >>>> Subject: That long-standing nasty Tcl/Tk-bug with autodocktools Re: Bitte weiterleiten (Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI)) > > > >>>> > > > >>>> Hi Stefano, > > > >>>> > > > >>>> some merry Christmas I hope you had and all the best for the New Year, > > > >>>> of course. The inter-annual time (as we say over here) is most likely > > > >>>> the most productive in the Open Source world :) Please forgive me > > > >>>> contacting you during all these festivities. > > > >>>> > > > >>>> I admit to know about this Tcl bug for some time, and I had even kind of > > > >>>> traced it down: the autodocktools do not pack their widgets right, i.e. > > > >>>> they are missing absolute and relative positions. Later versions than > > > >>>> 8.5 are apparently no longer tolerating it, and 8.6 is no longer any > > > >>>> recent version, I am afraid. Andreas is about to remove the package from > > > >>>> the distro as it is unusable as it is. > > > >>>> > > > >>>> How are your feelings about it all? Would you accept patches? Is there > > > >>>> something in your CVS that we should address, instead? > > > >>>> > > > >>>> All the best possible wishes > > > >>>> > > > >>>> Steffen > > > >>>> > > > >>>> On 29/12/15 08:40, Andreas Tille wrote: > > > >>>>> Hi Steffen, > > > >>>>> > > > >>>>> kannst Du das bitte mal an die Autoren weiterleiten (und den Bug in CC > > > >>>>> setzen). Ansonsten lasse ich das Paket entfernen, weil es ja > > > >>>>> offensichtlich zu nichts n?tze ist, wenn es nicht mal startet. > > > >>>>> > > > >>>>> Viele Gr??e > > > >>>>> > > > >>>>> Andreas. > > > >>>>> > > > >>>>> ----- Forwarded message from Sergei Golovan ----- > > > >>>>> > > > >>>>> Date: Thu, 24 Dec 2015 10:52:27 +0300 > > > >>>>> From: Sergei Golovan > > > >>>>> To: Andreas Tille > > > >>>>> Cc: Senthil Kumaran , 767145 at bugs.debian.org, Tcl/Tk Debian Packagers > > > >>>>> Subject: Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI) > > > >>>>> > > > >>>>> Hi Andreas, > > > >>>>> > > > >>>>> On Wed, Dec 23, 2015 at 11:42 PM, Andreas Tille wrote: > > > >>>>>> Hi Tcl/Tk packaging team, > > > >>>>>> > > > >>>>>> unfortunately I got no help on debian-mentors and since we somehow need > > > >>>>>> to tackle bug #767144 I wonder if you Tcl/Tk experts might be able to > > > >>>>>> provide some help. > > > >>>>> As far as I can see, you've stumbled on the change between Tcl/Tk 8.5 > > > >>>>> and 8.6. In Tcl/Tk 8.5 one could mix grid and pack geometry managers > > > >>>>> in one master window. It often works but sometimes leads to > > > >>>>> unpredictable results, sometimes an application which does that just > > > >>>>> hangs. In Tcl/Tk 8.6 this mixing of grid and pack was explicitly > > > >>>>> forbidden, hence this error message. > > > >>>>> > > > >>>>> I don't think that there is an easy way to fix this. You can't just > > > >>>>> revert to using Tcl/Tk 8.5 because Tkinter in Debian is already > > > >>>>> switched to Tk 8.6 (and I guess using custom Tkinter is not an > > > >>>>> option). So, one has to carefully find all mixed up packs and grids > > > >>>>> and make sure that only one of them is used in every particular master > > > >>>>> window. In plain Tcl/Tk I'd override the [pack] and [grid] routines to > > > >>>>> print some debug information (something like > > > >>>>> > > > >>>>> rename pack pack:orig > > > >>>>> proc pack {args} { > > > >>>>> puts stderr "pack: [info level -1] $args" > > > >>>>> pack:orig {*}$args > > > >>>>> } > > > >>>>> > > > >>>>> and similar for grid). This would help to trace where exactly the > > > >>>>> mixed geometry master windows appear. I don't know how you can do > > > >>>>> something similar in Python, but I'm pretty sure it's possible. > > > >>>>> > > > >>>>> Cheers! > > > >>> -- > > > >>> > > > >>> ----------------------------------------------------------------------- > > > >>> o > > > >>> / Michel F. Sanner Ph.D. The Scripps Research Institute > > > >>> o Associate Professor Department of Molecular Biology > > > >>> \ 10550 North Torrey Pines Road > > > >>> o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26 > > > >>> / Fax. (858) 784-2341 > > > >>> o sanner at scripps.edu http://www.scripps.edu/~sanner > > > >>> ----------------------------------------------------------------------- > > > >>> > > > >>> > > > > > > -- > > > > > > ----------------------------------------------------------------------- > > > o > > > / Michel F. Sanner Ph.D. The Scripps Research Institute > > > o Associate Professor Department of Molecular Biology > > > \ 10550 North Torrey Pines Road > > > o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26 > > > / Fax. (858) 784-2341 > > > o sanner at scripps.edu http://www.scripps.edu/~sanner > > > ----------------------------------------------------------------------- > > > > > > > > > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From owner at bugs.debian.org Wed May 4 11:57:17 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Wed, 04 May 2016 11:57:17 +0000 Subject: [Debian-med-packaging] Bug#822701: marked as done (samtools 1.3 fails to build against htslib 1.3.1.) References: <20160504115517.GA20921@falafel.plessy.net> <1461693748.2750823.590308017.767C5093@webmail.messagingengine.com> Message-ID: Your message dated Wed, 4 May 2016 20:55:17 +0900 with message-id <20160504115517.GA20921 at falafel.plessy.net> and subject line Re: Bug#822701: [Debian-med-packaging] Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure; has caused the Debian Bug report #822701, regarding samtools 1.3 fails to build against htslib 1.3.1. to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 822701: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822701 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Chris Lamb Subject: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure; Date: Tue, 26 Apr 2016 19:02:28 +0100 Size: 35738 URL: -------------- next part -------------- An embedded message was scrubbed... From: Charles Plessy Subject: Re: Bug#822701: [Debian-med-packaging] Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure; Date: Wed, 4 May 2016 20:55:17 +0900 Size: 2175 URL: From ftpmaster at ftp-master.debian.org Wed May 4 11:59:22 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 11:59:22 +0000 Subject: [Debian-med-packaging] Processing of fsa_1.15.9+dfsg-1_amd64.changes Message-ID: fsa_1.15.9+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: fsa_1.15.9+dfsg-1.dsc fsa_1.15.9+dfsg.orig.tar.xz fsa_1.15.9+dfsg-1.debian.tar.xz fsa-dbgsym_1.15.9+dfsg-1_amd64.deb fsa_1.15.9+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at an3as.eu Wed May 4 12:11:08 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 4 May 2016 14:11:08 +0200 Subject: [Debian-med-packaging] Missing testthat input for taxize In-Reply-To: <20160331173119.GB27477@an3as.eu> References: <20160331173119.GB27477@an3as.eu> Message-ID: <20160504121108.GE20381@an3as.eu> Hi again, I realised that taxize 0.7.5 was released meanwhile but the testthat input file keeps on missing? Since you did not answered my mail I wonder whether you might have received it. Kind regards Andreas. On Thu, Mar 31, 2016 at 07:31:19PM +0200, Andreas Tille wrote: > Hi Scott, > > I intend to package taxize for the Debian distribution as a precondition > for some R package. Since Debian provides automatic tests I intended to > run the testthat suite contained in the taxize source. Unfortunately the > main input file that usualy resides in the tests/ dir and controls the > call of the single tests in tests/testthat is missing. > > I think this is not intended and you might probably want to provide > this in your next release. > > Kind regards > > Andreas. > > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Wed May 4 12:14:31 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 12:14:31 +0000 Subject: [Debian-med-packaging] Processing of seaview_4.6-2~bpo8+1_amd64.changes Message-ID: seaview_4.6-2~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: seaview_4.6-2~bpo8+1.dsc seaview_4.6-2~bpo8+1.debian.tar.xz seaview_4.6-2~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 4 12:19:05 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 12:19:05 +0000 Subject: [Debian-med-packaging] fsa_1.15.9+dfsg-1_amd64.changes is NEW Message-ID: binary:fsa is NEW. source:fsa is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Wed May 4 12:20:44 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 12:20:44 +0000 Subject: [Debian-med-packaging] seaview_4.6-2~bpo8+1_amd64.changes is NEW Message-ID: binary:seaview is NEW. source:seaview is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From andreas at an3as.eu Wed May 4 12:19:15 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 4 May 2016 14:19:15 +0200 Subject: [Debian-med-packaging] Bug#777791: [PATCH] ball: ftbfs with GCC-5 In-Reply-To: <20160411184127.GH31347@an3as.eu> References: <20160107121229.GC26705@an3as.eu> <56A7A02D.6080501@danny-edel.de> <20160126193150.GD31910@an3as.eu> <570BB9B9.7020408@danny-edel.de> <20160411155403.GE31347@an3as.eu> <20160411155403.GE31347@an3as.eu> <570BE6E7.7060500@danny-edel.de> <20160411184127.GH31347@an3as.eu> Message-ID: <20160504121915.GF20381@an3as.eu> Any success with you alioth commits? Did you possibly pinged alioth admins via IRC? I'd love to get you properly working as any normal Debian Med member. If not I'd try to investigate. Kind regards Andreas. On Mon, Apr 11, 2016 at 08:41:27PM +0200, Andreas Tille wrote: > Hi Danny, > > On Mon, Apr 11, 2016 at 08:03:19PM +0200, Danny Edel wrote: > > > git://anonscm.debian.org/debian-med/ball.git > > > > sorry for the miswording -- I did use the git repository at the > > specified location, not collab-maint. If the patch didn't apply cleanly > > I can't say why. > > > > since I tried to > > > > > > git am 0001-Rework-patches-for-sid.patch > > > > > > which resulted in several conflicts. I wonder whether you could > > > rather commit to the official packaging repository. To enable you > > > doing this I've added you to the Debian Med team. > > > > Thanks! I will submit there as soon as the group membership is through. > > I can already see that I'm added in the alioth webinterface, but > > "groups" on git.debian.org doesn't yet include scm_debian-med. > > > > Trying to push anyway gives: > > > > danny at debwork ~/git/debian-med/ball $ git push -v > > Pushing to git.debian.org:/git/debian-med/ball.git > > Counting objects: 13, done. > > Delta compression using up to 2 threads. > > Compressing objects: 100% (13/13), done. > > Writing objects: 100% (13/13), 6.09 KiB | 0 bytes/s, done. > > Total 13 (delta 4), reused 0 (delta 0) > > > > remote: error: insufficient permission for adding an object to > > repository database ./objects > > > > remote: fatal: failed to write object > > > > error: unpack failed: unpack-objects abnormal exit > > > > To git.debian.org:/git/debian-med/ball.git > > = [up to date] pristine-tar -> pristine-tar > > = [up to date] upstream -> upstream > > ! [remote rejected] master -> master (unpacker error) > > updating local tracking ref 'refs/remotes/origin/pristine-tar' > > updating local tracking ref 'refs/remotes/origin/upstream' > > error: failed to push some refs to 'git.debian.org:/git/debian-med/ball.git' > > > > I will try to push again later tonight or tomorrow. I'm sure this is > > just an issue about the group membership update script not run yet. > > Sounds convincing. > > Thanks a lot for your patience > > Andreas. > > PS: The private CC I used bounced. May be you check the logs of your > mailserver. > > > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Wed May 4 12:24:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 12:24:34 +0000 Subject: [Debian-med-packaging] Processing of surankco_0.0.r5+dfsg-1~bpo8+1_amd64.changes Message-ID: surankco_0.0.r5+dfsg-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: surankco_0.0.r5+dfsg-1~bpo8+1.dsc surankco_0.0.r5+dfsg-1~bpo8+1.debian.tar.xz surankco_0.0.r5+dfsg-1~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 4 12:49:42 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 12:49:42 +0000 Subject: [Debian-med-packaging] Processing of picard-tools_2.1.1+dfsg-1~bpo8+1_amd64.changes Message-ID: picard-tools_2.1.1+dfsg-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: picard-tools_2.1.1+dfsg-1~bpo8+1.dsc picard-tools_2.1.1+dfsg-1~bpo8+1.debian.tar.xz picard-tools_2.1.1+dfsg-1~bpo8+1_all.deb libpicard-java_2.1.1+dfsg-1~bpo8+1_all.deb libpicard-java-doc_2.1.1+dfsg-1~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at an3as.eu Wed May 4 13:04:17 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 4 May 2016 15:04:17 +0200 Subject: [Debian-med-packaging] Please check whether I fixed syntax error in proteinortho properly In-Reply-To: <5719EF17.4060103@staff.uni-marburg.de> References: <20160310195755.GC2148@an3as.eu> <20160316130925.GB30138@an3as.eu> <56E96B3D.6010801@staff.uni-marburg.de> <20160316170252.GA4619@an3as.eu> <56EA9C2F.6000404@staff.uni-marburg.de> <20160317200202.GE31901@an3as.eu> <5719EF17.4060103@staff.uni-marburg.de> Message-ID: <20160504130417.GG20381@an3as.eu> Hi Marcus, On Fri, Apr 22, 2016 at 11:29:59AM +0200, Marcus Lechner wrote: > I followed your suggestions regarding the Makefile (also added > proteinortho5_tree for install, thanks) in the new update (5.13 -> > http://www.bioinf.uni-leipzig.de/Software/proteinortho/). > As there was a quite bad bug in 5.12, I kindly ask whether you could pack > the new version? Done. :-) > Regarding the stripping of all binaries: From my experience, many users that > download the tar-ball are actually not familiar with compiling and can get > started with the binaries. That's why they are inside. Would it be a useful > option to provide two tar-balls, one with and one without binaries for > either purpose? Yes. I would recommend to support a tarball with binaries and one with sources exclusively. If users have no idea how to build the binary from source they probably do not need the source at all - so the two different tarballs would serve different user groups. > Thanks a lot and best regards, You are welcome and thanks for your cooperation Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Wed May 4 13:04:44 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 13:04:44 +0000 Subject: [Debian-med-packaging] Processing of proteinortho_5.13+dfsg-1_amd64.changes Message-ID: proteinortho_5.13+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: proteinortho_5.13+dfsg-1.dsc proteinortho_5.13+dfsg.orig.tar.xz proteinortho_5.13+dfsg-1.debian.tar.xz proteinortho-dbgsym_5.13+dfsg-1_amd64.deb proteinortho_5.13+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at an3as.eu Wed May 4 13:29:30 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 4 May 2016 15:29:30 +0200 Subject: [Debian-med-packaging] Bug#818505: sortmerna FTBFS on !x86 In-Reply-To: <20160327181527.GA22036@angband.pl> References: <20160327053123.GA13867@an3as.eu> <20160327124932.GB1366@angband.pl> <1459092751.5616.13.camel@gmail.com> <20160327181527.GA22036@angband.pl> Message-ID: <20160504132930.GB25614@an3as.eu> On Sun, Mar 27, 2016 at 08:15:27PM +0200, Adam Borowski wrote: > > It might be also good to make a "sse2-support" package as mentioned in the > thread Gert linked to to reduce duplication of such detection logic. Please > say so if you think this is a good idea. Saying "so". :-) Yes, having an sse2-support package would be brilliant since this is definitely not the first time I'm stumbling upon this issue. Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Wed May 4 13:41:41 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 13:41:41 +0000 Subject: [Debian-med-packaging] picard-tools_2.1.1+dfsg-1~bpo8+1_amd64.changes is NEW Message-ID: binary:libpicard-java is NEW. binary:libpicard-java-doc is NEW. binary:picard-tools is NEW. source:picard-tools is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Wed May 4 13:42:02 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 13:42:02 +0000 Subject: [Debian-med-packaging] proteinortho_5.13+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 04 May 2016 14:55:07 +0200 Source: proteinortho Binary: proteinortho Architecture: source amd64 Version: 5.13+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: proteinortho - Detection of (Co-)orthologs in large-scale protein analysis Changes: proteinortho (5.13+dfsg-1) unstable; urgency=medium . * New upstream version (all patches applied upstream) * cme fix dpkg-control Checksums-Sha1: 84416228a4d4ecd07220066fa75793a39a5d53a1 2041 proteinortho_5.13+dfsg-1.dsc 36201ca5e130e031f3c41db64561f832c9c0600b 179736 proteinortho_5.13+dfsg.orig.tar.xz 501e796c6f701da8421e35a06a11adc88ea296a6 3976 proteinortho_5.13+dfsg-1.debian.tar.xz c56fde5fe3ab5fc99149b1b89452d141862edcd5 5760 proteinortho-dbgsym_5.13+dfsg-1_amd64.deb 2af0c29c1214a78a461be18ab36b4c6c71d116a4 250506 proteinortho_5.13+dfsg-1_amd64.deb Checksums-Sha256: ca27a72f737d5793d555b379e80dd08dd9e9df10ace15c2cf2aebe988c5128b2 2041 proteinortho_5.13+dfsg-1.dsc a4c7d82f8259b95c088c80dc7a96cd11a7e43b420b721ed4f38d40890ab0b04b 179736 proteinortho_5.13+dfsg.orig.tar.xz 7982590bc5853eca0e806fde17291b79b9b9aefe42c3d019f2ae7db743bc7011 3976 proteinortho_5.13+dfsg-1.debian.tar.xz 7b09f67bf419d1c8d25770a8cd64be4c6ba08f0505e26a5e7275bce4fcca6d72 5760 proteinortho-dbgsym_5.13+dfsg-1_amd64.deb 21df4a7604fb99817fdd4956e715db63be2adeb7ed4e8b9289608f48f9876aea 250506 proteinortho_5.13+dfsg-1_amd64.deb Files: 83e93ad1aedfa866d1fc99292862a94f 2041 science optional proteinortho_5.13+dfsg-1.dsc 0ca1cc4f5fd2865893c40f99a7a1825f 179736 science optional proteinortho_5.13+dfsg.orig.tar.xz 8f54e5de6d9e7cec66aa5d227d1c2a63 3976 science optional proteinortho_5.13+dfsg-1.debian.tar.xz ffee09275f7ae032be2facba56695a45 5760 debug extra proteinortho-dbgsym_5.13+dfsg-1_amd64.deb 32f7046bbd8a59474767c80d32b28a1c 250506 science optional proteinortho_5.13+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXKfJEAAoJEFeKBJTRxkbRhPcP/0zcAhFjXcFvIDu+FJDIjc6y T/JJA86hTr2WJbEXXN/hY0ECaL3bTwlSRXDE1W8Ttuukbpa3BN4aoG3mHG7N1Zvj OVY/SannAxLGnPslyf0VSu9G5NcBJzctoTigx12bokvjPeCcatGk1XMQEBmRAzkW GZMLlV95HGzI5r0YnF+jWji1tW57+FJamiMmh3Cmu63uXRX14xh0GvMkuHiG/gha EQh8kgR/5Ir0HYioJcXqA3kRfr3zl8+JgcYjtjUOBYz7D3nGFp86iZfSH2hobdTD exYLRXwIeWPGT+RRAWvspDwBz4yw6P8oStY934EFPlvikWPes8rACPXTSAEXmpMM Q8XykOkur8nrI7+tmvtniYgB0X7x8gak9IBzkM6h91xTw10qPFErxHJEqnRqThrH wA1FrCB98KWsycqRjyMFWEEM60CHfRWrVdUkVl/725aB5cy+7mREwoRYw+QZPC0D Dg2jVoGIdSphU6xS8SaCKtl3OxufLIOuNEhOCuL0kNhg15b6b870ZC/YUSti9Oxj FwrmG8hnU0uPc4Vb0rIIje9IRPb7ytpunBPBpsdgmVVPXXAgLOY1Kp7G+uMNKQEN XICpgY4MiALyIgAPPx01L5Sj+YIW7NZeYATtS61qrgtMmSBKXSleMjzUPLSnTuFi MPualFsnUAAHrxT72rD7 =/mMC -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 4 13:43:44 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 13:43:44 +0000 Subject: [Debian-med-packaging] surankco_0.0.r5+dfsg-1~bpo8+1_amd64.changes is NEW Message-ID: binary:surankco is NEW. source:surankco is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From tille at debian.org Wed May 4 14:00:47 2016 From: tille at debian.org (Andreas Tille) Date: Wed, 4 May 2016 16:00:47 +0200 Subject: [Debian-med-packaging] Bug#822382: There are two files with non-free source inside concavity (Was: Bug#822382: concavity: non-free files (NC)) In-Reply-To: <2413549.IrnaeTJCyG@deblab> References: <2413549.IrnaeTJCyG@deblab> Message-ID: <20160504140047.GC25614@an3as.eu> Hi, as you can read below it was spotted that two files inside the concavity source files that are considered as non-free by the Debian Free Software Guidelines (DFSG). The restriction to not selling the software makes it non-free since for instance it is not possible for vendors trying to sell the whole set of Debian packages on some media if there are these two files on it. As a consequence we need to remove concavity from Debian if the license of these files can not be clarified (preferably also as GPL-3+ as the rest of the code). Kind regards Andreas. On Sun, Apr 24, 2016 at 10:51:32AM +1000, Dmitry Smirnov wrote: > Source: concavity > Version: 0.1+dfsg-1 > Severity: serious > Usertags: dfsg > > Files: > pkgs/R3Shapes/ply.C > pkgs/R3Shapes/ply.h > Copyright: > 1994 the Board of Trustees of The Leland Stanford Junior University > License: > Permission to use, copy, modify and distribute this software and its > documentation for any purpose is hereby granted without fee, provided > that the above copyright notice and this permission notice appear in > all copies of this software and that you do not sell the software. > _____________________________^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > > Ironically this non-free license is documented in "copyright" file in > "License: as_is" paragraph. > > Please investigate. > > -- > Regards, > Dmitry Smirnov > GPG key : 4096R/53968D1B > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de From myrmecocystus at gmail.com Wed May 4 14:15:24 2016 From: myrmecocystus at gmail.com (Scott Chamberlain) Date: Wed, 04 May 2016 14:15:24 +0000 Subject: [Debian-med-packaging] Missing testthat input for taxize In-Reply-To: <20160504121108.GE20381@an3as.eu> References: <20160331173119.GB27477@an3as.eu> <20160504121108.GE20381@an3as.eu> Message-ID: Hi, I didn't receive the first email, sorry about that. I skip on tests on CRAN because it calls so many web services, that one is often down at any one point. So I .Rbuildignore tests/test-all.R You can see that here https://github.com/ropensci/taxize/blob/v0.7.5/.Rbuildignore#L19 in the version I sent to CRAN for this version. You can simply add that file https://github.com/ropensci/taxize/blob/master/tests/test-all.R back to tests/ dir. Soon I will fix this by not running tests on CRAN with testthat::skip_on_cran() - and that test-all.R file won't be ignored. Best, Scott On Wed, May 4, 2016 at 5:11 AM Andreas Tille wrote: > Hi again, > > I realised that taxize 0.7.5 was released meanwhile but the testthat > input file keeps on missing? Since you did not answered my mail I > wonder whether you might have received it. > > Kind regards > > Andreas. > > On Thu, Mar 31, 2016 at 07:31:19PM +0200, Andreas Tille wrote: > > Hi Scott, > > > > I intend to package taxize for the Debian distribution as a precondition > > for some R package. Since Debian provides automatic tests I intended to > > run the testthat suite contained in the taxize source. Unfortunately the > > main input file that usualy resides in the tests/ dir and controls the > > call of the single tests in tests/testthat is missing. > > > > I think this is not intended and you might probably want to provide > > this in your next release. > > > > Kind regards > > > > Andreas. > > > > > > -- > > http://fam-tille.de > > > > _______________________________________________ > > Debian-med-packaging mailing list > > Debian-med-packaging at lists.alioth.debian.org > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > > > > -- > http://fam-tille.de > -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at release.debian.org Wed May 4 16:39:06 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:06 +0000 Subject: [Debian-med-packaging] bowtie2 2.2.9-1 MIGRATED to testing Message-ID: FYI: The status of the bowtie2 source package in Debian's testing distribution has changed. Previous version: 2.2.8-1 Current version: 2.2.9-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-bioc-bsgenome 1.38.0-2 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-bsgenome source package in Debian's testing distribution has changed. Previous version: 1.38.0-1 Current version: 1.38.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-cran-lambda.r 1.1.7-3 MIGRATED to testing Message-ID: FYI: The status of the r-cran-lambda.r source package in Debian's testing distribution has changed. Previous version: 1.1.7-2 Current version: 1.1.7-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-bioc-genomicalignments 1.6.3-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-genomicalignments source package in Debian's testing distribution has changed. Previous version: 1.6.1-1 Current version: 1.6.3-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] r-bioc-aroma.light 3.0.0-2 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-aroma.light source package in Debian's testing distribution has changed. Previous version: 3.0.0-1 Current version: 3.0.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] python-pymummer 0.7.1-1 MIGRATED to testing Message-ID: FYI: The status of the python-pymummer source package in Debian's testing distribution has changed. Previous version: 0.7.0-1 Current version: 0.7.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-cran-r.utils 2.3.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-cran-r.utils source package in Debian's testing distribution has changed. Previous version: 2.1.0-1 Current version: 2.3.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] seqprep 1.2-1 MIGRATED to testing Message-ID: FYI: The status of the seqprep source package in Debian's testing distribution has changed. Previous version: 1.1-6 Current version: 1.2-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-cran-r.methodss3 1.7.1-1 MIGRATED to testing Message-ID: FYI: The status of the r-cran-r.methodss3 source package in Debian's testing distribution has changed. Previous version: 1.7.0-1 Current version: 1.7.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-cran-testthat 1.0.2-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-testthat source package in Debian's testing distribution has changed. Previous version: 0.11.0-1 Current version: 1.0.2-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-cran-xml2 0.1.2-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-xml2 source package in Debian's testing distribution has changed. Previous version: 0.1.2-1 Current version: 0.1.2-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 4 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 04 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] sleepyhead 1.0.0-beta-2+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the sleepyhead source package in Debian's testing distribution has changed. Previous version: 0.9.8-3 Current version: 1.0.0-beta-2+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Wed May 4 18:31:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 18:31:34 +0000 Subject: [Debian-med-packaging] Processing of mira_4.9.6-1_source.changes Message-ID: mira_4.9.6-1_source.changes uploaded successfully to localhost along with the files: mira_4.9.6-1.dsc mira_4.9.6.orig.tar.bz2 mira_4.9.6-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 4 18:31:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 18:31:34 +0000 Subject: [Debian-med-packaging] Processing of khmer_2.0+dfsg-6_source.changes Message-ID: khmer_2.0+dfsg-6_source.changes uploaded successfully to localhost along with the files: khmer_2.0+dfsg-6.dsc khmer_2.0+dfsg-6.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 4 19:26:49 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 19:26:49 +0000 Subject: [Debian-med-packaging] khmer_2.0+dfsg-6_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 04 May 2016 11:25:30 -0700 Source: khmer Binary: khmer-common khmer liboxli1 liboxli-dev Architecture: source Version: 2.0+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence analysis dev library liboxli1 - in-memory DNA sequence analysis library from the khmer project Changes: khmer (2.0+dfsg-6) unstable; urgency=medium . * Switch from deprecated ruby-ronn to asciidoctor for manpage generation * Bump Standards-Version to 3.9.8 Checksums-Sha1: 631dd25a329730895f4dc3a70f90b1b442b4e673 2630 khmer_2.0+dfsg-6.dsc 4c117900e6adc2ca746a2b2a63ee5da2c85df80f 10936 khmer_2.0+dfsg-6.debian.tar.xz Checksums-Sha256: 748bbeb7b2ab3d72a23c4d19b8363a4a9f8ef9b42094bf82fcd0229a681eaa02 2630 khmer_2.0+dfsg-6.dsc 174d67d46e821e1805e3aba6afc8b2c96607bfd667985eae2b9c8ea529619b41 10936 khmer_2.0+dfsg-6.debian.tar.xz Files: 194f17f4570fb1dd371cd3c0d5a16a6a 2630 science optional khmer_2.0+dfsg-6.dsc 5279d648ae7a6241fdb895e9823b4c48 10936 science optional khmer_2.0+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXKj8WAAoJEDwmdj9sZ+bi6gAP/A46acLfbjEeSzDVpbNTeMCv tNro2AOwn2oqEyL/AjPH1oREMavN7pKfCdk5ybnqxBCaHGtZsbhPpQp2OP4hP8KS hCaYBzTaYDrkmUJkGNLQYMngyONGGNHnA+0GIAH7fAa/SgmsBFGEsRnIuwwJQMZu l6ZAXUdjQuCLYjW0KrLWLFymB7ZKpJkSNcvOIgfgtttVSyHYafjdDnQqwdzx63S9 U+Q/sdYjbqLmQaAqfSd56M8Itghu3l5ACRcoTtpo6rAiGtmJQ6ysrUUnzkc9bf4i C94l5kNH28aEJKpNY0PYRBqUokEd002cbfJ6NiqiRTWeNTHk4ZlclUwd3OtdZOJw Uu0FED7vq/NOGNpPGimrgxUBfZ0iUawmWr2EI+3q1Ca8s7R7QiOVRZjXfO7CLvUS ToNoB1ISfN8BIXknFsQBpG+Oawvy1XPg+bTFqoufh9RfBtD/Ntu8iKWP4Bx5fP5X Ll4zc9MXd9gnjh3RaQL5cekUJKd2aOA2lCZTgwLzOWi8lMOlLcPaNc4OVoLoCH1q eU1lI4jvxM6TfMuDo53DqkCT/fAblJFJem8loUtrYVGSvOD2aWEDVS/ksGW2DAx9 CfMcQpthODfs+opREVlW8elHhtP/HDfqaRSrGo437EVBYWtkh4unTengiw5mtZ5o DF1tnCUI2gLFTw0EIWwr =gIHu -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 4 19:28:00 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 19:28:00 +0000 Subject: [Debian-med-packaging] mira_4.9.6-1_source.changes REJECTED Message-ID: ACL dm: NEW uploads are not allowed === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From andreas at an3as.eu Wed May 4 20:04:18 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 4 May 2016 22:04:18 +0200 Subject: [Debian-med-packaging] I'll take this (Was: mira_4.9.6-1_source.changes REJECTED) In-Reply-To: References: Message-ID: <20160504200417.GA4546@an3as.eu> On Wed, May 04, 2016 at 07:28:00PM +0000, Debian FTP Masters wrote: > > > ACL dm: NEW uploads are not allowed > > === > > Please feel free to respond to this email if you don't understand why > your files were rejected, or if you upload new files which address our > concerns. > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Wed May 4 22:28:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 22:28:01 +0000 Subject: [Debian-med-packaging] Processing of jaligner_1.0+dfsg-2_source.changes Message-ID: jaligner_1.0+dfsg-2_source.changes uploaded successfully to localhost along with the files: jaligner_1.0+dfsg-2.dsc jaligner_1.0+dfsg-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 4 23:13:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 23:13:07 +0000 Subject: [Debian-med-packaging] Processing of mira_4.9.6-1_source.changes Message-ID: mira_4.9.6-1_source.changes uploaded successfully to localhost along with the files: mira_4.9.6-1.dsc mira_4.9.6.orig.tar.bz2 mira_4.9.6-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 4 23:18:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 04 May 2016 23:18:17 +0000 Subject: [Debian-med-packaging] jaligner_1.0+dfsg-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 04 May 2016 15:23:47 -0700 Source: jaligner Binary: jaligner Architecture: source Version: 1.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: jaligner - Smith-Waterman algorithm with Gotoh's improvement Changes: jaligner (1.0+dfsg-2) unstable; urgency=medium . * Make build reproducible by switching to asciidoctor from ruby-ronn for manual page generation. Checksums-Sha1: 700f2c837c71ed2f04a48f8ba695968b411ae6ba 2047 jaligner_1.0+dfsg-2.dsc c7b102f3a2cfd20156a6c2d0e92d917e2cd6fd1f 7108 jaligner_1.0+dfsg-2.debian.tar.xz Checksums-Sha256: 4a1cdcfe0546fd59a13ba66ed7fa609add17aff2f617068ca442555676ce2885 2047 jaligner_1.0+dfsg-2.dsc 41eeb7eb475bf1bc00f67c88262d0c9c9396b530fde73de2a3db4a11cfd53a05 7108 jaligner_1.0+dfsg-2.debian.tar.xz Files: 0ecdf3ec9e62fb2f3c219f3f8cab8e19 2047 science optional jaligner_1.0+dfsg-2.dsc 711eba7c59a3ea8e326777aad3c5c21e 7108 science optional jaligner_1.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXKnaKAAoJEDwmdj9sZ+bi8ncQALwsTzmFxpTctHl8P0plrXin OBU9QRqDJvUqXIaHiSmdDOJveSmu62RCwISqpoAMPLsKIK7rYuEH+dw/D9qvF1f6 OOlX4jbhQnnH/7WNmrL9WGkKYfNMzXek3sWVa7R2xOiJMNTKXYUWOyqQD4aN0zVJ U/1z8raiW0Nk59AD5y5sMlr3ocYgHucZS+9UrcIFR0gFKC6ohlynCoBg5j5ItteW SkVLB4SYwWocw8p+8uTpoFzamYrhBjea+QJViWA0Vj46nRLV1LpzFQ0NrbBP7o51 6yxNXLpyfwQXGj/6j+WEIeCKjsW6CoFFEOi8l9gHqvY8SVHM1TsD8jCY2gxISUH9 VUd2jm5tRtzmRMHq5nzg6UZuLdVq+2gz8gkXPcblUmgGX53/l1sv1pNPisiyvlfk cyUDlxZqnhgw2y6DD9w6m8dOmMkdAMyFP6RKwWRThDT6FNM8IOg8OJQcasSuJOIj vK/TyoMZ4dSmpq3TBOcYfTbtsHiQYzZMqZKtESv1Cq4090N/LaUTuh/dtxuTVj60 vaozvkosi6VbbUcT7VNcZ8CsUQTZB3o4u3U/ABP6RyQnr0NxVjih3lJwMwecdJvb dwbRad+WDdiIMdwQBGhu5MMspWxfH9RWAaS+V5p8eFsrlRV2SaNwk17D9gKvCi9l nZSyorwlifShwdNV/DWN =71NW -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 5 00:28:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 00:28:23 +0000 Subject: [Debian-med-packaging] mira_4.9.6-1_source.changes REJECTED Message-ID: Source-only uploads to NEW are not allowed. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Thu May 5 05:45:00 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 05:45:00 +0000 Subject: [Debian-med-packaging] Processing of r-cran-taxize_0.7.4-1~bpo8+1_amd64.changes Message-ID: r-cran-taxize_0.7.4-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: r-cran-taxize_0.7.4-1~bpo8+1.dsc r-cran-taxize_0.7.4-1~bpo8+1.debian.tar.xz r-cran-taxize_0.7.4-1~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 05:48:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 05:48:35 +0000 Subject: [Debian-med-packaging] r-cran-taxize_0.7.4-1~bpo8+1_amd64.changes is NEW Message-ID: binary:r-cran-taxize is NEW. source:r-cran-taxize is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 5 05:55:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 05:55:01 +0000 Subject: [Debian-med-packaging] Processing of libbpp-seq_2.2.0-1~bpo8+1_amd64.changes Message-ID: libbpp-seq_2.2.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-seq_2.2.0-1~bpo8+1.dsc libbpp-seq_2.2.0-1~bpo8+1.debian.tar.xz libbpp-seq-dev_2.2.0-1~bpo8+1_amd64.deb libbpp-seq9_2.2.0-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 06:18:52 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 06:18:52 +0000 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes is NEW Message-ID: binary:libbpp-seq-dev is NEW. binary:libbpp-seq9 is NEW. source:libbpp-seq is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 5 07:15:19 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 07:15:19 +0000 Subject: [Debian-med-packaging] Processing of mira_4.9.6-1_amd64.changes Message-ID: mira_4.9.6-1_amd64.changes uploaded successfully to localhost along with the files: mira_4.9.6-1.dsc mira_4.9.6.orig.tar.bz2 mira_4.9.6-1.debian.tar.xz mira-assembler-dbgsym_4.9.6-1_amd64.deb mira-assembler_4.9.6-1_amd64.deb mira-doc_4.9.6-1_all.deb mira-rfam-12s-rrna_4.9.6-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 07:19:41 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 07:19:41 +0000 Subject: [Debian-med-packaging] mira_4.9.6-1_amd64.changes is NEW Message-ID: binary:mira-rfam-12s-rrna is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From owner at bugs.debian.org Thu May 5 08:23:29 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Thu, 05 May 2016 08:23:29 +0000 Subject: [Debian-med-packaging] Processed: severity of 821469 is serious, severity of 821471 is serious, severity of 821472 is serious ... References: <1462436191-2661-bts-ondrej@debian.org> Message-ID: Processing commands for control at bugs.debian.org: > severity 821469 serious Bug #821469 [acidbase] acidbase: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821471 serious Bug #821471 [adminer] adminer: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821472 serious Bug #821472 [arcanist] arcanist: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821475 serious Bug #821475 [auth2db-frontend] auth2db-frontend: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821476 serious Bug #821476 [collabtive] collabtive: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821478 serious Bug #821478 [dokuwiki] dokuwiki: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821479 serious Bug #821479 [dolibarr] dolibarr: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821480 serious Bug #821480 [dotclear] dotclear: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821481 serious Bug #821481 [d-push] d-push: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821482 serious Bug #821482 [drupal7] drupal7: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821483 serious Bug #821483 [drush] drush: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821484 serious Bug #821484 [freedombox-setup] freedombox-setup: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821485 serious Bug #821485 [fusiondirectory] fusiondirectory: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821498 serious Bug #821498 [galette] galette: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821499 serious Bug #821499 [ganglia-webfrontend] ganglia-webfrontend: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821500 serious Bug #821500 [glpi] glpi: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821501 serious Bug #821501 [gosa] gosa: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821502 serious Bug #821502 [gosa-dev] gosa-dev: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821503 serious Bug #821503 [hoteldruid] hoteldruid: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821504 serious Bug #821504 [htcheck-php] htcheck-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821505 serious Bug #821505 [icinga-web] icinga-web: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821506 serious Bug #821506 [icinga-web-config-icinga2-ido-mysql] icinga-web-config-icinga2-ido-mysql: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821507 serious Bug #821507 [icinga-web-config-icinga2-ido-pgsql] icinga-web-config-icinga2-ido-pgsql: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821508 serious Bug #821508 [ilohamail] ilohamail: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821509 serious Bug #821509 [kcachegrind-converters] kcachegrind-converters: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821511 serious Bug #821511 [letodms] letodms: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821515 serious Bug #821515 [libfpdf-tpl-php] libfpdf-tpl-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821516 serious Bug #821516 [libfpdi-php] libfpdi-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821518 serious Bug #821518 [libkohana2-modules-php] libkohana2-modules-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821519 serious Bug #821519 [libkohana2-php] libkohana2-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821520 serious Bug #821520 [libkohana3.1-core-php] libkohana3.1-core-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821521 serious Bug #821521 [libkohana3.2-core-php] libkohana3.2-core-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821522 serious Bug #821522 [libmarkdown-php] libmarkdown-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821523 serious Bug #821523 [src:owfs] libownet-php: PHP 7.0 Transition Bug #821691 [src:owfs] src:owfs: PHP 7.0 Transition Severity set to 'serious' from 'important' Severity set to 'serious' from 'important' > severity 821525 serious Bug #821525 [libphp-jabber] libphp-jabber: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821526 serious Bug #821526 [libphp-jpgraph] libphp-jpgraph: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821527 serious Bug #821527 [libphp-magpierss] libphp-magpierss: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821528 serious Bug #821528 [libphp-simplepie] libphp-simplepie: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821529 serious Bug #821529 [libphp-snoopy] libphp-snoopy: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821530 serious Bug #821530 [libsparkline-php] libsparkline-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821531 serious Bug #821531 [loganalyzer] loganalyzer: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821532 serious Bug #821532 [mlmmj-php-web] mlmmj-php-web: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821533 serious Bug #821533 [mlmmj-php-web-admin] mlmmj-php-web-admin: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821534 serious Bug #821534 [moodle] moodle: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821535 serious Bug #821535 [nagios3-cgi] nagios3-cgi: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821536 serious Bug #821536 [nagvis] nagvis: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821537 serious Bug #821537 [netmrg] netmrg: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821538 serious Bug #821538 [nordugrid-arc-ldap-monitor] nordugrid-arc-ldap-monitor: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821542 serious Bug #821542 [pgsnap] pgsnap: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821543 serious Bug #821543 [phabricator] phabricator: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821544 serious Bug #821544 [phamm] phamm: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821545 serious Bug #821545 [phoronix-test-suite] phoronix-test-suite: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821547 serious Bug #821547 [php5-lasso] php5-lasso: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821548 serious Bug #821548 [php5-librdf] php5-librdf: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821549 serious Bug #821549 [php5-midgard2] php5-midgard2: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821551 serious Bug #821551 [php5-pecl-http] php5-pecl-http: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821552 serious Bug #821552 [php5-pecl-http-dev] php5-pecl-http-dev: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821553 serious Bug #821553 [php5-pinba] php5-pinba: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821555 serious Bug #821555 [php5-ps] php5-ps: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821567 serious Bug #821567 [php-cache] php-cache: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821574 serious Bug #821574 [php-fpdf] php-fpdf: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821576 serious Bug #821576 [php-geshi] php-geshi: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821577 serious Bug #821577 [php-google-api-php-client] php-google-api-php-client: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821578 serious Bug #821578 [php-google-auth] php-google-auth: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821580 serious Bug #821580 [php-irods-prods] php-irods-prods: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821585 serious Bug #821585 [phpldapadmin] phpldapadmin: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821588 serious Bug #821588 [php-mail-mbox] php-mail-mbox: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821591 serious Bug #821591 [php-mf2] php-mf2: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821593 serious Bug #821593 [php-net-ftp] php-net-ftp: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821594 serious Bug #821594 [php-net-imap] php-net-imap: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821595 serious Bug #821595 [php-net-ipv6] php-net-ipv6: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821600 serious Bug #821600 [php-net-url2] php-net-url2: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821601 serious Bug #821601 [php-net-whois] php-net-whois: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821603 serious Bug #821603 [php-openid] php-openid: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821608 serious Bug #821608 [php-psr-cache] php-psr-cache: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821611 serious Bug #821611 [phpreports] phpreports: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821613 serious Bug #821613 [php-sepa-direct-debit] php-sepa-direct-debit: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821617 serious Bug #821617 [php-swiftmailer] php-swiftmailer: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821628 serious Bug #821628 [phpsysinfo] phpsysinfo: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821631 serious Bug #821631 [php-validate] php-validate: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821632 serious Bug #821632 [phpwebcounter] phpwebcounter: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821633 serious Bug #821633 [php-wikidiff2] php-wikidiff2: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821634 serious Bug #821634 [php-xajax] php-xajax: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821636 serious Bug #821636 [php-xml-rpc2] php-xml-rpc2: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821637 serious Bug #821637 [php-zend-search] php-zend-search: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821639 serious Bug #821639 [php-zeroc-ice] php-zeroc-ice: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821641 serious Bug #821641 [pluxml] pluxml: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821642 serious Bug #821642 [pnp4nagios-web] pnp4nagios-web: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821643 serious Bug #821643 [postfixadmin] postfixadmin: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821644 serious Bug #821644 [postfix-cluebringer-webui] postfix-cluebringer-webui: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821645 serious Bug #821645 [refdb-www] refdb-www: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821646 serious Bug #821646 [roundcube-core] roundcube-core: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821647 serious Bug #821647 [roundcube-mysql] roundcube-mysql: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821648 serious Bug #821648 [roundcube-pgsql] roundcube-pgsql: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821649 serious Bug #821649 [roundcube-plugins] roundcube-plugins: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821650 serious Bug #821650 [roundcube-sqlite3] roundcube-sqlite3: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821651 serious Bug #821651 [rtgui] rtgui: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821652 serious Bug #821652 [sbnc-php-dev] sbnc-php-dev: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821653 serious Bug #821653 [scuttle] scuttle: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821655 serious Bug #821655 [serverstats] serverstats: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821656 serious Bug #821656 [shaarli] shaarli: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821657 serious Bug #821657 [simpleid] simpleid: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821658 serious Bug #821658 [simpleid-ldap] simpleid-ldap: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821659 serious Bug #821659 [slbackup-php] slbackup-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821660 serious Bug #821660 [smarty3] smarty3: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821661 serious Bug #821661 [smarty-gettext] smarty-gettext: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821662 serious Bug #821662 [spotweb] spotweb: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821663 serious Bug #821663 [squirrelmail] squirrelmail: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821665 serious Bug #821665 [tweeper] tweeper: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821666 serious Bug #821666 [uwsgi-plugin-php] uwsgi-plugin-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821668 serious Bug #821668 [yate-scripts] yate-scripts: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821669 serious Bug #821669 [yubikey-ksm] yubikey-ksm: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821670 serious Bug #821670 [yubikey-val] yubikey-val: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821671 serious Bug #821671 [zoneminder] zoneminder: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821674 serious Bug #821674 [src:drush] src:drush: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821675 serious Bug #821675 [src:exactimage] src:exactimage: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821676 serious Bug #821676 [src:graphviz] src:graphviz: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821677 serious Bug #821677 [src:gdcm] RM: php5-gdcm php5-vtkgdcm --ROM;doesn't support PHP7.0 Severity set to 'serious' from 'important' > severity 821679 serious Bug #821679 [src:icinga-web] src:icinga-web: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821681 serious Bug #821681 [src:jscribble] src:jscribble: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821682 serious Bug #821682 [src:jsjac] src:jsjac: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821683 serious Bug #821683 [src:lasso] src:lasso: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821684 serious Bug #821684 [src:libexpect-php5] src:libexpect-php5: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821685 serious Bug #821685 [src:libjs-jcrop] src:libjs-jcrop: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821688 serious Bug #821688 [src:libpuzzle] src:libpuzzle: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821689 serious Bug #821689 [src:libvpx] src:libvpx: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821690 serious Bug #821690 [src:ming] src:ming: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821692 serious Bug #821692 [src:phoronix-test-suite] src:phoronix-test-suite: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821693 serious Bug #821693 [src:php5-midgard2] src:php5-midgard2: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821695 serious Bug #821695 [src:php-doc] src:php-doc: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821698 serious Bug #821698 [src:php-guzzle] src:php-guzzle: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821700 serious Bug #821700 [src:php-imlib] src:php-imlib: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821703 serious Bug #821703 [src:php-pecl-http] src:php-pecl-http: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821704 serious Bug #821704 [src:php-pinba] src:php-pinba: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821706 serious Bug #821706 [src:php-ps] src:php-ps: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821708 serious Bug #821708 [src:php-sabredav] src:php-sabredav: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821709 serious Bug #821709 [src:php-suhosin] src:php-suhosin: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821712 serious Bug #821712 [src:redland-bindings] src:redland-bindings: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821713 serious Bug #821713 [src:remctl] src:remctl: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821714 serious Bug #821714 [src:simplepie] src:simplepie: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821716 serious Bug #821716 [src:swig2.0] src:swig2.0: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821718 serious Bug #821718 [src:tarantool-php] src:tarantool-php: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821720 serious Bug #821720 [src:wikidiff2] src:wikidiff2: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821721 serious Bug #821721 [src:uwsgi] src:uwsgi: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821722 serious Bug #821722 [src:xhprof] src:xhprof: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821723 serious Bug #821723 [src:zeroc-ice] src:zeroc-ice: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821715 serious Bug #821715 [src:swig] src:swig: PHP 7.0 Transition Severity set to 'serious' from 'important' > severity 821539 serious Bug #821539 [ocsinventory-reports] ocsinventory-reports: PHP 7.0 Transition Severity set to 'serious' from 'important' > thanks Stopping processing here. Please contact me if you need assistance. -- 821469: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821469 821471: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821471 821472: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821472 821475: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821475 821476: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821476 821478: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821478 821479: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821479 821480: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821480 821481: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821481 821482: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821482 821483: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821483 821484: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821484 821485: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821485 821498: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821498 821499: 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bugs.debian.org with problems From ondrej at sury.org Thu May 5 08:20:58 2016 From: ondrej at sury.org (=?UTF-8?Q?Ond=C5=99ej_?= =?UTF-8?Q?Sur=C3=BD?=) Date: Thu, 5 May 2016 10:20:58 +0200 Subject: [Debian-med-packaging] Bug#821677: Bumping severity of PHP 7.0 transition bugs to serious Message-ID: <20160505082058.GA62336@lettie.labs.nic.cz> Dear maintainer(s), I am bumping the severity of this bug to serious, as we are going to remove src:php5 from Debian and your package is blocking the first step which is removal of php5 from testing. Please either update your package to support PHP 7.0 or remove the package from Debian unstable alltogether. Cheers, Ondrej From ftpmaster at ftp-master.debian.org Thu May 5 09:36:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 09:36:33 +0000 Subject: [Debian-med-packaging] Processing of fastqtl_2.184+dfsg-1_amd64.changes Message-ID: fastqtl_2.184+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: fastqtl_2.184+dfsg-1.dsc fastqtl_2.184+dfsg.orig.tar.xz fastqtl_2.184+dfsg-1.debian.tar.xz fastqtl-dbgsym_2.184+dfsg-1_amd64.deb fastqtl-doc_2.184+dfsg-1_all.deb fastqtl_2.184+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 10:11:38 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 10:11:38 +0000 Subject: [Debian-med-packaging] Processing of gdcm_2.6.3-5_source.changes Message-ID: gdcm_2.6.3-5_source.changes uploaded successfully to localhost along with the files: gdcm_2.6.3-5.dsc gdcm_2.6.3-5.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 10:19:22 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 10:19:22 +0000 Subject: [Debian-med-packaging] fastqtl_2.184+dfsg-1_amd64.changes is NEW Message-ID: binary:fastqtl is NEW. binary:fastqtl-doc is NEW. source:fastqtl is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 5 10:19:41 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 10:19:41 +0000 Subject: [Debian-med-packaging] gdcm_2.6.3-5_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 05 May 2016 09:39:26 +0000 Source: gdcm Binary: libgdcm2.6 libgdcm-tools libgdcm2-dev libgdcm2.6-dbg libgdcm-cil python-gdcm libvtkgdcm2.6 libvtkgdcm2-dev libvtkgdcm-cil python-vtkgdcm libvtkgdcm-tools gdcm-doc libgdcm-java libvtkgdcm-java Architecture: source Version: 2.6.3-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: gdcm-doc - Grassroots DICOM documentation libgdcm-cil - Grassroots DICOM CLI bindings libgdcm-java - Grassroots DICOM Java bindings libgdcm-tools - Grassroots DICOM tools and utilities libgdcm2-dev - Grassroots DICOM development libraries and headers libgdcm2.6 - Grassroots DICOM runtime libraries libgdcm2.6-dbg - Grassroots DICOM runtime libraries, debug version libvtkgdcm-cil - Grassroots DICOM VTK CLI bindings libvtkgdcm-java - Grassroots DICOM VTK Java bindings libvtkgdcm-tools - Grassroots DICOM VTK tools and utilities libvtkgdcm2-dev - Grassroots DICOM VTK development libraries and headers libvtkgdcm2.6 - Grassroots DICOM VTK runtime libraries python-gdcm - Grassroots DICOM Python bindings python-vtkgdcm - Grassroots DICOM VTK/Python bindings Changes: gdcm (2.6.3-5) unstable; urgency=medium . * d/control* +d/rules +d/php5-*: Really remove php bindings on all archs * d/control*: Update standards version to 3.9.8 Checksums-Sha1: 680348a622606dcc8b415eb4d4f3e85288a1c04c 3228 gdcm_2.6.3-5.dsc db87fb2e595c442271bf79f5341339c5f9107905 25372 gdcm_2.6.3-5.debian.tar.xz Checksums-Sha256: bc755806e9647dd75fe614ca2576c3a84e149c5599882d649aa91712799115de 3228 gdcm_2.6.3-5.dsc a120e5537f6e43c25f0e88fb16dbf9f24d4bec275ad6e074ea82247a6fd499a2 25372 gdcm_2.6.3-5.debian.tar.xz Files: a5dc2f5f44b629023695bb8835d35c1f 3228 libs optional gdcm_2.6.3-5.dsc 6ba113025df0e543839401976b11fc37 25372 libs optional gdcm_2.6.3-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXKxUNAAoJEPgeNoubJquYkPgH/RMDsemL1XAzFohEterg7L/B 7py7xaf+OlJUHuYfl+tC1XByWbKZmODus+K7pzF55tsSI/Q1HjRN39RrHT73BW7W 2uU98VJ4abuUrGW3Sf8dggE7mrGaZxshqQsHHnuMJ3oroS/CHz1pdRyOz6XtbdVN 1Gi5gHLtjXn2EWa+8UjpTrkX+QDhCZD6+OuQcrSiWqpgSj6C5ki2thSnm54jWF3P fHbbaZDB3qoa2o38jn83b8Bgf78xEGf0oyucDySXHLxvKAVaCKtgLq/WO6awWELl q8Mt+thW+ThbaJrqUIASoXoseYlz2mwlHgmXyJoq+VEw70QOkvtfAa7WFl07JD8= =iu3O -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From gw.fossdev at gmail.com Thu May 5 11:11:11 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Thu, 05 May 2016 13:11:11 +0200 Subject: [Debian-med-packaging] Bug#821677: Reassign to ftp.debian.org Message-ID: <1462446671.32403.8.camel@gmail.com> Control: reassign -1?ftp.debian.org Control: clone? -1 -2? Control: retitle -1?RM: php5-gdcm -- ROM;doesn't support PHP7.0 Control: retitle -2?RM: php5-vtkgdcm -- ROM;doesn't support PHP7.0 GDCM removed building the php packages because php 7 is not supported.? Please remove the outdated binaries.? best,? Gert? ? From owner at bugs.debian.org Thu May 5 11:15:07 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Thu, 05 May 2016 11:15:07 +0000 Subject: [Debian-med-packaging] Processed: Reassign to ftp.debian.org References: <1462446671.32403.8.camel@gmail.com> <20160418210220.83772.89341.reportbug@lettie.labs.nic.cz> Message-ID: Processing control commands: > reassign -1?ftp.debian.org Bug #821677 [src:gdcm] RM: php5-gdcm php5-vtkgdcm --ROM;doesn't support PHP7.0 Bug reassigned from package 'src:gdcm' to 'ftp.debian.org'. Ignoring request to alter found versions of bug #821677 to the same values previously set Ignoring request to alter fixed versions of bug #821677 to the same values previously set > clone? -1 -2? Bug #821677 [ftp.debian.org] RM: php5-gdcm php5-vtkgdcm --ROM;doesn't support PHP7.0 Bug 821677 cloned as bug 823495 823495 was blocked by: 821715 823495 was not blocking any bugs. Ignoring request to alter blocking bugs of bug #823495 to the same blocks previously set > retitle -1?RM: php5-gdcm -- ROM;doesn't support PHP7.0 Bug #821677 [ftp.debian.org] RM: php5-gdcm php5-vtkgdcm --ROM;doesn't support PHP7.0 Changed Bug title to 'RM: php5-gdcm -- ROM;doesn't support PHP7.0' from 'RM: php5-gdcm php5-vtkgdcm --ROM;doesn't support PHP7.0'. > retitle -2?RM: php5-vtkgdcm -- ROM;doesn't support PHP7.0 Bug #823495 [ftp.debian.org] RM: php5-gdcm php5-vtkgdcm --ROM;doesn't support PHP7.0 Changed Bug title to 'RM: php5-vtkgdcm -- ROM;doesn't support PHP7.0' from 'RM: php5-gdcm php5-vtkgdcm --ROM;doesn't support PHP7.0'. -- 821677: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821677 823495: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=823495 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Thu May 5 16:34:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 16:34:55 +0000 Subject: [Debian-med-packaging] Processing of vtk-dicom_0.7.7-1_source.changes Message-ID: vtk-dicom_0.7.7-1_source.changes uploaded successfully to localhost along with the files: vtk-dicom_0.7.7-1.dsc vtk-dicom_0.7.7.orig.tar.gz vtk-dicom_0.7.7-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 16:49:59 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 16:49:59 +0000 Subject: [Debian-med-packaging] Processing of libmialm_1.0.8-3_source.changes Message-ID: libmialm_1.0.8-3_source.changes uploaded successfully to localhost along with the files: libmialm_1.0.8-3.dsc libmialm_1.0.8-3.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From noreply at release.debian.org Thu May 5 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 05 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] theseus 3.3.0-5 MIGRATED to testing Message-ID: FYI: The status of the theseus source package in Debian's testing distribution has changed. Previous version: 3.3.0-4 Current version: 3.3.0-5 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Thu May 5 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 05 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] toppred 1.10-2 MIGRATED to testing Message-ID: FYI: The status of the toppred source package in Debian's testing distribution has changed. Previous version: 1.10-1 Current version: 1.10-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Thu May 5 17:15:14 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 17:15:14 +0000 Subject: [Debian-med-packaging] Processing of mialmpick_0.2.12-1_source.changes Message-ID: mialmpick_0.2.12-1_source.changes uploaded successfully to localhost along with the files: mialmpick_0.2.12-1.dsc mialmpick_0.2.12.orig.tar.xz mialmpick_0.2.12-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 17:23:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 17:23:58 +0000 Subject: [Debian-med-packaging] libmialm_1.0.8-3_source.changes REJECTED Message-ID: libmialm_1.0.8-3.dsc: Refers to non-existing file 'libmialm_1.0.8.orig.tar.xz' Perhaps you need to include the file in your upload? === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Thu May 5 17:24:08 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 17:24:08 +0000 Subject: [Debian-med-packaging] mialmpick_0.2.12-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 05 May 2016 16:59:25 +0000 Source: mialmpick Binary: mialmpick Architecture: source Version: 0.2.12-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: mialmpick - Tools for landmark picking in 3D volume data sets Changes: mialmpick (0.2.12-1) unstable; urgency=medium . * New upstream version * Update standards version to 3.9.8 * d/p/02: removed patch since it was apllied upstream Checksums-Sha1: 3a20bec166d6c20d955ef49221dae510bbf0c01c 1724 mialmpick_0.2.12-1.dsc 0651de75c01aa5ccf6def51ff219fa77bfe060a8 192756 mialmpick_0.2.12.orig.tar.xz 968ff763b4a1723c338659ca494a2d021de78863 3740 mialmpick_0.2.12-1.debian.tar.xz Checksums-Sha256: 45038446335b73b405f78b970b37c3cecd37526082233bd0afa424021ea8976d 1724 mialmpick_0.2.12-1.dsc b16c7ef0c865f442d4e6360d0ff87b4fe42093a8460621504adf17b98efe2914 192756 mialmpick_0.2.12.orig.tar.xz 6140cb0999e68766ca7efdc19c0c1c32ee2ccde42f0a5fea51c82520d1cbf384 3740 mialmpick_0.2.12-1.debian.tar.xz Files: ab5547997ccecebc443b814408ca0561 1724 science optional mialmpick_0.2.12-1.dsc 6a80cfe488ddcebf7705f15aa209c3ef 192756 science optional mialmpick_0.2.12.orig.tar.xz 21d2b8b8cb4792926600a56684ff4d1f 3740 science optional mialmpick_0.2.12-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXK3wRAAoJEPgeNoubJquYotQIALCtlgr/ezUxqtLYycxw3Edq eoEWmaHzZoPI2Eo8cbT2GbXGlaZI9xsDsI0AY4LjNcGhAokxZXWKPhbcxaQ8z2Ev /Jmn17tUFAoWZ6LWU9mJmnXMJYV9GvYftsTOKkL2ikfmoIuEiMW0OREfEvxCEpER kDwXD+Il32sYRFsyLt6YfuN2id4z6Hk2q9PuE3fd1aQMZOqc/+600bGl1/5gd3Jr +V/FDsZm/v7In5JPk4z0s0Xm0JJ/qvkFj6MHrPnZHVUapZ/05AFy2oP5g8FsZa1Z YZdEa9xqlfAUp5pvVF59dyVqvDMKy27tMfO2KYPzCsuIfdIgFxkMvKeXDCr13IQ= =rXQU -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 5 17:27:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 17:27:13 +0000 Subject: [Debian-med-packaging] vtk-dicom_0.7.7-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 05 May 2016 16:20:17 +0000 Source: vtk-dicom Binary: libvtk-dicom-dev libvtkdicom0.7 vtk-dicom-tools python-vtk-dicom Architecture: source Version: 0.7.7-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: libvtk-dicom-dev - DICOM for VTK - dev libvtkdicom0.7 - DICOM for VTK - lib python-vtk-dicom - DICOM for VTK - Python vtk-dicom-tools - DICOM for VTK - tools Changes: vtk-dicom (0.7.7-1) unstable; urgency=medium . * New upstream version * Update standards version to 3.9.8 Checksums-Sha1: 99cf17e9cc3423c6aa66bf44c6901b384f6f5cc2 1958 vtk-dicom_0.7.7-1.dsc 0e73996e44fee57bc8c8c9b86c7d0fbb34274410 1003902 vtk-dicom_0.7.7.orig.tar.gz 73bf7211cc1b18d66beb0281093c82034bc1087b 5336 vtk-dicom_0.7.7-1.debian.tar.xz Checksums-Sha256: d12f6daf7a20fe5242358ff92b0be7712f87db3a71dbc4e7afe378cc620e81aa 1958 vtk-dicom_0.7.7-1.dsc 0b065614460dccc23974f2d94bd751b05aad174d1b8c715d7a38c1d4154bfc79 1003902 vtk-dicom_0.7.7.orig.tar.gz 42884371ca9a28137cde9c10bd12fa839e252934f23437a3e4002b96afa3ff83 5336 vtk-dicom_0.7.7-1.debian.tar.xz Files: cc743abae41908a657077e461d5daad4 1958 graphics optional vtk-dicom_0.7.7-1.dsc 2a25becc0adbc03eb4545706f6d5ea5f 1003902 graphics optional vtk-dicom_0.7.7.orig.tar.gz b0c062974b47725b4b2db44df5574679 5336 graphics optional vtk-dicom_0.7.7-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXK3OEAAoJEPgeNoubJquYOScH/iUL+vgHK0QxNH9PeiYQuEfA 2HNf1FyBUJeTgigpVOy2+IivSjJaVNzJH4+7jlrgHdOIei7AATT7v56imRO1SiHI kNF6Z0lwGD8XfYP0Xz5LjlqZ/c5YaN/SPzlLXRxMgOwsfAOK5o1LmtX6DcOOMkUx j5KW1yUZrRB39UOygmoyHlTst+QntSiKBqGIwk7lab0aUxDLw/+MgCVspP+L3D17 bVigXI/UPlAZOSgPaNnmjwqD5rP30K0uXm5UNiwm3UtpvguWD5c85bWd3VgbqTcC yI/trevUMxMWpYNzdHoSA/1QfK0LCUm7yQFbd1w2VUvW2ZOToaiIC8czrt0k3cc= =0/OX -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 5 17:35:30 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 17:35:30 +0000 Subject: [Debian-med-packaging] Processing of libmialm_1.0.8-3_source.changes Message-ID: libmialm_1.0.8-3_source.changes uploaded successfully to localhost along with the files: libmialm_1.0.8-3.dsc libmialm_1.0.8-3.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 17:50:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 17:50:23 +0000 Subject: [Debian-med-packaging] libmialm_1.0.8-3_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 05 May 2016 16:43:40 +0000 Source: libmialm Binary: libmialm-dev libmialm3 libmialm-doc Architecture: source Version: 1.0.8-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: libmialm-dev - Development files for the MIA landmark library libmialm-doc - Documentation for the MIA landmark library libmialm3 - Landmark handling for the MIA tool chain Changes: libmialm (1.0.8-3) unstable; urgency=medium . * d/control: Update standards version to 3.9.8 * d/control, d/rules: remove the dbg package in favour of the automatically created debsysm package. Checksums-Sha1: c1cd003d94d8760318024b8f0051ca99c73ef04f 1763 libmialm_1.0.8-3.dsc 0c3b27d543ac63fd98bad5d6932fe6bd8da6cda8 7940 libmialm_1.0.8-3.debian.tar.xz Checksums-Sha256: 7a422c3ee66364a6381fb061cd2ca6b941a3d5c30400cf7fd31a57b0a8e563dc 1763 libmialm_1.0.8-3.dsc a2de735b88010a075f90c7713e91dd1da7caa9bc7791ad13683d31d7dce75ba7 7940 libmialm_1.0.8-3.debian.tar.xz Files: c5ba048d4bf9f28cf0840a268155f678 1763 science optional libmialm_1.0.8-3.dsc 0066548d8ae43868b5b82b93735163c9 7940 science optional libmialm_1.0.8-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXK4O7AAoJEPgeNoubJquY7qIH/3RNosCS75hv+V9mAximT3dQ hwXb5YVEfwvuvhXd7O4Qxg3AFY3dg0zfKmsY50iCoWaa8qtrEWl6erzO6vd9fr32 nzz7iAwYeLdqHEwc3zwzSBHpQSFNxk0Z2L30dOfRaQD2kWoEFg0w7K9cLDcWPcNp lkP12sqo28SEdj6+OY8wax2gEPWcPkAplrnhS00vyKOhNx8v0Yh0qBrIfHIVBR4i jwW1sfiz2cH5PLY1PvaTDfbWHQxX8J3Cwd2RRTHonGmv8qF4I/O8yirhNPMCCTDS i62UjaxyilnhKyDoN2eZWBFZl5nmp5Fj+0qoC89VOmVqsiNiidhdqUDR336aEYE= =WFS8 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 5 19:41:48 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 19:41:48 +0000 Subject: [Debian-med-packaging] Processing of iva_1.0.5-1_amd64.changes Message-ID: iva_1.0.5-1_amd64.changes uploaded successfully to localhost along with the files: iva_1.0.5-1.dsc iva_1.0.5.orig.tar.gz iva_1.0.5-1.debian.tar.xz iva_1.0.5-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 19:49:02 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 19:49:02 +0000 Subject: [Debian-med-packaging] iva_1.0.5-1_amd64.changes is NEW Message-ID: binary:iva is NEW. source:iva is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From jczlapinski at stephendurbinandassociates.com Thu May 5 19:49:04 2016 From: jczlapinski at stephendurbinandassociates.com (Julia Czlapinski) Date: Thu, 5 May 2016 15:49:04 -0400 Subject: [Debian-med-packaging] Hello Message-ID: <7A2E1872-072C-4E0F-960B-916EC2B8103A@stephendurbinandassociates.com> Testing 1,2,3 From ftpmaster at ftp-master.debian.org Thu May 5 19:51:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 19:51:54 +0000 Subject: [Debian-med-packaging] Processing of mypy_0.3.1-1_amd64.changes Message-ID: mypy_0.3.1-1_amd64.changes uploaded successfully to localhost along with the files: mypy_0.3.1-1.dsc mypy_0.3.1.orig.tar.gz mypy_0.3.1-1.debian.tar.xz mypy_0.3.1-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 5 22:24:47 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 05 May 2016 22:24:47 +0000 Subject: [Debian-med-packaging] mypy_0.3.1-1_amd64.changes is NEW Message-ID: binary:mypy is NEW. source:mypy is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From owner at bugs.debian.org Fri May 6 03:36:06 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 06 May 2016 03:36:06 +0000 Subject: [Debian-med-packaging] Processed: your mail References: Message-ID: Processing commands for control at bugs.debian.org: > forcemerge 822466 816569 Bug #822466 [mrs] mrs: FTBFS: error: 'log' was not declared in this scope Bug #816569 [mrs] mrs: FTBFS with GCC 6: was not declared in this scope Severity set to 'serious' from 'normal' Added tag(s) sid and stretch. Merged 816569 822466 > thanks Stopping processing here. Please contact me if you need assistance. -- 816569: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=816569 822466: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822466 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Fri May 6 06:06:50 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 06 May 2016 06:06:50 +0000 Subject: [Debian-med-packaging] Bug#822994: Removed package(s) from unstable Message-ID: We believe that the bug you reported is now fixed; the following package(s) have been removed from unstable: libgdcm-cil | 2.6.1-1 | powerpc ------------------- Reason ------------------- ROM; mono is not available anymore on powerpc ---------------------------------------------- Note that the package(s) have simply been removed from the tag database and may (or may not) still be in the pool; this is not a bug. The package(s) will be physically removed automatically when no suite references them (and in the case of source, when no binary references it). Please also remember that the changes have been done on the master archive and will not propagate to any mirrors until the next dinstall run at the earliest. Packages are usually not removed from testing by hand. Testing tracks unstable and will automatically remove packages which were removed from unstable when removing them from testing causes no dependency problems. The release team can force a removal from testing if it is really needed, please contact them if this should be the case. Bugs which have been reported against this package are not automatically removed from the Bug Tracking System. Please check all open bugs and close them or re-assign them to another package if the removed package was superseded by another one. The version of this package that was in Debian prior to this removal can still be found using http://snapshot.debian.org/. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 822994 at bugs.debian.org. The full log for this bug can be viewed at https://bugs.debian.org/822994 This message was generated automatically; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster at ftp-master.debian.org. Debian distribution maintenance software pp. Scott Kitterman (the ftpmaster behind the curtain) From ftpmaster at ftp-master.debian.org Fri May 6 06:07:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 06 May 2016 06:07:11 +0000 Subject: [Debian-med-packaging] Bug#822995: Removed package(s) from unstable Message-ID: We believe that the bug you reported is now fixed; the following package(s) have been removed from unstable: libvtkgdcm-cil | 2.6.1-1 | powerpc ------------------- Reason ------------------- ROM; mono is not available anymore on powerpc ---------------------------------------------- Note that the package(s) have simply been removed from the tag database and may (or may not) still be in the pool; this is not a bug. The package(s) will be physically removed automatically when no suite references them (and in the case of source, when no binary references it). Please also remember that the changes have been done on the master archive and will not propagate to any mirrors until the next dinstall run at the earliest. Packages are usually not removed from testing by hand. Testing tracks unstable and will automatically remove packages which were removed from unstable when removing them from testing causes no dependency problems. The release team can force a removal from testing if it is really needed, please contact them if this should be the case. Bugs which have been reported against this package are not automatically removed from the Bug Tracking System. Please check all open bugs and close them or re-assign them to another package if the removed package was superseded by another one. The version of this package that was in Debian prior to this removal can still be found using http://snapshot.debian.org/. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 822995 at bugs.debian.org. The full log for this bug can be viewed at https://bugs.debian.org/822995 This message was generated automatically; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster at ftp-master.debian.org. Debian distribution maintenance software pp. Scott Kitterman (the ftpmaster behind the curtain) From ftpmaster at ftp-master.debian.org Fri May 6 11:00:25 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 06 May 2016 11:00:25 +0000 Subject: [Debian-med-packaging] mypy_0.3.1-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 05 May 2016 06:00:25 -0700 Source: mypy Binary: mypy Architecture: source all Version: 0.3.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: mypy - Optional static typing for Python Closes: 823512 Changes: mypy (0.3.1-1) unstable; urgency=medium . * Initial release. 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From ftpmaster at ftp-master.debian.org Fri May 6 12:13:16 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 06 May 2016 12:13:16 +0000 Subject: [Debian-med-packaging] Processing of mypy_0.4-1_source.changes Message-ID: mypy_0.4-1_source.changes uploaded successfully to localhost along with the files: mypy_0.4-1.dsc mypy_0.4.orig.tar.gz mypy_0.4-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 6 12:19:25 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 06 May 2016 12:19:25 +0000 Subject: [Debian-med-packaging] mypy_0.4-1_source.changes REJECTED Message-ID: ACL dm: not allowed to upload source package 'mypy' === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Sat May 7 09:39:03 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 09:39:03 +0000 Subject: [Debian-med-packaging] Processing of mypy_0.4-1_source.changes Message-ID: mypy_0.4-1_source.changes uploaded successfully to localhost along with the files: mypy_0.4-1.dsc mypy_0.4.orig.tar.gz mypy_0.4-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 7 09:56:08 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 09:56:08 +0000 Subject: [Debian-med-packaging] mypy_0.4-1_source.changes REJECTED Message-ID: Signature for changes file was already seen at 2016-05-06 12:19:25.939507. Please refresh the signature of the changes file if you want to upload it again. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From sanvila at unex.es Sat May 7 13:03:45 2016 From: sanvila at unex.es (Santiago Vila) Date: Sat, 7 May 2016 15:03:45 +0200 (CEST) Subject: [Debian-med-packaging] Bug#823673: samtools: FTBFS in testing Message-ID: Package: samtools Version: 1.3.1-1 Severity: serious Dear maintainer: This package currently fails to build from source in stretch. ------------------------------------------------------------ === Testing mpileup.reg regressions === UNEXPECTED FAIL: Output mismatch for $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}' See FAIL-47.out.1 vs expected/47.out ------------------------------------------------------------ The full build log is attached. I see that this package required a change recently for htslib 1.3.1. However, if this only builds now with libhts >= 1.3.1, then the Build-Depends field should be updated accordingly. Thanks. -------------- next part -------------- A non-text attachment was scrubbed... Name: samtools_1.3.1-1_amd64-20160507-1455.gz Type: application/gzip Size: 12418 bytes Desc: URL: From owner at bugs.debian.org Sat May 7 13:30:04 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sat, 07 May 2016 13:30:04 +0000 Subject: [Debian-med-packaging] Bug#822741: marked as done (htslib 1.3.1 breaks samtools 1.3, at least at build time.) References: <20160507132610.GA16724@bubu.igloo> <1461693748.2750823.590308017.767C5093@webmail.messagingengine.com> Message-ID: Your message dated Sat, 7 May 2016 22:26:10 +0900 with message-id <20160507132610.GA16724 at bubu.igloo> and subject line Re: fails to build against htslib 1.3.1 has caused the Debian Bug report #822741, regarding htslib 1.3.1 breaks samtools 1.3, at least at build time. to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 822741: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822741 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Chris Lamb Subject: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure; Date: Tue, 26 Apr 2016 19:02:28 +0100 Size: 35738 URL: -------------- next part -------------- An embedded message was scrubbed... From: Charles Plessy Subject: Re: fails to build against htslib 1.3.1 Date: Sat, 7 May 2016 22:26:10 +0900 Size: 2833 URL: From noreply at release.debian.org Sat May 7 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] biomaj 1.2.3-7 MIGRATED to testing Message-ID: FYI: The status of the biomaj source package in Debian's testing distribution has changed. Previous version: 1.2.3-6 Current version: 1.2.3-7 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 7 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] camitk 4.0.0~beta-2 MIGRATED to testing Message-ID: FYI: The status of the camitk source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 4.0.0~beta-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 7 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] circlator 1.2.1-1 MIGRATED to testing Message-ID: FYI: The status of the circlator source package in Debian's testing distribution has changed. Previous version: 1.2.0-1 Current version: 1.2.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 7 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] mgltools-dejavu 1.5.7~rc1+cvs.20140424-1 MIGRATED to testing Message-ID: FYI: The status of the mgltools-dejavu source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 1.5.7~rc1+cvs.20140424-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 7 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] mgltools-opengltk 1.5.7~rc1+cvs.20140424-1 MIGRATED to testing Message-ID: FYI: The status of the mgltools-opengltk source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 1.5.7~rc1+cvs.20140424-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 7 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] mgltools-pmv 1.5.7~rc1+cvs.20140424-2 MIGRATED to testing Message-ID: FYI: The status of the mgltools-pmv source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 1.5.7~rc1+cvs.20140424-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 7 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] mgltools-pyautodock 1.5.7~rc1+cvs.20140424-1 MIGRATED to testing Message-ID: FYI: The status of the mgltools-pyautodock source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 1.5.7~rc1+cvs.20140424-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 7 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] mgltools-molkit 1.5.7~rc1+cvs.20140424-1 MIGRATED to testing Message-ID: FYI: The status of the mgltools-molkit source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 1.5.7~rc1+cvs.20140424-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 7 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] mgltools-gle 1.5.7~rc1+cvs.20140424-2 MIGRATED to testing Message-ID: FYI: The status of the mgltools-gle source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 1.5.7~rc1+cvs.20140424-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 7 16:39:15 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 07 May 2016 16:39:15 +0000 Subject: [Debian-med-packaging] roary 3.6.1+dfsg-2 MIGRATED to testing Message-ID: FYI: The status of the roary source package in Debian's testing distribution has changed. Previous version: 3.6.1+dfsg-1 Current version: 3.6.1+dfsg-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Sat May 7 18:01:05 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 18:01:05 +0000 Subject: [Debian-med-packaging] Processing of mypy_0.4-1_source.changes Message-ID: mypy_0.4-1_source.changes uploaded successfully to localhost along with the files: mypy_0.4-1.dsc mypy_0.4.orig.tar.gz mypy_0.4-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 7 18:22:20 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 18:22:20 +0000 Subject: [Debian-med-packaging] mypy_0.4-1_source.changes REJECTED Message-ID: Signature for changes file was already seen at 2016-05-06 12:19:25.939507. Please refresh the signature of the changes file if you want to upload it again. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From VGRAYSON at houstonisd.org Sat May 7 18:30:26 2016 From: VGRAYSON at houstonisd.org (Grayson, Vincent B) Date: Sat, 7 May 2016 13:30:26 -0500 Subject: [Debian-med-packaging] Re Message-ID: <3EC20FF49893764B83FA126B0688B6ED09ADD558@EXPRODMB05.AD.HISD.ORG> Welcome to PNC Financial Services. We give out loans of all kinds. If you are in need of urgent loan kindly contact us now for instant approval for just 2% interest rate. APPLICATION FORM NAME........... COUNTRY........ AMOUNT......... AGE............ PHONE NUMBER... ADDRESS........ DURATION....... PURPOSE........ Email:......... Mrs. Anita William C.E.O PNC Financial Services. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Sat May 7 18:36:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 18:36:13 +0000 Subject: [Debian-med-packaging] Processing of mypy_0.4-1_source.changes Message-ID: mypy_0.4-1_source.changes uploaded successfully to localhost along with the files: mypy_0.4-1.dsc mypy_0.4.orig.tar.gz mypy_0.4-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 7 18:50:42 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 18:50:42 +0000 Subject: [Debian-med-packaging] mypy_0.4-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 06 May 2016 05:12:05 -0700 Source: mypy Binary: mypy Architecture: source Version: 0.4-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: mypy - Optional static typing for Python Changes: mypy (0.4-1) unstable; urgency=medium . * New upstream release Checksums-Sha1: 2476838fe585d53421050c6e96edd6cfed46a72b 1891 mypy_0.4-1.dsc f32b91f6ebb95254ab1d43d13c95efd294bf300e 490231 mypy_0.4.orig.tar.gz 826d65529deb8f80c5dcd165e630c7c78b133612 2292 mypy_0.4-1.debian.tar.xz Checksums-Sha256: 772abb77c527df24d752a505aa3cd50f1548465741f42d2a0f8d9238b18ab77c 1891 mypy_0.4-1.dsc a7187a1ed197c55bf6fa5c7da1cef85f9f8132912e4cff246a69725568073724 490231 mypy_0.4.orig.tar.gz 2114677c80a9db56c16d2b7ef1097ef316efcc024ffde50b2a9fb19a6d0c866a 2292 mypy_0.4-1.debian.tar.xz Files: 64c5c7ee117ffa98083dbb2a37b1231f 1891 python optional mypy_0.4-1.dsc 7450489329c2c971f7ae64d3af18a0d6 490231 python optional mypy_0.4.orig.tar.gz 744b577389aebbfa924eb8a4b0e68f61 2292 python optional mypy_0.4-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXLjSwAAoJEDwmdj9sZ+biJNMP/2AQ7szeo5AlXmRqeNfwweij 7PcsX210tPDccsSLxkfhQ+wksDSl7YjuBvG7PWxD2TKBCdhn72u9UKzlBZLQE5QN Jz3TI5eVnW79DhL2z7GbHv2F/4mtSzeajnxy+nTvY4y+AolYPwm+jyyratptTv4n xT3f30r3EUTjsoK/IJqjoO95sQ7dpfFxqD2nqeNzuuCU9FrdooQKnLr+V2qiaVip eElGI3Ohw10JTNWnTOhn9nljRq9ZoznZkcuWYNiUg0Qme+IVbqoo13z+8czVvXb5 O3fUoJii32kS17U3DMLHJJPNdiuepZbUTcqXdH2H5r67kc2ppkMf7Rb0jC4z2amj DOf4JeTvpf+YJvixGfryTYaBwxRNpyYyO2zucf+3xWhgY0on8vd42psL4cS+w8bD ClbWl3rEsGJwq1MIzVJOJc7jXJVh50mgzEzkDEXJ827NuPvAFrL6OzNOXZfeWwpG nQK3GrKMZZp9IHoE63R1pWrOn+ImyrsZdPHnxg5b2susFNfoYbxtXXk/8J2SghVk 32GuksTafVMaEkyjmdPUvWxfpX+/bGX+KFoUh8dpKUbEtwkQj+2OIc4zCLKJt/4S GMe30fB+OKj8wx4XwfPJ2ouYGwig49QY9Te/evNbBdarxElAIUI+b1+8yQwns2na K8MdoXqk9psfi+5ql2k0 =ERwq -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sat May 7 20:11:39 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 20:11:39 +0000 Subject: [Debian-med-packaging] Processing of mothur_1.37.3-1_source.changes Message-ID: mothur_1.37.3-1_source.changes uploaded successfully to localhost along with the files: mothur_1.37.3-1.dsc mothur_1.37.3.orig.tar.gz mothur_1.37.3-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 7 21:54:03 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 21:54:03 +0000 Subject: [Debian-med-packaging] mothur_1.37.3-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sat, 07 May 2016 17:54:19 +0200 Source: mothur Binary: mothur mothur-mpi Architecture: source Version: 1.37.3-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: mothur - sequence analysis suite for research on microbiota mothur-mpi - mpi-enabled binary for mothur Changes: mothur (1.37.3-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * better description for mothur-mpi * propagate hardening options to uchime build * better hardening Checksums-Sha1: ad159cf118125400b3415cd844a156ddd3175f6a 2126 mothur_1.37.3-1.dsc eec7096d9bb0a6b1657a830e6cf00f03a261c085 3382727 mothur_1.37.3.orig.tar.gz ab992aeaf10774554891d24aff59eed641b104b2 11076 mothur_1.37.3-1.debian.tar.xz Checksums-Sha256: 90af3cb2e3d47f6c68eea5d3d1fd2fef860e3a105cd01ee5d1015af2879aadc4 2126 mothur_1.37.3-1.dsc 59dafa4d2dba637a7ff3e116bc2c66074e65a4e88e1a99141b33779bd88cf65a 3382727 mothur_1.37.3.orig.tar.gz 834d334f7446ac5896a8bc1d2586e11e92151b7a67341e411f681714aedef4a5 11076 mothur_1.37.3-1.debian.tar.xz Files: 2012a067bca68b17820e10714bc00850 2126 science optional mothur_1.37.3-1.dsc 776cefd60b1daf1ffb34edba35efc538 3382727 science optional mothur_1.37.3.orig.tar.gz 89098d6226373f5e272894f038246284 11076 science optional mothur_1.37.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXLkqwAAoJEFeKBJTRxkbRW2cQAJCb+u7XE0Xh6RYjZ62RZLKJ aliZM6UE7BE52XO7gWG8fRdQNHPqX4zLv4mMSTwu+/wkC/3c1rGC+JHANZ+AW7F4 EM3YYMCrDQKGtEaTVOcJJRoYO1ABqdMPwf2dgoRupHlxMU5YjJsFBfwOuIwoej4+ J3L3IYS6HuflGUJBGso59ip6cpxXpvpJ//1J9jx2u4zT3mG5iOwV5QHFrXJ8BtB0 1P1IcNtQ23a/yUcv51TF6B2DIrUiaW8qiJsswZ4lXr6eGXlQXox1hAZvOLar8bPI JCzpboOheD7rzfaIHlJZvlZd9p/2FfQrVB1EicR8bbTD/kYNc4rvNdtDYrxuI/1o lCpVEbT/iyLYcuiSFyyEInHSByK+Le5+Ww93FDTta+uhZvOv1OUk3QU7DsEmI0bx lvqnuPA1REcPFMddB4anTHru04jCEbj6qF7+HJZDzbroYaCOltgLKIg10GDqfW/j Op8KOzgwbuQ7kElgHaA1JvImHPkj3S4S36YfMjXcFYsr1Z+UlSmibAMac/Oerv5y 0+LJu5X2OBTG/qJIxxgbaV0kvWMzgl4v19SP6Nqrd+i5Gn1X1Wl35EMDJDxgZ2J2 fhbvAy4eVmJN1f1nDLbuO/XCMtNrT5UTUg/JAvnhrdJFJWL6CtYwqI+UWpTWyEJs jF1OpBbIU0QWftd/f9Rv =MFTk -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sat May 7 22:02:03 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 22:02:03 +0000 Subject: [Debian-med-packaging] Processing of pdb2pqr_2.1.1+dfsg-1_amd64.changes Message-ID: pdb2pqr_2.1.1+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: pdb2pqr_2.1.1+dfsg-1.dsc pdb2pqr_2.1.1+dfsg.orig.tar.xz pdb2pqr_2.1.1+dfsg-1.debian.tar.xz pdb2pqr-dbgsym_2.1.1+dfsg-1_amd64.deb pdb2pqr-doc_2.1.1+dfsg-1_all.deb pdb2pqr_2.1.1+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 7 22:23:44 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 22:23:44 +0000 Subject: [Debian-med-packaging] pdb2pqr_2.1.1+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sat, 07 May 2016 23:56:17 +0200 Source: pdb2pqr Binary: pdb2pqr pdb2pqr-doc Architecture: source amd64 all Version: 2.1.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Changed-By: Andreas Tille Description: pdb2pqr - Preparation of protein structures for electrostatics calculations pdb2pqr-doc - example files accompanying pdb2pqr Changes: pdb2pqr (2.1.1+dfsg-1) unstable; urgency=medium . * New upstream version * Add new options to d/watch * cme fix dpkg-control * drop wrapper and use links instead * fix interpreter lines by dos2unix Checksums-Sha1: 1b1d5873294ab00301403fa8f2168e1004c87045 2141 pdb2pqr_2.1.1+dfsg-1.dsc f32a6fdea111872ca6b3467f742f98dfdac91c7e 5191276 pdb2pqr_2.1.1+dfsg.orig.tar.xz 4ac8ea8a33d6cd660323bf3dd7041ec29cdcaff9 10408 pdb2pqr_2.1.1+dfsg-1.debian.tar.xz 12432700d829afbc897a150bc50c08bc9791b0c2 30026 pdb2pqr-dbgsym_2.1.1+dfsg-1_amd64.deb 0381b298621322212aed6b9ec09b32b224661d8c 474860 pdb2pqr-doc_2.1.1+dfsg-1_all.deb 81c2fad21c102092a5e73031186b1379fe9e2f56 364174 pdb2pqr_2.1.1+dfsg-1_amd64.deb Checksums-Sha256: 692b6d37627764bc3cf6e6a1d1df95e950294e97be7b24a70489023acae8801b 2141 pdb2pqr_2.1.1+dfsg-1.dsc aef49fcf96c8990275d956c02003f4b8398c665a0defb06c8655905bbf44c43b 5191276 pdb2pqr_2.1.1+dfsg.orig.tar.xz ee4c2e52dcf07f6456853b8b1a965808bfc6e42e0563b1c7dc60ffb302b13cbc 10408 pdb2pqr_2.1.1+dfsg-1.debian.tar.xz 68b4093355fc0e86a394d15dfc4eb7b163e76d217bc4474213cb2f14139ea076 30026 pdb2pqr-dbgsym_2.1.1+dfsg-1_amd64.deb ee0bc06468857753eac69b33c147442fe14c6f2d8c5704f50c6fc8db770a2a7f 474860 pdb2pqr-doc_2.1.1+dfsg-1_all.deb 8dbd9f766d5127fd5efd3f64cebe63aa367436b909ad88cf2eaa068f4bd03a8e 364174 pdb2pqr_2.1.1+dfsg-1_amd64.deb Files: cca90708765d4cff2a6fa4e4a086c9ad 2141 science optional pdb2pqr_2.1.1+dfsg-1.dsc 6ffad71b2b018b57f44cec20d93ef161 5191276 science optional pdb2pqr_2.1.1+dfsg.orig.tar.xz f4649bdb69a5587283dbd83ff00a7fd3 10408 science optional pdb2pqr_2.1.1+dfsg-1.debian.tar.xz fbd1a32370be50a10e4798b6fe211ae3 30026 debug extra pdb2pqr-dbgsym_2.1.1+dfsg-1_amd64.deb c2de8a03a88e91bc4538b9801b702691 474860 doc optional pdb2pqr-doc_2.1.1+dfsg-1_all.deb a03433d16e0d3fbe17675300ed1e8d60 364174 science optional pdb2pqr_2.1.1+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXLmUmAAoJEFeKBJTRxkbRReMP/2/+z5tr5EXzabdeA3HHGeOG nYkFnMGXesyjaJUjptsReH90bR83fR3Evc0XeVLdTe/Ok7qR7TORqyGqzTHsbROy 6hjIaYR+KGToyQ6pLOqWFh2g5bhOxEmYRGJYzXCOsaKN6fnfEtJgb8hsfWL+3a5c JZ5QYuG7D3Y/j9/KXVPEiDub83rL1TNAWuVLxxr66+fvKjb1MkLiF0dctyCXxfgq H8/XAuRv88eKNlMS3R0N3ZgNOvpj/yFaly+s7koSvEyor9F2LjKq+6NE/5a45CfZ Z/q9XvFVUgyWk5K76O3CI/mQOdGHyhTrpyuBTjRVWgchE0fdlukUd7lNL6Q0cwM/ F2XO41fvVQ1legBObkWkST6+cFlzt5b5a1oARlKXVx6Ugum8MnnIrfmlC02i6tdO dsFjQH6lLdiXraCS120etcNrP8qUKidRO+RAiHTiS/iwAxbnVvcS7aJCzKVshagB ljohBP72c36f8r4wmZ7LbkODChatcbLYevOLCEFX6wYU0VNEms+l/UK2i4LNtnhm di65X+P2PQ5HjjXGRfsxW95dqA7MlreOS1Ftp+vA76HVvtdHTBSLS5NTNsFELmpL a6o+57lmiewO8FvjUcyMBqT/LLK0kZmGuH2Dn+tNeBKyDweNy2W0fwrXTRLAYXiL iCB9xBKt8I1KJ2XNzGCp =dAPe -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sat May 7 22:52:19 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 22:52:19 +0000 Subject: [Debian-med-packaging] Processing of ffindex_0.9.9.7-1_amd64.changes Message-ID: ffindex_0.9.9.7-1_amd64.changes uploaded successfully to localhost along with the files: ffindex_0.9.9.7-1.dsc ffindex_0.9.9.7.orig.tar.gz ffindex_0.9.9.7-1.debian.tar.xz ffindex-dbg_0.9.9.7-1_amd64.deb ffindex_0.9.9.7-1_amd64.deb libffindex0-dev_0.9.9.7-1_amd64.deb libffindex0_0.9.9.7-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 7 23:18:48 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 07 May 2016 23:18:48 +0000 Subject: [Debian-med-packaging] ffindex_0.9.9.7-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sun, 08 May 2016 00:43:21 +0200 Source: ffindex Binary: ffindex libffindex0 libffindex0-dev ffindex-dbg Architecture: source amd64 Version: 0.9.9.7-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: ffindex - simple index/database for huge amounts of small files ffindex-dbg - simple index/database for huge amounts of small files (debug) libffindex0 - library for simple index/database for huge amounts of small files libffindex0-dev - library for simple index/database for huge amounts of small files Changes: ffindex (0.9.9.7-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * enable mpi Checksums-Sha1: 7e4c2dd6a8e1c93fd7887e8ba28b83aa7179dcf4 2204 ffindex_0.9.9.7-1.dsc 9569ab8cff5a00e8b4a1fad919a64cc4b8ea6ae4 36139 ffindex_0.9.9.7.orig.tar.gz a996d8cf19a8c8a0e3d9340271c3dbf8f12be87f 13048 ffindex_0.9.9.7-1.debian.tar.xz 1873018e24dd8b891bbdbba67379dbe7c0a73bc3 68124 ffindex-dbg_0.9.9.7-1_amd64.deb c51c4bd944999711633ce247123b21b0fec9ab1a 28996 ffindex_0.9.9.7-1_amd64.deb d005b74312dfb5bbaecd2a7134c8f4d3b4f2537b 17440 libffindex0-dev_0.9.9.7-1_amd64.deb cc04871633374c7849977ac2a4fd1dfc97f3d96c 16562 libffindex0_0.9.9.7-1_amd64.deb Checksums-Sha256: f5ef13a264126268d39c5f64ba04fa5230e4cd2e819dcb564e25d3c398079b59 2204 ffindex_0.9.9.7-1.dsc c4c6e6be9eaf352fed795635f09df55da0a5c00dfa6ca2e463690bee3504ca03 36139 ffindex_0.9.9.7.orig.tar.gz 3bd27d744615cd8cb1990ef60703cf0169aebb10236d4c510ed483aa3584691e 13048 ffindex_0.9.9.7-1.debian.tar.xz 4fd12e3e882d095175a157c5f4d9e4edab1f78ebe082dbc13aee8bc9c29ce338 68124 ffindex-dbg_0.9.9.7-1_amd64.deb 03547b9b23d72f3978e0c42000f42671362ece5f71073927e10959344545636b 28996 ffindex_0.9.9.7-1_amd64.deb b9355f431ad8b375ee4fa355387399c5420d0ab00bbb2f2097c10c1992823268 17440 libffindex0-dev_0.9.9.7-1_amd64.deb eb2de34112210b3ea031cea78ad55d745b6a5932be17d082cbb38ad924582cbf 16562 libffindex0_0.9.9.7-1_amd64.deb Files: cbb0107816556833feff3b34e26a06b2 2204 science optional ffindex_0.9.9.7-1.dsc 53adbd74459897f78fea9347d4eb0624 36139 science optional ffindex_0.9.9.7.orig.tar.gz 3fead39ee1471765ae0b329eff077b65 13048 science optional ffindex_0.9.9.7-1.debian.tar.xz 1aeec1e24f04710a30b6f4b54df4f5b6 68124 debug extra ffindex-dbg_0.9.9.7-1_amd64.deb 38c6524cdc0d3fd554f5fd4ea3bb34ab 28996 science optional ffindex_0.9.9.7-1_amd64.deb 1a89f9a6b3ba8fe2093635f8673c9c7a 17440 libdevel optional libffindex0-dev_0.9.9.7-1_amd64.deb 635dec1445cf4022bf53ed74373d24aa 16562 libs optional libffindex0_0.9.9.7-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXLnCAAAoJEFeKBJTRxkbRVJUQAJOQ7QI74EpAjHjic4pe56OJ +udJv2dU1pT2R68YHL0goaAPmx1Y3hnBmNSxCQd2eFgw4Bq6t2lvrcDoXXUgV02S ObAVctFIw/H10rmjUab0MThbMAtvtwhXH63u9ODbmjL0YpMEPV1t9Aon3roosx1/ KK86FKXJ1QMk7JXpQ7xHbArBzB8W0k/kpdRcz/9XPkulqRO5qx7Ly2W85I1DY3hl 5O2z84fCgLVmoVQkJkB7bbbApP1RN9jFlGdW6CRFeC7ZbsmVGpC17ci3CBm3WPxe nhB4HzmtO3uSEnngDLTDdJDpZQcm6WlDkeFjYOJtgGjfNbbc8zmLSqcwT9gNfULt 66KJxluatd+RdK8LO5TKGJPNnstOrQdqLgyzP+H0bf4sWilYR0GAhbK0KBIaruec 5+tdNSkiX4lQVrnB9KUEZjfPkRvqbB01CJAuaDVuh7+ULl5AZwYY1OI4hs3ZXBtR +VhnAbaOZj9kVlRtw551LdQv6HLk0jdoc4PpOFzrgrJmvQgt8aiRacEBfnf+gms/ sayxI/2jCvR+3F32LmhgCU7eJvVoTC8gtQGFhqfvHH4yjjM7+JOxNwbCrDj0p4F5 KSSdmJwhAHqWX9neyMBUdJ1rBbZoryHQ5SkdFJI1Rn5fIYKCgmfP/Rth/ZwLy7/k C0Tg5SIKscKh3tdVbbLZ =Gmdl -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 05:38:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 05:38:58 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-biocgenerics_0.18.0-1_amd64.changes Message-ID: r-bioc-biocgenerics_0.18.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-biocgenerics_0.18.0-1.dsc r-bioc-biocgenerics_0.18.0.orig.tar.gz r-bioc-biocgenerics_0.18.0-1.debian.tar.xz r-bioc-biocgenerics_0.18.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 05:51:47 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 05:51:47 +0000 Subject: [Debian-med-packaging] r-bioc-biocgenerics_0.18.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 07:33:05 +0200 Source: r-bioc-biocgenerics Binary: r-bioc-biocgenerics Architecture: source all Version: 0.18.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-biocgenerics - generic functions for Bioconductor Changes: r-bioc-biocgenerics (0.18.0-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 0ad45e1a2dbdfd2c616eb293297f8d7ceceb03f3 2113 r-bioc-biocgenerics_0.18.0-1.dsc e57c707d61293ee8953654ca9dbfbcff67e498c7 39200 r-bioc-biocgenerics_0.18.0.orig.tar.gz a97f8a30b934ec0db4ec6a0a725d4aaf8b923303 5324 r-bioc-biocgenerics_0.18.0-1.debian.tar.xz 335d43de74a561ec02b37bd6a5ad77a17da8ea42 475066 r-bioc-biocgenerics_0.18.0-1_all.deb Checksums-Sha256: 6e2f15df1f6d32660c806e43f2a0adf181502362fe4afc17768c59b8d9d0eab0 2113 r-bioc-biocgenerics_0.18.0-1.dsc e64eba4359c0e4eb298f7779f72b0d4a732fe543661c5657e109c0bb362257ca 39200 r-bioc-biocgenerics_0.18.0.orig.tar.gz a0f439f964c1a93e352a558def1cfed64d7d2e9d524dabf751654b0c6a1f6dbd 5324 r-bioc-biocgenerics_0.18.0-1.debian.tar.xz 180deded56dac910bfa8acaf87b8407e9d45b6bb668a4197f0e233be05bd050e 475066 r-bioc-biocgenerics_0.18.0-1_all.deb Files: eb078565b0d9491f87057ccbe899dddf 2113 gnu-r optional r-bioc-biocgenerics_0.18.0-1.dsc baaff00eb2c2b15396fed2f7f43e634c 39200 gnu-r optional r-bioc-biocgenerics_0.18.0.orig.tar.gz 585a2e9769ab3a8659251c80cbd7648a 5324 gnu-r optional r-bioc-biocgenerics_0.18.0-1.debian.tar.xz 82f6172039b858be46532f2bc0835fc4 475066 gnu-r optional r-bioc-biocgenerics_0.18.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLtAEAAoJEFeKBJTRxkbRklEP/1qBuS9NZgfKCwnUI2FlsilO kChMyVJ+gMrvDMYjZiwLAwA/A23gms78dzMcA5T9lPShzzbqHHPS4adIxGeTxONN BvomI09zKiLcQ6wRfBvYiu7Zu2TFPkAtZhoAjUIrZRvVk0wbRxIB6wp2dX+hDa9j W3ol0jGLYtYTc9ubSHx+FPuKHjwVkcX0l1DPuUws/Ap4Cw88EFzg79CCWioadA8t 8JvdbA+SuRAKqXzf+mEBZg4qj9eACGHM7NQ5x4PB95KD1f9A/sG9z9dzWBlJIffF 9oWy81fD9T6hdMH7CP6JoYq4vS5tPmaiCIr5YldJZZUdpGV1yZOGjEHyEQfK1DhG HRfexwjjUr8FIIBNdr326TGiKis1HOauCxhy3D6sgkjA4SQY5qDTyiWQl8uOGxgv eTY4zWaWjGjbWRBsRwmlR8wXZqn7ZoCNyE3u2yXIOpjcFajczG07v5P6672Y6NJx YtQ3QESmWKXxz0oKUS2SSUS61/yIOfeoxesmDxgLflRHwjO33CivkipJdoWJJPUp Xkw1VpL9uLUJbkXW7HCl7FtbwB+2Ux6scZk7VWG0Dr9nPlS25r9d59GMMHuyn2iG wCRf/ge6BUbZveDDU8goOsnazSMvpWjgl3UeoosMvuzPNl3W/e/27JN+lqqbEaH7 pivcqwGnIq2e7bTadeiC =RfN9 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 06:19:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:19:07 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-biobase_2.32.0-1_amd64.changes Message-ID: r-bioc-biobase_2.32.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-biobase_2.32.0-1.dsc r-bioc-biobase_2.32.0.orig.tar.gz r-bioc-biobase_2.32.0-1.debian.tar.xz r-bioc-biobase-dbgsym_2.32.0-1_amd64.deb r-bioc-biobase_2.32.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 06:24:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:24:07 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-s4vectors_0.10.0-1_amd64.changes Message-ID: r-bioc-s4vectors_0.10.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-s4vectors_0.10.0-1.dsc r-bioc-s4vectors_0.10.0.orig.tar.gz r-bioc-s4vectors_0.10.0-1.debian.tar.xz r-bioc-s4vectors-dbgsym_0.10.0-1_amd64.deb r-bioc-s4vectors_0.10.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 06:34:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:34:11 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-graph_1.50.0-1_source.changes Message-ID: r-bioc-graph_1.50.0-1_source.changes uploaded successfully to localhost along with the files: r-bioc-graph_1.50.0-1.dsc r-bioc-graph_1.50.0.orig.tar.gz r-bioc-graph_1.50.0-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 06:34:47 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:34:47 +0000 Subject: [Debian-med-packaging] r-bioc-biobase_2.32.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 08:10:13 +0200 Source: r-bioc-biobase Binary: r-bioc-biobase Architecture: source amd64 Version: 2.32.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-biobase - base functions for Bioconductor Changes: r-bioc-biobase (2.32.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 825fd5928b904092b56ac2046adcabc84b635157 2091 r-bioc-biobase_2.32.0-1.dsc 55a07ea6f077062be84e9151ff24e803fde52ab5 1675248 r-bioc-biobase_2.32.0.orig.tar.gz bd8cf5a3506ce2b5a1646743cc64f2554f4e53ec 7364 r-bioc-biobase_2.32.0-1.debian.tar.xz 59f34cc4b43f843fe9be626525463f1f4bc384c6 16918 r-bioc-biobase-dbgsym_2.32.0-1_amd64.deb 440aafa982ae1c716c4425f90b9fa934a8d8b1cb 1997682 r-bioc-biobase_2.32.0-1_amd64.deb Checksums-Sha256: 912a81359bad5e6193eafb79426b9ea756b32c59efe88fea23a5dd699857d75a 2091 r-bioc-biobase_2.32.0-1.dsc 31d02942da6d6505fbf8a216e250f6ec5fe62a943c4cb3a7c382e562d3669160 1675248 r-bioc-biobase_2.32.0.orig.tar.gz 3bdcc16574aa052dbdd9c7f2bd615a6eb2f341309b7dae2757f21912bfc76994 7364 r-bioc-biobase_2.32.0-1.debian.tar.xz 23b46eab95658e16a2d347a9eaade037b1f7897d69210b726f444c0581510c5f 16918 r-bioc-biobase-dbgsym_2.32.0-1_amd64.deb 412c23f7c82df6839edfa8725e02308fdeead197c09fe35eec57fd9c65639a20 1997682 r-bioc-biobase_2.32.0-1_amd64.deb Files: 873f912d2a695035680b606aeaccd706 2091 gnu-r optional r-bioc-biobase_2.32.0-1.dsc 8f3fa0b65c0fe3db21891ba6a13a2c91 1675248 gnu-r optional r-bioc-biobase_2.32.0.orig.tar.gz fe64a3faf9db1dfc1c60c757ed316df5 7364 gnu-r optional r-bioc-biobase_2.32.0-1.debian.tar.xz ac3af96aa085e39429ba17bcf04ffc7e 16918 debug extra r-bioc-biobase-dbgsym_2.32.0-1_amd64.deb 216ab8ae2164d6c98b4b44424d7d30f5 1997682 gnu-r optional r-bioc-biobase_2.32.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLtjbAAoJEFeKBJTRxkbR0TcP/30qJxtn+RbBYh4XW3+Nu0rH WcNFniklpr7YtH2Bs+ZYF6VJ5dMHHQcIEIC0VUaWz3MYWrvldh+T0T2dLAZ/3dUt SVbUxbPxxqIUJcxhLBhnZGsOi7BCvgpsZFWbTnn5it5AFlgwy+FK0EhCD6H/vvtb 9K1XR4qr4jt6wFtu+rR6G6dSx2WjJkawvECnzjDCBIsFCg3sg6mNY0kh+aj2A7+c oY7DM4eB4mL1/ul9Vnl/vZI2RGmVBqhD3TNBCD3sYMWMIi0keYIKLkAFxiPpHy0o w5k3HTEH8dpSVXIIG961R83DD6KMKH8ZlJ5Yp19hSyn1hiV9YW7BJuUZW0hbnHUy NQX3X2laLPqD2tlG9ekfNaHVbmNSYjZY7cTZIxLD8W6ru+Guv9zg7Petgl1RBHjf jhRox0GWpnLzohGOmvTyptQcPyXNpf5eqEC4izN6ulZqPrw0rnud85P5k26tTK9r swMYYyGw8sWBpZUK6jw67b0Yf/SgpGm+Jc0h5pXU487wEDNsETQUHJ/54+OX3Nqt Jjv3CelEAbWW0ZYSYehKlnV4RZcFcjS5hlgryFF4w98ZzN53H9/gUmbk9fWljf3t Mu3jfwlzAbS6o79eObyfcjvvk0gdfQVrHIIFmCLLYB0rJhgbGU+2hV/AXtKWR1QZ lcDlLCd8GOjlDwji8oah =AeLI -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 06:34:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:34:55 +0000 Subject: [Debian-med-packaging] r-bioc-s4vectors_0.10.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 08:17:19 +0200 Source: r-bioc-s4vectors Binary: r-bioc-s4vectors Architecture: source amd64 Version: 0.10.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-s4vectors - BioConductor S4 implementation of vectors and lists Changes: r-bioc-s4vectors (0.10.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 4c038aa2495de36f1fb123d3742c38a647388eb9 2145 r-bioc-s4vectors_0.10.0-1.dsc 908322177a5546a3d39a5ae210804786eb9b1934 226714 r-bioc-s4vectors_0.10.0.orig.tar.gz e856f1c5f8082ba8ed50d7f6a8225eb83d78caf6 3728 r-bioc-s4vectors_0.10.0-1.debian.tar.xz 461ba9a8d2540d6cc88cd0a35c25b87c0b07fa5a 104428 r-bioc-s4vectors-dbgsym_0.10.0-1_amd64.deb 2c15ef8b6f10045674e14e98b4b545574270819e 920048 r-bioc-s4vectors_0.10.0-1_amd64.deb Checksums-Sha256: 0c5eed04ece512620f9c0ed3d70ccf8b2461bb0d0a246872a4bf9d4f7d334a86 2145 r-bioc-s4vectors_0.10.0-1.dsc 6be0640f93ebbb530e15624229f2e2ca0ff03d911bf8174f31342d7b8da326d6 226714 r-bioc-s4vectors_0.10.0.orig.tar.gz b2e7f81555fe29234c49227f331bf6c822aaac237d8bcafd8459716fe54317a8 3728 r-bioc-s4vectors_0.10.0-1.debian.tar.xz 4b9f155530314499b854cf059d243e435173e22c14f9a6283cad89da86d8eace 104428 r-bioc-s4vectors-dbgsym_0.10.0-1_amd64.deb 215f3f06061358947b4b791a631caf0d238a651e6032407293f108ac6db35a24 920048 r-bioc-s4vectors_0.10.0-1_amd64.deb Files: fb7c9a082e7da1e2f3e960df69c01a80 2145 gnu-r optional r-bioc-s4vectors_0.10.0-1.dsc d02fc9645a1ab1a053b7c0972adbedd5 226714 gnu-r optional r-bioc-s4vectors_0.10.0.orig.tar.gz 536acb1a1795d3ccf0f8d0541fd0b5b7 3728 gnu-r optional r-bioc-s4vectors_0.10.0-1.debian.tar.xz 6c8e251f038b51fe647924103caa17e9 104428 debug extra r-bioc-s4vectors-dbgsym_0.10.0-1_amd64.deb f398eeabae04d1a563f0c0805db959d4 920048 gnu-r optional r-bioc-s4vectors_0.10.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLtqTAAoJEFeKBJTRxkbRLgQP/2jAJs47HW2mtozXIG4TkM+U uTMm6UJIbBk/FXGCjXUiYZYFIMGBpIB7+kpsjAjzhJeW1Q/c6uKyO+ERa8CoMwjg bVQ3lXWQDyb6ADttGwfGNrv89OHV7tDtqlFh1JeDbdgxJGmvcN+VzyX5anNP9R26 4mzFWalUbFsITCWz9h0MrN0fVHlNxS+D3JyCnr/GJTRPXtG77wYiNbM37hzzIzog ALe7Ln/b8DvMClGyXjL5T1OsRsyW7BHIAxE+5VJY4CpGyM8qYWsu23692FTMdE4C 8+VeQZsHqu4G8V6+d1VDUiShmAUSmsRDDTSy5/hu56VDqIsbtRkstmcAcAtNYkt0 t7b7YHlQdi3xCzNVAMmYXCI6rqm/DLB0tecmtd5aAlPUr/7jxElLEi2gekr3sETW ceIrsV57vSRSoSlyZTkLvtAtb1ySUrvnRdGfKZqn935kYMPhjrjFCf9xb1awkr80 a0XTM87BYuDXFSyhi6aPTNNaWaiHRT5t0A7xpZgZRW5hD9JdOGuvT/tV1Oxj5w// HP/Rqvxef2rcxRUwuwct8j5HcilmaUt6zev0wFkPm9fKMjYLGxzblokwX/Y4ea5x g7JLRrX25SpomqC0WWbtCrJqqz+sbUmCEkh9MapEYOGhDxpvM6bfIUwTxDFX+f+x Bpkt1cTrGD1rolAzfeAy =3p7C -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 06:39:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:39:11 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-snpstats_1.22.0+dfsg-1_amd64.changes Message-ID: r-bioc-snpstats_1.22.0+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-snpstats_1.22.0+dfsg-1.dsc r-bioc-snpstats_1.22.0+dfsg.orig.tar.xz r-bioc-snpstats_1.22.0+dfsg-1.debian.tar.xz r-bioc-snpstats-dbgsym_1.22.0+dfsg-1_amd64.deb r-bioc-snpstats_1.22.0+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 06:44:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:44:11 +0000 Subject: [Debian-med-packaging] Processing of pixelmed_20150917-1_amd64.changes Message-ID: pixelmed_20150917-1_amd64.changes uploaded successfully to localhost along with the files: pixelmed_20150917-1.dsc pixelmed_20150917.orig.tar.bz2 pixelmed_20150917-1.debian.tar.xz libpixelmed-java-doc_20150917-1_all.deb libpixelmed-java_20150917-1_all.deb pixelmed-apps_20150917-1_all.deb pixelmed-webstart-apps_20150917-1_all.deb pixelmed-www_20150917-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 06:48:41 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:48:41 +0000 Subject: [Debian-med-packaging] pixelmed_20150917-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 13 Jan 2016 15:05:06 +0100 Source: pixelmed Binary: libpixelmed-java libpixelmed-java-doc pixelmed-apps pixelmed-webstart-apps pixelmed-www Architecture: source all Version: 20150917-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libpixelmed-java - DICOM implementation containing Image Viewer and a ECG Viewer libpixelmed-java-doc - DICOM implementation containing Image Viewer and a ECG Viewer - d pixelmed-apps - DICOM implementation containing Image Viewer and a ECG Viewer - j pixelmed-webstart-apps - DICOM implementation containing Image Viewer and a ECG Viewer - j pixelmed-www - DICOM implementation containing Image Viewer and a ECG Viewer - j Changes: pixelmed (20150917-1) unstable; 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From ftpmaster at ftp-master.debian.org Sun May 8 06:48:47 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:48:47 +0000 Subject: [Debian-med-packaging] r-bioc-graph_1.50.0-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 08:24:51 +0200 Source: r-bioc-graph Binary: r-bioc-graph Architecture: source Version: 1.50.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-graph - handle graph data structures for BioConductor Changes: r-bioc-graph (1.50.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: ba56b02f8a28e24a6fcc3197e376fe1781c70213 2097 r-bioc-graph_1.50.0-1.dsc dbfc28021546d4f6a47e373ab103f204d7eb75bf 963602 r-bioc-graph_1.50.0.orig.tar.gz a538b393dc0b1e1581c789ed82e8c7f1c5a1e152 3816 r-bioc-graph_1.50.0-1.debian.tar.xz Checksums-Sha256: 99b122e48bbcca1037f1f9e68718e3833bbcc5b60d0c4a80f9eba254fdb98a34 2097 r-bioc-graph_1.50.0-1.dsc f112e7794333af1596f38292a67217f6702c3e80a25b0732cd60e45253d0457b 963602 r-bioc-graph_1.50.0.orig.tar.gz eddf7bfa0bd8ad313650e32e86f560487ac913606a0f417c8b92a703c803c28b 3816 r-bioc-graph_1.50.0-1.debian.tar.xz Files: 682805a00c7e550e5635fc60ecda3dfb 2097 gnu-r optional r-bioc-graph_1.50.0-1.dsc 3e65e4281e39a9b93caec2c4d8ae297c 963602 gnu-r optional r-bioc-graph_1.50.0.orig.tar.gz 97ae5be3a1aef72c65dcf53339ff8c4c 3816 gnu-r optional r-bioc-graph_1.50.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLt0QAAoJEFeKBJTRxkbRWdEP/390jibFyv5bl38qQV75qFSb vN8/x7EYjIHJSQVWyAG1FF3W25jdNZQ9hgxTHaCmDPGG9ivgdwOj3jH3Ck8uRgFj lprTTX7yycijwj26qtSdm+AFW3u09mz6UzwlfFPK9NxYgmoYhUdA5gwnlbkVNk5u ola6C7zDANUtTvjc6PjQ3pZ98myCg9j3QaBW4cDLAwu8wyoBPrHYrMlxenc8k4kf PpTudyeuiMIeqMQsduvnB359W6rDfGOpS+CuhYD4ot82vYEyNyx3UXvhv/tfpPTX x18l/YylwbC0wZMxtRa+jTXM5iGbM2OI+eYVS4aVI7XVsBnYSHxaNoU1bk25rA5F pAuxBu0jWaHeLQN6k91HBSgOrKV3wX/i5BsEZm9BTe/bqlBq4Cf2/tKNS8uCuMd4 w1hLcFetLc6Ab+0oqTLY55m5Nxddg1vNSsiaPgF/1CYOH136AJ7Roy+cTnj1zz16 gpp0lIHF/xu/pE+25LpGqNABbtbZymjOfFFRfLE19USVXHLHvX4lsjvU+xlgHzqy EPoNFA8cqGpWCt+foRggrTjv55Z0FNKThkcy6uZiuRjZmm6DY8b1MP/B9rw7IErk bMbr8ayXvFc52VRwS+O8hvUZjoabYpVJyrq25ZW7Jv1/PDasWw4IpVQ3UNpmV3Pc y3nxNM9qgJby7B4eOdDF =k8C7 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 06:48:56 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:48:56 +0000 Subject: [Debian-med-packaging] r-bioc-snpstats_1.22.0+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 08:29:42 +0200 Source: r-bioc-snpstats Binary: r-bioc-snpstats Architecture: source amd64 Version: 1.22.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-snpstats - BioConductor SnpMatrix and XSnpMatrix classes and methods Changes: r-bioc-snpstats (1.22.0+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 992d569491e7dba3af5f08b7f6a4d2d22ee7ea07 2215 r-bioc-snpstats_1.22.0+dfsg-1.dsc ff3da0924dad20dbb241ea35049cd462174c1eca 6664308 r-bioc-snpstats_1.22.0+dfsg.orig.tar.xz f6161484d4f25c76ed4dd98b7345390552e33b53 4176 r-bioc-snpstats_1.22.0+dfsg-1.debian.tar.xz 932e541f09567a8c7c03cc6bf5acb53aab905d69 194572 r-bioc-snpstats-dbgsym_1.22.0+dfsg-1_amd64.deb 61c07d7069a444796ff00ea25f87a148bc4495b8 7163808 r-bioc-snpstats_1.22.0+dfsg-1_amd64.deb Checksums-Sha256: f879ec9a8885cbba6e0e17f156090eab7312fc315b1a8d156c4cacec85284ae5 2215 r-bioc-snpstats_1.22.0+dfsg-1.dsc a17d709315c078333c9f18f50d1319d338320ccdbaa0139297ff34c1d23f7224 6664308 r-bioc-snpstats_1.22.0+dfsg.orig.tar.xz e0ab0ffebd5f986c256e6bc6abe2f988c01e2f36e0c11782510b175d073548a4 4176 r-bioc-snpstats_1.22.0+dfsg-1.debian.tar.xz b6547be1eab87b34159b271cb92d3746228c5c1b9e8e18e91afc1e4689d2d7f0 194572 r-bioc-snpstats-dbgsym_1.22.0+dfsg-1_amd64.deb f0b7c75b8820047e00d6d3f90df306b6b753f2aed6335a483f5824be88dce8da 7163808 r-bioc-snpstats_1.22.0+dfsg-1_amd64.deb Files: 5ff73377b202d3a127c39810a2770264 2215 gnu-r optional r-bioc-snpstats_1.22.0+dfsg-1.dsc 2c47393818d51d52f29a383ac1c24aac 6664308 gnu-r optional r-bioc-snpstats_1.22.0+dfsg.orig.tar.xz dc30f05e90946974a060cffec691983f 4176 gnu-r optional r-bioc-snpstats_1.22.0+dfsg-1.debian.tar.xz a97cb93315fe239a96f7217abc9be66a 194572 debug extra r-bioc-snpstats-dbgsym_1.22.0+dfsg-1_amd64.deb 62200e72110daa7be889b0b46540128f 7163808 gnu-r optional r-bioc-snpstats_1.22.0+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLt2HAAoJEFeKBJTRxkbRz5YP/3iGx4Ecnmu/hhR3psYEw0H/ I+MpWjVBHKyymDwxA9Yivt/3cWoD1qsYUxvDuZuOWRjeEOqjEzCm9vgJO7d/CAWr i1sEl3TjvLxubDl9bDRwphb3X8eCqW+/kvIALtuQZQZIvMRDH8YPxxb3yS6ibxsO VPnUlCacL46ggTSVXZuNA7igiejVHg2W3ougoDnRPtZiAJA6hzp8NIZKyC7CVQAo l+jm8r0DrBJ96UKZo85YDSqesA/fIQYGyn53DX7/fwzPwTwBupHmoYtN1uaZj03e cafgVKIPfZ1GIevfBMBwkvxQMogK6Q0b+2le/s9CqN5QB4xxJfX2ebzHMVruD+po 4s8rjuDG4ZfhRu+QLJ5bX2U7HuxxuoZn2vsSXfUaacuQyk45RWvi+pjAPYFnfLEM s34mFQxqu8r+BbHj6uLs6K+ygIeF2r8SRMgSW6uUZd/th8TKCTkHtAHAWG6QppZH tT6HoUCqoqt4v4JJZ17FVaefx8QFk4vTHrKIfyWnGP6L7VIUmgxvqV89N4NCfph5 abHuBgBDDKhveJpVSqXfD3CxqFgmhtijdpl50TEnGQnKm4njSCm9e5ufFzU+Cui4 lHbO5geBt9uI5IPE+A6lHq0+e0Ae8HNaBC1uM073HGfdhOm3I6jfe0icl3sPunxi 8IuPYHnaizb4Kqcir7/U =hohl -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 06:59:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 06:59:12 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-biocparallel_1.6.0-1_amd64.changes Message-ID: r-bioc-biocparallel_1.6.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-biocparallel_1.6.0-1.dsc r-bioc-biocparallel_1.6.0.orig.tar.gz r-bioc-biocparallel_1.6.0-1.debian.tar.xz r-bioc-biocparallel_1.6.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 07:09:14 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 07:09:14 +0000 Subject: [Debian-med-packaging] r-bioc-biocparallel_1.6.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 08:41:08 +0200 Source: r-bioc-biocparallel Binary: r-bioc-biocparallel Architecture: source all Version: 1.6.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-biocparallel - BioConductor facilities for parallel evaluation Changes: r-bioc-biocparallel (1.6.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 08fc7490fdf200f0237e1e053c8c28aa6890ee24 2240 r-bioc-biocparallel_1.6.0-1.dsc 2e660908aeb959cb7f633e7c22889a8cce4bb4d5 620320 r-bioc-biocparallel_1.6.0.orig.tar.gz 74608942cb6d713583f36a38cc5037377031de3a 3256 r-bioc-biocparallel_1.6.0-1.debian.tar.xz 27967d2cb05da63fad9db7cda688324a4226843d 626174 r-bioc-biocparallel_1.6.0-1_all.deb Checksums-Sha256: 8e04d69c31b4294a21175cdb4da4bc8d8fcefce0571ad57ad77479c2f8b6610d 2240 r-bioc-biocparallel_1.6.0-1.dsc da0322cfacbc1b317ef892a64ae3daf2e7058ed36ee8413eb175e8f7168c127a 620320 r-bioc-biocparallel_1.6.0.orig.tar.gz f682e865b586c4e52dfc64d867bc4398cff5deec5f5388dd2de3a30fd4c9efe6 3256 r-bioc-biocparallel_1.6.0-1.debian.tar.xz c2de40e6f4d86e16f9603114242e9a2873a3836e7a1e8708a10624c032ffa13f 626174 r-bioc-biocparallel_1.6.0-1_all.deb Files: 3477f1b02300d938a24a017487586798 2240 gnu-r optional r-bioc-biocparallel_1.6.0-1.dsc 733497f793cd432b061b3d06038b5d96 620320 gnu-r optional r-bioc-biocparallel_1.6.0.orig.tar.gz 8a3133785717d88924046297be9ea4c0 3256 gnu-r optional r-bioc-biocparallel_1.6.0-1.debian.tar.xz 09185b0d394ca5fe287ea854814f1ed3 626174 gnu-r optional r-bioc-biocparallel_1.6.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLuKpAAoJEFeKBJTRxkbRf8cP+wUpysuYqOxUmXioEzQMi3hx A6fomkJyQtiesnojMtJODBkwSQoCubqsTJHuPWcj/t9pru+2Yf0HULWBnU/yVmyT JyJMOB1XRikx+Yuvw8scS+h9K+eaFNdmIwjAqo8l8Q2NMAFV6NScSUI6fAsZxdO8 UmgzkD1rbkFtvUBFSifhZqulNnycUfq8a2TmNdMnI2xb4w0u5mEFy2zLb9mi8p3v 1gRBpwkgpQ3AUnGNHvI75FvUZ88OW7PdXzVLVgwUuXPMXBuzh/a6Lgh78v+/9lHh SdvT/2Gz536WgshHyaDI+Gp6nfkyuwmiHXVXK8bBCvlbXLIj/6I8h3u3WpmAohy7 EDLp3jZZB+3cpjzRPQkMZUqz9ocMYyaF8x9HafxY1AgOx/SdVL/YGoWe84KuuZ0f sPArA8U4zlpVqxISXjTmNcy2wPjJ7zTVw/5azYtWoOaaoCI728+GT9LfculaERtJ qAPtlqiJ8x1HizcBMeC5jkADlXFUZvYjqYRVk0laEBAjLpBSc8tu1JCETw2Ws77W QRnw0447SqJdGmc14S7ZKtoCNPge+7QFzDK3qEVF7BiNC+YQgxvm8CeWnH+xBsA1 VtoTMkRpE3R8jYr6dk/N/PgGHUBEcSwMTdicYS9K5ozdd6QZ5lxaOdvKjsy1joBZ Yimbh2dKSF191SSSK2ld =Ky2z -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 07:19:20 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 07:19:20 +0000 Subject: [Debian-med-packaging] Processing of sprai_0.9.9.14+dfsg-1~bpo8+1_amd64.changes Message-ID: sprai_0.9.9.14+dfsg-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: sprai_0.9.9.14+dfsg-1~bpo8+1.dsc sprai_0.9.9.14+dfsg-1~bpo8+1.debian.tar.xz sprai_0.9.9.14+dfsg-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 07:35:42 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 07:35:42 +0000 Subject: [Debian-med-packaging] sprai_0.9.9.14+dfsg-1~bpo8+1_amd64.changes is NEW Message-ID: binary:sprai is NEW. source:sprai is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Sun May 8 07:39:26 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 07:39:26 +0000 Subject: [Debian-med-packaging] Processing of fastaq_3.12.1-1~bpo8+1_amd64.changes Message-ID: fastaq_3.12.1-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: fastaq_3.12.1-1~bpo8+1.dsc fastaq_3.12.1-1~bpo8+1.debian.tar.xz fastaq_3.12.1-1~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 07:48:30 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 07:48:30 +0000 Subject: [Debian-med-packaging] fastaq_3.12.1-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 00:24:29 -0700 Source: fastaq Binary: fastaq Architecture: source all Version: 3.12.1-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Afif Elghraoui Description: fastaq - FASTA and FASTQ file manipulation tools Changes: fastaq (3.12.1-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. . fastaq (3.12.1-1) unstable; urgency=medium . * New upstream version. * Add new dependency on python3-pkg-resources. . fastaq (3.12.0-1) unstable; urgency=medium . * New upstream version. * Bump Standards-Version. 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From ftpmaster at ftp-master.debian.org Sun May 8 08:04:27 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 08:04:27 +0000 Subject: [Debian-med-packaging] Processing of python-pymummer_0.7.1-1~bpo8+1_amd64.changes Message-ID: python-pymummer_0.7.1-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: python-pymummer_0.7.1-1~bpo8+1.dsc python-pymummer_0.7.1-1~bpo8+1.debian.tar.xz python3-pymummer_0.7.1-1~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 08:29:31 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 08:29:31 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-biocinstaller_1.22.1-1_amd64.changes Message-ID: r-bioc-biocinstaller_1.22.1-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-biocinstaller_1.22.1-1.dsc r-bioc-biocinstaller_1.22.1.orig.tar.gz r-bioc-biocinstaller_1.22.1-1.debian.tar.xz r-bioc-biocinstaller_1.22.1-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 08:34:36 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 08:34:36 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-preprocesscore_1.34.0-1_amd64.changes Message-ID: r-bioc-preprocesscore_1.34.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-preprocesscore_1.34.0-1.dsc r-bioc-preprocesscore_1.34.0.orig.tar.gz r-bioc-preprocesscore_1.34.0-1.debian.tar.xz r-bioc-preprocesscore-dbgsym_1.34.0-1_amd64.deb r-bioc-preprocesscore_1.34.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 08:39:37 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 08:39:37 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-affyio_1.42.0-1_amd64.changes Message-ID: r-bioc-affyio_1.42.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-affyio_1.42.0-1.dsc r-bioc-affyio_1.42.0.orig.tar.gz r-bioc-affyio_1.42.0-1.debian.tar.xz r-bioc-affyio-dbgsym_1.42.0-1_amd64.deb r-bioc-affyio_1.42.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 09:55:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 09:55:35 +0000 Subject: [Debian-med-packaging] python-pymummer_0.7.1-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 00:43:50 -0700 Source: python-pymummer Binary: python3-pymummer Architecture: source all Version: 0.7.1-1~bpo8+1 Distribution: jessie-backports Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Afif Elghraoui Description: python3-pymummer - Python 3 interface to MUMmer Changes: python-pymummer (0.7.1-1~bpo8+1) jessie-backports; urgency=low . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Sun May 8 09:55:53 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 09:55:53 +0000 Subject: [Debian-med-packaging] r-bioc-affyio_1.42.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 10:36:53 +0200 Source: r-bioc-affyio Binary: r-bioc-affyio Architecture: source amd64 Version: 1.42.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-affyio - BioConductor tools for parsing Affymetrix data files Changes: r-bioc-affyio (1.42.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: b112e1340aeee361f18b40d2771c61245b6d8dde 2065 r-bioc-affyio_1.42.0-1.dsc 06536a05e5020835d7e26ee9776c11fecaa17497 106427 r-bioc-affyio_1.42.0.orig.tar.gz 454f20fcf6d46f5af0868ad668242f0512812b3a 2024 r-bioc-affyio_1.42.0-1.debian.tar.xz 6dd2a1c377309f3a6c4f5dda3a9877e8c8331ab5 161298 r-bioc-affyio-dbgsym_1.42.0-1_amd64.deb 33474ef0649c6fa8163da985e3dd3fb06c5f6658 76274 r-bioc-affyio_1.42.0-1_amd64.deb Checksums-Sha256: 58a4e38eabc219d5a7ed285aeebaf43af6b179de81d0f3833b0cdd544a789b35 2065 r-bioc-affyio_1.42.0-1.dsc 7c27eadb87af6ac52fb8ed209a7356fd5f6b4111906fd6b6bd92d0eb92dba767 106427 r-bioc-affyio_1.42.0.orig.tar.gz aee34271871497edd3d8a8a70f004f6fa683f9b8daa2de31395d102f29655f48 2024 r-bioc-affyio_1.42.0-1.debian.tar.xz 005b7e85d1ab8c45e046d64ff1b6ff2c0d1ff1f71e0d919ac4ca872dc9a0ddd4 161298 r-bioc-affyio-dbgsym_1.42.0-1_amd64.deb 7eb62229f8859c3ffee7d9326530c26527c63a21927fb6df44ebdf3ef9ef862d 76274 r-bioc-affyio_1.42.0-1_amd64.deb Files: aefdc264b2f92fae6109646296119720 2065 gnu-r optional r-bioc-affyio_1.42.0-1.dsc 3d7a7f037fe7e1a312b4bb80329d05e4 106427 gnu-r optional r-bioc-affyio_1.42.0.orig.tar.gz 81ef64cb8b9dbcdbab7f5a1e34861115 2024 gnu-r optional r-bioc-affyio_1.42.0-1.debian.tar.xz 7ebd0c818c95fdfc19315f5282dd2986 161298 debug extra r-bioc-affyio-dbgsym_1.42.0-1_amd64.deb 682142bc3abf153a208d22e89d677e0c 76274 gnu-r optional r-bioc-affyio_1.42.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLvsJAAoJEFeKBJTRxkbRGPAP/iFEsL4jt/iHnSPXoVqVQYHw 95P88Q+zGIXOxtf3Qb2C1mfMOOJSo7TRdGgn2HFUHSVHs9FkwqNvh5L0ryVPuUI2 E0n4MKE2WxOHiTLQAsBxicv4vF1RXLU4ecfh4aFTxhaKUssXVPzqqFdwXyqVgNJB DIxu0TEwwvb2lSeNZTG6rVs0o+W7564Ffasi0T2E86zU17m4mJYgDI9oqPpgnThV btIbMzCOXR9NdQoktT3f8jzNwaG6Onz4W229qu2kCVAxMQA7xYNsdLEYh4u/7Mzv xeBJXVw3WLkT2MamBaOyATVOFXzG5i1m3KXSCRz0SbQZNhw6yZuROAZKvgvW9+Ze Em9Ikd07wVFfsG22gUqxoqm4l3iGiaAHl9Ccghx9MA2CdkQf/QAD8HIe/uwytQC1 kBZTzmEi44OUJll5hK6/jva2l8LewPo/r1WWgQ6dMtfh4oGqGy3YmLJkuVJzf2GN RixEv6FvlJNVvRgFjPla28OwKtokVLy/0jmeq9jQw7gARMpAlyIdKQWdzy8pk5Vq dIMeEx3uqwGG09htjkFlizVxd4u+cLr2mnL1BBTiDCGgrlAj+VVXLVqeoesDcdl4 lag7VYda/iF0ZnJLk0GxZG6ATJd3/UU2lEwHBGMGx1gFX0Ejrnxc2S55PRMYWf85 R3+RYJLpKkXcNuQTT/P6 =OHO+ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 09:56:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 09:56:13 +0000 Subject: [Debian-med-packaging] r-bioc-biocinstaller_1.22.1-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 10:25:10 +0200 Source: r-bioc-biocinstaller Binary: r-bioc-biocinstaller Architecture: source all Version: 1.22.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-biocinstaller - Install/Update Bioconductor and CRAN Packages Changes: r-bioc-biocinstaller (1.22.1-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: df9ea6d960d0a281d2f42df71c73ad5e5dc59000 2157 r-bioc-biocinstaller_1.22.1-1.dsc 22a0aec1f56cfcbdcfac384e48c7a15b0bc49fdd 16263 r-bioc-biocinstaller_1.22.1.orig.tar.gz 9cb2152d3fccf9d6bd41b8217c03a1122d1a73f0 3576 r-bioc-biocinstaller_1.22.1-1.debian.tar.xz 39036b62d7dd76eccfe5ef7d8244a82400bfb626 57302 r-bioc-biocinstaller_1.22.1-1_all.deb Checksums-Sha256: 6524e4853f967769bdc02e83b97e7698b1302c47984c6c7d1fafe82f2da6e850 2157 r-bioc-biocinstaller_1.22.1-1.dsc 52d98e29ebf384c0fe1b1a6322bb5c243e30bfe924d1e9248c0f74467c8b7a6f 16263 r-bioc-biocinstaller_1.22.1.orig.tar.gz b2e27c25360728424dd22ad9b29f72f35d415ecf6d313a434d02cbc3c4415b25 3576 r-bioc-biocinstaller_1.22.1-1.debian.tar.xz 4fc51bda2dccf4df7c25e1974ad687416a0eda3593b5aeb351cb361d72542618 57302 r-bioc-biocinstaller_1.22.1-1_all.deb Files: a74515b111f4d9a5e95fb2383b404c4e 2157 gnu-r optional r-bioc-biocinstaller_1.22.1-1.dsc 2655fe7e7e95ae445a5df04912af6b0d 16263 gnu-r optional r-bioc-biocinstaller_1.22.1.orig.tar.gz bda3460a5630e910016dfe83cc29594b 3576 gnu-r optional r-bioc-biocinstaller_1.22.1-1.debian.tar.xz 1c2c5df2c11cba1a41aaf7b63ff6a8c8 57302 gnu-r optional r-bioc-biocinstaller_1.22.1-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLvhHAAoJEFeKBJTRxkbRk7gP/3ttgDN2JZvzie//zCtyItPZ hvnDpFzeyH//JfURcCiFTTkGjxvmYZhPAUmr0S03kXmH9bma6YKH5mdiL/TROaAn M3/YTtnBEDXYa11bq5ko0XYEjZYYnXWLT49MNPouIsGsjCvg5OBsbpvxr026ILrM U2T8bVf25R2OATgnpUiJZFWmUwaCl8iooHjpMIYtJ22ZKagyfOZXy3EUtN0MLA/a pGoVRNTNfAK03Tf4+olWII+lNvCf5pXZsLeFLxc1MXM63y9qnTvmTx6/mLHhyury TSGcL/K0A9v4YEtmxuzGlko9NRosbo1XfyjbtuHDAYEIJjVIUc0xYxJOTnanTd5u ygV0ieWuklK5YVn1diq8udo0JOGgNkqEUdqvShYgmDUfuHRJP/57aAJLWd8fXIte P0jgraLIL4QmJwszedZYloDRXdrnoFtUzG3BfvA2jPpG4ALxP7ooWUaE2stY3/a0 iSTzFseygeizVn6myjc8zEG1PU79YbN9nxQEtv9UNM1f5EbVvJdzvP9s4sxzHxGy Aomc/JUO9a08J22f35wlcaa7UyZ0tFHaTDdATrefsXMG1dVFnO6TY9swXvQ0lDUE SzQ3s48olvsImdKA0ZkOJTk4SBqS6+6Q+Nr/+33GrUUPj7oKcUxavHvATzGBDk9p 2wmxVSZWaBYQLu9eQggt =IazD -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 09:56:36 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 09:56:36 +0000 Subject: [Debian-med-packaging] r-bioc-preprocesscore_1.34.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 10:27:14 +0200 Source: r-bioc-preprocesscore Binary: r-bioc-preprocesscore Architecture: source amd64 Version: 1.34.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-preprocesscore - BioConductor collection of pre-processing functions Changes: r-bioc-preprocesscore (1.34.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: ca5b56183ec5348e8ffe29134410fa1fe57dd718 2172 r-bioc-preprocesscore_1.34.0-1.dsc 31a2e3cc50b73cccd600c98645fde22e1a853802 122756 r-bioc-preprocesscore_1.34.0.orig.tar.gz 1df6011d49aac3e25e12cd7cb00a248e52aa5c6c 1876 r-bioc-preprocesscore_1.34.0-1.debian.tar.xz 3527435ae107f64422449daec3e562ccbd2f8e1b 135974 r-bioc-preprocesscore-dbgsym_1.34.0-1_amd64.deb e59fbda885524d57b7245f816098e06d75af3bfa 124236 r-bioc-preprocesscore_1.34.0-1_amd64.deb Checksums-Sha256: 05f9717409cf222d7524dd99a5a8ffb3256d0b297e242a8b213c6902b6717ac5 2172 r-bioc-preprocesscore_1.34.0-1.dsc 8e99f5fd54f680d5cd36bf8f03395f1036cac3a53b89bf9f5a9e68a88c888e2d 122756 r-bioc-preprocesscore_1.34.0.orig.tar.gz 9fd8851a2384b5196546fdf86d39eeda2f7baac3a71d61e4ac834e4e316f5d32 1876 r-bioc-preprocesscore_1.34.0-1.debian.tar.xz a6218056048c6c4c445caf66d4115bd793b2d7694e7d11d1cb03d2491c26c5c6 135974 r-bioc-preprocesscore-dbgsym_1.34.0-1_amd64.deb fc4025e11f5a5a10f7d47aec013c0ba984022045e0ec624f77d55e6303517837 124236 r-bioc-preprocesscore_1.34.0-1_amd64.deb Files: 7889f3f034526f4c22062986cfa8d5d3 2172 gnu-r optional r-bioc-preprocesscore_1.34.0-1.dsc 1135fb620afece97fa5cf1e42cb3ec36 122756 gnu-r optional r-bioc-preprocesscore_1.34.0.orig.tar.gz 63ba7172abfe57c5d48f173f42c8a9fd 1876 gnu-r optional r-bioc-preprocesscore_1.34.0-1.debian.tar.xz 4be6a2bc9000ed2f9ed5caadfe467378 135974 debug extra r-bioc-preprocesscore-dbgsym_1.34.0-1_amd64.deb fc1cbe64757777e7dac4a38a7bcf9236 124236 gnu-r optional r-bioc-preprocesscore_1.34.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLvi/AAoJEFeKBJTRxkbRlcIP/jgl+NktrgqDhsgidbH0lXDX U9pZcykuydPmLs6wF/Yk793ro8LoQfxMP+i2BXfp99OTWLpzBSwx1wKRAMjVOI5V 8MgaJP6UWA/LaICwZU9Kh6js2GCe/FXBjCzSercih+quMYESMg6uBBS5+se8hy6f 2pioZL1t7Lj+Jkl+LW3FciL8MRQazGVQ7oLKRuESqddseh+0J5Hw+tzNyGBW+Fl9 iQsgS/3uvReaXmW8gFfPzBjhPfru8cCA6zXgiXSbT0nVsJimMChNE2bpc+y+ts0y KZpXHnHZoFOX2jPYXTyb2xCf5/gXX8qEfVQSkanmbS2XA1rbqtW9hbZIgbCP53Sn S3Whjfxwgmo3rX5y/mYKngV9MbonvN13HrcUK7nxvJG+E1RuJetpRnEZnbBjUN9h W/WPnYjTGOIdG3WE7XT446rFScZaIOihsfQEJnY/Ljst6KZzsbwxEiUhBXWJiP1B FHfI3q0t9OiER9yx6iyLRbP+env/ZkjaDMLnvSZIlmUfZ2ZP5n8sYYDynMZsU6/v vkOpISt8Pm1pfIWC49bT2drxTFmZaku6oW20Psfvf8ItYnPnHZ1gmRz2qWbugV/y sTr1idNND2TIRBKRWTyPoC4/+3orREApPtanlkRH3CJYJwt5/qWl5zpyhOdOLaaX 1UYJjhS32I+oj/FlFZqP =S+wL -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 10:05:02 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 10:05:02 +0000 Subject: [Debian-med-packaging] Processing of roary_3.6.1+dfsg-2~bpo8+1_amd64.changes Message-ID: roary_3.6.1+dfsg-2~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: roary_3.6.1+dfsg-2~bpo8+1.dsc roary_3.6.1+dfsg-2~bpo8+1.debian.tar.xz roary_3.6.1+dfsg-2~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 10:34:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 10:34:55 +0000 Subject: [Debian-med-packaging] roary_3.6.1+dfsg-2~bpo8+1_amd64.changes ACCEPTED into jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 01:59:19 -0700 Source: roary Binary: roary Architecture: source all Version: 3.6.1+dfsg-2~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Afif Elghraoui Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.1+dfsg-2~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. . roary (3.6.1+dfsg-2) unstable; urgency=medium . * Use correct argument format for easy_init to get rid of warning message. * Bump Standards-Version. . roary (3.6.1+dfsg-1) unstable; urgency=medium . * New upstream release. . roary (3.6.0+dfsg-4) unstable; urgency=medium . * Remove patch for PRANK. * Disable tests due to nondeterminism until upstream has fixed the issue. . roary (3.6.0+dfsg-3) unstable; urgency=medium . * Attempt to fix FTBFS in reproducibility tests by choosing a fixed random seed for PRANK. 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From ftpmaster at ftp-master.debian.org Sun May 8 12:15:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 12:15:35 +0000 Subject: [Debian-med-packaging] Processing of samtools_1.3.1-2_source.changes Message-ID: samtools_1.3.1-2_source.changes uploaded successfully to localhost along with the files: samtools_1.3.1-2.dsc samtools_1.3.1-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 12:19:24 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 12:19:24 +0000 Subject: [Debian-med-packaging] samtools_1.3.1-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sun, 08 May 2016 21:11:12 +0900 Source: samtools Binary: samtools samtools-test Architecture: source Version: 1.3.1-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Charles Plessy Description: samtools - processing sequence alignments in SAM and BAM formats samtools-test - test files for the samtools package Closes: 822701 Changes: samtools (1.3.1-2) unstable; urgency=medium . 952da10 Build-depends on htslib 1.3.1. 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From owner at bugs.debian.org Sun May 8 12:21:12 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sun, 08 May 2016 12:21:12 +0000 Subject: [Debian-med-packaging] Bug#822701: marked as done (samtools 1.3 fails to build against htslib 1.3.1.) References: <1461693748.2750823.590308017.767C5093@webmail.messagingengine.com> Message-ID: Your message dated Sun, 08 May 2016 12:19:24 +0000 with message-id and subject line Bug#822701: fixed in samtools 1.3.1-2 has caused the Debian Bug report #822701, regarding samtools 1.3 fails to build against htslib 1.3.1. to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 822701: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822701 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Chris Lamb Subject: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure; Date: Tue, 26 Apr 2016 19:02:28 +0100 Size: 35738 URL: -------------- next part -------------- An embedded message was scrubbed... From: Charles Plessy Subject: Bug#822701: fixed in samtools 1.3.1-2 Date: Sun, 08 May 2016 12:19:24 +0000 Size: 4908 URL: From owner at bugs.debian.org Sun May 8 12:30:07 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sun, 08 May 2016 12:30:07 +0000 Subject: [Debian-med-packaging] Processed (with 1 error): forcibly merging 822701 823673 References: <1462710398-3536-bts-plessy@debian.org> Message-ID: Processing commands for control at bugs.debian.org: > forcemerge 822701 823673 Bug #822701 {Done: Charles Plessy } [src:samtools] samtools 1.3 fails to build against htslib 1.3.1. Unable to merge bugs because: package of #823673 is 'samtools' not 'src:samtools' Failed to forcibly merge 822701: Did not alter merged bugs. > thanks Stopping processing here. Please contact me if you need assistance. -- 822701: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822701 823673: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=823673 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Sun May 8 12:45:37 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 12:45:37 +0000 Subject: [Debian-med-packaging] Processing of htslib_1.3.1-1~bpo8+1_source.changes Message-ID: htslib_1.3.1-1~bpo8+1_source.changes uploaded successfully to localhost along with the files: htslib_1.3.1-1~bpo8+1.dsc htslib_1.3.1-1~bpo8+1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From plessy at debian.org Sun May 8 12:45:35 2016 From: plessy at debian.org (Charles Plessy) Date: Sun, 8 May 2016 21:45:35 +0900 Subject: [Debian-med-packaging] Bug#823673: samtools: FTBFS in testing In-Reply-To: References: Message-ID: <20160508124535.GA16989@falafel.plessy.net> Version: 1.3.1-2 Le Sat, May 07, 2016 at 03:03:45PM +0200, Santiago Vila a ?crit : > > This package currently fails to build from source in stretch. > > ------------------------------------------------------------ > === Testing mpileup.reg regressions === > > UNEXPECTED FAIL: Output mismatch for $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}' > See FAIL-47.out.1 vs expected/47.out > ------------------------------------------------------------ > > The full build log is attached. > > I see that this package required a change recently for htslib 1.3.1. > However, if this only builds now with libhts >= 1.3.1, then the > Build-Depends field should be updated accordingly. Thanks for the report; the issue was already reported in #822701, which I just fixed by updating Build-Depends. Have a nice Sunday, -- Charles Plessy Tsurumi, Kanagawa, Japan From ftpmaster at ftp-master.debian.org Sun May 8 13:19:53 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 13:19:53 +0000 Subject: [Debian-med-packaging] htslib_1.3.1-1~bpo8+1_source.changes REJECTED Message-ID: Uploads not including architecture-independent packages are not allowed. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Sun May 8 13:25:53 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 13:25:53 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-iranges_2.6.0-1_amd64.changes Message-ID: r-bioc-iranges_2.6.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-iranges_2.6.0-1.dsc r-bioc-iranges_2.6.0.orig.tar.gz r-bioc-iranges_2.6.0-1.debian.tar.xz r-bioc-iranges-dbgsym_2.6.0-1_amd64.deb r-bioc-iranges_2.6.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 13:33:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 13:33:54 +0000 Subject: [Debian-med-packaging] r-bioc-iranges_2.6.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 15:16:51 +0200 Source: r-bioc-iranges Binary: r-bioc-iranges Architecture: source amd64 Version: 2.6.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-iranges - GNU R low-level containers for storing sets of integer ranges Changes: r-bioc-iranges (2.6.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 1950ff8d237a2e48848f18ba085353eba6babedf 2132 r-bioc-iranges_2.6.0-1.dsc 2e5f14194c393826efa525ad19a78d118a58e6b0 475270 r-bioc-iranges_2.6.0.orig.tar.gz db0ce3dad2182f8ff812a8aaff00f0c25ef5dd3f 4032 r-bioc-iranges_2.6.0-1.debian.tar.xz 793f2846dae806559be75dc77fe7de8dd7390a38 99504 r-bioc-iranges-dbgsym_2.6.0-1_amd64.deb a888aa0b0e11d52368e900af061078cb6e1a8956 1424460 r-bioc-iranges_2.6.0-1_amd64.deb Checksums-Sha256: 5df3e92e40ddbff7d2b6637c5f09c7a12def5100001c3307cae7a9161bba2c92 2132 r-bioc-iranges_2.6.0-1.dsc 7e9b8de889556bd85b0e83e68ea48108e89412108953ff584d0743342ff8e737 475270 r-bioc-iranges_2.6.0.orig.tar.gz ae0e78165ed9bb4380b07c5809b42c23e84d745f8c757fdd7da8ecb778c2c7ad 4032 r-bioc-iranges_2.6.0-1.debian.tar.xz 0c4b545d1b83c4bf7d3deebea84d7d160946992474d593d6a2af57538e706bfc 99504 r-bioc-iranges-dbgsym_2.6.0-1_amd64.deb e12ac26a5667ad059c4d51e1a6ebf929a3eb05202a4d9a96e96de2b56bcb087a 1424460 r-bioc-iranges_2.6.0-1_amd64.deb Files: a7e859a3b499410ae86a5b028b62c197 2132 gnu-r optional r-bioc-iranges_2.6.0-1.dsc a11f433b9288573e409c3c75fdd8b8c6 475270 gnu-r optional r-bioc-iranges_2.6.0.orig.tar.gz c122a49a1b59e997180286632d381ace 4032 gnu-r optional r-bioc-iranges_2.6.0-1.debian.tar.xz 62660f62bf743d2bcd9b59fe8b40bb32 99504 debug extra r-bioc-iranges-dbgsym_2.6.0-1_amd64.deb 6e8ec38e75b36b6ffca2a0f24cbc30ed 1424460 gnu-r optional r-bioc-iranges_2.6.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXLz1SAAoJEFeKBJTRxkbR1ewQAIpIMp/GerGjJFTssG+QXQxN A3YBJtRcszmiFyv9nmAo9HvvBx5H+VuJICepzs7homsKOiAEgKqfLBTVRpeZKoZx /WFJQQXz+0Sjvm1AkgF7l/u11WeJH73u81UvKnBZO0rClYzZTFsUSYDM+X5InZmm spVtRtqCtMsrg3AYlingaQw3/ikNm4F3ejLD3Dlm8k6u8Q3vKv/xT5u2irxSbdRt ai9YgizDXJ5yYHBjKcoWeDxtjUDAVtp0u/TQUIZZiRx82U7kqJOXyUOBnlr6QP9f ty3Zw5xA22IvLG4+KBgh7gXfyPbTFFhs4CjQMqbAzZg19VTEWdSkVDjD5cZkHvwV 11s6Nl5XBLfwk4ZtujPA9Zy5RGmD3ojbztPaT/6l7xOtiICoAOk4vbd2hZrwYccC z2tH1PqWiB3O9XtNhnOzhNNufJe5Hyt8zZFAZVqFXdyUiIm2g3drn3KvYNqcT62S LNcUqN3YUxKz3kdn0+w4auXJlpNdqC6/zNSrfWo4a+Ic/T5GaE9m9eDCzbYvMf17 k6JNFdYb2u+IK+q5612BKgeBUhyea6gbDpIwfE6B8GlEXhXSw13Ej7JhwfbROSsm Ax4xcSp5E3L6C8Uz3H6D1HwjhTuz2t/m6IkkBW22RpO0LbRab53RPyUA/MoxsnpX czsE8+fYmxJ6i3uV21HT =UN48 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Sun May 8 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 08 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] plink1.9 1.90~b3.36-160416-1 MIGRATED to testing Message-ID: FYI: The status of the plink1.9 source package in Debian's testing distribution has changed. Previous version: 1.90~b3.31-160203-1 Current version: 1.90~b3.36-160416-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 8 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 08 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] r-cran-beeswarm 0.2.3-1 MIGRATED to testing Message-ID: FYI: The status of the r-cran-beeswarm source package in Debian's testing distribution has changed. Previous version: 0.2.1-1 Current version: 0.2.3-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 8 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 08 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] adun.app 0.81-8 MIGRATED to testing Message-ID: FYI: The status of the adun.app source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 0.81-8 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 8 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 08 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] htslib 1.3.1-1 MIGRATED to testing Message-ID: FYI: The status of the htslib source package in Debian's testing distribution has changed. Previous version: 1.3-2 Current version: 1.3.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Sun May 8 17:07:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 17:07:07 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-xvector_0.12.0-1_amd64.changes Message-ID: r-bioc-xvector_0.12.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-xvector_0.12.0-1.dsc r-bioc-xvector_0.12.0.orig.tar.gz r-bioc-xvector_0.12.0-1.debian.tar.xz r-bioc-xvector-dbgsym_0.12.0-1_amd64.deb r-bioc-xvector_0.12.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 17:22:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 17:22:13 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-genomeinfodb_1.8.0-1_source.changes Message-ID: r-bioc-genomeinfodb_1.8.0-1_source.changes uploaded successfully to localhost along with the files: r-bioc-genomeinfodb_1.8.0-1.dsc r-bioc-genomeinfodb_1.8.0.orig.tar.gz r-bioc-genomeinfodb_1.8.0-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 17:22:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 17:22:13 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-affy_1.50.0-1_amd64.changes Message-ID: r-bioc-affy_1.50.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-affy_1.50.0-1.dsc r-bioc-affy_1.50.0.orig.tar.gz r-bioc-affy_1.50.0-1.debian.tar.xz r-bioc-affy-dbgsym_1.50.0-1_amd64.deb r-bioc-affy_1.50.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 17:23:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 17:23:07 +0000 Subject: [Debian-med-packaging] r-bioc-xvector_0.12.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 18:59:00 +0200 Source: r-bioc-xvector Binary: r-bioc-xvector Architecture: source amd64 Version: 0.12.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-xvector - BioConductor representation and manpulation of external sequences Changes: r-bioc-xvector (0.12.0-1) unstable; urgency=medium . * New upstream version * Fix versioned Depends * cme fix dpkg-control Checksums-Sha1: 66e00e910e0b8630c15fb8b2e6e40e8ed0005600 2116 r-bioc-xvector_0.12.0-1.dsc d72e891b25dfeaf435132457f64afaea41cb8c26 58159 r-bioc-xvector_0.12.0.orig.tar.gz 903d47890b3dd2c49f1d8e643b87761ab220466c 4032 r-bioc-xvector_0.12.0-1.debian.tar.xz ba6ad235be67fad5936339ec56397e1c38677051 83144 r-bioc-xvector-dbgsym_0.12.0-1_amd64.deb fd5e75e2209da74dfa0e3f1c38912b248f012b8d 334060 r-bioc-xvector_0.12.0-1_amd64.deb Checksums-Sha256: 9e59153737c23d944f613f53bb9ed71ab1742c54222eb6d7992c6cfa1c4ddeab 2116 r-bioc-xvector_0.12.0-1.dsc 17d78dae8b5f90b960afeb58a9bef28ef6fc043c26e0c8895543cfde99c42c31 58159 r-bioc-xvector_0.12.0.orig.tar.gz 69ccd6332410ed96a2390180c275e495f19825ed72b7f87d8de4b611a058b74b 4032 r-bioc-xvector_0.12.0-1.debian.tar.xz 738217e86949f2f7b6b94ba5c91d150fe5118b05d941e218b64faf380980efe1 83144 r-bioc-xvector-dbgsym_0.12.0-1_amd64.deb f8915687b2fa6a7ec6cc34a35a016a3e8dfa562b633a2eb4de4ea4db12d0e9e5 334060 r-bioc-xvector_0.12.0-1_amd64.deb Files: 7dfd426d5623993ead436e7523cda701 2116 gnu-r optional r-bioc-xvector_0.12.0-1.dsc 6005e6f59898835f6272676d9c3082b3 58159 gnu-r optional r-bioc-xvector_0.12.0.orig.tar.gz 8e4734f06f45c3018a2eb2cf9b8dc3bc 4032 gnu-r optional r-bioc-xvector_0.12.0-1.debian.tar.xz f6b24bb23dc3d9f88e54f47ee31c65b9 83144 debug extra r-bioc-xvector-dbgsym_0.12.0-1_amd64.deb 7d0941e213c7cd21f3e04e8bd29c4008 334060 gnu-r optional r-bioc-xvector_0.12.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL3EyAAoJEFeKBJTRxkbRoMgP/i8QngrOXDmjRqaEORgmcZ40 jlK4qAGWY1PX4+J8fS0Bi8zG2c6aAu+6GdI/9z/foF6nHe68GgWylL+vceVYp14/ qD+I8J56sV2hY7CiwA10zL/eKuck1OnMq0E1hmcQ5ntqhzX47IR4RIwntDUrTGjE LuiPoNH0afb5JEh6F4OQ35H6BW3EI96NwPTDaz+mEavMwM+zAXVg1Hu3FTSxZ328 cxal8Jb7dDkzFjgE/qqoYxdOnk4AiGb1xG7AmEGrW5LoGVb5V+FBi8sQRv/nCn4Y XSuqUFnHjWP8t8QWq54H1BjgVmkEH98eBmy3w+EAAXKAj2eSJbBLrC53E+U1l8PP hpCAQUMRBV/hxCsa+NmX+3/9xPPU+rDLkahT1kbD7L5ef76bHKDR3QpQJ+2KI21+ YCrQCr9hA+5Uw+D7WQ9BEMvr9V+6tvEh6IUDWosItYONiN6TBGh1ko1tlL1DawY8 uSmG3+O8uqxkD+z+Q4WCqfT5vooaCzBZEV2ISyVavfWAG5Lj7B72xJKBNiPY309D 4AJ+VqBqmlGjQz+/pdN0aWitc4dusoj3CXTHNFAmKfUtwcv51Q00/bPK3/6EwMye zDKrt7Md8GYhpAit8JPiBsXftfqPByLBJNYJj66mSA/DW4sHaMhrc082r322nn7G SUqIduofWQ6DXKmBYZVJ =sSuB -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 17:34:08 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 17:34:08 +0000 Subject: [Debian-med-packaging] r-bioc-affy_1.50.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 19:09:54 +0200 Source: r-bioc-affy Binary: r-bioc-affy Architecture: source amd64 Version: 1.50.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-affy - BioConductor methods for Affymetrix Oligonucleotide Arrays Changes: r-bioc-affy (1.50.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 29ff90788724f6a68ca63f340e331bb5ec61dfd5 2179 r-bioc-affy_1.50.0-1.dsc 3f0bf42b7f0a479aa071b4d240066fb1638230f9 1315016 r-bioc-affy_1.50.0.orig.tar.gz 7063308719ed041869586b26b14c9fd98c605a1c 4780 r-bioc-affy_1.50.0-1.debian.tar.xz c5988c29ebdec1b8a1f477a8e82aeb3becf363ff 30506 r-bioc-affy-dbgsym_1.50.0-1_amd64.deb 93f7bdacc4390080800c22862d3540e748fa13d2 1367706 r-bioc-affy_1.50.0-1_amd64.deb Checksums-Sha256: 8ffcc44ca2993b77e92e7a423ff3a13e677963eb174ed722690038b1978f9af7 2179 r-bioc-affy_1.50.0-1.dsc 45a14611da8bdee953139a2b1e1a2d2d1e208eac6b3558ec8f8234d01106c294 1315016 r-bioc-affy_1.50.0.orig.tar.gz 8b6779ab9413e4634a79898b521d99b635e666dfbe98b5230ec5c36927fda381 4780 r-bioc-affy_1.50.0-1.debian.tar.xz a86feb486166bc12ba749eb5abad693dd530f6834a9c0bb887cb84704e99a7d3 30506 r-bioc-affy-dbgsym_1.50.0-1_amd64.deb f4e643349ae1e7a55b5cb215a98dc6cae1573452a369c827773bc36b6c8526a3 1367706 r-bioc-affy_1.50.0-1_amd64.deb Files: 8e2f8e0582a616309a72b38fb400fc4a 2179 gnu-r optional r-bioc-affy_1.50.0-1.dsc 78f2eb708878df367a4bd92ad0bd8bc2 1315016 gnu-r optional r-bioc-affy_1.50.0.orig.tar.gz 0d014bf46e35c93028819a75c7a10acb 4780 gnu-r optional r-bioc-affy_1.50.0-1.debian.tar.xz 353f1b9e2b40bec2ecbcd7d9c133b0b5 30506 debug extra r-bioc-affy-dbgsym_1.50.0-1_amd64.deb cd1d344a0fc3c677f18cd321c8d3dfb7 1367706 gnu-r optional r-bioc-affy_1.50.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL3N+AAoJEFeKBJTRxkbRvHIP/1JjwC4jDfimt2Ddr3Mfch2K ClkGy5HaO0UffkRO8x4ppYW5xGRIcooy7pss5qP5lEGehNNqcpb6wV7urGpCTvoW siUkN9syftOZ4aK2UEHZWphNxD3p2deQ+LgUyudHVhLtwZrSs1r9ziPpgISpNats IzAcNC2uPbC3DgyR/WLes4+P7g0O4qtM+x8G486kZrBC28ah4JdoUzu03zsBuEbs 6bpweFJs4WIABBCcBOQ17xgvj82FPBJhy4IVjO7HHYQCIX2CqVx2OmNSHpVTrRDl Vx8CO429L7ceAP4VPQzP+MhwIGNZ5HqbFA7py/e92S899uNKHuVhmHI6++rof+8w 4cZKZQYWIFRu62Y/3RFa0Ts6JYucOOI9ypZVMNzXCynALc7oFLDUicgGz9BFez0b 2RNwm7Ttth89ghVA3aFgIAxwRxrJJDxkJSmYPVa7OCmyAYDqXw9/Jyi38ozGkg3P PVMUMfwy3qsGDuctoQ5K39D/f/7yrDZCBDmWEOSlmJkygTJoNsxbtjk3aQMsbSoe f4EiA9B2tRoj3n2P96VFrnkNxwepjeW0OD/anvYNlKun+0MHAa6GMxKy5BY5VMZn /YXdoG5cb9BP9WZZdxfmfbW53oYHgLCVdeHd0F+chNGY4RYrZpF42qlyyQJbjpWr S6262xIZkwA/+NLqAVgl =IxWi -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 17:34:15 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 17:34:15 +0000 Subject: [Debian-med-packaging] r-bioc-genomeinfodb_1.8.0-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 19:02:09 +0200 Source: r-bioc-genomeinfodb Binary: r-bioc-genomeinfodb Architecture: source Version: 1.8.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-genomeinfodb - BioConductor utilities for manipulating chromosome identifiers Changes: r-bioc-genomeinfodb (1.8.0-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 01b185f964333f4c1d41090e2a8cfd7502a88fab 2195 r-bioc-genomeinfodb_1.8.0-1.dsc 87f00a2aced09aec03fa06a32d8b0003db6f4a66 19364322 r-bioc-genomeinfodb_1.8.0.orig.tar.gz 8f4105c03fd26e57a740415b618f2d0df88e9c47 3764 r-bioc-genomeinfodb_1.8.0-1.debian.tar.xz Checksums-Sha256: fa005546600dbb1f4584202c08955b924e774e5cb46ba3401bab653f636c7c4b 2195 r-bioc-genomeinfodb_1.8.0-1.dsc 7a58779e21a004b4ecac122e858e08ca19f13adde0ef05c460b467d006ff8e39 19364322 r-bioc-genomeinfodb_1.8.0.orig.tar.gz c288a27b712654e4e17215f06e462315c1c901402617cb1b9b0d6b89625a4a24 3764 r-bioc-genomeinfodb_1.8.0-1.debian.tar.xz Files: ac0fc21fc461a59e19bb8d3df093f3fd 2195 gnu-r optional r-bioc-genomeinfodb_1.8.0-1.dsc cf0ec56ec72292363d0862831cbca111 19364322 gnu-r optional r-bioc-genomeinfodb_1.8.0.orig.tar.gz 3b5945b3cb5450f01c4385c1154c7a0e 3764 gnu-r optional r-bioc-genomeinfodb_1.8.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL3LOAAoJEFeKBJTRxkbRuBwQAITZF2tfcAOnQXML/h+XgZlV n4REFUo7BXMioxWiGuJgMyXwL/6QKEfjZCrdyoRyJMJHKxDSVlJrSsFjRKTFK03x nXOlpkMjNuCfGSFeciAMNeisLirhOymCOSqbdwDN1dBHbGnmt0pNCNtYiuaIuAdE qFWqGh4ugQoUtVS3WJNEZmxBQlq7qwzNTQHLPG9cMHB/TSJAuxOHQWiwRX2QaQJP 8ESd2wLHONyEbb5w7qwHNJrj7o8BTVEz2D7TQyLVWOwWflu/xjgpg5q5QkkdDRJB MqJMgwZ2gVPm7jmpQu2ra8uLdi45v1074E7YNDJmE0PN32fv1vuhE2WGSmOY0nPy 6NMxCDphHZ3SmeZIi/K6I6ZEAKUcBf3UBrVKLHMCbzBV7kGQo1uHROcntFwaw972 ckl6aLUqNj0zwqaInH79wFPuhA0ZJD3wjlhefaCyaYLyuJ9sCTfaQ8vuR88lbeqw F8PifKj/qG4PLjnVFDhy4yWa2R4eXM+lKA6x/FQeXQUj6csHfaFRvRsRt3POYkYb GaOj0jR1ZgVy00YGK5MiT31aaYtUOHVkuZxMEHHeolBUhrRMhHlLWoy+foZyfZPM U07OKbW+Qwbk0zq3DWxJYNkiHS4kHNas9AQ9270V3cb/jT/EZROLU97GjJzce4uN E7s9xhNZPN4KBkN5374i =GjRr -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 18:12:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 18:12:28 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-genomicranges_1.24.0-1_amd64.changes Message-ID: r-bioc-genomicranges_1.24.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-genomicranges_1.24.0-1.dsc r-bioc-genomicranges_1.24.0.orig.tar.gz r-bioc-genomicranges_1.24.0-1.debian.tar.xz r-bioc-genomicranges-dbgsym_1.24.0-1_amd64.deb r-bioc-genomicranges_1.24.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 18:17:29 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 18:17:29 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-annotationdbi_1.34.0-1_amd64.changes Message-ID: r-bioc-annotationdbi_1.34.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-annotationdbi_1.34.0-1.dsc r-bioc-annotationdbi_1.34.0.orig.tar.gz r-bioc-annotationdbi_1.34.0-1.debian.tar.xz r-bioc-annotationdbi_1.34.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 18:19:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 18:19:07 +0000 Subject: [Debian-med-packaging] r-bioc-annotationdbi_1.34.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 20:08:08 +0200 Source: r-bioc-annotationdbi Binary: r-bioc-annotationdbi Architecture: source all Version: 1.34.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-annotationdbi - GNU R Annotation Database Interface for BioConductor Changes: r-bioc-annotationdbi (1.34.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 00749ef5e6622eb64b5555fac743b21c210ca808 2232 r-bioc-annotationdbi_1.34.0-1.dsc 720c7ab0a7256b54747f411382ee638e9425897f 4271745 r-bioc-annotationdbi_1.34.0.orig.tar.gz e5ea292a30f33c9412e8e69498bc9ebb8a22feee 3972 r-bioc-annotationdbi_1.34.0-1.debian.tar.xz 255b364673814f5dfc6e30c368faa78d4f470391 4188356 r-bioc-annotationdbi_1.34.0-1_all.deb Checksums-Sha256: 5c9f2a180acdb066c93c5ec74bb6b5cadb7a413655981310abd8c7ece8523516 2232 r-bioc-annotationdbi_1.34.0-1.dsc 92f7e86eb49155526b8ce605a9db336f9c7c643c0baef89a2379600188312766 4271745 r-bioc-annotationdbi_1.34.0.orig.tar.gz e60d9dbb6cc88fbe1fc6c43e5184c94ab789e6c4be42fbe14fbcb84fe9851b51 3972 r-bioc-annotationdbi_1.34.0-1.debian.tar.xz c58188d73bc753b4cdd81a5af198581400e4066fcfbed4675345343c1088aa16 4188356 r-bioc-annotationdbi_1.34.0-1_all.deb Files: 63d499e63758c73b756c2a440ab14eb7 2232 gnu-r optional r-bioc-annotationdbi_1.34.0-1.dsc 4be6df912bdea3089dda58a617a30860 4271745 gnu-r optional r-bioc-annotationdbi_1.34.0.orig.tar.gz 36067b918e3b8544f366be14b3f54cf2 3972 gnu-r optional r-bioc-annotationdbi_1.34.0-1.debian.tar.xz b80c8ad9557da11cca54254c24c62550 4188356 gnu-r optional r-bioc-annotationdbi_1.34.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL4GTAAoJEFeKBJTRxkbRcoUP/A7biGc3kxrn/PtV3XeEbMXM bERh0iBMVcg04g5ReEe9d2/JfgZBGnlOEho938KmtAXAW1KHF0muWFoUeLgqQZcD W+Dk02zkoG3J/MoSLW5E5ZFF8qUEFZOL5t0Gtf2PpS2/Sl3CiJCHPVAAx+5V7nZ0 ej19X44f4xQyPuKkG8xLjuGol6FPswuNGie9SeUrWqRnrcbdyK9TvuDCP8gGxtet IAGoYLfi9v3H6RdXwnqRFfxyiZk/KAZ2EXvU9Oy9PWGsQ3DRQSRwWT5Rugs336DK s9gQd1Cg29UaYu3NCHQnj4zeHP/rp6O2E2t3ImkD0M8t8JTIFwfGtFo1HA68wjZq Syznu5dYCXommWVGM3mN5gOets22AKelddqYcHz4/w21KHQBNLlNhj4KoUWc23GW YcA/mJgVOnuAuFecnBZpZEvoCfJF0nExDztfzGGaQ5kwkEiM8+IgC8d5HV/lHqTX nnsaGGYH19ql1nuDoGzWe48p72g8fyGW2ZeSABJK59Q1bS+541AZycYJ3PnXsEgy lrFjGD1i8PsAcMN+VPhihtbjhbK8SyMvULCbbFjPOOtBhiz7C0yWFuIQp0OoxgMk NWiv1vaM6ciCWe85i8eC8SzewYXKFP7hXtZXDMYIfNoCL90FASi5BRzzkne/BzO0 pHKhLy5+yWJOLNnAyIqZ =iofn -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 18:19:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 18:19:17 +0000 Subject: [Debian-med-packaging] r-bioc-genomicranges_1.24.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 20:00:11 +0200 Source: r-bioc-genomicranges Binary: r-bioc-genomicranges Architecture: source amd64 Version: 1.24.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-genomicranges - BioConductor representation and manipulation of genomic intervals Changes: r-bioc-genomicranges (1.24.0-1) unstable; urgency=medium . * New upstream version * Adnjust versioned Build-Depends r-bioc-xvector Checksums-Sha1: f988edbf0c84eee09d76d47ef6edbb822a2c1468 2253 r-bioc-genomicranges_1.24.0-1.dsc 9cedfc46853e73a8c9d0bc47004aea11525d4a19 900358 r-bioc-genomicranges_1.24.0.orig.tar.gz 3a38e064d7a7b2621cfd95229dc3d1dd76991944 4964 r-bioc-genomicranges_1.24.0-1.debian.tar.xz 283c56ed5dc9c3c5c435417c206607a5a7e90e90 29368 r-bioc-genomicranges-dbgsym_1.24.0-1_amd64.deb 047045ece9b770542602e206ada111e0dd6be291 1302334 r-bioc-genomicranges_1.24.0-1_amd64.deb Checksums-Sha256: 5413608bc7c92857fdbe152c33d76ca4ea2522cf40977fa0ba043d6ce6244e90 2253 r-bioc-genomicranges_1.24.0-1.dsc 102b9f2cfcdd2e23a9cd01a05dac851a76e0762a070ecca9b6360f7a6d78dfc7 900358 r-bioc-genomicranges_1.24.0.orig.tar.gz e75f9b9ee394b5da5f1abe1e57fc63c6c1c5d9fdc104d8ba2bd0a8a1a7eb9cb2 4964 r-bioc-genomicranges_1.24.0-1.debian.tar.xz 93764c49bd40d1f730f1704b6cc636f77728dfef300620983fbc84ffb66aa548 29368 r-bioc-genomicranges-dbgsym_1.24.0-1_amd64.deb b849381a57cad75e2608dc0ff8df375e2be27d467d0625dfd8f5fe246c3340bb 1302334 r-bioc-genomicranges_1.24.0-1_amd64.deb Files: 4db9b16fc5a25dcbd084ae57c155c25f 2253 gnu-r optional r-bioc-genomicranges_1.24.0-1.dsc 2da5974fb10e4e9b80cc0eb9b9955289 900358 gnu-r optional r-bioc-genomicranges_1.24.0.orig.tar.gz f8b684c52f2c9ba66e4cbf7f31347517 4964 gnu-r optional r-bioc-genomicranges_1.24.0-1.debian.tar.xz 8d835c6c55f998d74b7be05c87fdbb97 29368 debug extra r-bioc-genomicranges-dbgsym_1.24.0-1_amd64.deb 14d529f418587b189ed74c99a809a780 1302334 gnu-r optional r-bioc-genomicranges_1.24.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL4DXAAoJEFeKBJTRxkbRGuMP+QH7ntywLFftqQfozX8S/xze Gh3ZjBBRBQwq6JPwp9hWRA5kEJ0agLcqJPsneRts1YguWMl2ofZTMmsb+tXzl/0i kQePW5xJLgg+2b/LkIXoS+wz7vlJiI0DQm1PK8eQagh14msakd+LqoBMNt9DvVk3 4vS/2SPoMECrO1RvEl2rrJ89PVUWSBT7RzAHDsO/Afs62Yd30ErcQtIJG/uYqnuR 5cC+dUISOi0uUNFxV0WqUY4NP73YW+fEfYXsFgVqcT1ye4TibYAUmXSntozAojri W6gPLiB6uGtjiPNwB6XIYEJDlidc2cg2UcCVV0eJXTAwE128WunlNuS4UwI6Xq5E LZwW09xeEhowspVZdILH1I+TXDOcpfseXirW3IeC0qIaLHJWxG1kI4o9f5HEEVcW 62Ee8RvTi2wSAVwMrRPmSd/J/3uSoPH8OkSbCA6YosU72urO721EJU4Yl8MwvQWB hU+4Da7VXWStS9bEFvM4usrrecOOwTY92Z/jE0ZYJfur0cfRHcuYukr/+kU5hz+1 a/c0x/TeYOshFTiBxzV0DCt8Zeo+VohQIhO16k9eZBXSjEd8sPPRWirykM0raAMq kPp+/AHMm3cEPWbgCe4eyHF4nXfhUlwkUvU31hWURQSkTXRfVIFcDE+BRIeqfgXf O1eFmf4Zne2p7EqCzjvq =l+39 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 18:37:30 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 18:37:30 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-hypergraph_1.44.0-1_amd64.changes Message-ID: r-bioc-hypergraph_1.44.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-hypergraph_1.44.0-1.dsc r-bioc-hypergraph_1.44.0.orig.tar.gz r-bioc-hypergraph_1.44.0-1.debian.tar.xz r-bioc-hypergraph_1.44.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 18:42:32 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 18:42:32 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-biostrings_2.40.0-1_source.changes Message-ID: r-bioc-biostrings_2.40.0-1_source.changes uploaded successfully to localhost along with the files: r-bioc-biostrings_2.40.0-1.dsc r-bioc-biostrings_2.40.0.orig.tar.gz r-bioc-biostrings_2.40.0-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 18:50:47 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 18:50:47 +0000 Subject: [Debian-med-packaging] r-bioc-biostrings_2.40.0-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 20:25:16 +0200 Source: r-bioc-biostrings Binary: r-bioc-biostrings Architecture: source Version: 2.40.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-biostrings - GNU R string objects representing biological sequences Changes: r-bioc-biostrings (2.40.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * Bumped versioned (Build-)Depends Checksums-Sha1: 8a4ff1325daf39da119a81fc90797ebc5b9657e3 2185 r-bioc-biostrings_2.40.0-1.dsc ef5e8e299fbd56f3bbbaeff007e5f9ed43d967f7 12713237 r-bioc-biostrings_2.40.0.orig.tar.gz 63b45f2bc5cb9b0c359d56fc165d17acb530413d 3952 r-bioc-biostrings_2.40.0-1.debian.tar.xz Checksums-Sha256: dd31576458c143f66635e97bb3ee80861a9eaa34e1884bca141afb51561dc256 2185 r-bioc-biostrings_2.40.0-1.dsc 49be778c869afd35c42b7e28152ec137859dc384913ef0be0dc577127e84fe0d 12713237 r-bioc-biostrings_2.40.0.orig.tar.gz 9d9d40a985e4c53ac737cd4f46b054c9244c08e976cf8a321d99bdee729b8b79 3952 r-bioc-biostrings_2.40.0-1.debian.tar.xz Files: 607a065bdb025ee500713abe3ebb0267 2185 gnu-r optional r-bioc-biostrings_2.40.0-1.dsc 68614590e21fa020042ad63da3d0a02b 12713237 gnu-r optional r-bioc-biostrings_2.40.0.orig.tar.gz c7c5a4b62beb2f793cc2bb9990803d69 3952 gnu-r optional r-bioc-biostrings_2.40.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL4bKAAoJEFeKBJTRxkbR54kP/0Y9MeQCbBagOMQtb9TiV8+N C2o8L2W0cg5jCq3EyzLL1ikPikE/ioJuopp2fZ9iCZD8OKJq1aGwIYQJahEFlRq3 /1XnSCR57R+6H3fUgblOaoAPj2l1kzXZ8CLpxMBXUKe2DEw9Uyj322JVDm1w2JbQ BwfgdJH+TMtPQCKlW0uRa7xxA+DG6x/LoaqksMOMZBSO3jGQETiop7vIIoneKcCR juxmNi+OZiDa4o42UU9v9EylelCgvxzrRt8OUOgjyNfZCTKw7Pl6gMoHc3nTwAVv TqU8lFPHWOpZwvWzXcDIyYhdQU8vXBXPGTCjE/jvXhbVQgBXrn52YTTfORsgPWbd RF+261njQOPDv5D4likm/lBI5nDspN2luv4Q/LDJlq1iI7Wt5Wee13exUrottWZJ buyXnCWrlVyaT2MpEhg2KFAw2XmxTCLRbBiD6nQSPfaTy/JG/FV8NR+RKESXtnyO noKfmqF5J02QCoqL0qPxRavbr4dNPcZNphU9taF0/e/zRP236D8xFVLYsRF5JFvK 2VRb4r+HK/3QUPMB73TR+nQgWEt4XwVDMDyvTAd1iLp3nMeiYGvOnYtyYIQoIvnx vGxgIU0LPSj+K43kHJpR9R1DPMLqCAXhOdPu0TKyMwzebofZuDJMQUF1MFn0U48E FYgkq9t0HvuYKqCLqfzC =5MrP -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 18:51:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 18:51:01 +0000 Subject: [Debian-med-packaging] r-bioc-hypergraph_1.44.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 20:31:28 +0200 Source: r-bioc-hypergraph Binary: r-bioc-hypergraph Architecture: source all Version: 1.44.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-hypergraph - BioConductor hypergraph data structures Changes: r-bioc-hypergraph (1.44.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: fbef117dd6ec3c06144e2cd90017333b49b128e4 2144 r-bioc-hypergraph_1.44.0-1.dsc 2477420b1621f048e2ce3c701203725bcc7aa476 8396 r-bioc-hypergraph_1.44.0.orig.tar.gz 1090bf2f0e9ff04a5b101a493a2735ca1b0ed387 3468 r-bioc-hypergraph_1.44.0-1.debian.tar.xz 3cfd52875c25643f795778b0adb3fc236afaf6da 99612 r-bioc-hypergraph_1.44.0-1_all.deb Checksums-Sha256: 9015e2801e05f337cdd0929c4c3c18cbc0b12eb52430fe58640451f97f4e5dbb 2144 r-bioc-hypergraph_1.44.0-1.dsc e9d790709e107619b1aae223cf3ac7f60c421d08bbf50feff65a195500ef7e83 8396 r-bioc-hypergraph_1.44.0.orig.tar.gz cd049d9198c94c771c92f03788d8d28420b44c5b9157945386ff91561681cd47 3468 r-bioc-hypergraph_1.44.0-1.debian.tar.xz 9f8b007abd81fce62d5d57e716a7ef45c46bee912e8e9cea51c57ed0f66d6df7 99612 r-bioc-hypergraph_1.44.0-1_all.deb Files: 9316f7ed99b654158ab92bf2864c699c 2144 gnu-r optional r-bioc-hypergraph_1.44.0-1.dsc 1ac5c12abf4d2dc348df58debdf4e6f0 8396 gnu-r optional r-bioc-hypergraph_1.44.0.orig.tar.gz 05aef60936affec941c990c426f47e5c 3468 gnu-r optional r-bioc-hypergraph_1.44.0-1.debian.tar.xz 2c1bd9ecce6081c98201eb4816049d97 99612 gnu-r optional r-bioc-hypergraph_1.44.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL4abAAoJEFeKBJTRxkbRxq0P/2CQu/0Q3f2oX2KuxxbcWSVe 39Nmov9tingKvGA3dwBPX6+HknidHt1prDVGeMScjYHo4iml1zBzOGjx4ln+ToZo 2NNCHLaotTtlVMFM24t97Sk3SkPqC2EYY3+qnXBD/MN2klXz2cY5NUDVP0kqxk9F cTIIfqJzHjXdEo/+yhXon2s/0a6shckiyRt5XOd3ZvIT61cVn4YVOr72PrdN7sb4 0KqdPPWOOpfqUvS8G4OiavTOmHKtCLVuVPsfPtA5WWMlh11qJ4TwjdganRAyQsoN /v7Ic53vyJSRms8GKvS9dFJPczXO6Q7w/F7XlF8K+aUYhL2YYabU1VpQO0/Td2+Y OJURkKUAXuAKtNoKuI41XNdvs2lnmO7S2O4/g5espPBjnuNdf/kS/mWEavmqM5/U s2qrJsJQg3dhgoCecb9FbIsbIkZZAMD9g3l06glxAVJYgZFQMTwvWYCcrx4SCPWN U843EbajJPOlokX9i7JNllRC0jBJZlEGTBSrmkshxMIzW7bvIueX7K3wmu7NgR8v SMdcrn3JenYBciurYfJ4oftEiKnvmGopmOQd5tFAG9LOCyMZ4ubhGOXK4PzSloFY P6AVyb7MMY/y9M5mDNcBSGjOpJPos68DL8Vl3+/Onph6bcj5HV83EB5PDN3XQ3kt 4wHo6RzdbUn+7xgcyAqo =5GzU -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 18:52:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 18:52:40 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-annotate_1.50.0+dfsg-1_amd64.changes Message-ID: r-bioc-annotate_1.50.0+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-annotate_1.50.0+dfsg-1.dsc r-bioc-annotate_1.50.0+dfsg.orig.tar.xz r-bioc-annotate_1.50.0+dfsg-1.debian.tar.xz r-bioc-annotate_1.50.0+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 19:02:41 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 19:02:41 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-biomart_2.28.0-1_amd64.changes Message-ID: r-bioc-biomart_2.28.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-biomart_2.28.0-1.dsc r-bioc-biomart_2.28.0.orig.tar.gz r-bioc-biomart_2.28.0-1.debian.tar.xz r-bioc-biomart_2.28.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 19:07:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 19:07:06 +0000 Subject: [Debian-med-packaging] r-bioc-annotate_1.50.0+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 20:46:23 +0200 Source: r-bioc-annotate Binary: r-bioc-annotate Architecture: source amd64 Version: 1.50.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-annotate - BioConductor annotation for microarrays Changes: r-bioc-annotate (1.50.0+dfsg-1) unstable; urgency=medium . * New upstream version * Use new uscan options in debian/watch * cme fix dpkg-control Checksums-Sha1: c8530024a6f19d24dca43f433bfd62e6ef950a5c 2176 r-bioc-annotate_1.50.0+dfsg-1.dsc 7cbacd32fd8a5b3c8d17e00e3bd964575fc07472 1756244 r-bioc-annotate_1.50.0+dfsg.orig.tar.xz 4647ecb175fb507bf151cfa1c9297beab7ca1b90 3800 r-bioc-annotate_1.50.0+dfsg-1.debian.tar.xz 85d2c7318c7f631a018d11d8d060049c98f180b4 1878486 r-bioc-annotate_1.50.0+dfsg-1_amd64.deb Checksums-Sha256: 9ac4a882290d33ca5aca66fa52ed1c3281f1def365977eef11a9d7db03075a0b 2176 r-bioc-annotate_1.50.0+dfsg-1.dsc 06aaaa9ce6a31f78373f92c68050da49e73a64e00654397d3b671b025d2791e0 1756244 r-bioc-annotate_1.50.0+dfsg.orig.tar.xz 29eb08cde8a71670897c3a72aeb31a7c081e8415a24384df52bc62e7e48baef5 3800 r-bioc-annotate_1.50.0+dfsg-1.debian.tar.xz 8fe815b40f712c0e4c08e44af1b921c210f3edb4e7b1a556fd69888ede9b67f9 1878486 r-bioc-annotate_1.50.0+dfsg-1_amd64.deb Files: 5fefb8eda7561d56db800286a1c380c0 2176 gnu-r optional r-bioc-annotate_1.50.0+dfsg-1.dsc 0a1c8a52508b9a951c0580e92f7cb042 1756244 gnu-r optional r-bioc-annotate_1.50.0+dfsg.orig.tar.xz 70ba8647b2e88108741ab7c8260b45fa 3800 gnu-r optional r-bioc-annotate_1.50.0+dfsg-1.debian.tar.xz 95f52250eaa32680113e54f9cfd03b06 1878486 gnu-r optional r-bioc-annotate_1.50.0+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL4pHAAoJEFeKBJTRxkbRCNcQAIg2dM8RV7A+0vrVvScU5uM5 j+AglNaq5s3l+Iw6GwyTclsn6LCTaoigCjRnJf0CrNdJXnN/Ub/hgQ/NGyr0ZjG4 PLRJNY82YBhbRlbVlvt4Uo0C2a1DeGedZ0X/yRk69VZJEqiKZpVXUBuZ0vbEwnAp WfBSbDPR//H2THsufNEtWkFLuheDREhn8fGKn7xH2v1UpIh3pts+ELQ6DG9Ntk6D w7SZUyjh378iRBbd3Hbm8ALaEDk9shoD7ZmOlBLsKashv6glVsG0XJPHbWt77VZt CBAuLLBAPRC2Gf7Nc2/RAmxKSL/3/MITsI3eZ79BQU1jN/wMHuDwYKdUZF18vdwZ rNUaoK7wVGwSNNCeiYpLytvS2INbp5s/0zf5wnYth+lVabCE+5DRc6deL5ixNVZx p7ze5wDWdzgvt6bNgmVl9oq+GJ631IoDIRe+MR4cMbeDRNJkSUH7UDOXCHZ0Ff27 HxQHeamg3U7ew3LI6cW+gD8nf9vU8GQDupDdqijZ6C0r5kfot+9f94/gnQ/tl0lP 4oAWxEHmmXsQwikmPQ4BFVIVdZtJV319PlMB91OpZWVgiruAlloRu4s84V599AyK VKjEyOycLq5nnfwQGZHiw4P37HpDvNvsmUuKdg6W9Bn3pXYPG9CxzZo+LKaTG78C 0RcpJGvy8YLUQOP+cIST =T0WV -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 19:07:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 19:07:13 +0000 Subject: [Debian-med-packaging] r-bioc-biomart_2.28.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 20:55:38 +0200 Source: r-bioc-biomart Binary: r-bioc-biomart Architecture: source all Version: 2.28.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-biomart - GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase a Changes: r-bioc-biomart (2.28.0-1) unstable; urgency=medium . * New upstream version * We can not use autopkgtests since the use of biomart is basically downloading external databases Checksums-Sha1: a33a27146b16b67c2d717fdcfaa41f98ef8a8a8f 2129 r-bioc-biomart_2.28.0-1.dsc 53df2203243234579e79df282884b037c20d7422 274747 r-bioc-biomart_2.28.0.orig.tar.gz 76c6da39f42f226d9f0879c0a9bf36f55a8b4970 4780 r-bioc-biomart_2.28.0-1.debian.tar.xz 139149d8f589fb9a382a6ab4eb2f519d54060253 386346 r-bioc-biomart_2.28.0-1_all.deb Checksums-Sha256: b762ccc6f7144d6d633df9e56b24b42ed723368e78d2a7d7b5c3cbec3c552755 2129 r-bioc-biomart_2.28.0-1.dsc bbd42d7938e72fa2d232c3ec21765678242d92cef51abca17fd44d98ac321cbc 274747 r-bioc-biomart_2.28.0.orig.tar.gz 1b276e7d82da2058defeffe4e738c734581076acc208d5b32627ca4fbe99c61d 4780 r-bioc-biomart_2.28.0-1.debian.tar.xz 561bacd5396944b18a07c662e7250f221d8e966c2cad40f48e0594c8fad948d4 386346 r-bioc-biomart_2.28.0-1_all.deb Files: 38dc284e8e03d753955a2e6986f8d4dd 2129 gnu-r optional r-bioc-biomart_2.28.0-1.dsc 043ed61b4e19c085968db0f9524c57b7 274747 gnu-r optional r-bioc-biomart_2.28.0.orig.tar.gz 4e1332105d461fd2625f91781a2664cf 4780 gnu-r optional r-bioc-biomart_2.28.0-1.debian.tar.xz cc413d0ab6efc02c5089640e331cde4f 386346 gnu-r optional r-bioc-biomart_2.28.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL4wXAAoJEFeKBJTRxkbRywcQAJQMcTSvMZz8PW7i61R2jnQL M1qzlSRBNYNGbBkqIlPdlOGxH7ILpqoJJ22c2CvTKTJtlTsmlfZaSm+66FqXzEwU qt1tGz2ioPjY2HRfYXyv+se/14McC9Jv5kQL8lnLucAve9BQIAdJJHbjyF7uH2/C tOgPXjBo/W9YS/a9Cnc/ml1TijTDdun5mmixZYBBD5OW6NTSnVJM30ipW0hLIPPa 3O8Fm1TSLOIPYCco8kW/CZc5vEirYBhGECAjYnMhNurXFot5UhpZIK/UFqDjfIGa 8P59pMFLRfeV1xagnlvjJtpd3OPuYtg48VRNIRf1N3SbcmYKaUfSg4nkO/luJ0cS TZBYYSHSYLSUwt24HDWFLqxMOp3Dejmnmus86p2Y8FzwmskA0dPd4Cs9a6uAapzz iOJegHQhGimZa/pgRkCmlDob02PJAbqo4qtMlt7/zrmbV8VNRd3qBKKdsRoDfpW1 pR0RXfpSkwpVfyAmzR3fWLU/adr35VX245MfMkbNMn4erRlpQrbKGFGwCrkyo/WR aEs2Z9nL6tOWoGnsm+ZeXBv6P/4JXuQVJTCwHNes+UhPZl0bJquR1MtEXqKVpiwy 6IPjU9yHpvNW18mFjyQjXT9DyzUYindfUIqdLSwRlqu19+Zi3l0Z9BYCsBXwFEPS uqhHTMRemO8hdw3SwUt8 =FPAu -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 19:12:51 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 19:12:51 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-summarizedexperiment_1.2.0-1_amd64.changes Message-ID: r-bioc-summarizedexperiment_1.2.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-summarizedexperiment_1.2.0-1.dsc r-bioc-summarizedexperiment_1.2.0.orig.tar.gz r-bioc-summarizedexperiment_1.2.0-1.debian.tar.xz r-bioc-summarizedexperiment_1.2.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 19:20:19 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 19:20:19 +0000 Subject: [Debian-med-packaging] r-bioc-summarizedexperiment_1.2.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 19:12:19 +0200 Source: r-bioc-summarizedexperiment Binary: r-bioc-summarizedexperiment Architecture: source all Version: 1.2.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-summarizedexperiment - BioConductor assay container Changes: r-bioc-summarizedexperiment (1.2.0-1) unstable; urgency=medium . * New upstream version * Fix versioned Depends Checksums-Sha1: 69243cd98da57a93440daf07eb97a8d513d53fe4 2303 r-bioc-summarizedexperiment_1.2.0-1.dsc d3a41e0071ad92256218a4600dd20d8bd2a5acac 964033 r-bioc-summarizedexperiment_1.2.0.orig.tar.gz e84f90964043fdec766e7994bdcb6de309e6ad50 4220 r-bioc-summarizedexperiment_1.2.0-1.debian.tar.xz f73e2d2ca325255d9ef226bbb916430a719a95cd 1292420 r-bioc-summarizedexperiment_1.2.0-1_all.deb Checksums-Sha256: 6e7bfc8849ee92902dfe6fe9391a3781583c967194497f375cdc29bd1b422f74 2303 r-bioc-summarizedexperiment_1.2.0-1.dsc 0832e1742fb4bee3d9f454c33954b983cf13ca37ebabdbdfa947b9489be0cbdd 964033 r-bioc-summarizedexperiment_1.2.0.orig.tar.gz eddf57db320f2116e04f106610d10dfd4d07926d72d8b8c8c5f1017942266091 4220 r-bioc-summarizedexperiment_1.2.0-1.debian.tar.xz 76e1242e65b240ead1a23a652bd30bd913d5daa0e096464bedcb8826606183df 1292420 r-bioc-summarizedexperiment_1.2.0-1_all.deb Files: 50fa74d48bc36970596a980c19446b02 2303 gnu-r optional r-bioc-summarizedexperiment_1.2.0-1.dsc d6974a246da6bbc061289bddd1ad73b7 964033 gnu-r optional r-bioc-summarizedexperiment_1.2.0.orig.tar.gz e5f421ad50e36426a5f853e0a56cd547 4220 gnu-r optional r-bioc-summarizedexperiment_1.2.0-1.debian.tar.xz 6dcf0e436da714c14054de98bb7db7e5 1292420 gnu-r optional r-bioc-summarizedexperiment_1.2.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL47xAAoJEFeKBJTRxkbRvpQP/R2o0ZPorrld0D3UNbR8EnoF N1MmE9Bl5kw9UOkyj/m3lMWj2I6/C62D8jfjJ/9cdBXSRUYTOqX+7oN8PJeaMzB/ sRN6d1rDojPhtYAO3UZqaDJM8IYy6YkUKaZ9D403WgpVDbiZZ/qxjcSFchmzoRKb H+lhm6Qym/DymNQa/GGZzUWXSORZz39bSf6CqPEFlCBbA8PeRAE2KzQa5THhHeqy Ccf9tx5HBhzMcbeMgYdcerdJ/aZg6S+oSyvSjnXuYRVRn27+8jaOgxmuGf929aOm hbk9eDbmI/7rCZQR5f1N3HA/JAay438cfbVsqpakQ/2PssBNq8iQy/PfiwY52SN0 8eGf+0+Nnft8xqrWkXw+NfvGzjleEI/robYormcn57ZfiBGHTMnrJIgxOSE/wnL6 cBT9/hxGuvS0IPPTy9A3wnsPx8KJ58Yy0m7by9SIQ9SGfI9AUbWTC+Ux9npbV0fY 4nsCq+MO+KQRMY0BdRwmSmPFg7Pzr3TRQIM2wYjPHnkBsiCpufpym+0hVOgpRMQm mZgffVOH/upvDQxRxXgMfqQ+JufY6pvRdcFjZyJJltHjZhpRPeDUHdC54QzG119z yjiVlKBJY1Cxdm+QN/Ic2j/D3650asG9ibOijGokpIjm2VDwKUcIWqT7adARjQ9+ fhc83x2I3YbKOjHosWb9 =o84A -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 19:32:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 19:32:58 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-makecdfenv_1.48.0-1_source.changes Message-ID: r-bioc-makecdfenv_1.48.0-1_source.changes uploaded successfully to localhost along with the files: r-bioc-makecdfenv_1.48.0-1.dsc r-bioc-makecdfenv_1.48.0.orig.tar.gz r-bioc-makecdfenv_1.48.0-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 19:34:44 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 19:34:44 +0000 Subject: [Debian-med-packaging] r-bioc-makecdfenv_1.48.0-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 21:22:40 +0200 Source: r-bioc-makecdfenv Binary: r-bioc-makecdfenv Architecture: source Version: 1.48.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-makecdfenv - BioConductor CDF Environment Maker Changes: r-bioc-makecdfenv (1.48.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 6dad10da9dae09a71c2e4c9985ac305137532107 2152 r-bioc-makecdfenv_1.48.0-1.dsc d95f873b8f9af530a6b9ed5df9a9a64d3ce28a60 3306370 r-bioc-makecdfenv_1.48.0.orig.tar.gz 0339f7cd064a687e365c32724a0993a5f33d5ce6 4396 r-bioc-makecdfenv_1.48.0-1.debian.tar.xz Checksums-Sha256: b6ad17617d9514c0cfab4c090b57863cf62d8dddbaa085eca4c5ef7a1f1bf98a 2152 r-bioc-makecdfenv_1.48.0-1.dsc 0d47edfaa8b2602032aa6b3e0b820636a48819096104c47a8fd9c65c1f2c0668 3306370 r-bioc-makecdfenv_1.48.0.orig.tar.gz 74ede29ebb6ae2714c4189c6f8f6b9fe60e5b120784e82c2082303221267a65a 4396 r-bioc-makecdfenv_1.48.0-1.debian.tar.xz Files: f283f50b13651a17b8ebc3f9f6bd922c 2152 gnu-r optional r-bioc-makecdfenv_1.48.0-1.dsc fc548dd4bb0a416647236ae9715ca4bb 3306370 gnu-r optional r-bioc-makecdfenv_1.48.0.orig.tar.gz 50ae8710d9bc1eabb3094e1dfaecda5f 4396 gnu-r optional r-bioc-makecdfenv_1.48.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXL5MaAAoJEFeKBJTRxkbRaxsP/2OJLaKoH/67IXXc0Wi+LwTH qme+Gl5flAHT+ZfLEYuOzFcj/PzLaLxRC4BGDEP+UR5FpSlTvtK6f/uxJZVdsKek Y/wD52m8bILtrkkYb+J7cvJ3K5fUODF2+8UMfKUtJ+KQLDxL75fbK2XJTgqHTrEr 1KQ+T/cdqyyQ8fJmjFRPxMtL1UQjQf1rJG2mx116U+yNxAGYHMQ7U5dInq06NvqT Ee7ZwsWkY3nQbmMgitKCAbHSiiJSc4FPI8Dc0beAheGkFXPUkFWoDr+1euetYhK0 fuWnrLIJg92xloS151gIh9+e2d1qot0RNKDoxoqLUK/8TQekMvjUoQSHMBi5+MMN jH8YpZLrzJS2EHeFpD2EUQG0YGBbP2tVBFIpTOt9SpS1QYS/st2v+vNvOYc8DqFn nN8kk6slDRi1+agmT1DyRlWqTPxJan5r9FFvs243c29+rxrf27VwxejtPuATaSaJ dsy6wt3GdXq9I1C29GUyk3kZ7PC2/53euBaV5mpcpOC9eR8B+Bg6hYZP3Rnzv2Rn VFpGV1C6FKlCY/cfCCglILhtbzTXWZnJgYfEkvvy+OTLyGb2nbKE3qPnby1s2pQY 9V1RjMUG0ZFtS1tzgXJNLuJV0svIYaQPmHS4VHNEWDDDwWY07qh8abCT/DN8HKQi 4SJXXcyy8H4br3tGZJdG =eBkW -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 8 21:13:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 21:13:40 +0000 Subject: [Debian-med-packaging] Processing of htslib_1.3.1-1~bpo8+1_amd64.changes Message-ID: htslib_1.3.1-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: htslib_1.3.1-1~bpo8+1.dsc htslib_1.3.1-1~bpo8+1.debian.tar.xz libhts1_1.3.1-1~bpo8+1_amd64.deb libhts-dev_1.3.1-1~bpo8+1_amd64.deb htslib-test_1.3.1-1~bpo8+1_all.deb tabix_1.3.1-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From afif at ghraoui.name Sun May 8 21:15:55 2016 From: afif at ghraoui.name (Afif Elghraoui) Date: Sun, 8 May 2016 14:15:55 -0700 Subject: [Debian-med-packaging] htslib_1.3.1-1~bpo8+1_source.changes REJECTED In-Reply-To: References: Message-ID: <572FAC8B.6070307@ghraoui.name> Hi, Charles, I guess you ran out of time for the day to take care of this. I went ahead and made the build and binary upload. Knowing you like to keep track of the build logs, please find them attached. :) Thanks and regards Afif ??? ????? 8 ???? 2016 ?06:19? ??? Debian FTP Masters: > > > Uploads not including architecture-independent packages are not allowed. > > === > > Please feel free to respond to this email if you don't understand why > your files were rejected, or if you upload new files which address our > concerns. > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- Afif Elghraoui | ???? ??????? http://afif.ghraoui.name -------------- next part -------------- sbuild (Debian sbuild) 0.68.0 (15 Jan 2016) on afif-1215B +==============================================================================+ | htslib 1.3.1-1~bpo8+1 (amd64) 08 May 2016 13:54 | +==============================================================================+ Package: htslib Version: 1.3.1-1~bpo8+1 Source Version: 1.3.1-1~bpo8+1 Distribution: jessie-backports Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/htslib-aHK0ED/htslib-1.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/htslib-aHK0ED' with '<>' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-amd64-sbuild-f5a3f6b6-de37-46ec-b4fd-b7d7e351aa9b' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Ign http://ftp.us.debian.org jessie InRelease Hit http://ftp.us.debian.org jessie Release.gpg Hit http://ftp.us.debian.org jessie Release Hit http://ftp.us.debian.org jessie/main Sources Hit http://ftp.us.debian.org jessie/main amd64 Packages Hit http://ftp.us.debian.org jessie/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /home/afif/??????/debian/med/htslib/htslib_1.3.1-1~bpo8+1.dsc exists in /home/afif/??????/debian/med/htslib; copying to chroot +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/<>/resolver-YX_a4L/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Ign file: ./ InRelease Get:1 file: ./ Release.gpg [299 B] Get:2 file: ./ Release [2119 B] Ign file: ./ Translation-en Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/822 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11866 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9), dh-exec, libcurl4-gnutls-dev, libssl-dev, zlib1g-dev, autoconf Filtered Build-Depends: debhelper (>= 9), dh-exec, libcurl4-gnutls-dev, libssl-dev, zlib1g-dev, autoconf dpkg-deb: building package `sbuild-build-depends-htslib-dummy' in `/<>/resolver-mGXQsc/apt_archive/sbuild-build-depends-htslib-dummy.deb'. OK Ign file: ./ InRelease Get:1 file: ./ Release.gpg [299 B] Get:2 file: ./ Release [2119 B] Ign file: ./ Translation-en Reading package lists... Reading package lists... Install htslib build dependencies (apt-based resolver) ------------------------------------------------------ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf bsdmainutils debhelper dh-exec file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libffi6 libglib2.0-0 libgnutls-deb0-28 libgssapi-krb5-2 libhogweed2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libnettle4 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl-dev libssl1.0.0 libtasn1-6 libunistring0 libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation dh-make gettext-doc groff libcurl4-doc libcurl3-dbg libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config gnutls-bin krb5-doc krb5-user less www-browser libmail-box-perl Recommended packages: automake automaken curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libsasl2-modules libssl-doc xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf bsdmainutils debhelper dh-exec file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libffi6 libglib2.0-0 libgnutls-deb0-28 libgssapi-krb5-2 libhogweed2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libnettle4 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl-dev libssl1.0.0 libtasn1-6 libunistring0 libxml2 m4 man-db po-debconf sbuild-build-depends-htslib-dummy zlib1g-dev 0 upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 15.0 MB/15.0 MB of archives. After this operation, 48.1 MB of additional disk space will be used. Get:1 http://ftp.us.debian.org/debian/ jessie/main libpipeline1 amd64 1.4.0-1 [27.9 kB] Get:2 http://ftp.us.debian.org/debian/ jessie/main libssl1.0.0 amd64 1.0.1k-3+deb8u4 [1039 kB] Get:3 http://ftp.us.debian.org/debian/ jessie/main groff-base amd64 1.22.2-8 [1183 kB] Get:4 http://ftp.us.debian.org/debian/ jessie/main bsdmainutils amd64 9.0.6 [183 kB] Get:5 http://ftp.us.debian.org/debian/ jessie/main man-db amd64 2.7.0.2-5 [1000 kB] Get:6 http://ftp.us.debian.org/debian/ jessie/main libasprintf0c2 amd64 0.19.3-2 [31.3 kB] Get:7 http://ftp.us.debian.org/debian/ jessie/main libnettle4 amd64 2.7.1-5+deb8u1 [176 kB] Get:8 http://ftp.us.debian.org/debian/ jessie/main libhogweed2 amd64 2.7.1-5+deb8u1 [126 kB] Get:9 http://ftp.us.debian.org/debian/ jessie/main libffi6 amd64 3.1-2+b2 [20.1 kB] Get:10 http://ftp.us.debian.org/debian/ jessie/main libp11-kit0 amd64 0.20.7-1 [81.2 kB] Get:11 http://ftp.us.debian.org/debian/ jessie/main libtasn1-6 amd64 4.2-3+deb8u1 [48.9 kB] Get:12 http://ftp.us.debian.org/debian/ jessie/main libgnutls-deb0-28 amd64 3.3.8-6+deb8u3 [694 kB] Get:13 http://ftp.us.debian.org/debian/ jessie/main libkeyutils1 amd64 1.5.9-5+b1 [12.0 kB] Get:14 http://ftp.us.debian.org/debian/ jessie/main libkrb5support0 amd64 1.12.1+dfsg-19+deb8u2 [59.1 kB] Get:15 http://ftp.us.debian.org/debian/ jessie/main libk5crypto3 amd64 1.12.1+dfsg-19+deb8u2 [115 kB] Get:16 http://ftp.us.debian.org/debian/ jessie/main libkrb5-3 amd64 1.12.1+dfsg-19+deb8u2 [303 kB] Get:17 http://ftp.us.debian.org/debian/ jessie/main libgssapi-krb5-2 amd64 1.12.1+dfsg-19+deb8u2 [152 kB] Get:18 http://ftp.us.debian.org/debian/ jessie/main libidn11 amd64 1.29-1+b2 [136 kB] Get:19 http://ftp.us.debian.org/debian/ jessie/main libsasl2-modules-db amd64 2.1.26.dfsg1-13+deb8u1 [67.1 kB] Get:20 http://ftp.us.debian.org/debian/ jessie/main libsasl2-2 amd64 2.1.26.dfsg1-13+deb8u1 [105 kB] Get:21 http://ftp.us.debian.org/debian/ jessie/main libldap-2.4-2 amd64 2.4.40+dfsg-1+deb8u2 [218 kB] Get:22 http://ftp.us.debian.org/debian/ jessie/main libmagic1 amd64 1:5.22+15-2+deb8u1 [249 kB] Get:23 http://ftp.us.debian.org/debian/ jessie/main libxml2 amd64 2.9.1+dfsg1-5+deb8u1 [801 kB] Get:24 http://ftp.us.debian.org/debian/ jessie/main libglib2.0-0 amd64 2.42.1-1+b1 [2401 kB] Get:25 http://ftp.us.debian.org/debian/ jessie/main libcroco3 amd64 0.6.8-3+b1 [135 kB] Get:26 http://ftp.us.debian.org/debian/ jessie/main librtmp1 amd64 2.4+20150115.gita107cef-1 [59.8 kB] Get:27 http://ftp.us.debian.org/debian/ jessie/main libssh2-1 amd64 1.4.3-4.1+deb8u1 [125 kB] Get:28 http://ftp.us.debian.org/debian/ jessie/main libcurl3-gnutls amd64 7.38.0-4+deb8u3 [251 kB] Get:29 http://ftp.us.debian.org/debian/ jessie/main libsigsegv2 amd64 2.10-4+b1 [29.2 kB] Get:30 http://ftp.us.debian.org/debian/ jessie/main libunistring0 amd64 0.9.3-5.2+b1 [288 kB] Get:31 http://ftp.us.debian.org/debian/ jessie/main file amd64 1:5.22+15-2+deb8u1 [60.4 kB] Get:32 http://ftp.us.debian.org/debian/ jessie/main gettext-base amd64 0.19.3-2 [121 kB] Get:33 http://ftp.us.debian.org/debian/ jessie/main m4 amd64 1.4.17-4 [254 kB] Get:34 http://ftp.us.debian.org/debian/ jessie/main autoconf all 2.69-8 [340 kB] Get:35 http://ftp.us.debian.org/debian/ jessie/main gettext amd64 0.19.3-2 [1240 kB] Get:36 http://ftp.us.debian.org/debian/ jessie/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:37 http://ftp.us.debian.org/debian/ jessie/main po-debconf all 1.0.16+nmu3 [220 kB] Get:38 http://ftp.us.debian.org/debian/ jessie/main debhelper all 9.20150101 [813 kB] Get:39 http://ftp.us.debian.org/debian/ jessie/main libcurl4-gnutls-dev amd64 7.38.0-4+deb8u3 [327 kB] Get:40 http://ftp.us.debian.org/debian/ jessie/main zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] Get:41 http://ftp.us.debian.org/debian/ jessie/main libssl-dev amd64 1.0.1k-3+deb8u4 [1273 kB] Get:42 http://ftp.us.debian.org/debian/ jessie/main dh-exec amd64 0.14 [23.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.0 MB in 18s (813 kB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11866 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.4.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.0-1) ... Selecting previously unselected package libssl1.0.0:amd64. Preparing to unpack .../libssl1.0.0_1.0.1k-3+deb8u4_amd64.deb ... Unpacking libssl1.0.0:amd64 (1.0.1k-3+deb8u4) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-8_amd64.deb ... Unpacking groff-base (1.22.2-8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6_amd64.deb ... Unpacking bsdmainutils (9.0.6) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.0.2-5_amd64.deb ... Unpacking man-db (2.7.0.2-5) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.19.3-2_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.19.3-2) ... Selecting previously unselected package libnettle4:amd64. Preparing to unpack .../libnettle4_2.7.1-5+deb8u1_amd64.deb ... Unpacking libnettle4:amd64 (2.7.1-5+deb8u1) ... Selecting previously unselected package libhogweed2:amd64. Preparing to unpack .../libhogweed2_2.7.1-5+deb8u1_amd64.deb ... Unpacking libhogweed2:amd64 (2.7.1-5+deb8u1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.1-2+b2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2+b2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../libp11-kit0_0.20.7-1_amd64.deb ... Unpacking libp11-kit0:amd64 (0.20.7-1) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../libtasn1-6_4.2-3+deb8u1_amd64.deb ... Unpacking libtasn1-6:amd64 (4.2-3+deb8u1) ... Selecting previously unselected package libgnutls-deb0-28:amd64. Preparing to unpack .../libgnutls-deb0-28_3.3.8-6+deb8u3_amd64.deb ... Unpacking libgnutls-deb0-28:amd64 (3.3.8-6+deb8u3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../libkeyutils1_1.5.9-5+b1_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-5+b1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../libkrb5support0_1.12.1+dfsg-19+deb8u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.12.1+dfsg-19+deb8u2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../libk5crypto3_1.12.1+dfsg-19+deb8u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.12.1+dfsg-19+deb8u2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../libkrb5-3_1.12.1+dfsg-19+deb8u2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.12.1+dfsg-19+deb8u2) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../libgssapi-krb5-2_1.12.1+dfsg-19+deb8u2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.12.1+dfsg-19+deb8u2) ... Selecting previously unselected package libidn11:amd64. Preparing to unpack .../libidn11_1.29-1+b2_amd64.deb ... Unpacking libidn11:amd64 (1.29-1+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-13+deb8u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.26.dfsg1-13+deb8u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-13+deb8u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.26.dfsg1-13+deb8u1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../libldap-2.4-2_2.4.40+dfsg-1+deb8u2_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.40+dfsg-1+deb8u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.22+15-2+deb8u1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.22+15-2+deb8u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.1+dfsg1-5+deb8u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.1+dfsg1-5+deb8u1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.42.1-1+b1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.42.1-1+b1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-3+b1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.8-3+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../librtmp1_2.4+20150115.gita107cef-1_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20150115.gita107cef-1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../libssh2-1_1.4.3-4.1+deb8u1_amd64.deb ... Unpacking libssh2-1:amd64 (1.4.3-4.1+deb8u1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../libcurl3-gnutls_7.38.0-4+deb8u3_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.38.0-4+deb8u3) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.10-4+b1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.10-4+b1) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.22+15-2+deb8u1_amd64.deb ... Unpacking file (1:5.22+15-2+deb8u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.3-2_amd64.deb ... Unpacking gettext-base (0.19.3-2) ... Selecting previously unselected package m4. Preparing to unpack .../archives/m4_1.4.17-4_amd64.deb ... Unpacking m4 (1.4.17-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../autoconf_2.69-8_all.deb ... Unpacking autoconf (2.69-8) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.3-2_amd64.deb ... Unpacking gettext (0.19.3-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ... Unpacking intltool-debian (0.35.0+20060710.1) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ... Unpacking po-debconf (1.0.16+nmu3) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20150101_all.deb ... Unpacking debhelper (9.20150101) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../libcurl4-gnutls-dev_7.38.0-4+deb8u3_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.38.0-4+deb8u3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../libssl-dev_1.0.1k-3+deb8u4_amd64.deb ... Unpacking libssl-dev:amd64 (1.0.1k-3+deb8u4) ... Selecting previously unselected package dh-exec. Preparing to unpack .../dh-exec_0.14_amd64.deb ... Unpacking dh-exec (0.14) ... Selecting previously unselected package sbuild-build-depends-htslib-dummy. Preparing to unpack .../sbuild-build-depends-htslib-dummy.deb ... Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.4.0-1) ... Setting up libssl1.0.0:amd64 (1.0.1k-3+deb8u4) ... Setting up groff-base (1.22.2-8) ... Setting up bsdmainutils (9.0.6) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.7.0.2-5) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.19.3-2) ... Setting up libnettle4:amd64 (2.7.1-5+deb8u1) ... Setting up libhogweed2:amd64 (2.7.1-5+deb8u1) ... Setting up libffi6:amd64 (3.1-2+b2) ... Setting up libp11-kit0:amd64 (0.20.7-1) ... Setting up libtasn1-6:amd64 (4.2-3+deb8u1) ... Setting up libgnutls-deb0-28:amd64 (3.3.8-6+deb8u3) ... Setting up libkeyutils1:amd64 (1.5.9-5+b1) ... Setting up libkrb5support0:amd64 (1.12.1+dfsg-19+deb8u2) ... Setting up libk5crypto3:amd64 (1.12.1+dfsg-19+deb8u2) ... Setting up libkrb5-3:amd64 (1.12.1+dfsg-19+deb8u2) ... Setting up libgssapi-krb5-2:amd64 (1.12.1+dfsg-19+deb8u2) ... Setting up libidn11:amd64 (1.29-1+b2) ... Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-13+deb8u1) ... Setting up libsasl2-2:amd64 (2.1.26.dfsg1-13+deb8u1) ... Setting up libldap-2.4-2:amd64 (2.4.40+dfsg-1+deb8u2) ... Setting up libmagic1:amd64 (1:5.22+15-2+deb8u1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-5+deb8u1) ... Setting up libglib2.0-0:amd64 (2.42.1-1+b1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-3+b1) ... Setting up librtmp1:amd64 (2.4+20150115.gita107cef-1) ... Setting up libssh2-1:amd64 (1.4.3-4.1+deb8u1) ... Setting up libcurl3-gnutls:amd64 (7.38.0-4+deb8u3) ... Setting up libsigsegv2:amd64 (2.10-4+b1) ... Setting up libunistring0:amd64 (0.9.3-5.2+b1) ... Setting up file (1:5.22+15-2+deb8u1) ... Setting up gettext-base (0.19.3-2) ... Setting up m4 (1.4.17-4) ... Setting up autoconf (2.69-8) ... Setting up gettext (0.19.3-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up debhelper (9.20150101) ... Setting up libcurl4-gnutls-dev:amd64 (7.38.0-4+deb8u3) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up libssl-dev:amd64 (1.0.1k-3+deb8u4) ... Setting up dh-exec (0.14) ... Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-18+deb8u4) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.26 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18+deb8u4 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt25-1 Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8.3 autoconf_2.69-8 base-files_8+deb8u4 base-passwd_3.5.37 bash_4.3-11+b1 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7+b3 coreutils_8.23-4 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4+b1 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150101 debian-archive-keyring_2014.3 debianutils_4.4+b1 dh-exec_0.14 diffutils_1:3.3-1+b1 dmsetup_2:1.02.90-2.2 dpkg_1.17.26 dpkg-dev_1.17.26 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2+deb8u1 findutils_4.4.2-9+b1 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.3-2 gettext-base_0.19.3-2 gnupg_1.4.18-7+deb8u1 gpgv_1.4.18-7+deb8u1 grep_2.20-4.1 groff-base_1.22.2-8 gzip_1.6-4 hostname_3.15 init_1.22 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8.3 libasan1_4.9.2-10 libasprintf0c2_0.19.3-2 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1+b1 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7+b3 libc-bin_2.19-18+deb8u4 libc-dev-bin_2.19-18+deb8u4 libc6_2.19-18+deb8u4 libc6-dev_2.19-18+deb8u4 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcilkrts5_4.9.2-10 libcloog-isl4_0.18.2-1+b2 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3+b1 libcryptsetup4_2:1.6.6-5 libcurl3-gnutls_7.38.0-4+deb8u3 libcurl4-gnutls-dev_7.38.0-4+deb8u3 libdb5.3_5.3.28-9 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.26 libfakeroot_1.20.2-1 libffi6_3.1-2+b2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2+deb8u1 libgdbm3_1.8.3-13.1 libglib2.0-0_2.42.1-1+b1 libgmp10_2:6.0.0+dfsg-6 libgnutls-deb0-28_3.3.8-6+deb8u3 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libgssapi-krb5-2_1.12.1+dfsg-19+deb8u2 libhogweed2_2.7.1-5+deb8u1 libidn11_1.29-1+b2 libisl10_0.12.2-2 libitm1_4.9.2-10 libk5crypto3_1.12.1+dfsg-19+deb8u2 libkeyutils1_1.5.9-5+b1 libkmod2_18-3 libkrb5-3_1.12.1+dfsg-19+deb8u2 libkrb5support0_1.12.1+dfsg-19+deb8u2 libldap-2.4-2_2.4.40+dfsg-1+deb8u2 liblocale-gettext-perl_1.05-8+b1 liblsan0_4.9.2-10 liblzma5_5.1.1alpha+20120614-2+b3 libmagic1_1:5.22+15-2+deb8u1 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1+b1 libncursesw5_5.9+20140913-1+b1 libnettle4_2.7.1-5+deb8u1 libp11-kit0_0.20.7-1 libpam-modules_1.1.8-3.1+deb8u1+b1 libpam-modules-bin_1.1.8-3.1+deb8u1+b1 libpam-runtime_1.1.8-3.1+deb8u1 libpam0g_1.1.8-3.1+deb8u1+b1 libpcre3_2:8.35-3.3+deb8u4 libpipeline1_1.4.0-1 libprocps3_2:3.3.9-9 libquadmath0_4.9.2-10 libreadline6_6.3-8+b3 librtmp1_2.4+20150115.gita107cef-1 libsasl2-2_2.1.26.dfsg1-13+deb8u1 libsasl2-modules-db_2.1.26.dfsg1-13+deb8u1 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1+b1 libsepol1_2.3-2 libsigsegv2_2.10-4+b1 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libss2_1.42.12-1.1 libssh2-1_1.4.3-4.1+deb8u1 libssl-dev_1.0.1k-3+deb8u4 libssl1.0.0_1.0.1k-3+deb8u4 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-17+deb8u4 libtasn1-6_4.2-3+deb8u1 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1+b1 libtsan0_4.9.2-10 libubsan0_4.9.2-10 libudev1_215-17+deb8u4 libunistring0_0.9.3-5.2+b1 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3+b2 libuuid1_2.25.2-6 libxml2_2.9.1+dfsg1-5+deb8u1 linux-libc-dev_3.16.7-ckt25-1 login_1:4.2-3+deb8u1 lsb-base_4.1+Debian13+nmu1 m4_1.4.17-4 make_4.0-8.1 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-6 multiarch-support_2.19-18+deb8u4 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1+b1 passwd_1:4.2-3+deb8u1 patch_2.7.5-1 perl_5.20.2-3+deb8u4 perl-base_5.20.2-3+deb8u4 perl-modules_5.20.2-3+deb8u4 po-debconf_1.0.16+nmu3 procps_2:3.3.9-9 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.2.2-4+b1 sensible-utils_0.0.9 startpar_0.59-3 systemd_215-17+deb8u4 systemd-sysv_215-17+deb8u4 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2+b1 tzdata_2016c-0+deb8u1 udev_215-17+deb8u4 util-linux_2.25.2-6 xz-utils_5.1.1alpha+20120614-2+b3 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- dpkg-source: warning: extracting unsigned source package (htslib_1.3.1-1~bpo8+1.dsc) dpkg-source: info: extracting htslib in htslib-1.3.1 dpkg-source: info: unpacking htslib_1.3.1.orig.tar.gz dpkg-source: info: unpacking htslib_1.3.1-1~bpo8+1.debian.tar.xz dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying literal_version.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LC_ALL=POSIX LOGNAME=afif PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=jessie-amd64-sbuild SCHROOT_CHROOT_NAME=jessie-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=afif SCHROOT_SESSION_ID=jessie-amd64-sbuild-f5a3f6b6-de37-46ec-b4fd-b7d7e351aa9b SCHROOT_UID=1000 SCHROOT_USER=afif SHELL=/bin/sh TERM=xterm USER=afif XDG_RUNTIME_DIR=/run/user/1000 XDG_SEAT=seat0 XDG_SESSION_ID=1 XDG_VTNR=7 dpkg-buildpackage ----------------- dpkg-buildpackage: source package htslib dpkg-buildpackage: source version 1.3.1-1~bpo8+1 dpkg-buildpackage: source distribution jessie-backports dpkg-buildpackage: source changed by Charles Plessy dpkg-source --before-build htslib-1.3.1 dpkg-buildpackage: host architecture amd64 dpkg-source: info: using options from htslib-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$ fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make -j2 distclean make[1]: Entering directory '/<>' rm -f test/*.tmp test/*.tmp.* rm -f libhts.so libhts.so.* rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h rm -f libhts.a bgzip htsfile tabix test/fieldarith test/hfile test/sam test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *-uninstalled.pc make[1]: Leaving directory '/<>' dh_clean -O--parallel rm -f debian/libhts1.substvars rm -f debian/libhts1.*.debhelper rm -rf debian/libhts1/ rm -f debian/libhts-dev.substvars rm -f debian/libhts-dev.*.debhelper rm -rf debian/libhts-dev/ rm -f debian/htslib-test.substvars rm -f debian/htslib-test.*.debhelper rm -rf debian/htslib-test/ rm -f debian/tabix.substvars rm -f debian/tabix.*.debhelper rm -rf debian/tabix/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *-stamp dpkg-source -b htslib-1.3.1 dpkg-source: info: using options from htslib-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$ dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building htslib using existing ./htslib_1.3.1.orig.tar.gz dpkg-source: info: building htslib in htslib_1.3.1-1~bpo8+1.debian.tar.xz dpkg-source: info: building htslib in htslib_1.3.1-1~bpo8+1.dsc debian/rules build dh build --parallel dh_testdir -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' autoconf ./configure --enable-libcurl checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \ # re-try later LDLIBS=-lhts \ PACKAGE_VERSION="1.3.1-1~bpo8+1" \ libdir=/usr/lib/x86_64-linux-gnu make -j2 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>' gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.3.1"' > version.h gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/thread_pool.o cram/thread_pool.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/vlen.o cram/vlen.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/zfio.o cram/zfio.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile_libcurl.o hfile_libcurl.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o kfunc.pico kfunc.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o knetfile.pico knetfile.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o kstring.pico kstring.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o bgzf.pico bgzf.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o faidx.pico faidx.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile.pico hfile.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile_net.pico hfile_net.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hts.pico hts.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o md5.pico md5.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o regidx.pico regidx.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o sam.pico sam.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o tbx.pico tbx.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcf.pico vcf.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcfutils.pico vcfutils.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/files.pico cram/files.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/sam_header.pico cram/sam_header.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/thread_pool.pico cram/thread_pool.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/vlen.pico cram/vlen.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/zfio.pico cram/zfio.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -shared -Wl,-soname,libhts.so.1 -pthread -Wl,-z,relro -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico hfile_libcurl.pico -lz -lm -lcurl -lcrypto ln -sf libhts.so libhts.so.1 ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o hfile_libcurl.o ranlib libhts.a gcc -pthread -Wl,-z,relro -o bgzip bgzip.o libhts.a -lz -lcurl -lcrypto gcc -pthread -Wl,-z,relro -o htsfile htsfile.o libhts.a -lz -lcurl -lcrypto gcc -pthread -Wl,-z,relro -o tabix tabix.o libhts.a -lz -lcurl -lcrypto gcc -pthread -Wl,-z,relro -o test/fieldarith test/fieldarith.o libhts.a -lz -lcurl -lcrypto gcc -pthread -Wl,-z,relro -o test/hfile test/hfile.o libhts.a -lz -lcurl -lcrypto gcc -pthread -Wl,-z,relro -o test/sam test/sam.o libhts.a -lz -lcurl -lcrypto gcc -pthread -Wl,-z,relro -o test/test-regidx test/test-regidx.o libhts.a -lz -lcurl -lcrypto gcc -pthread -Wl,-z,relro -o test/test_view test/test_view.o libhts.a -lz -lcurl -lcrypto gcc -pthread -Wl,-z,relro -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lcurl -lcrypto gcc -pthread -Wl,-z,relro -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lcurl -lcrypto make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test make -j2 test make[2]: Entering directory '/<>' test/fieldarith test/fieldarith.sam test/hfile test/sam test/ce.fa test/faidx.fa test/test-regidx cd test && REF_PATH=: ./test.pl test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=3.0 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=3.0 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=3.0 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=3.0 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=3.0 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=3.0 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=3.0 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=3.0 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=3.0 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ WARNING: Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=3.0 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ .. ok test_vcf_api: /<>/test/test-vcf-api /tmp/xLOo4Mo2HC/test-vcf-api.bcf .. ok test_vcf_sweep: /<>/test/test-vcf-sweep /tmp/xLOo4Mo2HC/test-vcf-api.bcf .. ok test_vcf_various: /<>/htsfile -ch /<>/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /<>/htsfile -c /<>/test/formatcols.vcf .. ok test_vcf_various: /<>/htsfile -c /<>/test/noroundtrip.vcf .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/xLOo4Mo2HC/headernul0.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/xLOo4Mo2HC/headernul1.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/xLOo4Mo2HC/headernul678.bam .. ok Number of tests: total .. 39 passed .. 39 failed .. 0 make[2]: Leaving directory '/<>' rm -f test/*.tmp test/*.tmp.* test/*.o test/*.dSYM \ test/fieldarith test/hfile test/test_view test/test-vcf-api test/test-vcf-sweep make[1]: Leaving directory '/<>' fakeroot debian/rules binary dh binary --parallel dh_testroot -O--parallel dh_prep -O--parallel rm -f debian/libhts1.substvars rm -f debian/libhts1.*.debhelper rm -rf debian/libhts1/ rm -f debian/libhts-dev.substvars rm -f debian/libhts-dev.*.debhelper rm -rf debian/libhts-dev/ rm -f debian/htslib-test.substvars rm -f debian/htslib-test.*.debhelper rm -rf debian/htslib-test/ rm -f debian/tabix.substvars rm -f debian/tabix.*.debhelper rm -rf debian/tabix/ debian/rules override_dh_auto_install make[1]: Entering directory '/<>' rm /<>/test/sam /<>/test/test-regidx dh_auto_install -- \ prefix=/usr \ libdir=/usr/lib/x86_64-linux-gnu \ PACKAGE_VERSION="1.3.1-1~bpo8+1" install -d debian/libhts1 install -d debian/libhts-dev install -d debian/htslib-test install -d debian/tabix make -j2 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr libdir=/usr/lib/x86_64-linux-gnu PACKAGE_VERSION=1.3.1-1\~bpo8\+1 make[2]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/include /<>/debian/tmp/usr/include/htslib /<>/debian/tmp/usr/lib/x86_64-linux-gnu /<>/debian/tmp/usr/share/man/man1 /<>/debian/tmp/usr/share/man/man5 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig if test -n ""; then mkdir -p -m 755 /<>/debian/tmp; fi install -p -m 644 libhts.so /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1~bpo8+1 sed -e 's#@includedir@#/usr/include#g;s#@libdir@#/usr/lib/x86_64-linux-gnu#g;s#@PACKAGE_VERSION@#1.3.1-1~bpo8+1#g' htslib.pc.in > /<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.3.1-1~bpo8+1 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so ln -sf libhts.so.1.3.1-1~bpo8+1 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1 install -p bgzip htsfile tabix /<>/debian/tmp/usr/bin if test -n ""; then install -p /<>/debian/tmp; fi install -p -m 644 htslib/*.h /<>/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a install -p -m 644 htsfile.1 tabix.1 /<>/debian/tmp/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /<>/debian/tmp/usr/share/man/man5 make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_install -O--parallel install -d debian/libhts1/usr/lib/x86_64-linux-gnu cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1 debian/libhts1/usr/lib/x86_64-linux-gnu/ cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1\~bpo8\+1 debian/libhts1/usr/lib/x86_64-linux-gnu/ install -d debian/libhts-dev/usr/include cp -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -d debian/libhts-dev/usr/lib/x86_64-linux-gnu cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a debian/libhts-dev/usr/lib/x86_64-linux-gnu/ cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so debian/libhts-dev/usr/lib/x86_64-linux-gnu/ install -d debian/libhts-dev/usr/share/man/man5 cp -a debian/tmp/usr/share/man/man5/faidx.5 debian/libhts-dev/usr/share/man/man5/ cp -a debian/tmp/usr/share/man/man5/sam.5 debian/libhts-dev/usr/share/man/man5/ cp -a debian/tmp/usr/share/man/man5/vcf.5 debian/libhts-dev/usr/share/man/man5/ install -d debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp -a debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ install -d debian/htslib-test//usr/share/htslib-test cp -a ./test/aux\#aux_java.cram debian/htslib-test//usr/share/htslib-test/ cp -a ./test/auxf\#values.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/auxf.fa debian/htslib-test//usr/share/htslib-test/ cp -a ./test/auxf.fa.fai debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c1\#bounds.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c1\#clip.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c1\#noseq.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c1\#pad1.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c1\#pad2.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c1\#pad3.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c1\#unknown.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c1.fa debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c1.fa.fai debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c2\#pad.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c2.fa debian/htslib-test//usr/share/htslib-test/ cp -a ./test/c2.fa.fai debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#1.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#2.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#5.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#5b.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#5b_java.cram debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#large_seq.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#supp.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#tag_depadded.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#tag_padded.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#unmap.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#unmap1.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce\#unmap2.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce.fa debian/htslib-test//usr/share/htslib-test/ cp -a ./test/ce.fa.fai debian/htslib-test//usr/share/htslib-test/ cp -a ./test/compare_sam.pl debian/htslib-test//usr/share/htslib-test/ cp -a ./test/cross_validate.sh debian/htslib-test//usr/share/htslib-test/ cp -a ./test/faidx.fa debian/htslib-test//usr/share/htslib-test/ cp -a ./test/fieldarith.c debian/htslib-test//usr/share/htslib-test/ cp -a ./test/fieldarith.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/formatcols.vcf debian/htslib-test//usr/share/htslib-test/ cp -a ./test/hfile.c debian/htslib-test//usr/share/htslib-test/ cp -a ./test/noroundtrip-out.vcf debian/htslib-test//usr/share/htslib-test/ cp -a ./test/noroundtrip.vcf debian/htslib-test//usr/share/htslib-test/ cp -a ./test/sam.c debian/htslib-test//usr/share/htslib-test/ cp -a ./test/test-regidx.c debian/htslib-test//usr/share/htslib-test/ cp -a ./test/test-vcf-api.c debian/htslib-test//usr/share/htslib-test/ cp -a ./test/test-vcf-api.out debian/htslib-test//usr/share/htslib-test/ cp -a ./test/test-vcf-hdr-in.vcf debian/htslib-test//usr/share/htslib-test/ cp -a ./test/test-vcf-hdr.out debian/htslib-test//usr/share/htslib-test/ cp -a ./test/test-vcf-sweep.c debian/htslib-test//usr/share/htslib-test/ cp -a ./test/test-vcf-sweep.out debian/htslib-test//usr/share/htslib-test/ cp -a ./test/test.pl debian/htslib-test//usr/share/htslib-test/ cp -a ./test/test_view.c debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#blank.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#large_aux.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#large_aux2.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#large_aux_java.cram debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#minimal.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#pair.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#repeated.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#rg.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#tlen.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#tlen2.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#triplet.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx\#unsorted.sam debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx.fa debian/htslib-test//usr/share/htslib-test/ cp -a ./test/xx.fa.fai debian/htslib-test//usr/share/htslib-test/ install -d debian/tabix/usr/bin cp -a ./tabix debian/tabix/usr/bin/ cp -a ./bgzip debian/tabix/usr/bin/ dh_installdocs -O--parallel install -g 0 -o 0 -d debian/libhts1/usr/share/doc/libhts1 install -g 0 -o 0 -m 644 -p debian/copyright debian/libhts1/usr/share/doc/libhts1/copyright install -g 0 -o 0 -d debian/libhts-dev/usr/share/doc/libhts-dev install -g 0 -o 0 -m 644 -p debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright install -g 0 -o 0 -d debian/htslib-test/usr/share/doc/htslib-test install -g 0 -o 0 -m 644 -p debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright install -g 0 -o 0 -d debian/tabix/usr/share/doc/tabix install -g 0 -o 0 -m 644 -p debian/copyright debian/tabix/usr/share/doc/tabix/copyright debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs NEWS install -o 0 -g 0 -p -m644 debian/changelog debian/libhts1/usr/share/doc/libhts1/changelog.Debian install -o 0 -g 0 -p -m644 NEWS debian/libhts1/usr/share/doc/libhts1/changelog install -o 0 -g 0 -p -m644 debian/changelog debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -o 0 -g 0 -p -m644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog install -o 0 -g 0 -p -m644 debian/changelog debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian install -o 0 -g 0 -p -m644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -o 0 -g 0 -p -m644 debian/changelog debian/tabix/usr/share/doc/tabix/changelog.Debian install -o 0 -g 0 -p -m644 NEWS debian/tabix/usr/share/doc/tabix/changelog make[1]: Leaving directory '/<>' dh_installman -O--parallel man --recode UTF-8 ./sam\.5 > sam\.5\.new chmod 644 sam.5.new mv -f sam.5.new sam.5 man --recode UTF-8 ./vcf\.5 > vcf\.5\.new chmod 644 vcf.5.new mv -f vcf.5.new vcf.5 man --recode UTF-8 ./faidx\.5 > faidx\.5\.new chmod 644 faidx.5.new mv -f faidx.5.new faidx.5 install -d debian/tabix/usr/share/man/man1/ install -p -m644 tabix.1 debian/tabix/usr/share/man/man1/tabix.1 man --recode UTF-8 ./tabix\.1 > tabix\.1\.new chmod 644 tabix.1.new mv -f tabix.1.new tabix.1 dh_lintian -O--parallel install -d debian/libhts1/usr/share/lintian/overrides install -p -m644 debian/libhts1.lintian-overrides debian/libhts1/usr/share/lintian/overrides/libhts1 install -d debian/tabix/usr/share/lintian/overrides install -p -m644 debian/tabix.lintian-overrides debian/tabix/usr/share/lintian/overrides/tabix dh_perl -O--parallel (grep -s -v perl:Depends debian/htslib-test.substvars; echo perl:Depends=perl) > debian/htslib-test.substvars.new mv debian/htslib-test.substvars.new debian/htslib-test.substvars dh_link -O--parallel rm -f debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1 ln -sf libhts.so.1.3.1-1\~bpo8\+1 debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1 rm -f debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so ln -sf libhts.so.1.3.1-1\~bpo8\+1 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz ln -sf tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz dh_compress -O--parallel cd debian/libhts1 chmod a-x usr/share/doc/libhts1/changelog.Debian usr/share/doc/libhts1/changelog gzip -9nf usr/share/doc/libhts1/changelog.Debian usr/share/doc/libhts1/changelog cd '/<>' cd debian/libhts-dev chmod a-x usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man5/faidx.5 usr/share/doc/libhts-dev/changelog.Debian usr/share/doc/libhts-dev/changelog gzip -9nf usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man5/faidx.5 usr/share/doc/libhts-dev/changelog.Debian usr/share/doc/libhts-dev/changelog cd '/<>' cd debian/htslib-test chmod a-x usr/share/doc/htslib-test/changelog.Debian usr/share/doc/htslib-test/changelog gzip -9nf usr/share/doc/htslib-test/changelog.Debian usr/share/doc/htslib-test/changelog cd '/<>' cd debian/tabix chmod a-x usr/share/man/man1/tabix.1 usr/share/doc/tabix/changelog.Debian usr/share/doc/tabix/changelog gzip -9nf usr/share/man/man1/tabix.1 usr/share/doc/tabix/changelog.Debian usr/share/doc/tabix/changelog cd '/<>' dh_fixperms -O--parallel find debian/libhts1 -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libhts1 ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts1/usr/share/doc -type f ! -regex 'debian/libhts1/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts1/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/libhts1/usr/share/man debian/libhts1/usr/man/ debian/libhts1/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts1 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts1/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts1/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts1 -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts1/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/libhts1/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/libhts1/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libhts1/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts-dev -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libhts-dev ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts-dev/usr/share/doc -type f ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts-dev/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/libhts-dev/usr/share/man debian/libhts-dev/usr/man/ debian/libhts-dev/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts-dev -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts-dev/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts-dev/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts-dev -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/libhts-dev/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/libhts-dev/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/libhts-dev/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w find debian/htslib-test -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/htslib-test ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/htslib-test/usr/share/doc -type f ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/htslib-test/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/htslib-test/usr/share/man debian/htslib-test/usr/man/ debian/htslib-test/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/htslib-test -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/htslib-test/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/htslib-test/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/htslib-test -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/htslib-test/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/htslib-test/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/htslib-test/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w find debian/tabix -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/tabix ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tabix/usr/share/doc -type f ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/tabix/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/tabix/usr/share/man debian/tabix/usr/man/ debian/tabix/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/tabix -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/tabix/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/tabix/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/tabix -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/tabix/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/tabix/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/tabix/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x find debian/tabix/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w find debian/tabix/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 644 dh_strip -O--parallel strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1\~bpo8\+1 strip --strip-debug debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.a strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix dh_makeshlibs -O--parallel rm -f debian/libhts1/DEBIAN/shlibs install -d debian/libhts1/DEBIAN echo 'libhts 1 libhts1' >>debian/libhts1/DEBIAN/shlibs echo "# Automatically added by dh_makeshlibs">> debian/libhts1.postinst.debhelper sed "" /usr/share/debhelper/autoscripts/postinst-makeshlibs >> debian/libhts1.postinst.debhelper echo '# End automatically added section' >> debian/libhts1.postinst.debhelper echo "# Automatically added by dh_makeshlibs">> debian/libhts1.postrm.debhelper sed "" /usr/share/debhelper/autoscripts/postrm-makeshlibs >> debian/libhts1.postrm.debhelper echo '# End automatically added section' >> debian/libhts1.postrm.debhelper chmod 644 debian/libhts1/DEBIAN/shlibs chown 0:0 debian/libhts1/DEBIAN/shlibs dpkg-gensymbols -plibhts1 -Idebian/libhts1.symbols -Pdebian/libhts1 "-edebian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1~bpo8+1\ " (grep -s -v misc:Pre-Depends debian/libhts1.substvars; echo misc:Pre-Depends=multiarch-support) > debian/libhts1.substvars.new mv debian/libhts1.substvars.new debian/libhts1.substvars rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/htslib-test/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -O--parallel dpkg-shlibdeps -Tdebian/libhts1.substvars debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1\~bpo8\+1 install -o 0 -g 0 -d debian/libhts-dev/DEBIAN install -o 0 -g 0 -d debian/htslib-test/DEBIAN install -o 0 -g 0 -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/tabix dh_installdeb -O--parallel printf '#!/bin/sh set -e ' > debian/libhts1/DEBIAN/postinst cat debian/libhts1.postinst.debhelper >> debian/libhts1/DEBIAN/postinst chown 0:0 debian/libhts1/DEBIAN/postinst chmod 755 debian/libhts1/DEBIAN/postinst printf '#!/bin/sh set -e ' > debian/libhts1/DEBIAN/postrm cat debian/libhts1.postrm.debhelper >> debian/libhts1/DEBIAN/postrm chown 0:0 debian/libhts1/DEBIAN/postrm chmod 755 debian/libhts1/DEBIAN/postrm dh_gencontrol -O--parallel echo misc:Depends= >> debian/libhts1.substvars dpkg-gencontrol -plibhts1 -ldebian/changelog -Tdebian/libhts1.substvars -Pdebian/libhts1 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/libhts1/DEBIAN/control chown 0:0 debian/libhts1/DEBIAN/control echo misc:Depends= >> debian/libhts-dev.substvars dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -Pdebian/libhts-dev dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/libhts-dev/DEBIAN/control chown 0:0 debian/libhts-dev/DEBIAN/control echo misc:Depends= >> debian/htslib-test.substvars dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -Pdebian/htslib-test dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/htslib-test/DEBIAN/control chown 0:0 debian/htslib-test/DEBIAN/control echo misc:Depends= >> debian/tabix.substvars dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/tabix/DEBIAN/control chown 0:0 debian/tabix/DEBIAN/control dh_md5sums -O--parallel (cd debian/libhts1 >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/libhts1/DEBIAN/md5sums chown 0:0 debian/libhts1/DEBIAN/md5sums (cd debian/libhts-dev >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/libhts-dev/DEBIAN/md5sums chown 0:0 debian/libhts-dev/DEBIAN/md5sums (cd debian/htslib-test >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/htslib-test/DEBIAN/md5sums chown 0:0 debian/htslib-test/DEBIAN/md5sums (cd debian/tabix >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/tabix/DEBIAN/md5sums chown 0:0 debian/tabix/DEBIAN/md5sums dh_builddeb -O--parallel dpkg-deb --build debian/libhts1 .. dpkg-deb --build debian/libhts-dev .. dpkg-deb: building package `libhts-dev' in `../libhts-dev_1.3.1-1~bpo8+1_amd64.deb'. dpkg-deb: building package `libhts1' in `../libhts1_1.3.1-1~bpo8+1_amd64.deb'. dpkg-deb --build debian/htslib-test .. dpkg-deb: building package `htslib-test' in `../htslib-test_1.3.1-1~bpo8+1_all.deb'. dpkg-deb --build debian/tabix .. dpkg-deb: building package `tabix' in `../tabix_1.3.1-1~bpo8+1_amd64.deb'. dpkg-genchanges -v1.3-1~bpo8+1 >../htslib_1.3.1-1~bpo8+1_amd64.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build htslib-1.3.1 dpkg-source: info: using options from htslib-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$ dpkg-buildpackage: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 20160508-1403 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ htslib_1.3.1-1~bpo8+1_amd64.changes: ------------------------------------ Format: 1.8 Date: Sun, 08 May 2016 21:28:33 +0900 Source: htslib Binary: libhts1 libhts-dev htslib-test tabix Architecture: source amd64 all Version: 1.3.1-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Charles Plessy Description: htslib-test - Test data for HTSlib libhts-dev - Development files for the HTSlib libhts1 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Changes: htslib (1.3.1-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. . htslib (1.3.1-1) unstable; urgency=medium . 36bf59a Merge tag '1.3.1' into debian/unstable 559f8b4 Remove add_largefile.patch, applied upstream. 7163afb Update symbols file. Missing _vcf_parse_format at Base and fai_read at Base. c2c1df3 Build-depend on libcurl4-gnutls-dev and libssl-dev. 3b219b8 Enable libcurl. 9101580 Conforms to the Policy version 3.9.8. . htslib (1.3-2) unstable; urgency=medium . * Team upload . [ Steffen Moeller and Jon Ison ] * Introduction of EDAM annotation . [ Sascha Steinbiss ] * Include upstream patch for large file support * Run configure as part of the build Checksums-Sha1: d25e7c489e4ab1430903ab9689d7c8fd4be17211 1297 htslib_1.3.1-1~bpo8+1.dsc 9ca088e4868e2103863621526e9dacece7b3a8df 10184 htslib_1.3.1-1~bpo8+1.debian.tar.xz 310d59963cc32a3e1a7f7d0ed605d9b72b86ee10 258274 libhts1_1.3.1-1~bpo8+1_amd64.deb 239456eae30f7ebd0b51baa4064a5a060c16f136 314518 libhts-dev_1.3.1-1~bpo8+1_amd64.deb 6859a47faadfc5ecaf933cd8135e2bd21d6afe20 541970 htslib-test_1.3.1-1~bpo8+1_all.deb f6a9ef47c4c40ae11c3c4b71953c8e9a03d4b696 252512 tabix_1.3.1-1~bpo8+1_amd64.deb Checksums-Sha256: ef1ef59e9c7ceded58cece6aa038e4f8d3122471faa8e4040e2e62faba5b3cd7 1297 htslib_1.3.1-1~bpo8+1.dsc 0d9042864ed450aced897c28619b41be0f59a01bcd2e54fc81de469c768c97ea 10184 htslib_1.3.1-1~bpo8+1.debian.tar.xz 7e287505056ce63092ebb7e98692cd422d64cdc4a94125a3225d59830f534d02 258274 libhts1_1.3.1-1~bpo8+1_amd64.deb 99c691e26162b294885ac8adfa3faac20f67e1610b2d9ba950698534d906875f 314518 libhts-dev_1.3.1-1~bpo8+1_amd64.deb 89eaa484d3c2a65f4218b6b3ff8ef9fe28516c9cb66fef6da5de95e3cf46a008 541970 htslib-test_1.3.1-1~bpo8+1_all.deb 2400ead2311b752517966823a4305321604a31300c64139157ce537eeadc04b4 252512 tabix_1.3.1-1~bpo8+1_amd64.deb Files: 20fdd8e86fb45c40c948d18be2ab2705 1297 science optional htslib_1.3.1-1~bpo8+1.dsc 4e640df2495ac0db5f05185adf0503de 10184 science optional htslib_1.3.1-1~bpo8+1.debian.tar.xz e775e6f537ddc42dd5a98c44e6cbb34d 258274 libs optional libhts1_1.3.1-1~bpo8+1_amd64.deb f0328cdee36237653c3c6ffebdd6f49d 314518 libdevel optional libhts-dev_1.3.1-1~bpo8+1_amd64.deb 235bb571c18167415039e985724bc871 541970 science optional htslib-test_1.3.1-1~bpo8+1_all.deb 5d8de035b31a8e2ab6e915508f8bf1c9 252512 science optional tabix_1.3.1-1~bpo8+1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libhts1_1.3.1-1~bpo8+1_amd64.deb -------------------------------- new debian package, version 2.0. size 258274 bytes: control archive=5305 bytes. 1041 bytes, 22 lines control 365 bytes, 5 lines md5sums 135 bytes, 7 lines * postinst #!/bin/sh 132 bytes, 7 lines * postrm #!/bin/sh 17 bytes, 1 lines shlibs 16657 bytes, 637 lines symbols Package: libhts1 Source: htslib Version: 1.3.1-1~bpo8+1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 685 Pre-Depends: multiarch-support Depends: libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), libssl1.0.0 (>= 1.0.0), zlib1g (>= 1:1.2.0.2) Section: libs Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: C library for high-throughput sequencing data formats HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ?csi? (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. drwxr-xr-x root/root 0 2016-05-08 14:03 ./ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/libhts.so.1 -> libhts.so.1.3.1-1~bpo8+1 -rw-r--r-- root/root 633152 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1~bpo8+1 drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/libhts1/ -rw-r--r-- root/root 1561 2016-05-08 13:48 ./usr/share/doc/libhts1/changelog.Debian.gz -rw-r--r-- root/root 2350 2016-04-22 01:45 ./usr/share/doc/libhts1/changelog.gz -rw-r--r-- root/root 5776 2016-05-08 13:48 ./usr/share/doc/libhts1/copyright drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/lintian/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 105 2016-05-08 13:48 ./usr/share/lintian/overrides/libhts1 libhts-dev_1.3.1-1~bpo8+1_amd64.deb ----------------------------------- new debian package, version 2.0. size 314518 bytes: control archive=1758 bytes. 1037 bytes, 24 lines control 1924 bytes, 30 lines md5sums Package: libhts-dev Source: htslib Version: 1.3.1-1~bpo8+1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1176 Depends: libhts1 (= 1.3.1-1~bpo8+1) Section: libdevel Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: Development files for the HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ?csi? (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains development files for the HTSlib: headers, static library, manual pages, etc. drwxr-xr-x root/root 0 2016-05-08 14:03 ./ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/include/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/include/htslib/ -rw-r--r-- root/root 11423 2016-04-22 01:45 ./usr/include/htslib/bgzf.h -rw-r--r-- root/root 14648 2016-04-22 01:45 ./usr/include/htslib/cram.h -rw-r--r-- root/root 4562 2016-04-22 01:45 ./usr/include/htslib/faidx.h -rw-r--r-- root/root 7111 2016-04-22 01:45 ./usr/include/htslib/hfile.h -rw-r--r-- root/root 21950 2016-04-22 01:45 ./usr/include/htslib/hts.h -rw-r--r-- root/root 2451 2016-04-22 01:45 ./usr/include/htslib/hts_defs.h -rw-r--r-- root/root 4195 2016-04-22 01:45 ./usr/include/htslib/kbitset.h -rw-r--r-- root/root 2716 2016-04-22 01:45 ./usr/include/htslib/kfunc.h -rw-r--r-- root/root 21540 2016-04-22 01:45 ./usr/include/htslib/khash.h -rw-r--r-- root/root 3990 2016-04-22 01:45 ./usr/include/htslib/khash_str2int.h -rw-r--r-- root/root 5086 2016-04-22 01:45 ./usr/include/htslib/klist.h -rw-r--r-- root/root 2828 2016-04-22 01:45 ./usr/include/htslib/knetfile.h -rw-r--r-- root/root 8900 2016-04-22 01:45 ./usr/include/htslib/kseq.h -rw-r--r-- root/root 10125 2016-04-22 01:45 ./usr/include/htslib/ksort.h -rw-r--r-- root/root 7071 2016-04-22 01:45 ./usr/include/htslib/kstring.h -rw-r--r-- root/root 5798 2016-04-22 01:45 ./usr/include/htslib/regidx.h -rw-r--r-- root/root 17089 2016-04-22 01:45 ./usr/include/htslib/sam.h -rw-r--r-- root/root 12666 2016-04-22 01:45 ./usr/include/htslib/synced_bcf_reader.h -rw-r--r-- root/root 2910 2016-04-22 01:45 ./usr/include/htslib/tbx.h -rw-r--r-- root/root 39884 2016-04-22 01:45 ./usr/include/htslib/vcf.h -rw-r--r-- root/root 1586 2016-04-22 01:45 ./usr/include/htslib/vcf_sweep.h -rw-r--r-- root/root 4659 2016-04-22 01:45 ./usr/include/htslib/vcfutils.h drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 921556 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/libhts.a lrwxrwxrwx root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/libhts.so -> libhts.so.1.3.1-1~bpo8+1 drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 279 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 1561 2016-05-08 13:48 ./usr/share/doc/libhts-dev/changelog.Debian.gz -rw-r--r-- root/root 2350 2016-04-22 01:45 ./usr/share/doc/libhts-dev/changelog.gz -rw-r--r-- root/root 5776 2016-05-08 13:48 ./usr/share/doc/libhts-dev/copyright drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/man/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/man/man5/ -rw-r--r-- root/root 2080 2016-05-08 14:03 ./usr/share/man/man5/faidx.5.gz -rw-r--r-- root/root 1535 2016-05-08 14:03 ./usr/share/man/man5/sam.5.gz -rw-r--r-- root/root 1854 2016-05-08 14:03 ./usr/share/man/man5/vcf.5.gz htslib-test_1.3.1-1~bpo8+1_all.deb ---------------------------------- new debian package, version 2.0. size 541970 bytes: control archive=2709 bytes. 944 bytes, 22 lines control 4585 bytes, 66 lines md5sums Package: htslib-test Source: htslib Version: 1.3.1-1~bpo8+1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 4180 Depends: perl Section: science Priority: optional Homepage: https://github.com/samtools/htslib Description: Test data for HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ?csi? (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains test files and scripts for the HTSlib. drwxr-xr-x root/root 0 2016-05-08 14:03 ./ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/htslib-test/ -rw-r--r-- root/root 1561 2016-05-08 13:48 ./usr/share/doc/htslib-test/changelog.Debian.gz -rw-r--r-- root/root 2350 2016-04-22 01:45 ./usr/share/doc/htslib-test/changelog.gz -rw-r--r-- root/root 5776 2016-05-08 13:48 ./usr/share/doc/htslib-test/copyright drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/htslib-test/ -rw-r--r-- root/root 3774 2016-04-22 01:45 ./usr/share/htslib-test/aux#aux_java.cram -rw-r--r-- root/root 727 2016-04-22 01:45 ./usr/share/htslib-test/auxf#values.sam -rw-r--r-- root/root 29 2016-04-22 01:45 ./usr/share/htslib-test/auxf.fa -rw-r--r-- root/root 18 2016-04-22 01:45 ./usr/share/htslib-test/auxf.fa.fai -rw-r--r-- root/root 148 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./usr/share/htslib-test/ce.fa.fai -rwxr-xr-x root/root 5562 2016-04-22 01:45 ./usr/share/htslib-test/compare_sam.pl -rwxr-xr-x root/root 3204 2016-04-22 01:45 ./usr/share/htslib-test/cross_validate.sh -rw-r--r-- root/root 231 2016-04-22 01:45 ./usr/share/htslib-test/faidx.fa -rw-r--r-- root/root 2430 2016-04-22 01:45 ./usr/share/htslib-test/fieldarith.c -rw-r--r-- root/root 916 2016-04-22 01:45 ./usr/share/htslib-test/fieldarith.sam -rw-r--r-- root/root 240 2016-04-22 01:45 ./usr/share/htslib-test/formatcols.vcf -rw-r--r-- root/root 6852 2016-04-22 01:45 ./usr/share/htslib-test/hfile.c -rw-r--r-- root/root 325 2016-04-22 01:45 ./usr/share/htslib-test/noroundtrip-out.vcf -rw-r--r-- root/root 271 2016-04-22 01:45 ./usr/share/htslib-test/noroundtrip.vcf -rw-r--r-- root/root 7440 2016-04-22 01:45 ./usr/share/htslib-test/sam.c -rw-r--r-- root/root 4292 2016-04-22 01:45 ./usr/share/htslib-test/test-regidx.c -rw-r--r-- root/root 10142 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-api.c -rw-r--r-- root/root 1936 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-api.out -rw-r--r-- root/root 2024 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-hdr-in.vcf -rw-r--r-- root/root 1349 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-hdr.out -rw-r--r-- root/root 3823 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-sweep.c -rw-r--r-- root/root 92 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-sweep.out -rwxr-xr-x root/root 9964 2016-04-22 01:45 ./usr/share/htslib-test/test.pl -rw-r--r-- root/root 6405 2016-04-22 01:45 ./usr/share/htslib-test/test_view.c -rw-r--r-- root/root 0 2016-04-22 01:45 ./usr/share/htslib-test/xx#blank.sam -rw-r--r-- root/root 905485 2016-04-22 01:45 ./usr/share/htslib-test/xx#large_aux.sam -rw-r--r-- root/root 651 2016-04-22 01:45 ./usr/share/htslib-test/xx#large_aux2.sam -rw-r--r-- root/root 22668 2016-04-22 01:45 ./usr/share/htslib-test/xx#large_aux_java.cram -rw-r--r-- root/root 254 2016-04-22 01:45 ./usr/share/htslib-test/xx#minimal.sam -rw-r--r-- root/root 304 2016-04-22 01:45 ./usr/share/htslib-test/xx#pair.sam -rw-r--r-- root/root 298 2016-04-22 01:45 ./usr/share/htslib-test/xx#repeated.sam -rw-r--r-- root/root 517 2016-04-22 01:45 ./usr/share/htslib-test/xx#rg.sam -rw-r--r-- root/root 1028 2016-04-22 01:45 ./usr/share/htslib-test/xx#tlen.sam -rw-r--r-- root/root 1096 2016-04-22 01:45 ./usr/share/htslib-test/xx#tlen2.sam -rw-r--r-- root/root 267 2016-04-22 01:45 ./usr/share/htslib-test/xx#triplet.sam -rw-r--r-- root/root 320 2016-04-22 01:45 ./usr/share/htslib-test/xx#unsorted.sam -rw-r--r-- root/root 51 2016-04-22 01:45 ./usr/share/htslib-test/xx.fa -rw-r--r-- root/root 29 2016-04-22 01:45 ./usr/share/htslib-test/xx.fa.fai tabix_1.3.1-1~bpo8+1_amd64.deb ------------------------------ new debian package, version 2.0. size 252512 bytes: control archive=1028 bytes. 908 bytes, 19 lines control 433 bytes, 7 lines md5sums Package: tabix Source: htslib Version: 1.3.1-1~bpo8+1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1016 Depends: libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), libssl1.0.0 (>= 1.0.0), zlib1g (>= 1:1.2.0.2) Section: science Priority: optional Homepage: https://github.com/samtools/htslib Description: generic indexer for TAB-delimited genome position files Tabix indexes files where some columns indicate sequence coordinates: name (usually a chromosome), start and stop. The input data file must be position sorted and compressed by bgzip (provided in this package), which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines by chromosomal coordinates. Fast data retrieval also works over network if an URI is given as a file name. . This version of tabix is built from the HTSlib source. drwxr-xr-x root/root 0 2016-05-08 14:03 ./ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/bin/ -rwxr-xr-x root/root 445712 2016-05-08 14:03 ./usr/bin/bgzip -rwxr-xr-x root/root 536008 2016-05-08 14:03 ./usr/bin/tabix drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/tabix/ -rw-r--r-- root/root 1561 2016-05-08 13:48 ./usr/share/doc/tabix/changelog.Debian.gz -rw-r--r-- root/root 2350 2016-04-22 01:45 ./usr/share/doc/tabix/changelog.gz -rw-r--r-- root/root 5776 2016-05-08 13:48 ./usr/share/doc/tabix/copyright drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/lintian/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 129 2015-09-07 16:20 ./usr/share/lintian/overrides/tabix drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/man/ drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2016-05-08 14:03 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz -rw-r--r-- root/root 2797 2016-05-08 14:03 ./usr/share/man/man1/tabix.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 50084 Build-Time: 314 Distribution: jessie-backports Host Architecture: amd64 Install-Time: 198 Job: /home/afif/??????/debian/med/htslib/htslib_1.3.1-1~bpo8+1.dsc Machine Architecture: amd64 Package: htslib Package-Time: 539 Source-Version: 1.3.1-1~bpo8+1 Space: 50084 Status: successful Version: 1.3.1-1~bpo8+1 -------------------------------------------------------------------------------- Finished at 20160508-1403 Build needed 00:08:59, 50084k disc space From ftpmaster at ftp-master.debian.org Sun May 8 21:52:32 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 21:52:32 +0000 Subject: [Debian-med-packaging] htslib_1.3.1-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 21:28:33 +0900 Source: htslib Binary: libhts1 libhts-dev htslib-test tabix Architecture: source amd64 all Version: 1.3.1-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Charles Plessy Description: htslib-test - Test data for HTSlib libhts-dev - Development files for the HTSlib libhts1 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Changes: htslib (1.3.1-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. . htslib (1.3.1-1) unstable; urgency=medium . 36bf59a Merge tag '1.3.1' into debian/unstable 559f8b4 Remove add_largefile.patch, applied upstream. 7163afb Update symbols file. Missing _vcf_parse_format at Base and fai_read at Base. c2c1df3 Build-depend on libcurl4-gnutls-dev and libssl-dev. 3b219b8 Enable libcurl. 9101580 Conforms to the Policy version 3.9.8. . htslib (1.3-2) unstable; urgency=medium . * Team upload . [ Steffen Moeller and Jon Ison ] * Introduction of EDAM annotation . 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From ftpmaster at ftp-master.debian.org Sun May 8 23:01:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 23:01:04 +0000 Subject: [Debian-med-packaging] Processing of dcmtk_3.6.1~20160216-1_amd64.changes Message-ID: dcmtk_3.6.1~20160216-1_amd64.changes uploaded successfully to ftp-master.debian.org along with the files: dcmtk_3.6.1~20160216-1.dsc dcmtk_3.6.1~20160216.orig.tar.gz dcmtk_3.6.1~20160216-1.debian.tar.xz dcmtk-dbgsym_3.6.1~20160216-1_amd64.deb dcmtk-doc_3.6.1~20160216-1_all.deb dcmtk_3.6.1~20160216-1_amd64.deb libdcmtk-dev_3.6.1~20160216-1_amd64.deb libdcmtk8-dbgsym_3.6.1~20160216-1_amd64.deb libdcmtk8_3.6.1~20160216-1_amd64.deb Greetings, Your Debian queue daemon (running on host coccia.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 23:04:21 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 23:04:21 +0000 Subject: [Debian-med-packaging] Processing of dcmtk_3.6.1~20160216-1_amd64.changes Message-ID: dcmtk_3.6.1~20160216-1_amd64.changes uploaded successfully to localhost along with the files: dcmtk_3.6.1~20160216-1.dsc dcmtk_3.6.1~20160216.orig.tar.gz dcmtk_3.6.1~20160216-1.debian.tar.xz dcmtk-dbgsym_3.6.1~20160216-1_amd64.deb dcmtk-doc_3.6.1~20160216-1_all.deb dcmtk_3.6.1~20160216-1_amd64.deb libdcmtk-dev_3.6.1~20160216-1_amd64.deb libdcmtk8-dbgsym_3.6.1~20160216-1_amd64.deb libdcmtk8_3.6.1~20160216-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 8 23:20:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 08 May 2016 23:20:17 +0000 Subject: [Debian-med-packaging] dcmtk_3.6.1~20160216-1_amd64.changes is NEW Message-ID: binary:libdcmtk8 is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ixi44 at gmx.de Mon May 9 03:33:21 2016 From: ixi44 at gmx.de (DHL World Wide Delivery) Date: Mon, 9 May 2016 04:33:21 +0100 Subject: [Debian-med-packaging] New Parcel Message-ID: <0LqylH-1bVOGQ2SHL-00eZ3D@mail.gmx.com> - This mail is in HTML. Some elements may be ommited in plain text. - Dear debian-med-packaging at lists.alioth.debian.org, A parcel arrived our head office since 5/2/2016 and couldn't be delivered due to incorrect address. Please click on the URL to verify ownership details for proper delivery https://en.tracking.dhl.com/Parcel/ConfirmAddress/tracking?Emailid=admin at DHLdomain.com Thanks. DHL Customer Service 2016 -------------- next part -------------- An HTML attachment was scrubbed... URL: From plessy at debian.org Mon May 9 04:29:09 2016 From: plessy at debian.org (Charles Plessy) Date: Mon, 9 May 2016 13:29:09 +0900 Subject: [Debian-med-packaging] htslib_1.3.1-1~bpo8+1_source.changes REJECTED In-Reply-To: <572FAC8B.6070307@ghraoui.name> References: <572FAC8B.6070307@ghraoui.name> Message-ID: <20160509042908.GD19224@falafel.plessy.net> Le Sun, May 08, 2016 at 02:15:55PM -0700, Afif Elghraoui a ?crit : > > I guess you ran out of time for the day to take care of this. I went > ahead and made the build and binary upload. > > Knowing you like to keep track of the build logs, please find them > attached. :) Thanks Afif :) Indeed, one reason why I uploaded source instead of binary was to ensure the build logs would be stored automagically on buildd.debian.org. Some time ago I used to send the build logs to logs at buildd.debian.org, but since there are no sanity checks, I stopped doing this after making a mistake or two... Have a nice day, -- Charles From ftpmaster at ftp-master.debian.org Mon May 9 06:31:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 09 May 2016 06:31:07 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-rsamtools_1.24.0-1_amd64.changes Message-ID: r-bioc-rsamtools_1.24.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-rsamtools_1.24.0-1.dsc r-bioc-rsamtools_1.24.0.orig.tar.gz r-bioc-rsamtools_1.24.0-1.debian.tar.xz r-bioc-rsamtools-dbgsym_1.24.0-1_amd64.deb r-bioc-rsamtools_1.24.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 9 06:33:53 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 09 May 2016 06:33:53 +0000 Subject: [Debian-med-packaging] r-bioc-rsamtools_1.24.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 21:06:24 +0200 Source: r-bioc-rsamtools Binary: r-bioc-rsamtools Architecture: source amd64 Version: 1.24.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i Changes: r-bioc-rsamtools (1.24.0-1) unstable; urgency=medium . * New upstream version * Fix versioned Dependencies Checksums-Sha1: b87493c0a14a31c628dfd9482e3207d7987cb330 2232 r-bioc-rsamtools_1.24.0-1.dsc d17c0f04b8c2ec5f2599eb25da3227ae8ad6df70 2985011 r-bioc-rsamtools_1.24.0.orig.tar.gz 32762b152db8c85d88ff54be7a2e6792ca5f7afc 6892 r-bioc-rsamtools_1.24.0-1.debian.tar.xz fe9d705d4bd8f7ee245120cf0362943a64627815 788152 r-bioc-rsamtools-dbgsym_1.24.0-1_amd64.deb c5f437765228734dc223bfa04de4eabddd3034ee 3239680 r-bioc-rsamtools_1.24.0-1_amd64.deb Checksums-Sha256: 91b7d5d16fbcd0e0c57ac452123debd8efafed03a6e1001db168f2cac891cee1 2232 r-bioc-rsamtools_1.24.0-1.dsc 8be9a332fbe5c300ea8e54c598510d4d161eaa3d4f1183bfa216cdcb90ce0d70 2985011 r-bioc-rsamtools_1.24.0.orig.tar.gz 0735f10382d4418a5dcec1651bb1d56bd939173ac0fa73a7f25706a942814a1e 6892 r-bioc-rsamtools_1.24.0-1.debian.tar.xz 73c6b89d4542ab2e92d22fba5fbbcd5af4094df9f148966c8ab6d4788d46ccea 788152 r-bioc-rsamtools-dbgsym_1.24.0-1_amd64.deb 9849a9a967d6c9e123959e4a261337315c5546caece53d52b67a03453fb4df06 3239680 r-bioc-rsamtools_1.24.0-1_amd64.deb Files: fefca573cabfcb75c4c6ba152f49f8bd 2232 gnu-r optional r-bioc-rsamtools_1.24.0-1.dsc a640f51170f24fa02bc429e5bb7b622e 2985011 gnu-r optional r-bioc-rsamtools_1.24.0.orig.tar.gz 4bcc922c1128fd17aada497583ba4abe 6892 gnu-r optional r-bioc-rsamtools_1.24.0-1.debian.tar.xz 4feec3e1ed34da3122abf4c246fb671c 788152 debug extra r-bioc-rsamtools-dbgsym_1.24.0-1_amd64.deb adc0aa54c980b588b5bfedd44d809640 3239680 gnu-r optional r-bioc-rsamtools_1.24.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMC2+AAoJEFeKBJTRxkbR7KYP/36XKhdCjdbNMzrqvsM+XeHj QvZlm3/yDqDQjDk0wUNqIWO3tbUistyUq+IqbrMC9SewUQ8P86y20fregq2dZlJp tdW3eFr3r+9KqPKF1a6e8tOjdeJIXJtWtNgp9K2nn24e9XBcxAmi0u6WyVArIJlT ykk0aSEc73n1Z3EHAk0SQj9tZ/jvzwJVoXPczrJyqOUlBM/7/Gy71GZaJyy8+b1h q4pibl94Py6o3jV/p4P1LbvkOAd584/9wuk79/BPOiLt8TFZIbzp3AO3m9Enr0/b NzzUGkaN2Ao5tyE5jhbkBmspLQKjCnI+aY3uBPp9ZMP+FA1UQnfhVzBr8qKdNkqu OWtTWnbZjiuEvtUU9CoOy835FCI3jMvWivOsplAeE4+ai3kMM/sjgZUMyTfqCsVl J/1eOs0NqW9gnC7ELB9f+CFU8HGp2VB7ju4peM+mOm/fQX9ThR/xUxmfnMZJD+Ni hqeQpNME1ICBmZ6lZPjk1FSvGueRtwZP1C6az5vQ0pdTyXovGY4Ko/r2tSWlWgQH JuxXtyIPTvAsTYs15+26odOyE1nCuHRJz2xbsjsOf8HsuKoz42vKOaXDdnTyoVeT y17hCrXTuoTriS1D9NEKlOL1gfq08ahE4mkmPA9fYMFcM9CAlbKE9s774uG2hRbi Of4xqszTfIl3yn6Z0+Qm =ossV -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 9 06:51:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 09 May 2016 06:51:11 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-altcdfenvs_2.34.0-1_amd64.changes Message-ID: r-bioc-altcdfenvs_2.34.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-altcdfenvs_2.34.0-1.dsc r-bioc-altcdfenvs_2.34.0.orig.tar.gz r-bioc-altcdfenvs_2.34.0-1.debian.tar.xz r-bioc-altcdfenvs_2.34.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 9 07:05:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 09 May 2016 07:05:13 +0000 Subject: [Debian-med-packaging] r-bioc-altcdfenvs_2.34.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 09 May 2016 08:37:16 +0200 Source: r-bioc-altcdfenvs Binary: r-bioc-altcdfenvs Architecture: source all Version: 1:2.34.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-altcdfenvs - BioConductor alternative CDF environments Changes: r-bioc-altcdfenvs (1:2.34.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 0db0e66f7e432b110662bc3cbc72e03a2cdd5fe8 2183 r-bioc-altcdfenvs_2.34.0-1.dsc 2b7a1fba70c9d166c4a556cbda5804b64900a66a 379423 r-bioc-altcdfenvs_2.34.0.orig.tar.gz 670a494a2daee43ec82f187423fad64a7a938a25 3928 r-bioc-altcdfenvs_2.34.0-1.debian.tar.xz 5463ff1774669a2f600bcb2c6ef57260908f49ae 500448 r-bioc-altcdfenvs_2.34.0-1_all.deb Checksums-Sha256: 08c816a32cbfdf3bbc8b16300ba0fcb2d818bed9687649fa2416d7b861fcd1f3 2183 r-bioc-altcdfenvs_2.34.0-1.dsc 8a600c4b0c937bfab42dd8ea9bfd5b2fe81c0708e8578e2e80a0d155c0c42c01 379423 r-bioc-altcdfenvs_2.34.0.orig.tar.gz 75f31d97e624e81603e89242cf0169523ca93c11f2f8f77cfc9ffffbcab4445d 3928 r-bioc-altcdfenvs_2.34.0-1.debian.tar.xz 024a564134c715b0acb428e43f7b7266e8d4b95eabbb3a3ae9a0e5cbbddd4ade 500448 r-bioc-altcdfenvs_2.34.0-1_all.deb Files: 80300231e13a1fdcd00d633ba1767fdb 2183 gnu-r optional r-bioc-altcdfenvs_2.34.0-1.dsc b2b88d6e2e128e933c26213c00725769 379423 gnu-r optional r-bioc-altcdfenvs_2.34.0.orig.tar.gz e450697e184bfc1bfb9a2c7874aef04a 3928 gnu-r optional r-bioc-altcdfenvs_2.34.0-1.debian.tar.xz 968411de8741687d7429d9fdfe455e09 500448 gnu-r optional r-bioc-altcdfenvs_2.34.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMDLZAAoJEFeKBJTRxkbRYRsP/jJPq54fbJHtDpS7IGBkzHLs r/KdeMlh66OnrhGvkwHQfRA31JKW8B3LXrXUIqvkESGR/kdsmvqAp4MB4NPHdhOl /IpBwlwhfND4vjhUESxbivI+DkQ1QB4sdsna1BLhIB87Bs1vi6dkcC3YILewvb1t 3UdDVYIMS3iPPztKMBPIYKrzfd+lNIXGuh7DNLR+tNqFjc7jUwgXVqdSRMZ3E1Ce JV+j0INCljFaSroifEHbWnHyLpJ4Mipr0sPpA7ujY5Dy7qnEUpklYMzUGEkmvAJh 6qnoIsoOO3j8cPBkTc/CG85S+YxA5u/q9fCl6ya9CxalSAVFpbl9YvwFJY8qtkhq DKmiloCi1l0T0BBx9Jphx+6AIELQOPmq09gVLWFCT1ulU4SRG0dwQqH5Ezp7JErW dFbAAU8Qif1w4yXoYUe0rmqYHOyd67utf1Juw54v8yJ9JFAidqccfviqZmEpx0Cm Q8DOxWS7BCrsUOyytuDsklq2JO+rFwhDPJ5X1gtzCNeUxWBX0IU+MSUORKMMrTM0 5ZT3j8qfrQIjeEI+BOgtpmwR+EbfHdnjCN6VA9bB7R/6Uwezyvgvjuho3omc7LwC xXCdS337fXd0eqIr36TMB0IJCc9XUUvzeyAW4cgsWB9GZxtGskvOZuQbaVrG+7NA 751dIbUvowAbYs/LPz+f =RTdB -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 9 07:36:21 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 09 May 2016 07:36:21 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-genomicalignments_1.8.0-1_amd64.changes Message-ID: r-bioc-genomicalignments_1.8.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-genomicalignments_1.8.0-1.dsc r-bioc-genomicalignments_1.8.0.orig.tar.gz r-bioc-genomicalignments_1.8.0-1.debian.tar.xz r-bioc-genomicalignments-dbgsym_1.8.0-1_amd64.deb r-bioc-genomicalignments_1.8.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 9 07:48:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 09 May 2016 07:48:34 +0000 Subject: [Debian-med-packaging] r-bioc-genomicalignments_1.8.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 09 May 2016 09:24:38 +0200 Source: r-bioc-genomicalignments Binary: r-bioc-genomicalignments Architecture: source amd64 Version: 1.8.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-genomicalignments - BioConductor representation and manipulation of short genomic ali Changes: r-bioc-genomicalignments (1.8.0-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: f2c4a456de4c9f288c3f012e381ab0c92f398f0f 2263 r-bioc-genomicalignments_1.8.0-1.dsc 0bdf81288de49b11dd9f175de206ebdf849797ff 2127649 r-bioc-genomicalignments_1.8.0.orig.tar.gz ee5138168c0c6f44c521d8a0859fb03636b9a746 6644 r-bioc-genomicalignments_1.8.0-1.debian.tar.xz ba416f7bdb301d53f3546f05ef09647cf389dd54 53406 r-bioc-genomicalignments-dbgsym_1.8.0-1_amd64.deb 1738d8b743bc15996f086000463a418494bc339c 1448082 r-bioc-genomicalignments_1.8.0-1_amd64.deb Checksums-Sha256: 2108fe7c478eb3131c3bf298429727b567b6e44df52c2f008e089bca03ce1a5d 2263 r-bioc-genomicalignments_1.8.0-1.dsc b29b189c057f68ca775a07f547a9ccf8caf74e343515fab84e5d35843b7e98f8 2127649 r-bioc-genomicalignments_1.8.0.orig.tar.gz 62d7ac203acdb8fc9d3f936c214ee9c3681e57797269047a44ecbc4833f55594 6644 r-bioc-genomicalignments_1.8.0-1.debian.tar.xz 7e7d34c2ae35663e4d992acba4316a8e99ba8f1ae0085c745260b5107b5f57b6 53406 r-bioc-genomicalignments-dbgsym_1.8.0-1_amd64.deb 2f8236e87473a5f9db1c270cc52dfd2dd2832dbcb0822ca6544471d6ed4a6dbf 1448082 r-bioc-genomicalignments_1.8.0-1_amd64.deb Files: ba163d4a08ff40dcd7d25e87ca6eaaf0 2263 gnu-r optional r-bioc-genomicalignments_1.8.0-1.dsc 76035bb5d2da199c937c6be59f06bdd4 2127649 gnu-r optional r-bioc-genomicalignments_1.8.0.orig.tar.gz a423770a4293a2c0a3bfcd2e8ee60875 6644 gnu-r optional r-bioc-genomicalignments_1.8.0-1.debian.tar.xz ecded98aa9c958b853d7d74933edf782 53406 debug extra r-bioc-genomicalignments-dbgsym_1.8.0-1_amd64.deb 71a1157cd9b33bc16763bc9dc2ec6714 1448082 gnu-r optional r-bioc-genomicalignments_1.8.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMDzOAAoJEFeKBJTRxkbREewQAIZFbAv/S3pznEI+TUinACLe gwslePVvOu7OCfy0TxhDqSP52ErtgJcJKkhUexc2gaJ3JkWxBmNRwXgvR8UvBWNW 8zqcU46RgdJ24omCzyj/W6eXp3XmtklNVU8EH7r9jhIMzZZLKH3NLEc3N7kZ868X CVvBJSWDBr/0+PkIEB1Uur8rcm+ZLMRMV9UgBBwUPRQqqrwYIchXbycT6JvKK3jN nzk4hYfmNos//72FaPG1x2y0qNriVkxSQCBW9EidQwG7qVfFRYHcKnQT6yaoGwXk B0DN2G35JrRhHwgw5cz9+aPazucWnylom9nH+DptCA4W3O9ltdTG2SNFMbRsWXfb P0qbHjmOdKkLu+mCgCS/3WGyrTdW/dK468ca6o33bAOMhb9qwMCweIhTe/qMTulE hFppqb10icUXEqMl3BM4wXMJ0puwlSgSc0/7eNJlPuuSMlOvbwk+JriVnd8MqYf1 oXH6/vS+W2fDRp57qDqIdXxQwt9IAG2HgnxMn2HJFRoNwl30hs1lDXGk3cT5KkNT yd4Wf6Wmt8QB2eCQA2G6zwMEAnTywdssC2Q7T5LqiZl5MIO9dis2gKVdTqd0A01n Tylwx5dDCU+Ot1PVlrsJ6rxDV2tW9YQU5Hz88GsS8+qKUGFTlgR/RANMq75BGfnx GgCDs08qpCWD2F1h9VkK =Qn8f -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From tille at debian.org Mon May 9 08:51:13 2016 From: tille at debian.org (Andreas Tille) Date: Mon, 9 May 2016 10:51:13 +0200 Subject: [Debian-med-packaging] Bug#807580: Most files contain license clarification now In-Reply-To: <20160428173904.GC7597@an3as.eu> References: <20151211083457.GI21887@an3as.eu> <20151214083825.GC23979@an3as.eu> <20151219061354.GA32401@an3as.eu> <20151220050701.GB1720@falafel.plessy.net> <20160316135411.GC30138@an3as.eu> <20160428173904.GC7597@an3as.eu> Message-ID: <20160509085113.GF8125@an3as.eu> Hi, I reviewed the copyright of the new version of r-cran-rtracklayer (1.32.0). Licenses of most files are clarified and probably re-fetched from GitHub[1]. Only four remaining files are featuring the old non-free copyright statement which is IMHO just an oversight. I opened an issue on Github[2] to clarify this. I propose to upgrade the remaining BioConductor packages to the recently released new version independently from this bug report since I assume that the issue can be dealt with in the near future. What do you think? Kind regards Andreas. [1] https://github.com/jstjohn/KentLib [2] https://github.com/jstjohn/KentLib/issues/2 -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Mon May 9 09:06:50 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 09 May 2016 09:06:50 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-shortread_1.30.0-1_source.changes Message-ID: r-bioc-shortread_1.30.0-1_source.changes uploaded successfully to localhost along with the files: r-bioc-shortread_1.30.0-1.dsc r-bioc-shortread_1.30.0.orig.tar.gz r-bioc-shortread_1.30.0-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 9 09:54:22 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 09 May 2016 09:54:22 +0000 Subject: [Debian-med-packaging] r-bioc-shortread_1.30.0-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 09 May 2016 10:58:41 +0200 Source: r-bioc-shortread Binary: r-bioc-shortread Architecture: source Version: 1.30.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-shortread - GNU R classes and methods for high-throughput short-read sequenci Changes: r-bioc-shortread (1.30.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 9adfa687e2e38254a781d6c8aab1b32e0d406436 2221 r-bioc-shortread_1.30.0-1.dsc a74beba720281182a4a0e07a1b280ef86d501269 5147162 r-bioc-shortread_1.30.0.orig.tar.gz 90355287ca4885967cd6907a28c2ea5a35c0c5d1 5144 r-bioc-shortread_1.30.0-1.debian.tar.xz Checksums-Sha256: 76de346393ca32bf5d2e05a8087fedf27a2ec07ad540820e4cd59b38efecafb8 2221 r-bioc-shortread_1.30.0-1.dsc 4faeae2ec2d7c6bc4d6d598547ecb91e0bfa76b454d439ba53d771b888b69d62 5147162 r-bioc-shortread_1.30.0.orig.tar.gz b86c891bdf057cb5240ed0842f61cf462c860217caeca0578079fe911660bfe1 5144 r-bioc-shortread_1.30.0-1.debian.tar.xz Files: fad8440aa0f0fbfb497f81533ba7cd16 2221 gnu-r optional r-bioc-shortread_1.30.0-1.dsc ab549461deb0c38d9f42af31f963efc1 5147162 gnu-r optional r-bioc-shortread_1.30.0.orig.tar.gz 6a01ab61c565ad32d7a0e43d4a12207f 5144 gnu-r optional r-bioc-shortread_1.30.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMFLMAAoJEFeKBJTRxkbRR6wP/1xVYogc6/njj0DcfvP31mVF H+HVrlLafTGXmQysbWhsC/WP4CYvS7pWrHIwqYXvRtCIzez6G25BMbe8zZN6DKfi PQ5Ff17GAltBqxDhukBusJauwiWfXsTaG+nqHo9wE0pz3pQNv0TFEUXuLth1tbK1 zxWM6rGpny0Xh5ea11+aIrLtfuwkCjGIScFXovi7v8olKEG7ziwo/q3peUQeq440 tNXJgcTcf7JFcw9CijD6s3wi3gUIOO/+gNBbUSljOT+N7u4nUC8IoK/9ARwiaefz LfgLCmSzrP34kAwD2sSlO9lTyFu/QoWnxrF7dZdV+6UNplfqsy8UQL7Vg9pi5cGv wXOlpNqw5pkuHneufRTomMrL9J6MxHbGRrrBS6Jo6vV3eKBAnem7h/5R8WjZXyx2 0oRFPvmFehPrJ0Ye7Tgw7Cspn+gj/ZNbOPl/KQkUf99XSY0n+ERWaWlSNjoHvFRy wcZ7zdfqbDhUUl6YgO3xJoMACea0YaQ3eo2t9TYjmftZiVHCtu69Yzhg25BCCk9m rnvHpwludbVpBng/Uy73IvopdLw6FdFllR3E6vfWGHCsiRLxVuKPXysUb68R7tOH U8oqhacpruqp1MVyXsRi5vMddhJnBYpnuVewJXOwaILOo2Z6OQKfYkJwFSHoTlIb io3L7d3yZFvl3jxwWbcV =QiEX -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Mon May 9 11:36:05 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Mon, 09 May 2016 11:36:05 +0000 Subject: [Debian-med-packaging] Bug#823673: marked as done (samtools: FTBFS in testing) References: <20160509113256.GE16724@bubu.igloo> Message-ID: Your message dated Mon, 9 May 2016 20:32:56 +0900 with message-id <20160509113256.GE16724 at bubu.igloo> and subject line Re: [Debian-med-packaging] Bug#823673: samtools: FTBFS in testing has caused the Debian Bug report #823673, regarding samtools: FTBFS in testing to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 823673: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=823673 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Santiago Vila Subject: samtools: FTBFS in testing Date: Sat, 7 May 2016 15:03:45 +0200 (CEST) Size: 21839 URL: -------------- next part -------------- An embedded message was scrubbed... From: Charles Plessy Subject: Re: [Debian-med-packaging] Bug#823673: samtools: FTBFS in testing Date: Mon, 9 May 2016 20:32:56 +0900 Size: 1956 URL: From rrs at debian.org Mon May 9 14:28:49 2016 From: rrs at debian.org (Ritesh Raj Sarraf) Date: Mon, 09 May 2016 19:58:49 +0530 Subject: [Debian-med-packaging] Bug#823842: python-fitbit: cannot generate auth token Message-ID: <146280412902.14589.16231283848132804670.reportbug@learner.researchut.com> Package: python-fitbit Version: 0.2-1 Severity: normal As per the documentation, the ./gather_keys_oauth2.py should help in generating an auth token. But when using the same, I get the following error from the fitbit server "The app you're trying to connect did not provide valid information to Fitbit. Please report this issue to them. Developer information: invalid_request - Invalid redirect_uri parameter value" On the terminal, I get the following: rrs at learner:/var/tmp/Debian-Build/temp/python-fitbit-0.2$ ./gather_keys_oauth2.py XXXXXX xxxxxxxxxxxxxxxxxxx [09/May/2016:19:53:44] ENGINE Listening for SIGHUP. [09/May/2016:19:53:44] ENGINE Listening for SIGTERM. [09/May/2016:19:53:44] ENGINE Listening for SIGUSR1. [09/May/2016:19:53:44] ENGINE Bus STARTING CherryPy Checker: The Application mounted at '' has an empty config. [09/May/2016:19:53:44] ENGINE Started monitor thread 'Autoreloader'. [09/May/2016:19:53:44] ENGINE Started monitor thread '_TimeoutMonitor'. [09/May/2016:19:53:44] ENGINE Serving on http://127.0.0.1:8080 [09/May/2016:19:53:44] ENGINE Bus STARTED Created new window in existing browser session. [14429:14456:0509/195345:ERROR:nss_util.cc(839)] After loading Root Certs, loaded==false: NSS error code: -8018 PS: Also, could you please ship gather_keys_oauth2.py in the binary package ? -- System Information: Debian Release: stretch/sid APT prefers testing APT policy: (990, 'testing'), (500, 'unstable-debug'), (500, 'unstable'), (101, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.5.0-2-amd64 (SMP w/4 CPU cores) Locale: LANG=en_IN.utf8, LC_CTYPE=en_IN.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages python-fitbit depends on: ii libjs-jquery 1.11.3+dfsg-4 ii libjs-underscore 1.7.0~dfsg-1 ii python-dateutil 2.4.2-1 ii python-pkg-resources 20.10.1-1 ii python-requests-oauthlib 0.4.0-1 pn python:any python-fitbit recommends no packages. python-fitbit suggests no packages. -- debconf-show failed From owner at bugs.debian.org Mon May 9 14:45:07 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Mon, 09 May 2016 14:45:07 +0000 Subject: [Debian-med-packaging] Processed: Re: python-fitbit: cannot generate auth token References: <1462805026.8317.4.camel@debian.org> <146280412902.14589.16231283848132804670.reportbug@learner.researchut.com> Message-ID: Processing control commands: > retitle -1 add versioned dependency on?python-requests-oauthlib Bug #823842 [python-fitbit] python-fitbit: cannot generate auth token Changed Bug title to 'add versioned dependency on?python-requests-oauthlib' from 'python-fitbit: cannot generate auth token'. -- 823842: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=823842 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From rrs at debian.org Mon May 9 14:43:46 2016 From: rrs at debian.org (Ritesh Raj Sarraf) Date: Mon, 09 May 2016 20:13:46 +0530 Subject: [Debian-med-packaging] Bug#823842: python-fitbit: cannot generate auth token In-Reply-To: <146280412902.14589.16231283848132804670.reportbug@learner.researchut.com> References: <146280412902.14589.16231283848132804670.reportbug@learner.researchut.com> Message-ID: <1462805026.8317.4.camel@debian.org> Control: retitle -1 add versioned dependency on?python-requests-oauthlib The actual bug filed is incorrect, hence I've retitled. On Mon, 2016-05-09 at 19:58 +0530, Ritesh Raj Sarraf wrote: > Package: python-fitbit > Version: 0.2-1 > Severity: normal > > As per the documentation, the ./gather_keys_oauth2.py should help in > generating an auth token. But when using the same, I get the following > error from the fitbit server > > "The app you're trying to connect did not provide valid information to > Fitbit. Please report this issue to them. > > Developer information: invalid_request - Invalid redirect_uri parameter > value" > > > On the terminal, I get the following: > > > rrs at learner:/var/tmp/Debian-Build/temp/python-fitbit-0.2$ > ./gather_keys_oauth2.py XXXXXX xxxxxxxxxxxxxxxxxxx > [09/May/2016:19:53:44] ENGINE Listening for SIGHUP. > [09/May/2016:19:53:44] ENGINE Listening for SIGTERM. > [09/May/2016:19:53:44] ENGINE Listening for SIGUSR1. > [09/May/2016:19:53:44] ENGINE Bus STARTING > CherryPy Checker: > The Application mounted at '' has an empty config. > > [09/May/2016:19:53:44] ENGINE Started monitor thread 'Autoreloader'. > [09/May/2016:19:53:44] ENGINE Started monitor thread '_TimeoutMonitor'. > [09/May/2016:19:53:44] ENGINE Serving on http://127.0.0.1:8080 > [09/May/2016:19:53:44] ENGINE Bus STARTED > Created new window in existing browser session. > [14429:14456:0509/195345:ERROR:nss_util.cc(839)] After loading Root Certs, > loaded==false: NSS error code: -8018 > > With a proper callback url in place, this doesn't fail. So it was my bad assuming this to be a buggy behavior. OTOH, I think now I have encountered a bug, which I believe has already been reported and fixed upstream. https://github.com/orcasgit/python-fitbit/issues/70 I cannot verify the fix because the dependent python-requests-oauthlib is outdated in Debian. What we need today is 0.6+ This leads to errors like the following. ERROR: Missing access token parameter. Please check that you are using the correct client_secret You can close this window ? File "./gather_keys_oauth2.py", line 46, in index ????self.oauth.fetch_access_token(code, self.redirect_uri) ? File "/media/SSHD/var/tmp/Debian-Build/temp/python-fitbit-0.2/fitbit/api.py", line 153, in fetch_access_token ????code=code) ? File "/usr/lib/python2.7/dist-packages/requests_oauthlib/oauth2_session.py", line 160, in fetch_token ????self._client.parse_request_body_response(r.text, scope=self.scope) ? File "/usr/lib/python2.7/dist- packages/oauthlib/oauth2/rfc6749/clients/base.py", line 409, in parse_request_body_response ????self.token = parse_token_response(body, scope=scope) ? File "/usr/lib/python2.7/dist-packages/oauthlib/oauth2/rfc6749/parameters.py", line 376, in parse_token_response ????validate_token_parameters(params) ? File "/usr/lib/python2.7/dist-packages/oauthlib/oauth2/rfc6749/parameters.py", line 386, in validate_token_parameters ????raise MissingTokenError(description="Missing access token parameter.") > > PS: Also, could you please ship gather_keys_oauth2.py in the binary > package ? It'd still be very helpful to see this packaged in the binary package. -- Ritesh Raj Sarraf | http://people.debian.org/~rrs Debian - The Universal Operating System -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: This is a digitally signed message part URL: From andreas at an3as.eu Mon May 9 15:01:52 2016 From: andreas at an3as.eu (Andreas Tille) Date: Mon, 9 May 2016 17:01:52 +0200 Subject: [Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer) Message-ID: <20160509150152.GH8125@an3as.eu> Hi, usually R packages are building without problems but I faced an issue now which I have no clue about. I try to upgrade r-bioc-rtracklayer[1] and I have updated SVN to something that should build version 1.32.0. Unfortunately when using pbuilder I get: dh_testroot dh_prep dh_installdirs -A mkdir -p "." dh_installdirs usr/lib/R/site-library echo "R:Depends=r-base-core (>= 3.3.0-1), r-api-3" >> debian/r-bioc-rtracklayer.substvars if test -f /usr/bin/xvfb-run; then \ xvfb-run -a \ R CMD INSTALL -l /build/r-bioc-rtracklayer-1.32.0/debian/r-bioc-rtracklayer/usr/lib/R/site-library --clean \ . \ "--built-timestamp=\"Mon, 09 May 2016 12:46:31 +0200\"" \ ; \ else \ R CMD INSTALL -l /build/r-bioc-rtracklayer-1.32.0/debian/r-bioc-rtracklayer/usr/lib/R/site-library \ --clean . \ "--built-timestamp=\"Mon, 09 May 2016 12:46:31 +0200\"" \ ; \ fi * installing *source* package 'rtracklayer' ... configure: error: cannot find sources (rtracklayer) in . or .. ERROR: configuration failed for package 'rtracklayer' * removing '/build/r-bioc-rtracklayer-1.32.0/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer' /usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed make: *** [R_any_arch] Error 1 dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2 The issue is that the configure scripts seeks a dir rtracklayer either in . or .. but pbuilder renames the build directory to r-bioc-rtracklayer-1.32.0. The package builds fine with debuild. This is the first time I'm observing and I wonder whether there is a better way to fix this than patching the configure script. Unfortunately I'm not that comfortable with cdbs hooks to know how to possibly set a symlink to the proper dir in advance or something like this. Any help would be welcome Andreas. [1] svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/ -- http://fam-tille.de From noreply at release.debian.org Mon May 9 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] r-cran-evaluate 0.9-1 MIGRATED to testing Message-ID: FYI: The status of the r-cran-evaluate source package in Debian's testing distribution has changed. Previous version: 0.5.5-1 Current version: 0.9-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] r-cran-etm 0.6-2-3 MIGRATED to testing Message-ID: FYI: The status of the r-cran-etm source package in Debian's testing distribution has changed. Previous version: 0.6-2-1 Current version: 0.6-2-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-cran-magrittr 1.5-3 MIGRATED to testing Message-ID: FYI: The status of the r-cran-magrittr source package in Debian's testing distribution has changed. Previous version: 1.5-1 Current version: 1.5-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] r-cran-futile.logger 1.4.1-3 MIGRATED to testing Message-ID: FYI: The status of the r-cran-futile.logger source package in Debian's testing distribution has changed. Previous version: 1.4.1-1 Current version: 1.4.1-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] r-cran-cmprsk 2.2-7-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-cmprsk source package in Debian's testing distribution has changed. Previous version: 2.2-7-1 Current version: 2.2-7-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] r-bioc-hilbertvis 1.28.0-2 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-hilbertvis source package in Debian's testing distribution has changed. Previous version: 1.28.0-1 Current version: 1.28.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-cran-qtl 1.39-5-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-qtl source package in Debian's testing distribution has changed. Previous version: 1.37-11-1 Current version: 1.39-5-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] r-cran-doparallel 1.0.10-1 MIGRATED to testing Message-ID: FYI: The status of the r-cran-doparallel source package in Debian's testing distribution has changed. Previous version: 1.0.8-1 Current version: 1.0.10-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-cran-rocr 1.0-7-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-rocr source package in Debian's testing distribution has changed. Previous version: 1.0-7-1 Current version: 1.0-7-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] snap 2013-11-29-2 MIGRATED to testing Message-ID: FYI: The status of the snap source package in Debian's testing distribution has changed. Previous version: 2013-11-29-1 Current version: 2013-11-29-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 9 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 09 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-cran-ggplot2 2.1.0-3 MIGRATED to testing Message-ID: FYI: The status of the r-cran-ggplot2 source package in Debian's testing distribution has changed. Previous version: 2.0.0-2 Current version: 2.1.0-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From tille at debian.org Mon May 9 18:09:21 2016 From: tille at debian.org (Andreas Tille) Date: Mon, 9 May 2016 20:09:21 +0200 Subject: [Debian-med-packaging] Bug#807580: [jstjohn/KentLib] Four files do contain old licensing statement (#2) In-Reply-To: References: Message-ID: <20160509180921.GA11437@an3as.eu> Hi Jim, you probably remember my constant nagging abou the licensing of your library code. Inside the bug report in Debian BTS[1] you mentioned MPL yourself. Since I did not received any definitive answer stronger than "looking at Mozilla Public LIcense, ... I can release it under that as well." I was searching the web for potential new releases of the code. I found something at Github which has only four files left with a non-free license and I mentioned this in the according bug report there[2]. From what I can see when inspecting the whole directory it looks pretty much like an unwanted leftover since all other files have later copyright and a free license. It would be really great if you could clarify this. Thanks a lot for your cooperation Andreas. [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=807580#112 [2] https://github.com/jstjohn/KentLib/issues/2 On Mon, May 09, 2016 at 08:56:16AM -0700, John St. John wrote: > Hi Andreas, this issue should be taken up directly with Jim Kent. If he gives the OK I am more than happy to update those problematic headers. This is not my code, so I am not sure what was intended between the conflicting statement in the README that was part of the Kent source tree at the time, and header comments in the individual libraries you mentioned. > > --- > You are receiving this because you authored the thread. > Reply to this email directly or view it on GitHub: > https://github.com/jstjohn/KentLib/issues/2#issuecomment-217906316 -- http://fam-tille.de From andreas at an3as.eu Mon May 9 18:37:49 2016 From: andreas at an3as.eu (Andreas Tille) Date: Mon, 9 May 2016 20:37:49 +0200 Subject: [Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer) In-Reply-To: <20160509150152.GH8125@an3as.eu> References: <20160509150152.GH8125@an3as.eu> Message-ID: <20160509183749.GB11437@an3as.eu> Hi again, I solved this by simply removing the whole configure script in a quilt patch. Kind regards Andreas. On Mon, May 09, 2016 at 05:01:52PM +0200, Andreas Tille wrote: > Hi, > > usually R packages are building without problems but I faced an issue > now which I have no clue about. I try to upgrade r-bioc-rtracklayer[1] > and I have updated SVN to something that should build version 1.32.0. > > Unfortunately when using pbuilder I get: > > dh_testroot > dh_prep > dh_installdirs -A > mkdir -p "." > dh_installdirs usr/lib/R/site-library > echo "R:Depends=r-base-core (>= 3.3.0-1), r-api-3" >> debian/r-bioc-rtracklayer.substvars > if test -f /usr/bin/xvfb-run; then \ > xvfb-run -a \ > R CMD INSTALL -l /build/r-bioc-rtracklayer-1.32.0/debian/r-bioc-rtracklayer/usr/lib/R/site-library --clean \ > . \ > "--built-timestamp=\"Mon, 09 May 2016 12:46:31 +0200\"" \ > ; \ > else \ > R CMD INSTALL -l /build/r-bioc-rtracklayer-1.32.0/debian/r-bioc-rtracklayer/usr/lib/R/site-library \ > --clean . \ > "--built-timestamp=\"Mon, 09 May 2016 12:46:31 +0200\"" \ > ; \ > fi > * installing *source* package 'rtracklayer' ... > configure: error: cannot find sources (rtracklayer) in . or .. > ERROR: configuration failed for package 'rtracklayer' > * removing '/build/r-bioc-rtracklayer-1.32.0/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer' > /usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed > make: *** [R_any_arch] Error 1 > dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2 > > > The issue is that the configure scripts seeks a dir rtracklayer either > in . or .. but pbuilder renames the build directory to > r-bioc-rtracklayer-1.32.0. The package builds fine with debuild. > > This is the first time I'm observing and I wonder whether there is a > better way to fix this than patching the configure script. > Unfortunately I'm not that comfortable with cdbs hooks to know how to > possibly set a symlink to the proper dir in advance or something like > this. > > Any help would be welcome > > Andreas. > > [1] svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/ > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From edd at debian.org Mon May 9 18:55:42 2016 From: edd at debian.org (Dirk Eddelbuettel) Date: Mon, 9 May 2016 13:55:42 -0500 Subject: [Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer) In-Reply-To: <20160509183749.GB11437@an3as.eu> References: <20160509150152.GH8125@an3as.eu> <20160509183749.GB11437@an3as.eu> Message-ID: <22320.56622.851567.367229@max.nulle.part> On 9 May 2016 at 20:37, Andreas Tille wrote: | Hi again, | | I solved this by simply removing the whole configure script in a quilt patch. That sounds crazy so I took a look. BioConductor just had a 3.3 release (matching the R release cycle) and they seemingly simplified it a lot. Compare these two: https://github.com/Bioconductor-mirror/rtracklayer/blob/release-3.2/configure.ac https://github.com/Bioconductor-mirror/rtracklayer/blob/release-3.3/configure.ac I did not look too closely at the older one but the newer does check for OpenSSL present or not __and then uses this in src/Makevars.in__ so if it were me I consider switching to this. Or rather, I take the 'self-directory' test out in 3.2. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org From tille at debian.org Mon May 9 19:10:22 2016 From: tille at debian.org (Andreas Tille) Date: Mon, 9 May 2016 21:10:22 +0200 Subject: [Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer) In-Reply-To: <22320.56622.851567.367229@max.nulle.part> References: <20160509150152.GH8125@an3as.eu> <20160509183749.GB11437@an3as.eu> <22320.56622.851567.367229@max.nulle.part> Message-ID: <20160509191022.GC11437@an3as.eu> Hi Dirk, On Mon, May 09, 2016 at 01:55:42PM -0500, Dirk Eddelbuettel wrote: > > On 9 May 2016 at 20:37, Andreas Tille wrote: > | Hi again, > | > | I solved this by simply removing the whole configure script in a quilt patch. > > That sounds crazy so I took a look. BioConductor just had a 3.3 release > (matching the R release cycle) and they seemingly simplified it a lot. > Compare these two: > > https://github.com/Bioconductor-mirror/rtracklayer/blob/release-3.2/configure.ac > > https://github.com/Bioconductor-mirror/rtracklayer/blob/release-3.3/configure.ac I can confirm that I did compared the old and the new release. Since the old release did not had a configure script (*without* the .ac!) in its release tarball I came to the conclusion that this might be unneeded and in fact it is. My guess is that it will be recreated from configure.ac (as it should be). > I did not look too closely at the older one but the newer does check for > OpenSSL present or not __and then uses this in src/Makevars.in__ so if it > were me I consider switching to this. I can confirm that I also added Build-Depends: libssl-dev. > Or rather, I take the 'self-directory' > test out in 3.2. You probably mean 3.3, right? Version 3.2 has no such test as far as I can see. Kind regards Andreas. -- http://fam-tille.de From dispenda-03 at muaraenimkab.go.id Mon May 9 13:49:56 2016 From: dispenda-03 at muaraenimkab.go.id (Rita) Date: Mon, 9 May 2016 20:49:56 +0700 (WIB) Subject: [Debian-med-packaging] ? Message-ID: <1070363267.14015.1462801796397.JavaMail.zimbra@muaraenimkab.go.id> Did you get my previous mail? When can i call you? From edd at debian.org Mon May 9 19:37:37 2016 From: edd at debian.org (Dirk Eddelbuettel) Date: Mon, 9 May 2016 14:37:37 -0500 Subject: [Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer) In-Reply-To: <20160509191022.GC11437@an3as.eu> References: <20160509150152.GH8125@an3as.eu> <20160509183749.GB11437@an3as.eu> <22320.56622.851567.367229@max.nulle.part> <20160509191022.GC11437@an3as.eu> Message-ID: <22320.59137.142872.903240@max.nulle.part> On 9 May 2016 at 21:10, Andreas Tille wrote: | > Or rather, I take the 'self-directory' | > test out in 3.2. | | You probably mean 3.3, right? Version 3.2 has no such test as far as I | can see. Sorry, meant whichever version (of rtracklayer) gave you that issue. I would rather not remove configure wholesale. I am reasonably fluent at writing these so I may be able to help you just modify the existing one by taking the offending test out, but I'm at work now so ... Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org From kent at soe.ucsc.edu Tue May 10 00:32:33 2016 From: kent at soe.ucsc.edu (Jim Kent) Date: Mon, 9 May 2016 17:32:33 -0700 Subject: [Debian-med-packaging] Bug#807580: [jstjohn/KentLib] Four files do contain old licensing statement (#2) In-Reply-To: <20160509180921.GA11437@an3as.eu> References: <20160509180921.GA11437@an3as.eu> Message-ID: Hmm, the license statements are like so on these 4: /* hmmstats.h - Stuff for doing statistical analysis in general and * hidden Markov models in particular. * * This file is copyright 2000 Jim Kent, but license is hereby * granted for all use - public, private or commercial. */ not what is in the github note: * Copyright (C) 2000 Jim Kent. This source code may be freely used * * for personal, academic, and non-profit purposes. Commercial use * * permitted only by explicit agreement with Jim Kent (jim_kent at pacbell.net) * On Mon, May 9, 2016 at 11:09 AM, Andreas Tille wrote: > Hi Jim, > > you probably remember my constant nagging abou the licensing of your > library code. Inside the bug report in Debian BTS[1] you mentioned MPL > yourself. Since I did not received any definitive answer stronger than > > "looking at Mozilla Public LIcense, ... I can release it under > that as well." > > I was searching the web for potential new releases of the code. I found > something at Github which has only four files left with a non-free > license and I mentioned this in the according bug report there[2]. From > what I can see when inspecting the whole directory it looks pretty much > like an unwanted leftover since all other files have later copyright and > a free license. > > It would be really great if you could clarify this. > > Thanks a lot for your cooperation > > Andreas. > > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=807580#112 > [2] https://github.com/jstjohn/KentLib/issues/2 > > On Mon, May 09, 2016 at 08:56:16AM -0700, John St. John wrote: > > Hi Andreas, this issue should be taken up directly with Jim Kent. If he > gives the OK I am more than happy to update those problematic headers. This > is not my code, so I am not sure what was intended between the conflicting > statement in the README that was part of the Kent source tree at the time, > and header comments in the individual libraries you mentioned. > > > > --- > > You are receiving this because you authored the thread. > > Reply to this email directly or view it on GitHub: > > https://github.com/jstjohn/KentLib/issues/2#issuecomment-217906316 > > -- > http://fam-tille.de > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tille at debian.org Tue May 10 07:02:39 2016 From: tille at debian.org (Andreas Tille) Date: Tue, 10 May 2016 09:02:39 +0200 Subject: [Debian-med-packaging] Bug#807580: [jstjohn/KentLib] Four files do contain old licensing statement (#2) In-Reply-To: References: <20160509180921.GA11437@an3as.eu> Message-ID: <20160510070239.GB30189@an3as.eu> Hi Jim, thanks for the clarification. Do you maintain somewhere some official repository where we could fetch these files from. I assumed Github would be official ... Thanks for your quick and helpful response Andreas. On Mon, May 09, 2016 at 05:32:33PM -0700, Jim Kent wrote: > Hmm, the license statements are like so on these 4: > > /* hmmstats.h - Stuff for doing statistical analysis in general and > > * hidden Markov models in particular. > > * > > * This file is copyright 2000 Jim Kent, but license is hereby > > * granted for all use - public, private or commercial. */ > > not what is in the github note: > > * Copyright (C) 2000 Jim Kent. This source code may be freely used * > * for personal, academic, and non-profit purposes. Commercial use * > * permitted only by explicit agreement with Jim Kent (jim_kent at pacbell.net) > * > > > > > > On Mon, May 9, 2016 at 11:09 AM, Andreas Tille wrote: > > > Hi Jim, > > > > you probably remember my constant nagging abou the licensing of your > > library code. Inside the bug report in Debian BTS[1] you mentioned MPL > > yourself. Since I did not received any definitive answer stronger than > > > > "looking at Mozilla Public LIcense, ... I can release it under > > that as well." > > > > I was searching the web for potential new releases of the code. I found > > something at Github which has only four files left with a non-free > > license and I mentioned this in the according bug report there[2]. From > > what I can see when inspecting the whole directory it looks pretty much > > like an unwanted leftover since all other files have later copyright and > > a free license. > > > > It would be really great if you could clarify this. > > > > Thanks a lot for your cooperation > > > > Andreas. > > > > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=807580#112 > > [2] https://github.com/jstjohn/KentLib/issues/2 > > > > On Mon, May 09, 2016 at 08:56:16AM -0700, John St. John wrote: > > > Hi Andreas, this issue should be taken up directly with Jim Kent. If he > > gives the OK I am more than happy to update those problematic headers. This > > is not my code, so I am not sure what was intended between the conflicting > > statement in the README that was part of the Kent source tree at the time, > > and header comments in the individual libraries you mentioned. > > > > > > --- > > > You are receiving this because you authored the thread. > > > Reply to this email directly or view it on GitHub: > > > https://github.com/jstjohn/KentLib/issues/2#issuecomment-217906316 > > > > -- > > http://fam-tille.de > > -- http://fam-tille.de From tille at debian.org Tue May 10 08:02:02 2016 From: tille at debian.org (Andreas Tille) Date: Tue, 10 May 2016 10:02:02 +0200 Subject: [Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer) In-Reply-To: <22320.59137.142872.903240@max.nulle.part> References: <20160509150152.GH8125@an3as.eu> <20160509183749.GB11437@an3as.eu> <22320.56622.851567.367229@max.nulle.part> <20160509191022.GC11437@an3as.eu> <22320.59137.142872.903240@max.nulle.part> Message-ID: <20160510080202.GC30189@an3as.eu> Hi Dirk, On Mon, May 09, 2016 at 02:37:37PM -0500, Dirk Eddelbuettel wrote: > > Sorry, meant whichever version (of rtracklayer) gave you that issue. I would > rather not remove configure wholesale. > > I am reasonably fluent at writing these so I may be able to help you just > modify the existing one by taking the offending test out Hmmm, its no problem to kick out the relevant test (I managed on my local disk successfully). But are you *really* sure that editing autogenerated files that are actually not supposed to be edited manually but under control of autoconf is the best solution for the problem? I never ever had the need to edit a configure file and if there was ever any need to fix a broken one using dh-autoreconf was the working solution. Moreover I noticed that after *removing* configure the option -DUSE_SSL was used while when I just skipped the test inside the configure file it was *not* included which seems like the configure file is broken in several ways. So it sounds reasonable to me to stick to my initial strategy and to assume that the configure file was delivered by accident and thus removing it. Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Tue May 10 08:24:51 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 08:24:51 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-rtracklayer_1.32.0-1_amd64.changes Message-ID: r-bioc-rtracklayer_1.32.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-rtracklayer_1.32.0-1.dsc r-bioc-rtracklayer_1.32.0.orig.tar.gz r-bioc-rtracklayer_1.32.0-1.debian.tar.xz r-bioc-rtracklayer-dbgsym_1.32.0-1_amd64.deb r-bioc-rtracklayer_1.32.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 10 09:05:09 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 09:05:09 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-qvalue_2.4.0-1_amd64.changes Message-ID: r-bioc-qvalue_2.4.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-qvalue_2.4.0-1.dsc r-bioc-qvalue_2.4.0.orig.tar.gz r-bioc-qvalue_2.4.0-1.debian.tar.xz r-bioc-qvalue_2.4.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From gw.fossdev at gmail.com Tue May 10 09:31:07 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Tue, 10 May 2016 11:31:07 +0200 Subject: [Debian-med-packaging] Bug#811944: fastml: Fixed Message-ID: <1462872667.6378.8.camel@gmail.com> Control: tags -1 pending? Hi all,? I've added another patch that really fixes the compile errors with g++- 6.? I suspect the the first patch also fixed some problems with template instantiation in general, and was not necessarily related to g++-6 only.? Best,? Gert? From owner at bugs.debian.org Tue May 10 09:33:05 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 10 May 2016 09:33:05 +0000 Subject: [Debian-med-packaging] Processed: fastml: Fixed References: <1462872667.6378.8.camel@gmail.com> <20160120035508.GB4951@jirafa.cyrius.com> Message-ID: Processing control commands: > tags -1 pending? Bug #811944 [fastml] fastml: FTBFS with GCC 6: template instantiation depth exceeds maximum Added tag(s) pending. -- 811944: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811944 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From gw.fossdev at gmail.com Tue May 10 09:15:16 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Tue, 10 May 2016 11:15:16 +0200 Subject: [Debian-med-packaging] Bug#811944: fastml: Fixed in git Message-ID: <1462871716.6378.5.camel@gmail.com> Hello all,? I've added a patch to the repo that fixes the bug, i.e. removes the artificial limit on the template depth that showed as compile error.? However, it doesn't actually fix compiling with g++-6. I continue investigating.? Best,? Gert? ?? From ftpmaster at ftp-master.debian.org Tue May 10 09:52:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 09:52:34 +0000 Subject: [Debian-med-packaging] r-bioc-qvalue_2.4.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 10 May 2016 10:23:55 +0200 Source: r-bioc-qvalue Binary: r-bioc-qvalue Architecture: source all Version: 2.4.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-qvalue - GNU R package for Q-value estimation for FDR control Changes: r-bioc-qvalue (2.4.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * Drop references to r-cran-qvalue in d/control Checksums-Sha1: b5616f377cf215e2b2d48946ae45c32feb252508 2156 r-bioc-qvalue_2.4.0-1.dsc 4a14159fdf5c27e662a45a6de8bc4078c5bad91c 2757609 r-bioc-qvalue_2.4.0.orig.tar.gz 5d2e73afa9498da6952c1c653660c54819cfb415 4960 r-bioc-qvalue_2.4.0-1.debian.tar.xz 16d0fe595906e56f9f7ca26754a7e426b3374c9f 3051610 r-bioc-qvalue_2.4.0-1_all.deb Checksums-Sha256: 40c7faeb1da2a234c6440ed507fa6fe627c737418f84d0f484b98273755de294 2156 r-bioc-qvalue_2.4.0-1.dsc 61e769882eff74caf77e500ee5040901fb0b9f5e26ae27e8d9ae048e9f1a3ca4 2757609 r-bioc-qvalue_2.4.0.orig.tar.gz fe47e999812a2a3c25e238ec8713049a72961d441a98b98a82b4cf58f9afd825 4960 r-bioc-qvalue_2.4.0-1.debian.tar.xz 30da9f9f8469319e51b25898eb8c96390be0ce999d857ae0ea5c3be1fd0b399f 3051610 r-bioc-qvalue_2.4.0-1_all.deb Files: df6479be7452afdd8a9e165a2dd82bc2 2156 gnu-r optional r-bioc-qvalue_2.4.0-1.dsc 3169b778c987e91a8fc0fdfd17d09532 2757609 gnu-r optional r-bioc-qvalue_2.4.0.orig.tar.gz 885dac55e7e47a46e10bd8a8d2e1698a 4960 gnu-r optional r-bioc-qvalue_2.4.0-1.debian.tar.xz 43a63b0b57f70a054dfb9509e7129d54 3051610 gnu-r optional r-bioc-qvalue_2.4.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMaMnAAoJEFeKBJTRxkbRMkkP/1+wl8krCLVn18vEiqhoGFA6 k3Cf9Mvuarb2NQI8YiJQcvHBnunDDA9OMUAzld4QI31tKs/bhSD3jKnBTZJoEHMq 9pideMs4MVzFYE18RDFN4stzSjx26iBGBw7PRGnwSPxOJBCiK7ZXHEKiXBUFqI2D ULmJpK8Y00/YHXjyG/MiPYyrqfhomqKF0mnSgfK6q1JulyHEtIamLGHrTT10lHCM e3lPxrCTrkU23lm4O4U+MK/FyrDvn1XH+JKPBCcsape1Z5K32VGsqY4cWuPoMQMP bmdEIisN5DbHP+LcYya8ILJsu35POzmFppPttVPRQywi7EUmMsEzkSBTDmXTU0IC Cds/QZe7PfZsa86jf1omRI3fCZXu8YQQ2o0iIVC77m16zR4zEdR4T1MN5cIn2b7F D3K5Sh1Ae8lShDoo2gfoKwMOktvjiT/qNTiCBDsDYXO6o1fAtvvUTK4b13RVNJ5M bx011ESf6Tjm25VClB4UueFUXW5rXbvSuqZp3PRtpDjxwpirEjnxUefZVUmS1EUu +mZHn9qjVMjGG4ux6F1ycughCJy2GLEN5LY9nPMF9OYsf1mpKalzR80zx3QpTdkg CRt76hBWVoPJeuXPWTX+msqFomkQ5nxZZXlfW5s66IJrbAsMVmi9gS1qMW29Ttva tCSBEr1M7satY0KZ0ehY =9kXU -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 10 09:52:42 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 09:52:42 +0000 Subject: [Debian-med-packaging] r-bioc-rtracklayer_1.32.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 09 May 2016 12:46:31 +0200 Source: r-bioc-rtracklayer Binary: r-bioc-rtracklayer Architecture: source amd64 Version: 1.32.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-rtracklayer - GNU R interface to genome browsers and their annotation tracks Closes: 807580 Changes: r-bioc-rtracklayer (1.32.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * Add missing Build-Depends: libssl-dev * debian/copyright: Clarify license of files in src/ucsc/* Closes: #807580 Checksums-Sha1: 95a19603c4a35641ca1a6191a2cb46efc37ff97f 2203 r-bioc-rtracklayer_1.32.0-1.dsc fc81ef3b8ff7b59480a8ccd487b949e1950558ff 1378515 r-bioc-rtracklayer_1.32.0.orig.tar.gz 733df3dac9cf6bd1ac99b3264b5712b49c8179cc 26416 r-bioc-rtracklayer_1.32.0-1.debian.tar.xz 7e63f6e77b98e93df268023fe058115330d263dc 389154 r-bioc-rtracklayer-dbgsym_1.32.0-1_amd64.deb bcdc6e7b97c2279a4ced92dba77d1542b56dfb3b 1785322 r-bioc-rtracklayer_1.32.0-1_amd64.deb Checksums-Sha256: 816426156cc3e76885dc5e4f7dcf4aa17d4fee619eeb78f3e55247e2e51ff09d 2203 r-bioc-rtracklayer_1.32.0-1.dsc db16ffb9bf90c83ec01a3d27b503c82360c7f7aa315a6cdfdad587855e983c5b 1378515 r-bioc-rtracklayer_1.32.0.orig.tar.gz c63bb7639814a25d86887f2087f0adc0aefce07a73663338a58038d07bf3ed7a 26416 r-bioc-rtracklayer_1.32.0-1.debian.tar.xz b623acd508506448c1c7a9e2ba9dbcce21f385e6c39d79323266459634b93e93 389154 r-bioc-rtracklayer-dbgsym_1.32.0-1_amd64.deb 7f07d2d59cd439b9733d8d4a9ed2581435f942e620b08102245ee55922f648d9 1785322 r-bioc-rtracklayer_1.32.0-1_amd64.deb Files: de8d07cac42cf85d2ba097935e2f32e2 2203 gnu-r optional r-bioc-rtracklayer_1.32.0-1.dsc 4bce1825ba9ae241fc9856c76ed71b98 1378515 gnu-r optional r-bioc-rtracklayer_1.32.0.orig.tar.gz bf98891534092a94c38c7c4b292632cd 26416 gnu-r optional r-bioc-rtracklayer_1.32.0-1.debian.tar.xz 449409cdae89e563268afa7472d88079 389154 debug extra r-bioc-rtracklayer-dbgsym_1.32.0-1_amd64.deb 970121a85f22e6f27ac0a282974d6682 1785322 gnu-r optional r-bioc-rtracklayer_1.32.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMZm3AAoJEFeKBJTRxkbRIwMP/2gRhGJHrT227Kfwi2jKIImk v90QFwKUCDm5cKyfO66yeh2mSML+ASn+H09+I1hvWVZBXK9nyiTgmr355ZEfbepn 5WYJaMUuF/yZqlxtsfKDjzM/RV0XztNlW1lZJjcNlOsqYiM8b4xqpNYr52gHYkNP Bes+WdNtIBcDAkLHqaxwmDePUvevij1Z66sVEs/VBRgNqBdPuKfKZ5wouTx9ucL4 qogOIlvZq3x0V/KsXu17BljiJ3x/8oZJ0KfqP8Kizql+dQjFSpZrniseACqpPmmn 9JJXtkRY5Aq41dP/3bOsPcKiYOYKQeZnR2UiSCwE6v0fcSIhu+z2DBvpflKRG/WH oKXDrJUuc9SoR9Ubr9QYmun1eCVSo0hRcceo75Uv0ou1X0s8t1mghKh3/HfXQffK BMqtQRr4Inp9DwTBBjBH9wstj0zgXZ915fLQJvliNosSYAjh2UQbKVdJAP8F+FQx 5ExtPY5k5MvKxu3h9MSPNyc4WhusCDkOzsXkDwxouQ6qWAoc58mif6+2YmuYC/do sdYKhC17RdNtHwcSj9XSB9YqzWRcwjBh0JhTIG536NvUo/0hyNep6OlH9LVE3qqD l1URrDX38b5BTzoB6qMi26NDL4SyYGI7ybgaSas76s0XfeQKKbB2zuNz/EqXYx73 zr/vgKeEoDDlgUCsg31B =XYm+ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Tue May 10 09:57:17 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 10 May 2016 09:57:17 +0000 Subject: [Debian-med-packaging] Bug#807580: marked as done (r-bioc-rtracklayer: src/ucsc/* is copied from another project with non-DFSG free license) References: <144975652407.12037.11224768774270851776.reportbug@mrcdev> Message-ID: Your message dated Tue, 10 May 2016 09:52:42 +0000 with message-id and subject line Bug#807580: fixed in r-bioc-rtracklayer 1.32.0-1 has caused the Debian Bug report #807580, regarding r-bioc-rtracklayer: src/ucsc/* is copied from another project with non-DFSG free license to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 807580: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=807580 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: "Michael R. Crusoe" Subject: r-bioc-rtracklayer: src/ucsc/* is stolen from another project with non-DFSG free license Date: Thu, 10 Dec 2015 06:08:44 -0800 Size: 3307 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#807580: fixed in r-bioc-rtracklayer 1.32.0-1 Date: Tue, 10 May 2016 09:52:42 +0000 Size: 6030 URL: From owner at bugs.debian.org Tue May 10 10:12:04 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 10 May 2016 10:12:04 +0000 Subject: [Debian-med-packaging] Bug#822381: marked as done (libbpp-popgen: FTBFS: error: 'const class bpp::CodonAlphabet' has no member named 'isStop') References: <1462874928.6378.33.camel@gmail.com> <20160424005033.GB21104@jirafa.cyrius.com> Message-ID: Your message dated Tue, 10 May 2016 12:08:48 +0200 with message-id <1462874928.6378.33.camel at gmail.com> and subject line Fixed with 2.2.0-1 has caused the Debian Bug report #822381, regarding libbpp-popgen: FTBFS: error: 'const class bpp::CodonAlphabet' has no member named 'isStop' to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 822381: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822381 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Martin Michlmayr Subject: libbpp-popgen: FTBFS: error: 'const class bpp::CodonAlphabet' has no member named 'isStop' Date: Sat, 23 Apr 2016 17:50:33 -0700 Size: 3971 URL: -------------- next part -------------- An embedded message was scrubbed... From: Gert Wollny Subject: Fixed with 2.2.0-1 Date: Tue, 10 May 2016 12:08:48 +0200 Size: 3238 URL: From ftpmaster at ftp-master.debian.org Tue May 10 10:20:46 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 10:20:46 +0000 Subject: [Debian-med-packaging] Processing of fastml_3.1-3_amd64.changes Message-ID: fastml_3.1-3_amd64.changes uploaded successfully to localhost along with the files: fastml_3.1-3.dsc fastml_3.1-3.debian.tar.xz fastml-dbgsym_3.1-3_amd64.deb fastml_3.1-3_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 10 10:23:30 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 10:23:30 +0000 Subject: [Debian-med-packaging] fastml_3.1-3_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 10 May 2016 09:46:15 +0000 Source: fastml Binary: fastml Architecture: source amd64 Version: 3.1-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: fastml - maximum likelihood ancestral amino-acid sequence reconstruction Closes: 811944 Changes: fastml (3.1-3) unstable; urgency=medium . * Team upload . [ Gert Wollny ] * d/p/remove-template-depth.patch add patch to not restrict template depth. (Default with g++-6 is 900) * d/p/g++-6.patch: fix compilation with g++-6, Closes: #811944 * d/control: Update standards version to 3.9.8 . [ Andreas Tille ] * cme fix dpkg-control * Better hardening Checksums-Sha1: fe7d70d59c2494287dad7c54a5aa4ceea1c619f3 1868 fastml_3.1-3.dsc 50a2b087d6b4ff4b4fdd3185d73d18f57e25b631 10044 fastml_3.1-3.debian.tar.xz 52568efa027cc0009d4352e7f04c1b5d697c8c43 16227892 fastml-dbgsym_3.1-3_amd64.deb 9d033bc22c22336744fb0e3f7b88eb8320d52bfe 990576 fastml_3.1-3_amd64.deb Checksums-Sha256: 036f6123ac7fbcfd4cd8c55e5b4f117c27337a7c5e7ab9fedc75b5c47bd0f863 1868 fastml_3.1-3.dsc 4ae5319d80c8e9964365de6f1047afece6b5d2e6c46e1fad60515b32d7977e65 10044 fastml_3.1-3.debian.tar.xz 47c7d80ac0f5fd72a0688b4022f39565848967376db087857e395a28d218f18d 16227892 fastml-dbgsym_3.1-3_amd64.deb c625a51dfec777098017918fbdb7df8e2432e2552a70d3c9aa1d44698d3b74e4 990576 fastml_3.1-3_amd64.deb Files: f6b98ef41e20401598bd1ddb04d0ecc7 1868 science optional fastml_3.1-3.dsc 687fd5fc12920f4bf3040279cb253a67 10044 science optional fastml_3.1-3.debian.tar.xz fde24ed45c0d36a5e7006f1f64aee7f7 16227892 debug extra fastml-dbgsym_3.1-3_amd64.deb 895d04f20b3811d9c33c4ab2d2fe6043 990576 science optional fastml_3.1-3_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMbTQAAoJEFeKBJTRxkbRYkgP/RA4Mr69X/C0WYYIPhvJrD2F z0lhfRm0NvcF4Io5Hikm+4Iq1CdM7GWF76h6XRhItQ6KLn5eY1IhlZCytw64Hqit vka2dL6TtXNRLqWw1/wtMwOZiOLjfYDV4GM68A/SUEVYb99gt/Xq8Q61gBUJl1Lj h2BSLXVg+4KtZ5K9juSE/27gDCVvDTmSUCTuo/5pjks1tDk0D2ohNIXiJp0twcyq Ectz97Mlx0SibaNtQbiFS3XbWUmEI6/d5XehFWMDkKj9D2k1nMyY2HWYo1GMjKRJ LAzniUzIuyqMBZq/GpSGX5uADn8fQ8DedRMfgEySM9f1TMJDYh5uzJ8Av4ZSmwBP bXr5au5+lS0085RauL47kKbP1Yf891MwdZFlkZnvzhU2y8HCrRncRjY2772jec6A g2CEMS7UMr9nQvw2AdZ4kEJe8ZlPcN9TNjZo7eWQwOFg8cBSpwP/Ma0gLw46V0Ze tBxKHQ3KER+JPVRlPsDhpZBSeviFw/h+Kuhm9YJIllsMLk+C7/+1baErRFm23Ylb 2vKJTbmEw98LjAL0il/LVToPr2fmmwuTdStrEpTAoG0QTSQ/Mr/4VDZKEQViz8ZH 3fffGXWit3/kpj6Vz3z6psErK0ndM95glLLjkrC/YnP3qEu8LRFjC5GTMEuZkS3N x00Whtlqa0gQYfxk4HUT =MIgc -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From andreas at an3as.eu Tue May 10 10:25:26 2016 From: andreas at an3as.eu (Andreas Tille) Date: Tue, 10 May 2016 12:25:26 +0200 Subject: [Debian-med-packaging] Several enhancements for FastML available as Debian patches Message-ID: <20160510102526.GF30189@an3as.eu> Hi, I'd like to inform you that we have assembled a set of patches for the Debian packaging of FastML. The latest ones are helpful to build the source with GCC version 6 (Thanks to Gert Wollny for the patch). I'd recommend you cherry pick from here https://anonscm.debian.org/cgit/debian-med/fastml.git/tree/debian/patches the commented patches - most of them are not really Debian specific. Kind regards and thanks for providing FastML as free software Andreas. -- http://fam-tille.de From owner at bugs.debian.org Tue May 10 10:27:16 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 10 May 2016 10:27:16 +0000 Subject: [Debian-med-packaging] Bug#811944: marked as done (fastml: FTBFS with GCC 6: template instantiation depth exceeds maximum) References: <20160120035508.GB4951@jirafa.cyrius.com> Message-ID: Your message dated Tue, 10 May 2016 10:23:30 +0000 with message-id and subject line Bug#811944: fixed in fastml 3.1-3 has caused the Debian Bug report #811944, regarding fastml: FTBFS with GCC 6: template instantiation depth exceeds maximum to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 811944: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811944 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Martin Michlmayr Subject: fastml: FTBFS with GCC 6: template instantiation depth exceeds maximum Date: Tue, 19 Jan 2016 19:55:08 -0800 Size: 6474 URL: -------------- next part -------------- An embedded message was scrubbed... From: Gert Wollny Subject: Bug#811944: fixed in fastml 3.1-3 Date: Tue, 10 May 2016 10:23:30 +0000 Size: 5723 URL: From ftpmaster at ftp-master.debian.org Tue May 10 11:42:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 11:42:04 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-genomicfeatures_1.24.0-1_amd64.changes Message-ID: r-bioc-genomicfeatures_1.24.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-genomicfeatures_1.24.0-1.dsc r-bioc-genomicfeatures_1.24.0.orig.tar.gz r-bioc-genomicfeatures_1.24.0-1.debian.tar.xz r-bioc-genomicfeatures_1.24.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 10 11:47:05 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 11:47:05 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-bsgenome_1.40.0-1_amd64.changes Message-ID: r-bioc-bsgenome_1.40.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-bsgenome_1.40.0-1.dsc r-bioc-bsgenome_1.40.0.orig.tar.gz r-bioc-bsgenome_1.40.0-1.debian.tar.xz r-bioc-bsgenome_1.40.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 10 11:47:05 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 11:47:05 +0000 Subject: [Debian-med-packaging] Processing of prottest_3.4.2+dfsg-1_amd64.changes Message-ID: prottest_3.4.2+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: prottest_3.4.2+dfsg-1.dsc prottest_3.4.2+dfsg.orig.tar.xz prottest_3.4.2+dfsg-1.debian.tar.xz prottest_3.4.2+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 10 11:49:05 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 11:49:05 +0000 Subject: [Debian-med-packaging] prottest_3.4.2+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 10 May 2016 13:34:08 +0200 Source: prottest Binary: prottest Architecture: source all Version: 3.4.2+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: prottest - selection of best-fit models of protein evolution Changes: prottest (3.4.2+dfsg-1) unstable; urgency=medium . * New upstream version * Use repack and compress option in watch file * Drop libnb-absolutelayout-java Build-Depends * Cleanup d/copyright from files removed upstream * cme fix dpkg-control Checksums-Sha1: f08e375dc64da077fed2b11b44215e200e036052 2060 prottest_3.4.2+dfsg-1.dsc 554e7e0d7b8f499867787631b73fcf524020b27e 254984 prottest_3.4.2+dfsg.orig.tar.xz e9f828fe525679efc86ee7fa8c2fdc2f30d734d9 5124 prottest_3.4.2+dfsg-1.debian.tar.xz 0e425ac37b2cdec70fca750a3081b7cb705aeb4e 346570 prottest_3.4.2+dfsg-1_all.deb Checksums-Sha256: 159a11143cf832a8bad5cb896394d53171b281a1c3e5585abb5e36c327f8e4cf 2060 prottest_3.4.2+dfsg-1.dsc b2cfcb76e40ada8b00b36c83e81c6af7df2f9f11d7556e6e1501e4f76b4add36 254984 prottest_3.4.2+dfsg.orig.tar.xz 9cc26a309dbd83c960220c1e277d1c69c01b1ccdb9b087a7373762924841767f 5124 prottest_3.4.2+dfsg-1.debian.tar.xz 8ee4c58eadf84b0583542b95ad9c0263272111c3a75a073aa6411ab03259bc04 346570 prottest_3.4.2+dfsg-1_all.deb Files: d3b9ce9c7199d168af232a4dc7cdf900 2060 science optional prottest_3.4.2+dfsg-1.dsc 30c9eeead6bcc890f69c6b3074956755 254984 science optional prottest_3.4.2+dfsg.orig.tar.xz 240e35245c9ab7601ae09181fecacf7c 5124 science optional prottest_3.4.2+dfsg-1.debian.tar.xz 767a034a93072d0d2e8329269c35a0ed 346570 science optional prottest_3.4.2+dfsg-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMckAAAoJEFeKBJTRxkbRg7UP/1PDFFn92hjePdLtHD0aTj9i tTVEDwtbryotx90vctPsCc9/Zp89ayHB2c6WggLc/ITlDGS1CwWLUwKklx5wbK/z EKIa6ca4MNnzzqV9XFnqw3QRR6w8PSRKtL33L7NseK3S6NMrAS5ppIHrXfQYpeWd 0/nZ/dhkvH3dQ5mBLDOqfQq3pbI1x2W9F9vgGclrPv9d0O7P7NmW2XoyQxMlr4hT rZBgxdl84G1SZyYtKQsL1c2gnEtF01x2fSrJRQY1pIrw/Uk6FXUqj0wuVMvmDW+p /QxHtcM1r7rk4cHmzDRAhkgVHg1OPi3YZl7KvPi/GaXexgY3GmPpmnzxd9j3+j3y u1loCwhgaBWdico3z7cUMHzKIHwg6ZaYtqlYGAW4ILy5dNLUKoatUcxiGYH404D0 i40y0nyf6rc1f/zH0oDKYOZ7eTVOscWudeUGIrSXy3WzKiDBDLY4HpVwoliqw3qO kw1Usb07nOu1lo5Yl44qPWeUvjPEpCtf0O7jlxb5z6EqLZebk7+h0s9HHLZScRwA /1QO5QgIWhqaH/CrG0elLuFVIfhhevJl7/2NhLWUAoY0uJcJKs84V0U+dG3yElL4 FJR9SOhV3CCLm36UxyMUmWdvuYlFn6/UfNmhADqIlMOR0GAXEqWTlV2h8aB0mNcC eL1kdGWg3XYgFnsM1E8M =mukK -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 10 11:49:21 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 11:49:21 +0000 Subject: [Debian-med-packaging] r-bioc-bsgenome_1.40.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 10 May 2016 13:41:01 +0200 Source: r-bioc-bsgenome Binary: r-bioc-bsgenome Architecture: source all Version: 1.40.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-bsgenome - BioConductor infrastructure for Biostrings-based genome data pack Changes: r-bioc-bsgenome (1.40.0-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 133f2fe8035c8cd0fcd584be4dd6f05523136cfb 2135 r-bioc-bsgenome_1.40.0-1.dsc 8f79a96435e461fa31284ce3d36a0051323fdba7 6059554 r-bioc-bsgenome_1.40.0.orig.tar.gz 8680c56d7050989c63d511217b328ca3341d0f3c 9744 r-bioc-bsgenome_1.40.0-1.debian.tar.xz 59862aa5d0123c1a746e2b562e2b6f08de5089bf 6444414 r-bioc-bsgenome_1.40.0-1_all.deb Checksums-Sha256: 3489f730bba8387d7b71c965b1f5239f92530e695073fa98c8dad458c5ca9ca9 2135 r-bioc-bsgenome_1.40.0-1.dsc 847c3cc4136ae60735996ece3eaa6529de6335171d2cca2091af2eed0fe1e321 6059554 r-bioc-bsgenome_1.40.0.orig.tar.gz fa790777028082eafc105d43d79ff9e8ed509b3bd393e519fc4794c446457bb1 9744 r-bioc-bsgenome_1.40.0-1.debian.tar.xz 7dad632a8546abfddd4f8fa69d58c4f0383a31abac9140097c46b1eb211609d2 6444414 r-bioc-bsgenome_1.40.0-1_all.deb Files: 5e81402b876ea98b77e4a46ae4e7de9a 2135 gnu-r optional r-bioc-bsgenome_1.40.0-1.dsc b7e0f0e41dc3fc8416db84afc95214a5 6059554 gnu-r optional r-bioc-bsgenome_1.40.0.orig.tar.gz 7e6347d23882489654961dba07746df2 9744 gnu-r optional r-bioc-bsgenome_1.40.0-1.debian.tar.xz 44bc3d624044e43697587c3781097890 6444414 gnu-r optional r-bioc-bsgenome_1.40.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMcn1AAoJEFeKBJTRxkbRQM8P/i18jq8rY/ygaqI86PF3jT95 kMgudJVtffh9hUj5eGGuPAN9bgTmRowQ2/W2s7uaJ3O4h5URbmWqdZXdQYUPZiDG Ytfn1617y+WuwqXtKkasDsr635ZCDSoM8v8CJe7ZNRH68AQULd7W6OqHAglvmu0i 8RU+ROEGvSrbDBa49kVYB+5rX5un6xRlPAGeoo/x2Dr4vpGUiRhsLc4rqHCpS+iA PzST/Z20UH2hcCQpW7C0Qr/Sx/ub3cRaC1/mBGSbiWBGwRS2Ej/fnMwKsQZyAGBj PfXZa43Rf/MgKLWWF1Zm9JX7V1jyEapWF1GiOrePfen6N6zCTUOUxydRT6OJlr0d zsdsTgUUlp+uzGQsBoh1j/wVvqD6IzhoEQXaB5aXE/ojbsDMY5IF758kGCmF5q3F Kw9YxJALzueSFS4GHwLTsnbkvRjz8QClJwYw1+k1Zc7KVWf72AL4mOC9pDj/cuNc 0kMcNvsxaQPUy6h6SlIpmWLNqBHaNXr+WNBARMBHnTm7P0R1KukkgvKp5FaNcVoM nUuG60xcR5IrC4jFVC15b7wVFEiEr2CY+3hUXvOCz1fWKDGKpMOrSZR3A/eD+i01 l3AuK1k17zQMoV9EfU8aFWeTOS7SXRXrXlANztVXT1MRT1S46UbTo0EA0tJKr4vj zK31M1BRGa2/7xESG+pH =7vPA -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 10 11:49:27 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 11:49:27 +0000 Subject: [Debian-med-packaging] r-bioc-genomicfeatures_1.24.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 10 May 2016 13:25:15 +0200 Source: r-bioc-genomicfeatures Binary: r-bioc-genomicfeatures Architecture: source all Version: 1.24.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-genomicfeatures - GNU R tools for making and manipulating transcript centric annota Changes: r-bioc-genomicfeatures (1.24.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: e617ef6a9f9cfae89398682deaa997e20e461cfc 2253 r-bioc-genomicfeatures_1.24.0-1.dsc 24f8a618c3f6a012749c84f52d1503130bcb5398 827275 r-bioc-genomicfeatures_1.24.0.orig.tar.gz 7dd45cc9ff4cac693742bad5ae29b70724af748b 6260 r-bioc-genomicfeatures_1.24.0-1.debian.tar.xz 5f30448638bad17116079a24b0f2fd01de58c7c0 1050434 r-bioc-genomicfeatures_1.24.0-1_all.deb Checksums-Sha256: 197524407f575019ffa13bfea7a3474feeb5f9d692593d7f2b5e0b31b3536e76 2253 r-bioc-genomicfeatures_1.24.0-1.dsc 4e2cd1f3252220579fda30cacb424ba280a7945bcd9bd6a56adfe5bc0ceed8e5 827275 r-bioc-genomicfeatures_1.24.0.orig.tar.gz cf1a1da4026e01a97ebb73f596218cbabf410239969eafa0d1ea1ac431d3b2f0 6260 r-bioc-genomicfeatures_1.24.0-1.debian.tar.xz e63227a60e2ca97b1123e048272dd04baaefd91925a767d1c2490758874d56f9 1050434 r-bioc-genomicfeatures_1.24.0-1_all.deb Files: cb7b1c0e0e08e3b6736f5827b9f94d0d 2253 gnu-r optional r-bioc-genomicfeatures_1.24.0-1.dsc 9b127207f96c60923bb2f45b633b56a1 827275 gnu-r optional r-bioc-genomicfeatures_1.24.0.orig.tar.gz 0b45f05cfdd3117029989d44d0108ae5 6260 gnu-r optional r-bioc-genomicfeatures_1.24.0-1.debian.tar.xz 2292cb3823e87789ec1ffd9d25d8cabc 1050434 gnu-r optional r-bioc-genomicfeatures_1.24.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMcgDAAoJEFeKBJTRxkbRTYEP/00/jYcW9NQaPCiuc5Fudf/1 GYhz2x7tJCB3cXRMpgNBHyXNaaBk3bkT8D+MR+Sd3iFy5swq6uHczBpmyCLLDmwB IiETo1YAWG3WNPH/6J9ocs0onzgRDiYs7lE82VPHk+GSrVglJZV6lJ5x/RY3UncT 9oRwrS42RLzvWluEzssri1lCtaXL+obuZQ8gjLyaY1CFPgjMovjKGm7LV2v0Ufi6 2sFmr9DRFq/fjL9kiPHSxbeI2wARAUAKh0U0g6k37tGOE9rQNOj6g+3eXLSJQA44 UNjx/2L3KlOiyU9/y45k/PVsYEWTL0p0gsyBSfAFKGW/1Kv5LThcES4g1AQ0V9dU llKRpPgZQc6m3jx0PSjmIjmdkNapgowvXHGXXZAWSOOhWUMSprFNuWt89t1iI6L1 I+xvBhPHiIbuIR9YgAwbjIFER1De3qDOrM20OE3zHe7xndbadw2VXJN1jWuJwyKi csNI1GW66F/2ioMQ7wP458KDEInxkCH+v/jSgZVU96J3DZKXLvPG2dWFVMPyv/hs lpD1aMr6aANdhPArcRf+757H7Es+xOPOP0R7f5oM4PRZsf6du6Qs3VzQxmR2l1dl wc+qzUL8g6bjY+5rUJNGuYJFLxItywY09lUDz3zGgo7s/6N44pull/VSXcLleYei /IXQ19KCKzCQHlNhlPLd =EfwR -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From edd at debian.org Tue May 10 12:13:57 2016 From: edd at debian.org (Dirk Eddelbuettel) Date: Tue, 10 May 2016 07:13:57 -0500 Subject: [Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer) In-Reply-To: <20160510080202.GC30189@an3as.eu> References: <20160509150152.GH8125@an3as.eu> <20160509183749.GB11437@an3as.eu> <22320.56622.851567.367229@max.nulle.part> <20160509191022.GC11437@an3as.eu> <22320.59137.142872.903240@max.nulle.part> <20160510080202.GC30189@an3as.eu> Message-ID: <22321.53381.449662.136549@max.nulle.part> On 10 May 2016 at 10:02, Andreas Tille wrote: | Hmmm, its no problem to kick out the relevant test (I managed on my | local disk successfully). But are you *really* sure that editing | autogenerated files that are actually not supposed to be edited manually | but under control of autoconf is the best solution for the problem? Of course editing configure.ac and re-creating configure is better. | I never ever had the need to edit a configure file and if there was ever I had to once or twice in the 20+ years here when the autoconf toolchain had issues, which can happen. | any need to fix a broken one using dh-autoreconf was the working | solution. Moreover I noticed that after *removing* configure the option | -DUSE_SSL was used while when I just skipped the test inside the | configure file it was *not* included which seems like the configure file | is broken in several ways. So it sounds reasonable to me to stick to my | initial strategy and to assume that the configure file was delivered by | accident and thus removing it. I can't comment on the specifics here but in general that is A Bad Idea. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org From tille at debian.org Tue May 10 13:02:08 2016 From: tille at debian.org (Andreas Tille) Date: Tue, 10 May 2016 15:02:08 +0200 Subject: [Debian-med-packaging] Bug#823920: ITP: jmodeltest -- HPC selection of models of nucleotide substitution Message-ID: <20160510130208.10541.56321.reportbug@mail.an3as.eu> Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name : jmodeltest Version : 2.1.10 Upstream Author : Diego Darriba * URL : https://github.com//ddarriba/jmodeltest2 * License : GPL Programming Lang: Java Description : HPC selection of models of nucleotide substitution jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model- averaged phylogenetic trees (both topology and branch length), heuristic filtering and automatic logging of user activity. This package is maintained by the Debian Med team at https://anonscm.debian.org/git/debian-med/jmodeltest.git From owner at bugs.debian.org Tue May 10 14:00:17 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 10 May 2016 14:00:17 +0000 Subject: [Debian-med-packaging] Processed: your mail References: Message-ID: Processing commands for control at bugs.debian.org: > affects 822785 = Bug #822785 [src:dcmtk] dcmjpls: Big Endian Transfer Syntax not handlled correctly Removed indication that 822785 affects src:gdcm and src:dcmtk > End of message, stopping processing here. Please contact me if you need assistance. -- 822785: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822785 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Tue May 10 15:10:16 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 15:10:16 +0000 Subject: [Debian-med-packaging] Processing of mypy_0.4.1-1_source.changes Message-ID: mypy_0.4.1-1_source.changes uploaded successfully to localhost along with the files: mypy_0.4.1-1.dsc mypy_0.4.1.orig.tar.gz mypy_0.4.1-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From debian at danny-edel.de Tue May 10 15:39:55 2016 From: debian at danny-edel.de (Danny Edel) Date: Tue, 10 May 2016 17:39:55 +0200 Subject: [Debian-med-packaging] Bug#777791: [PATCH] ball: ftbfs with GCC-5 In-Reply-To: <20160504121915.GF20381@an3as.eu> References: <20160107121229.GC26705@an3as.eu> <56A7A02D.6080501@danny-edel.de> <20160126193150.GD31910@an3as.eu> <570BB9B9.7020408@danny-edel.de> <20160411155403.GE31347@an3as.eu> <20160411155403.GE31347@an3as.eu> <570BE6E7.7060500@danny-edel.de> <20160411184127.GH31347@an3as.eu> <20160504121915.GF20381@an3as.eu> Message-ID: <573200CB.1050700@danny-edel.de> On 05/04/2016 02:19 PM, Andreas Tille wrote: > Any success with you alioth commits? Did you possibly pinged alioth > admins via IRC? I'd love to get you properly working as any normal > Debian Med member. If not I'd try to investigate. Hello Andreas, sorry for the late reply, but I have been able to commit now. Thank you for fixing this. I mirrored my changes as "fix-debian-bug-777791" branch to debian-med/ball.git, and deleted the temporary mirror. The work I pushed is equal to the patch from the last email, so it can be ignored now. I then rebuilt the package on a fresh sid cowbuilder, but now there's a new problem (see attachment for the exact error message) near the end of the build, involving a static_cast. I will look into that of course, but I did not want to overwrite the "master" branch before contacting you, especially not with a not-anymore-working solution. Will report back here, - Danny -------------- next part -------------- [ 79%] Building CXX object source/PYTHON/EXTENSIONS/CMakeFiles/VIEWmodule.dir/VIEWmodule/sipVIEWpart2.o /build/ball-1.4.3~beta1/build/source/PYTHON/EXTENSIONS/VIEWmodule/sipVIEWpart2.cpp: In function 'void* cast_Box(void*, const sipTypeDef*)': /build/ball-1.4.3~beta1/build/source/PYTHON/EXTENSIONS/VIEWmodule/sipVIEWpart2.cpp:3184:45: error: invalid static_cast from type 'BALL::VIEW::Box*' to type 'BALL::VIEW::Vertex2*' return static_cast(sipCpp); ^ source/PYTHON/EXTENSIONS/CMakeFiles/VIEWmodule.dir/build.make:383: recipe for target 'source/PYTHON/EXTENSIONS/CMakeFiles/VIEWmodule.dir/VIEWmodule/sipVIEWpart2.o' failed From ftpmaster at ftp-master.debian.org Tue May 10 16:04:27 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 16:04:27 +0000 Subject: [Debian-med-packaging] iva_1.0.5-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 05 May 2016 09:32:57 +0000 Source: iva Binary: iva Architecture: source amd64 Version: 1.0.5-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: iva - iterative virus sequence assembler Closes: 772547 Changes: iva (1.0.5-1) unstable; urgency=low . * Initial release (Closes: #772547) Checksums-Sha1: 26e0c01d1d5c68fa97542a8ef55c3b507f06bc6c 2098 iva_1.0.5-1.dsc b2d23dd778f192efdda6d971e209bef4dd4d9167 8762199 iva_1.0.5.orig.tar.gz 85dbd6fc778dfdb400ad87856504cf6b8e1eccfc 5412 iva_1.0.5-1.debian.tar.xz ae922a4cc9856ee8905a8de4a5f017334da45a8a 8576960 iva_1.0.5-1_amd64.deb Checksums-Sha256: 510d6f3016d00108d42504f3cce737faf7b50976afb11005ec3d3b5c1169d0cd 2098 iva_1.0.5-1.dsc 05ad4a24fb30047aaefc13fa4f7f29246e0cbea7835a0acd83c11cf44da10a3c 8762199 iva_1.0.5.orig.tar.gz 2348da190d10b40dad09dd1ccb5cf530682958352349e2ce7a45899954d3a047 5412 iva_1.0.5-1.debian.tar.xz c5638437eb12199b68c97ffa8f30fe58c6400525f40a3e0c02e5a8a54a667657 8576960 iva_1.0.5-1_amd64.deb Files: cd1c997f818767020a29f5b18ebad305 2098 science optional iva_1.0.5-1.dsc 43fce4144519ec9854b4ec967962cbd7 8762199 science optional iva_1.0.5.orig.tar.gz 3160305f586bb04c262a547d870eb803 5412 science optional iva_1.0.5-1.debian.tar.xz 823dbe60cdbccc9449a0b989ebaca847 8576960 science optional iva_1.0.5-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXK5+TAAoJEFeKBJTRxkbRfqoP/0eq3/ZckFMwC5LlPxn3yMst 9KlvIfTJxjHxuhgwAW9bwSHrOz2utLCYTbBkDsAd4r5tyZ83gWmshOiR3WOMYRMz Xt1PX8xBAFOm5cV76nHolwEYCm9siTPa+RK5T87Uk/DOn+zMGzmrYp8sBfrneGTw s+4sKD9LclkWCC0R18Bxv2RoIiBMMFmc0mUFSmzF3JyykBqJH3d9iY45DOOSMoAr phDNGAMbtPsT1fCNr+F3KRRbVRjdB+mofv/eugdte1C8hFnGll6OmzR0Nys/0dDj x0oso8RP4mwpu94swePlc3K7Lu2wIEbY3afMffiN6LPyvow9EJ3rvoPxIfgm+xXj +VR80yk0HyyEq1kPCQFhkmjUk2RDC3075nzZsoTiZ9/RG3pmJD12gys7WBWU7CiY vbx4/QMiTqNgvji2pv8WH/jPnhGULYkARhpGpuCCgyBJU80SdvrYkuWzRLrqOKt4 H6OmOIBRbch5arCZ6CECPFVQNm0ga9aAFOtK1qqcedKfEqBPZ0AI833j0FksfSJO Qn8w2VDjx5aZ9xrmQ4ovvqp1iUdue79bfNUtEDGpTOvz71KSBLrtIUtCHkLr9JyP 3lgAUptCH8ymBT7nLkMhkZd0dmOn8OZtFCGxNQqHIK/b9MFS0QGzjQuFQXF1yfVR snLAHnwT2e/Z4/b+gMiS =UMBV -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Tue May 10 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 10 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] jaligner 1.0+dfsg-2 MIGRATED to testing Message-ID: FYI: The status of the jaligner source package in Debian's testing distribution has changed. Previous version: 1.0+dfsg-1 Current version: 1.0+dfsg-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 10 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 10 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] proteinortho 5.13+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the proteinortho source package in Debian's testing distribution has changed. Previous version: 5.12+dfsg-1 Current version: 5.13+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 10 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 10 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] khmer 2.0+dfsg-6 MIGRATED to testing Message-ID: FYI: The status of the khmer source package in Debian's testing distribution has changed. Previous version: 2.0+dfsg-5 Current version: 2.0+dfsg-6 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Tue May 10 16:39:47 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 16:39:47 +0000 Subject: [Debian-med-packaging] mypy_0.4.1-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 10 May 2016 08:08:14 -0700 Source: mypy Binary: mypy Architecture: source Version: 0.4.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: mypy - Optional static typing for Python Changes: mypy (0.4.1-1) unstable; urgency=medium . * New upstream release Checksums-Sha1: c265cbc2aed83c60bf0ea9b057c1bc2cc4c58b78 1905 mypy_0.4.1-1.dsc 7f2799c5132f2534034d78d4d209909a73326b27 518028 mypy_0.4.1.orig.tar.gz cc8421cffdc9a99f7103a7d40a51691c01bf1ae6 2284 mypy_0.4.1-1.debian.tar.xz Checksums-Sha256: b78856a3b2e024a14a3e476f8648dd4433437e5a5874a633543a7404c988c34c 1905 mypy_0.4.1-1.dsc 1cee2474c573a54d06cbcda46e2afa58c36a69d54281cb9a9c7ec9ea10ba1b77 518028 mypy_0.4.1.orig.tar.gz d68e5e9c4ef07d04a90b7abcccbced76de0c1d24438957c76f91b44cf7ed10f5 2284 mypy_0.4.1-1.debian.tar.xz Files: dd481ce910dc944370f4cb2b5af7e4b2 1905 python optional mypy_0.4.1-1.dsc 9e20367f11e3fc0194c03b350ba5e611 518028 python optional mypy_0.4.1.orig.tar.gz 72a1689b2a2f53c8d6af2039d02780cd 2284 python optional mypy_0.4.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXMfm5AAoJEDwmdj9sZ+bixCAQAKaE9aNduM9r/bHZmDcjzSK9 sfleVVuFub1VCZAg6twrWZ5Fq7DCLkfN1B23qQOQOeM5yk3q3C0p8hW6uD01vik2 xkyy0AOjWYz8/yG8OoMcJN1eCii7x3L4/SqtDb5PC53HrYxP39okRqs+UnrXwE0G 61Rd45H0du5ip4/YAFmizx4w2HtgE0lVA29aOXVPDD/yKrOs1MGG/wUiXYPYliTd cPY7I++jlTtn6BiGRz6LVWvbBgr68bZi7AZwWhVvhxGLenstQZ+6t4Xul8BEWD1o rMdPa7OY896Eef7pignzPvNwB2aXEJCVQwWIWbfjXZxtzpGnaygTg+Mj5JvYsRn1 6tTTt8tCgvUgfl6t6PZb5WXTU0XF/DAs0JiEH5ookomuu8PUPpF2raNNIqo4S7IO TebjEcvKMUgYTkrl0NnDcj9utuqREl6eYUnYcByq2tpafk1nTpXeUE3uwVRSTHOR Uu22YODqIdGuD1ljpnGAhXA+Jn54XU96lKgFVBy2nSGoNR51s75c8O5r7ZSf39mo rOceD59HIUM9bUlHYOJEP2iIz0BpSGTB54m736jxRBJNt9ozjH5lvUlCC/dg3+FS g6CJjGItEnVcVSovv3/dUxciDDfToTnPOnAJBqBaPR5ZIO65JStC7RMW15BKkNzn 01Uj7LJwZio+B+0RACZ8 =cPyr -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From andreas at an3as.eu Tue May 10 17:13:28 2016 From: andreas at an3as.eu (Andreas Tille) Date: Tue, 10 May 2016 19:13:28 +0200 Subject: [Debian-med-packaging] Bug#777791: [PATCH] ball: ftbfs with GCC-5 In-Reply-To: <573200CB.1050700@danny-edel.de> References: <20160107121229.GC26705@an3as.eu> <56A7A02D.6080501@danny-edel.de> <20160126193150.GD31910@an3as.eu> <570BB9B9.7020408@danny-edel.de> <20160411155403.GE31347@an3as.eu> <20160411155403.GE31347@an3as.eu> <570BE6E7.7060500@danny-edel.de> <20160411184127.GH31347@an3as.eu> <20160504121915.GF20381@an3as.eu> <573200CB.1050700@danny-edel.de> Message-ID: <20160510171328.GA18647@an3as.eu> Hi Danny, On Tue, May 10, 2016 at 05:39:55PM +0200, Danny Edel wrote: > > sorry for the late reply, but I have been able to commit now. Thank you > for fixing this. I admit I did nothing than writing alioth admins ... but nice to know. :-) > I mirrored my changes as "fix-debian-bug-777791" branch to > debian-med/ball.git, and deleted the temporary mirror. The work I > pushed is equal to the patch from the last email, so it can be ignored now. > > I then rebuilt the package on a fresh sid cowbuilder, but now there's a > new problem (see attachment for the exact error message) near the end of > the build, involving a static_cast. Ahhh, Ball is a beast somehow - but the name beast ist just taken in our package name space. ;-) > I will look into that of course, > but I did not want to overwrite the "master" branch before contacting > you, especially not with a not-anymore-working solution. > > Will report back here, Thanks a lot. Your work is really appreciated. Please also be bold and commit to master. I have no time to look the next 2-3 days - but I'd like to see the changes in master since I see no point in deriving for this package what we are doing anywhere else. Kind regards and thanks again Andreas. -- http://fam-tille.de From debian at danny-edel.de Tue May 10 20:55:11 2016 From: debian at danny-edel.de (Danny Edel) Date: Tue, 10 May 2016 22:55:11 +0200 Subject: [Debian-med-packaging] Bug#777791: [PATCH] ball: ftbfs with GCC-5 In-Reply-To: <20160510171328.GA18647@an3as.eu> References: <20160107121229.GC26705@an3as.eu> <56A7A02D.6080501@danny-edel.de> <20160126193150.GD31910@an3as.eu> <570BB9B9.7020408@danny-edel.de> <20160411155403.GE31347@an3as.eu> <20160411155403.GE31347@an3as.eu> <570BE6E7.7060500@danny-edel.de> <20160411184127.GH31347@an3as.eu> <20160504121915.GF20381@an3as.eu> <573200CB.1050700@danny-edel.de> <20160510171328.GA18647@an3as.eu> Message-ID: <57324AAF.9040601@danny-edel.de> On 05/10/2016 07:13 PM, Andreas Tille wrote: > Thanks a lot. Your work is really appreciated. Please also be bold and > commit to master. I have no time to look the next 2-3 days - but I'd > like to see the changes in master since I see no point in deriving for > this package what we are doing anywhere else. Hi Andreas, I have backported a fix for the Python issue and ball now builds in a fresh sid cowbuilder. I also un-deleted the 0001-missingSigned.patch, since I realized it is needed on ARM, where "char" is "unsigned char" by default, causing FTBFS when assigning -1 to a "const char". This may be a candidate for a pullrequest to the newly moved upstream github repository. All patches are uploaded to "master", the work-in-progress branch is deleted. To me the resulting package (now without any weird hacks and old packages from snapshot.d.o) seems usable: I started BALLView and loaded random projects from /usr/share/BALL-1.4/data/projects, and I get molecule renderings on my screen -- but I have no idea if these are the right ones : ) Cheers, - Danny -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 473 bytes Desc: OpenPGP digital signature URL: From gw.fossdev at gmail.com Tue May 10 21:41:26 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Tue, 10 May 2016 23:41:26 +0200 Subject: [Debian-med-packaging] Bug#816569: mrs: FTBFS with GCC 6: was not declared in this scope Message-ID: <1462916486.11343.6.camel@gmail.com> Control: block -1 by ?823978 Hi,? I've added a patch to the packaging svn that fixes the problem, but building with g++-6 still doesn't work because of some boost-regex linking problem (see block request), Best,? Gert? From owner at bugs.debian.org Tue May 10 21:45:10 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 10 May 2016 21:45:10 +0000 Subject: [Debian-med-packaging] Processed: re: mrs: FTBFS with GCC 6: was not declared in this scope References: <1462916486.11343.6.camel@gmail.com> <20160303025644.GC16926@jirafa.cyrius.com> Message-ID: Processing control commands: > block -1 by ?823978 Bug #816569 [mrs] mrs: FTBFS with GCC 6: was not declared in this scope Bug #822466 [mrs] mrs: FTBFS: error: 'log' was not declared in this scope 816569 was not blocked by any bugs. 816569 was not blocking any bugs. Added blocking bug(s) of 816569: 823978 822466 was not blocked by any bugs. 822466 was not blocking any bugs. Added blocking bug(s) of 822466: 823978 -- 816569: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=816569 822466: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822466 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Tue May 10 21:46:37 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 21:46:37 +0000 Subject: [Debian-med-packaging] Processing of roary_3.6.2+dfsg-1_amd64.changes Message-ID: roary_3.6.2+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: roary_3.6.2+dfsg-1.dsc roary_3.6.2+dfsg.orig.tar.gz roary_3.6.2+dfsg-1.debian.tar.xz roary_3.6.2+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 10 22:46:39 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 10 May 2016 22:46:39 +0000 Subject: [Debian-med-packaging] roary_3.6.2+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 10 May 2016 21:30:25 +0000 Source: roary Binary: roary Architecture: source all Version: 3.6.2+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.6.2+dfsg-1) unstable; urgency=medium . * New upstream release. * Drop patches applied by upstream. 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From steve at sumost.ca Tue May 10 23:46:53 2016 From: steve at sumost.ca (Steve M. Robbins) Date: Tue, 10 May 2016 18:46:53 -0500 Subject: [Debian-med-packaging] [pkg-boost-devel] Processed: re: mrs: FTBFS with GCC 6: was not declared in this scope In-Reply-To: References: <1462916486.11343.6.camel@gmail.com> <20160303025644.GC16926@jirafa.cyrius.com> Message-ID: <5146882.K2Vjy8fmcx@riemann> Hi Gert, Boost 1.58 (and 1.60) is compiled with the default gcc (currently 5) and default gcc flags. For gcc 5, this means the C++03 api. So if mrs requires -std=c++11, I think you're out of luck with Debian's boost, until it is built with -std=c++11. At least, this is my understanding. Appreciate confirmation or refutation from more knowledgeable folks! -Steve -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 819 bytes Desc: This is a digitally signed message part. URL: From gw.fossdev at gmail.com Wed May 11 08:28:44 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Wed, 11 May 2016 10:28:44 +0200 Subject: [Debian-med-packaging] [pkg-boost-devel] Processed: re: mrs: FTBFS with GCC 6: was not declared in this scope In-Reply-To: <5146882.K2Vjy8fmcx@riemann> References: <1462916486.11343.6.camel@gmail.com> <20160303025644.GC16926@jirafa.cyrius.com> <5146882.K2Vjy8fmcx@riemann> Message-ID: <1462955324.11343.15.camel@gmail.com> Hello Steve,? Am Dienstag, den 10.05.2016, 18:46 -0500 schrieb Steve M. Robbins: > So if mrs requires -std=c++11, I think you're out of luck with > Debian's boost, ?until it is built with -std=c++11.??At least, this > is my understanding. ? This is also exactly my understanding. Now I also remember that I have seen this before with boost and the use of enums. With C++11 enums can be strongly typed, boost enebles/disables this in the headers regardless of what was used when compiling boost itself.? The only way to work around this was not to use certain functionality.? best,? Gert? From ftpmaster at ftp-master.debian.org Wed May 11 08:41:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 08:41:55 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-variantannotation_1.18.0-1_amd64.changes Message-ID: r-bioc-variantannotation_1.18.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-variantannotation_1.18.0-1.dsc r-bioc-variantannotation_1.18.0.orig.tar.gz r-bioc-variantannotation_1.18.0-1.debian.tar.xz r-bioc-variantannotation-dbgsym_1.18.0-1_amd64.deb r-bioc-variantannotation_1.18.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 11 08:47:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 08:47:01 +0000 Subject: [Debian-med-packaging] Processing of mpj_0.44+dfsg-1_amd64.changes Message-ID: mpj_0.44+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: mpj_0.44+dfsg-1.dsc mpj_0.44+dfsg.orig.tar.xz mpj_0.44+dfsg-1.debian.tar.xz libmpj-java_0.44+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From kwejes_ubaliana at goo.jp Wed May 11 08:42:20 2016 From: kwejes_ubaliana at goo.jp (Ms. Laura Sebastiani) Date: Wed, 11 May 2016 17:42:20 +0900 (JST) Subject: [Debian-med-packaging] ORDER INQUIRY:: Message-ID: <380894817.76634072.1462956140455.JavaMail.root@goo.jp> Dear Seller, We are very interested in your product. We need your best quote and more specifications of your products for immediate purchase. Please send your reply ASAP. Regards, Ms. Laura Sebastiani. C.E.O 79 Turkey ways Road... Email:uffromabelettronica2 at gmail.com From ftpmaster at ftp-master.debian.org Wed May 11 09:52:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 09:52:54 +0000 Subject: [Debian-med-packaging] mpj_0.44+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 11 May 2016 10:38:23 +0200 Source: mpj Binary: libmpj-java Architecture: source all Version: 0.44+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libmpj-java - Java library for parallel applications for multicore processors a Changes: mpj (0.44+dfsg-1) unstable; urgency=medium . * New upstream version * Moved packaging to Debian Java team * Use compression options of uscan in d/watch * Fix clean target * Install all JARs build by the project * Try to add build time tests but failed Checksums-Sha1: 66697c5efa95b16f069eb036344d156d29a01b3a 2033 mpj_0.44+dfsg-1.dsc b0bb17e657c17901888b5b95bb217bf096e30e4b 1947092 mpj_0.44+dfsg.orig.tar.xz a9b523a260f5749ee532230cd8c97ba3588756bf 4832 mpj_0.44+dfsg-1.debian.tar.xz 03c4aa9b46d84ae858fc910b377d84b79ead0878 436394 libmpj-java_0.44+dfsg-1_all.deb Checksums-Sha256: bcf2e2de7ad21be8e8686f65577834cc19ddd3600379e97b5e36f02821d3f9c6 2033 mpj_0.44+dfsg-1.dsc 75ab5bbb2e40359c75cb30222b6d85d2ba0d1291a0fcef0c6b0b4f465436bb75 1947092 mpj_0.44+dfsg.orig.tar.xz d4d335468c7da00609262b89893bb21ecb1c3660723419dad2e88332ca6d1c67 4832 mpj_0.44+dfsg-1.debian.tar.xz ea1d546050d3e4878379c12dbc1056435b9cb35de821ceb11ef47ded94243354 436394 libmpj-java_0.44+dfsg-1_all.deb Files: c22feafd5d32ede4eeafc75ce2254aef 2033 java optional mpj_0.44+dfsg-1.dsc 7ca244eaebaaa16827d7bbbb9d1436a3 1947092 java optional mpj_0.44+dfsg.orig.tar.xz 48617fe17ba83466a818710825ea1977 4832 java optional mpj_0.44+dfsg-1.debian.tar.xz b366696ec0f14076a104b07d72666517 436394 java optional libmpj-java_0.44+dfsg-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMvESAAoJEFeKBJTRxkbRYu8P/17DzVW7oEZLe5oS00zqMfkt dJNoVABq7wqDWv2RGl5ebQ8msNKnYGaycQLq58JrNUghveWbMte9oScBkn9+nzPZ zV4EaWSdmbPHaHdhr5ko12G8XvW/EiETo+4UdP5aMiT/+YNA0ZnjgZdByj+ZI8Zn 9Etgdz+Res15olFDjpuiBHJjIAeoIfRxaw17T6CzvTBRuzKCvrhIkC6DWkME6rL8 67PRv7R2ua1Za/jke3Zk+iyqRtDDLnBK4o3Qlr/OIPPUBKhJMB1EJbCR7/L5JmdZ TV/8kA1trf+fmVrLNmqh1Nf12hSW6HyL4u/pKUDWEhkmYUsBkAssV3hpqdEXqAYX ThR9/maZHVxXL5NnhGlrnol/b9GkmvXl9wKWzkaWOPru/jPGIutsv4yG5O6xyPIZ xKFIgLwaAg5KwQHyrTVaJ/7jUutbPB2tbED5FafCSKogXUnw7yxGoVX1rZtYURtX WXW7P4z3E+r/JtOe30lpKOVMAX7iUa76cJ968uJdztr6kdVdgYoA22XBF+qr9DsA q0G+aFHw+iRy4ZfVPYIXQUgtElBwZC0218GqYWyVaRKMtr1jT87cmlmyTQ6FnkZg +LfHWosC50SeIpPNs6vlKusiuNE2xrWarVWr5+RTQ9hMst8/Ody2k484H3EPw/ih YHucO3GHLMyQM3K7q76G =bDll -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 11 09:55:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 09:55:40 +0000 Subject: [Debian-med-packaging] r-bioc-variantannotation_1.18.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 11 May 2016 10:05:34 +0200 Source: r-bioc-variantannotation Binary: r-bioc-variantannotation Architecture: source amd64 Version: 1.18.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-variantannotation - BioConductor annotation of genetic variants Changes: r-bioc-variantannotation (1.18.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 24e60266545b2c3bbe5515978705acc73ec042ec 2276 r-bioc-variantannotation_1.18.0-1.dsc 57548f51c636eb2db26830a4c731c1c1d6c5c7d7 1636465 r-bioc-variantannotation_1.18.0.orig.tar.gz 9eb2dc836c94ae58b7a9f17c9a49d1efcb3f162c 7184 r-bioc-variantannotation_1.18.0-1.debian.tar.xz f3858a35cba543354e6caa73126287947263f740 65698 r-bioc-variantannotation-dbgsym_1.18.0-1_amd64.deb b23c41095a3fd83e8be3949ebbf447a857881085 2176460 r-bioc-variantannotation_1.18.0-1_amd64.deb Checksums-Sha256: fc3f92b35d143fa55a810ad0e3707b997f31ad0c973c5879354aac257eefb97d 2276 r-bioc-variantannotation_1.18.0-1.dsc 59710b00b5e8bcdb8aa0f30bb60b4fa37aab13b732283824ab5e56b0d52c55d6 1636465 r-bioc-variantannotation_1.18.0.orig.tar.gz 4fdb41075353574729898a952fc8ceeef3f1cb81f7250b0b36695ea67f4ee966 7184 r-bioc-variantannotation_1.18.0-1.debian.tar.xz 4beba5ae47b3ddcaefd1a727435b9cec0dd6d7a730e6a09e2dbd5a4ed5c2663e 65698 r-bioc-variantannotation-dbgsym_1.18.0-1_amd64.deb 9ebd58c261882bd1410c76ea3b8ffca4c07e1302d6fc54641f5e8f93d955b4e5 2176460 r-bioc-variantannotation_1.18.0-1_amd64.deb Files: 17482526e1ea3a108fa1cff4053a4e3b 2276 gnu-r optional r-bioc-variantannotation_1.18.0-1.dsc 0cd04a0d92f368d534e6eb7bcaafd5d3 1636465 gnu-r optional r-bioc-variantannotation_1.18.0.orig.tar.gz d171a656c3da1eddabcfb97545fd5d85 7184 gnu-r optional r-bioc-variantannotation_1.18.0-1.debian.tar.xz 47fa7ff658041b879519b850fed80a6c 65698 debug extra r-bioc-variantannotation-dbgsym_1.18.0-1_amd64.deb f583216f6b881037fa3c70c2dacce792 2176460 gnu-r optional r-bioc-variantannotation_1.18.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXMu+YAAoJEFeKBJTRxkbRhL8P/2bg9KW0+EPH3lhE1nnQ0PRv TyexBH6n7frGdGVsMDrZWPp0jc2dARj01pNk4uFrdBBjglgOExUW2AVA3M57oEDD D/u70KdF8kjrflCppVwv6RcG20FOSCH/IOjc7KthCiFL3zA5439m4R3Zkg8eAZOi Qp5Ny6rRhpgUMrFlAQZtUPfRdToRaHTk4bdo205jKx2IMcCAr2kaEH/of2XKU36f CSUc3bLyjeWNNnVIfJrMQ1cArawNpscniyVgWGTKzpXqDeTBsavBBGun2B1QhtvM tj4TmId2rXXZ3DF9JFaYQgUgRFDqugx67DEj2m54/lhKK/tkvuh/8UJyBlXtq3G8 ChHlx0e/PHJ2kgkOMaJ6RLie7dnLTpUq8oU+MnmeTlO5jXE+SA5FzmvM7nHTkz7k T70jHCXtuHGbCL+75BWLS8kpGTVg7LfZidGq92C3baXohvz5a4wZqyX60yI6YWkv QYTo++nm0Fcc68ubAs9E17RqDkwBj6NQYDeU+g5o99Nfhyl2eM+lNbvU03w6sVDy ki6z/u5ngGmDVxtmTnxleDc9WMrh/ukXD1BlwBs1iNkjRg29T+bPhjlwL1Tm035H biA+Yyhyb/ROIFyKcBESzxsmTY/MjtnXKT5Df8FBtUe7cINqtDPiSFuE1yWoghJg x0C8aIJ5NBbFXuTy6i+w =ddmW -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From gw.fossdev at gmail.com Wed May 11 10:13:20 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Wed, 11 May 2016 12:13:20 +0200 Subject: [Debian-med-packaging] Bug#824013: libzeep: FTBFS with g++6 and libboost-1.60 also compiled with g++-6 Message-ID: <146296160007.29988.16888204778007802937.reportbug@rohan.bai-gerddie.de> Source: libzeep Version: 3.0.2-3 Severity: important Tags: patch Control: block 816569 by -1 When compiled against libboost1.60 that is compiled with g++-6 compilation fails because std::tie and boost::fusion::tie are both availabe with equal signatures (see below). The attached patch fixes this. Currently, boost1.60 is still compiled with g++-5 and not yet the default, but this will probably change soon. error log: g++ -MD -c -o obj/doctype.o src/doctype.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -I. -fPIC -pthread -shared -std=c++0x -Wall src/doctype.cpp: In member function 'virtual boost::fusion::tuple zeep::xml::doctype::state_repeated_zero_or_once::allow(const string&)': src/doctype.cpp:135:20: error: call of overloaded 'tie(bool&, bool&)' is ambiguous tie(result, done) = m_sub->allow(name); ^ In file included from /usr/include/boost/fusion/tuple.hpp:13:0, from /usr/include/boost/fusion/include/tuple.hpp:11, from /usr/include/boost/tr1/tuple.hpp:58, from src/doctype.cpp:12: /usr/include/boost/fusion/tuple/tuple_tie.hpp:30:5: note: candidate: boost::fusion::tuple boost::fusion::tie(T& ...) [with T = {bool, bool}] tie(T&... arg) ^~~ In file included from /usr/include/c++/6/functional:55:0, from /usr/include/boost/fusion/support/detail/as_fusion_element.hpp:15, from /usr/include/boost/fusion/algorithm/transformation/push_back.hpp:11, from /usr/include/boost/fusion/view/iterator_range/detail/segmented_iterator_range.hpp:20, from /usr/include/boost/fusion/view/iterator_range/detail/segments_impl.hpp:14, from /usr/include/boost/fusion/view/iterator_range/iterator_range.hpp:22, from /usr/include/boost/fusion/view/iterator_range.hpp:11, from /usr/include/boost/fusion/sequence/intrinsic/detail/segmented_begin.hpp:13, from /usr/include/boost/fusion/sequence/intrinsic/begin.hpp:18, from /usr/include/boost/fusion/mpl/begin.hpp:12, from /usr/include/boost/fusion/sequence/intrinsic/detail/segmented_size.hpp:18, from /usr/include/boost/fusion/sequence/intrinsic/size.hpp:17, from /usr/include/boost/fusion/container/vector/vector.hpp:32, from /usr/include/boost/fusion/tuple/tuple.hpp:23, from /usr/include/boost/fusion/tuple.hpp:11, from /usr/include/boost/fusion/include/tuple.hpp:11, from /usr/include/boost/tr1/tuple.hpp:58, from src/doctype.cpp:12: /usr/include/c++/6/tuple:1521:5: note: candidate: constexpr std::tuple<_Elements& ...> std::tie(_Elements& ...) [with _Elements = {bool, bool}] tie(_Elements&... __args) noexcept ^~~ src/doctype.cpp:143:20: error: call of overloaded 'tie(bool&, bool&)' is ambiguous tie(result, done) = m_sub->allow(name); ^ Best, Gert -- System Information: Debian Release: stretch/sid APT prefers unstable-debug APT policy: (500, 'unstable-debug'), (500, 'unstable'), (500, 'testing'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.5.0-2-amd64 (SMP w/2 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) -------------- next part -------------- A non-text attachment was scrubbed... Name: libzeep-3.0-g++-6-boost1.60.patch Type: text/x-diff Size: 3494 bytes Desc: not available URL: From gw.fossdev at gmail.com Wed May 11 10:21:14 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Wed, 11 May 2016 12:21:14 +0200 Subject: [Debian-med-packaging] Bug#816569: Also need to fix libzeep first Message-ID: <1462962074.11343.31.camel@gmail.com> Control: block 816569 by 824013 The fix will have to wait until libboost1.60 becomes the default and is build by using g++-6. In addition libzeep needs then to be fixed first (see blocker).? cheers,? Gert? From owner at bugs.debian.org Wed May 11 10:24:08 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Wed, 11 May 2016 10:24:08 +0000 Subject: [Debian-med-packaging] Processed: Also need to fix libzeep first References: <1462962074.11343.31.camel@gmail.com> <20160303025644.GC16926@jirafa.cyrius.com> Message-ID: Processing control commands: > block 816569 by 824013 Bug #816569 [mrs] mrs: FTBFS with GCC 6: was not declared in this scope Bug #822466 [mrs] mrs: FTBFS: error: 'log' was not declared in this scope 816569 was blocked by: 823978 816569 was not blocking any bugs. Added blocking bug(s) of 816569: 824013 822466 was blocked by: 823978 822466 was not blocking any bugs. Added blocking bug(s) of 822466: 824013 -- 816569: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=816569 822466: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822466 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From plessy at debian.org Wed May 11 13:48:28 2016 From: plessy at debian.org (Charles Plessy) Date: Wed, 11 May 2016 22:48:28 +0900 Subject: [Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer) In-Reply-To: <20160509150152.GH8125@an3as.eu> References: <20160509150152.GH8125@an3as.eu> Message-ID: <20160511134828.GA15539@bubu.igloo> Le Mon, May 09, 2016 at 05:01:52PM +0200, Andreas Tille a ?crit : > > * installing *source* package 'rtracklayer' ... > configure: error: cannot find sources (rtracklayer) in . or .. > ERROR: configuration failed for package 'rtracklayer' > The issue is that the configure scripts seeks a dir rtracklayer either > in . or .. but pbuilder renames the build directory to > r-bioc-rtracklayer-1.32.0. The package builds fine with debuild. Hi Andreas, Dirk and everybody, the source of the problem here is the command AC_INIT("rtracklayer") in configure.ac. According to the autoconf manual, it is an obsolete use of the AC_INIT macro to pass it a single agument: https://www.gnu.org/software/autoconf/manual/autoconf-2.69/html_node/Obsolete-Macros.html ? Macro: AC_INIT (unique-file-in-source-dir) Formerly AC_INIT used to have a single argument, and was equivalent to: AC_INIT AC_CONFIG_SRCDIR(unique-file-in-source-dir) See AC_INIT and AC_CONFIG_SRCDIR. Indeed, replacing AC_INIT("rtracklayer") with just AC_INIT or AC_INIT(rtracklayer, 1.32.0) and running autoreconf -f removes the line ac_unique_file=""rtracklayer"" in the configure script. As a temporary workaround, the simplest for us would be to run "touch rtracklayer" somewhere in debian/rules. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From ftpmaster at ftp-master.debian.org Wed May 11 15:38:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 15:38:55 +0000 Subject: [Debian-med-packaging] Processing of prottest_3.4.2+dfsg-2_amd64.changes Message-ID: prottest_3.4.2+dfsg-2_amd64.changes uploaded successfully to localhost along with the files: prottest_3.4.2+dfsg-2.dsc prottest_3.4.2+dfsg-2.debian.tar.xz prottest_3.4.2+dfsg-2_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From noreply at release.debian.org Wed May 11 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 11 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] gdcm 2.6.3-5 MIGRATED to testing Message-ID: FYI: The status of the gdcm source package in Debian's testing distribution has changed. Previous version: 2.6.3-3 Current version: 2.6.3-5 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 11 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 11 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] mialmpick 0.2.12-1 MIGRATED to testing Message-ID: FYI: The status of the mialmpick source package in Debian's testing distribution has changed. Previous version: 0.2.11-1 Current version: 0.2.12-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 11 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 11 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] libmialm 1.0.8-3 MIGRATED to testing Message-ID: FYI: The status of the libmialm source package in Debian's testing distribution has changed. Previous version: 1.0.8-2 Current version: 1.0.8-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From lamby at debian.org Wed May 11 16:35:27 2016 From: lamby at debian.org (Chris Lamb) Date: Wed, 11 May 2016 17:35:27 +0100 Subject: [Debian-med-packaging] Bug#824048: python-biopython: FTBFS: AssertionError: 10 != 1 Message-ID: <1462984527.2366877.604901465.716271DC@webmail.messagingengine.com> Source: python-biopython Version: 1.66+dfsg-2 Severity: serious Justification: fails to build from source User: reproducible-builds at lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org Dear Maintainer, python-biopython fails to build from source in unstable/amd64: [..] cp -a Doc/Tutorial.tex /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \ cp -a Doc/Tutorial /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \ cp -a Doc/examples /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \ cp -a Tests /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build; \ cd /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home python2.7 run_tests.py --offline test_Ace ... ok test_AlignIO ... ok test_AlignIO_ClustalIO ... ok test_AlignIO_EmbossIO ... ok test_AlignIO_FastaIO ... ok test_AlignIO_PhylipIO ... ok test_AlignIO_convert ... ok test_Application ... ok test_BWA_tool ... ok test_BioSQL_mysql_connector ... skipping. Install mysql.connector if you want to use mysql with BioSQL test_BioSQL_sqlite3 ... ok test_CAPS ... ok test_CelFile ... ok test_Chi2 ... ok test_ClustalOmega_tool ... ok test_Clustalw_tool ... ok test_Cluster ... ok test_CodonTable ... ok test_CodonUsage ... ok test_ColorSpiral ... ok test_Compass ... ok test_Consensus ... ok test_Crystal ... ok test_DSSP_tool ... ok test_Dialign_tool ... ok test_DocSQL ... ok test_EMBL_unittest ... ok test_Emboss ... ok test_EmbossPrimer ... ok test_Entrez ... ok test_Entrez_online ... skipping. internet not available test_Enzyme ... ok test_FSSP ... ok test_Fasttree_tool ... ok test_File ... ok test_GACrossover ... ok test_GAMutation ... ok test_GAOrganism ... ok test_GAQueens ... ok test_GARepair ... ok test_GASelection ... ok test_GenBank ... ok test_GenBank_unittest ... ok test_GenomeDiagram ... ok test_GraphicsBitmaps ... ok test_GraphicsChromosome ... ok test_GraphicsDistribution ... ok test_GraphicsGeneral ... ok test_HMMCasino ... ok test_HMMGeneral ... ok test_KDTree ... ok test_KEGG ... ok test_KEGG_online ... skipping. internet not available test_KGML_graphics ... ok test_KGML_graphics_online ... skipping. internet not available test_KGML_nographics ... ok test_KeyWList ... ok test_Location ... ok test_LogisticRegression ... ok test_MMCIF ... ok test_Mafft_tool ... ok test_MarkovModel ... ok test_Medline ... ok test_Motif ... ok test_Muscle_tool ... ok test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_NCBI_BLAST_tools.py:280: UserWarning: NCBI BLAST+ deltablast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -save_each_pssm,-save_pssm_after_last_round) ",".join(sorted(missing)))) /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_NCBI_BLAST_tools.py:280: UserWarning: NCBI BLAST+ psiblast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -save_each_pssm,-save_pssm_after_last_round) ",".join(sorted(missing)))) FAIL test_NCBI_qblast ... skipping. internet not available test_NNExclusiveOr ... ok test_NNGene ... ok test_NNGeneral ... ok test_Nexus ... ok test_PAML_baseml ... ok test_PAML_codeml ... ok test_PAML_yn00 ... ok test_PDB ... ok test_PDB_KDTree ... ok test_ParserSupport ... ok test_Pathway ... ok test_Phd ... ok test_Phylo ... ok test_PhyloXML ... ok test_Phylo_CDAO ... ok test_Phylo_NeXML ... ok test_Phylo_depend ... /usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') ok test_PopGen_FDist_nodepend ... ok test_PopGen_FastSimCoal ... skipping. Install fastsimcoal if you want to use Bio.PopGen.SimCoal.Controller.FastSimCoalController. test_PopGen_GenePop_nodepend ... ok test_PopGen_SimCoal_nodepend ... ok test_Prank_tool ... ok test_Probcons_tool ... ok test_ProtParam ... ok test_QCPSuperimposer ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/QCPSuperimposer/__init__.py:22: BiopythonExperimentalWarning: Bio.PDB.QCPSuperimposer is an experimental submodule which may undergo significant changes prior to its future official release. BiopythonExperimentalWarning) ok test_Restriction ... ok test_SCOP_Astral ... ok test_SCOP_Cla ... ok test_SCOP_Des ... ok test_SCOP_Dom ... ok test_SCOP_Hie ... ok test_SCOP_Raf ... ok test_SCOP_Residues ... ok test_SCOP_Scop ... ok test_SCOP_online ... skipping. internet not available test_SVDSuperimposer ... ok test_SearchIO_blast_tab ... ok test_SearchIO_blast_tab_index ... ok test_SearchIO_blast_text ... ok test_SearchIO_blast_xml ... ok test_SearchIO_blast_xml_index ... ok test_SearchIO_blat_psl ... ok test_SearchIO_blat_psl_index ... ok test_SearchIO_exonerate ... ok test_SearchIO_exonerate_text_index ... ok test_SearchIO_exonerate_vulgar_index ... ok test_SearchIO_fasta_m10 ... ok test_SearchIO_fasta_m10_index ... ok test_SearchIO_hmmer2_text ... ok test_SearchIO_hmmer2_text_index ... ok test_SearchIO_hmmer3_domtab ... ok test_SearchIO_hmmer3_domtab_index ... ok test_SearchIO_hmmer3_tab ... ok test_SearchIO_hmmer3_tab_index ... ok test_SearchIO_hmmer3_text ... ok test_SearchIO_hmmer3_text_index ... ok test_SearchIO_model ... ok test_SearchIO_write ... ok test_SeqIO ... ok test_SeqIO_AbiIO ... ok test_SeqIO_FastaIO ... ok test_SeqIO_Insdc ... ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_convert ... ok test_SeqIO_features ... ok test_SeqIO_index ... ok test_SeqIO_online ... skipping. internet not available test_SeqIO_write ... ok test_SeqRecord ... ok test_SeqUtils ... ok test_Seq_objs ... ok test_SffIO ... ok test_SubsMat ... ok test_SwissProt ... ok test_TCoffee_tool ... ok test_TogoWS ... skipping. internet not available test_TreeConstruction ... ok test_Tutorial ... ok test_UniGene ... ok test_Uniprot ... ok test_Wise ... ok test_align ... ok test_bgzf ... ok test_codonalign ... ok test_geo ... ok test_kNN ... ok test_lowess ... ok test_motifs ... ok test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_prodoc ... ok test_prosite1 ... ok test_prosite2 ... ok test_psw ... ok test_py3k ... ok test_raxml_tool ... ok test_seq ... ok test_translate ... ok test_trie ... ok Bio.Align docstring test ... ok Bio.Align.Generic docstring test ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Generic.py:55: BiopythonDeprecationWarning: With the introduction of the MultipleSeqAlignment class in Bio.Align, this base class is deprecated and is likely to be removed in a future release of Biopython. warnings.warn("With the introduction of the MultipleSeqAlignment class in Bio.Align, this base class is deprecated and is likely to be removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning) ok Bio.Align.Applications._Clustalw docstring test ... ok Bio.Align.Applications._ClustalOmega docstring test ... ok Bio.Align.Applications._MSAProbs docstring test ... ok Bio.Align.Applications._Mafft docstring test ... ok Bio.Align.Applications._Muscle docstring test ... ok Bio.Align.Applications._Probcons docstring test ... ok Bio.Align.Applications._Prank docstring test ... ok Bio.Align.Applications._TCoffee docstring test ... ok Bio.AlignIO docstring test ... ok Bio.AlignIO.StockholmIO docstring test ... ok Bio.Alphabet docstring test ... ok Bio.Application docstring test ... ok Bio.bgzf docstring test ... ok Bio.codonalign docstring test ... ok Bio.Blast.Applications docstring test ... ok Bio.Emboss.Applications docstring test ... ok Bio.GenBank docstring test ... ok Bio.KEGG.Compound docstring test ... ok Bio.KEGG.Enzyme docstring test ... ok Bio.NMR.xpktools docstring test ... ok Bio.Motif docstring test ... ok Bio.motifs docstring test ... ok Bio.motifs.applications._alignace docstring test ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/applications/_alignace.py:54: BiopythonDeprecationWarning: The AlignACE application wrapper is deprecated and is likely to be removed in a future release of Biopython, since an up to date version of the AlignACE software cannot be obtained anymore. If you have a copy of AlignACE 4, please consider contacting the Biopython developers. developers.""", BiopythonDeprecationWarning) /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/applications/_alignace.py:122: BiopythonDeprecationWarning: The CompareACE application wrapper is deprecated and is likely to be removed in a future release of Biopython, since an up to date version of the AlignACE software cannot be obtained anymore. If you have a copy of AlignACE 4, please consider contacting the Biopython developers. developers.""", BiopythonDeprecationWarning) ok Bio.motifs.applications._xxmotif docstring test ... ok Bio.pairwise2 docstring test ... ok Bio.Phylo.Applications._Raxml docstring test ... ok Bio.SearchIO docstring test ... ok Bio.SearchIO._model docstring test ... ok Bio.SearchIO._model.query docstring test ... ok Bio.SearchIO._model.hit docstring test ... ok Bio.SearchIO._model.hsp docstring test ... ok Bio.SearchIO.BlastIO docstring test ... ok Bio.SearchIO.HmmerIO docstring test ... ok Bio.SearchIO.FastaIO docstring test ... ok Bio.SearchIO.BlatIO docstring test ... ok Bio.SearchIO.ExonerateIO docstring test ... ok Bio.Seq docstring test ... ok Bio.SeqIO docstring test ... ok Bio.SeqIO.FastaIO docstring test ... ok Bio.SeqIO.AceIO docstring test ... ok Bio.SeqIO.PhdIO docstring test ... ok Bio.SeqIO.QualityIO docstring test ... ok Bio.SeqIO.SffIO docstring test ... ok Bio.SeqFeature docstring test ... ok Bio.SeqRecord docstring test ... ok Bio.SeqUtils docstring test ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils/__init__.py:560: BiopythonDeprecationWarning: The quick_FASTA_reader has been deprecated and will be removed in a future release of Biopython. Please try function SimpleFastaParser from Bio.SeqIO.FastaIO instead. "instead.", BiopythonDeprecationWarning) ok Bio.SeqUtils.MeltingTemp docstring test ... ok Bio.Sequencing.Applications._Novoalign docstring test ... ok Bio.Sequencing.Applications._bwa docstring test ... ok Bio.Sequencing.Applications._samtools docstring test ... ok Bio.Wise docstring test ... ok Bio.Wise.psw docstring test ... ok Bio.Affy.CelFile docstring test ... ok Bio.Statistics.lowess docstring test ... ok Bio.PDB.Polypeptide docstring test ... ok Bio.PDB.Selection docstring test ... ok ====================================================================== FAIL: test_blastp (test_NCBI_BLAST_tools.Pairwise) Pairwise BLASTP search ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_NCBI_BLAST_tools.py", line 103, in test_blastp self.assertEqual(10, stdoutdata.count("Query= ")) AssertionError: 10 != 1 ---------------------------------------------------------------------- Ran 228 tests in 101.627 seconds FAILED (failures = 1) Skipping any tests requiring internet access Python version: 2.7.11+ (default, May 9 2016, 15:54:33) [GCC 5.3.1 20160429] Operating system: posix linux2 E: pybuild pybuild:274: test: plugin custom failed with: exit code=1: set -e; \ mkdir -p /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home; \ mkdir -p /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc/examples; \ cp -a Doc/Tutorial.tex /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \ cp -a Doc/Tutorial /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \ cp -a Doc/examples /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \ cp -a Tests /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build; \ cd /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home python2.7 run_tests.py --offline dh_auto_test: pybuild --test -i python{version} -p 2.7 --test --system=custom --test-args=set -e; \ mkdir -p {build_dir}/home; \ mkdir -p {build_dir}/Doc/examples; \ cp -a Doc/Tutorial.tex {build_dir}/Doc; \ cp -a Doc/Tutorial {build_dir}/Doc; \ cp -a Doc/examples {build_dir}/Doc; \ cp -a Tests {build_dir}; \ cd {build_dir}/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline --dir . returned exit code 13 debian/rules:69: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 25 make[1]: Leaving directory '/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg' debian/rules:51: recipe for target 'build' failed make: *** [build] Error 2 [..] The full build log is attached. Regards, -- ,''`. : :' : Chris Lamb `. `'` lamby at debian.org / chris-lamb.co.uk `- -------------- next part -------------- A non-text attachment was scrubbed... Name: python-biopython.1.66+dfsg-2.unstable.amd64.log.txt.gz Type: application/octet-stream Size: 24435 bytes Desc: not available URL: From ftpmaster at ftp-master.debian.org Wed May 11 16:45:27 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 16:45:27 +0000 Subject: [Debian-med-packaging] prottest_3.4.2+dfsg-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 11 May 2016 17:25:05 +0200 Source: prottest Binary: prottest Architecture: source all Version: 3.4.2+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: prottest - selection of best-fit models of protein evolution Changes: prottest (3.4.2+dfsg-2) unstable; urgency=medium . * Adapt to libmpj-java settings * Fix wrapper scripts Checksums-Sha1: 72d7f981084e03f929fa43142495315243c71f62 2077 prottest_3.4.2+dfsg-2.dsc eb19587d89daed4b047ea818b013b83fadd86a9c 5276 prottest_3.4.2+dfsg-2.debian.tar.xz b3d5be8a5ca4eabd88b4349dec598095e24308d5 346646 prottest_3.4.2+dfsg-2_all.deb Checksums-Sha256: ffed645eab5da60398ebb52b601c0e37ee2e4c71774e2019c31c16cbd52b3023 2077 prottest_3.4.2+dfsg-2.dsc 523ce8a16780ea3ae389842200c2b7c204d4f77ee98f73734b350a3c99778cf3 5276 prottest_3.4.2+dfsg-2.debian.tar.xz d84ab07ff109582aa4f5deeb1eb9ff30f72c9aa4bc97875e8b3d71c7a0fb3c74 346646 prottest_3.4.2+dfsg-2_all.deb Files: ad7920b136bb06aa08a14c994642d97c 2077 science optional prottest_3.4.2+dfsg-2.dsc 029fff9901f160cb22c0f59b42d0bc6a 5276 science optional prottest_3.4.2+dfsg-2.debian.tar.xz 9ea9165c9c0e1f33bf801ea57873275f 346646 science optional prottest_3.4.2+dfsg-2_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXM1DaAAoJEFeKBJTRxkbRxMoP/iswj03Mdc5AwCVfiKrMF5zX 50BRx1TUMXY5JClgJCqkC6WtuS8k3bW48vcs4C6eLOhlsdOozNgaQcTG2RrONyXa 3C3gMRU5xGlToIp8Gx9VoW5epsvmL6O86sw5Z3J/wHaP+qru+OMI4Qo7SkGslLIN SVty0QrmUCcVKZ63pUb8+bHtxhdEQpkqKoacnk7b3q/dKpNdzHgn0KJOf23F6FoD xyFKVSnDp9hafssEUNXDeTyA/9lM/yTX1nkeqzaXQDLvpSHP6QGLMLYIOoOltJ9A 7HkK8nxAvpkZ0D+iakEjXLNMdo835zHMdNm/yIFQHXAhFunuY/a3RQFN/9kq5net 1If/1FeEnn9R5t64CoDsh0Lqx3WmX3Ja99ThDXG2+SuTJLX8Mfke10g6i9vAe7gv zwfl9ZZNKoBlPqJdQXkXRIccdzop5hxHzZMqXfxsjNBRjjxKq/hm0uUMyofODQTq Qhn2BL+VGg72OYbTD/5IcxQIrU2BF6W558D4j0rDK6WLYDoEIHU5QJnz1d8jQ3TY RM2jcpuGni03bDalj1S8Lf6vjYbyJtkuf2pO4pF0WLJ90JX7s6kqFDxLjMSOfFTt sb/1lVEXfr4zpDsMnip1lUq/hR1o1alXvQnn4e7vrk95vAQtYNjRlR4UE1AGBE10 eXs8WuiNR8drDtp/JVZP =ZqN+ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Wed May 11 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 11 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] vtk-dicom 0.7.7-1 MIGRATED to testing Message-ID: FYI: The status of the vtk-dicom source package in Debian's testing distribution has changed. Previous version: 0.7.6-1 Current version: 0.7.7-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From andreas at an3as.eu Wed May 11 20:08:49 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 11 May 2016 22:08:49 +0200 Subject: [Debian-med-packaging] Bug#824048: Any change in blastp? (Was: Bug#824048: python-biopython: FTBFS: AssertionError: 10 != 1) In-Reply-To: <1462984527.2366877.604901465.716271DC@webmail.messagingengine.com> References: <1462984527.2366877.604901465.716271DC@webmail.messagingengine.com> Message-ID: <20160511200849.GA28855@an3as.eu> On Wed, May 11, 2016 at 05:35:27PM +0100, Chris Lamb wrote: > ... > Bio.PDB.Selection docstring test ... ok > ====================================================================== > FAIL: test_blastp (test_NCBI_BLAST_tools.Pairwise) > Pairwise BLASTP search > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_NCBI_BLAST_tools.py", line 103, in test_blastp > self.assertEqual(10, stdoutdata.count("Query= ")) > AssertionError: 10 != 1 > > ---------------------------------------------------------------------- > Ran 228 tests in 101.627 seconds > > FAILED (failures = 1) Does any body know about a recent change in blastp? Kind regards Andreas. -- http://fam-tille.de From debian-backports at lists.debian.org Wed May 11 22:03:22 2016 From: debian-backports at lists.debian.org (Alexander Wirt) Date: Wed, 11 May 2016 22:03:22 +0000 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED Message-ID: This package is not even in unstable. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Wed May 11 22:03:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 22:03:33 +0000 Subject: [Debian-med-packaging] picard-tools_2.1.1+dfsg-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 04 May 2016 14:22:19 +0200 Source: picard-tools Binary: picard-tools libpicard-java libpicard-java-doc Architecture: source all Version: 2.1.1+dfsg-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libpicard-java - Java library to manipulate SAM and BAM files libpicard-java-doc - Documentation for the java picard library picard-tools - Command line tools to manipulate SAM and BAM files Changes: picard-tools (2.1.1+dfsg-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Wed May 11 22:03:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 22:03:34 +0000 Subject: [Debian-med-packaging] r-cran-taxize_0.7.4-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 21 Apr 2016 16:29:27 +0200 Source: r-cran-taxize Binary: r-cran-taxize Architecture: source all Version: 0.7.4-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-taxize - GNU R taxonomic information from around the web Changes: r-cran-taxize (0.7.4-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Wed May 11 22:03:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 22:03:35 +0000 Subject: [Debian-med-packaging] seaview_4.6-2~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 04 May 2016 14:07:07 +0200 Source: seaview Binary: seaview Architecture: source amd64 Version: 1:4.6-2~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: seaview - Multiplatform interface for sequence alignment and phylogeny Changes: seaview (1:4.6-2~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Wed May 11 22:03:36 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 22:03:36 +0000 Subject: [Debian-med-packaging] sprai_0.9.9.14+dfsg-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 03 May 2016 22:18:01 -0700 Source: sprai Binary: sprai Architecture: source amd64 Version: 0.9.9.14+dfsg-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Afif Elghraoui Description: sprai - single-pass sequencing read accuracy improver Changes: sprai (0.9.9.14+dfsg-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Wed May 11 22:03:37 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 11 May 2016 22:03:37 +0000 Subject: [Debian-med-packaging] surankco_0.0.r5+dfsg-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 04 Apr 2016 15:01:27 +0200 Source: surankco Binary: surankco Architecture: source all Version: 0.0.r5+dfsg-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: surankco - Supervised Ranking of Contigs in de novo Assemblies Changes: surankco (0.0.r5+dfsg-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Thu May 12 03:46:18 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 03:46:18 +0000 Subject: [Debian-med-packaging] Processing of bcftools_1.3.1-1~bpo8+1_amd64.changes Message-ID: bcftools_1.3.1-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: bcftools_1.3.1-1~bpo8+1.dsc bcftools_1.3.1-1~bpo8+1.debian.tar.xz bcftools_1.3.1-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 12 03:49:46 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 03:49:46 +0000 Subject: [Debian-med-packaging] bcftools_1.3.1-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 11 May 2016 20:10:13 -0700 Source: bcftools Binary: bcftools Architecture: source amd64 Version: 1.3.1-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Afif Elghraoui Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Closes: 812268 Changes: bcftools (1.3.1-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. . bcftools (1.3.1-1) unstable; urgency=medium . * Imported Upstream version 1.3.1 * Remove backported patches * Refresh remaining patches * Bump htslib minimum dependency * Bump Standards-Version to 3.9.8 * Add a manpage for the color-chrs command . bcftools (1.3-3) unstable; urgency=medium . * Backport upstream patch to fix build on arm64, armel, and ppc64el (Closes: #812268) . bcftools (1.3-2) unstable; urgency=medium . * Backport upstream patch to be able to build plugin with GSL2 * Bump Standards-Version * Use encrypted protocols for VCS URLs Checksums-Sha1: 96e90b4ff3f2d1f8b57a35d44bbdbb0cc130aa04 2035 bcftools_1.3.1-1~bpo8+1.dsc dee3595b027a569f307ffa3b548062e934f26a9e 6100 bcftools_1.3.1-1~bpo8+1.debian.tar.xz a199a956be14245239cd59621eb436f9ffd91db8 327098 bcftools_1.3.1-1~bpo8+1_amd64.deb Checksums-Sha256: d00e79143c687d11813bf64c9c49613958227d5eb2e01da9d859cd05b6fc3e97 2035 bcftools_1.3.1-1~bpo8+1.dsc ab40025e494344f8012e62c5e78eeebc1526917a2cb6e6bd4be87752ed6cfffc 6100 bcftools_1.3.1-1~bpo8+1.debian.tar.xz dd42194ea877c77a753b5edbe0ff0ef25709b46e8a431c45eadd53b5b57a9f3d 327098 bcftools_1.3.1-1~bpo8+1_amd64.deb Files: 2a9b453f5bd6677f2210993e7cae0ad0 2035 science optional bcftools_1.3.1-1~bpo8+1.dsc b0f73123b2c869af32cf06e03a3a3d54 6100 science optional bcftools_1.3.1-1~bpo8+1.debian.tar.xz 1119d17e3fe4023bf45170605b25a10f 327098 science optional bcftools_1.3.1-1~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXM/uDAAoJEM6uatOv6Cb7LdoP/RAU5N1ZedSfFwb1pqiq92Lh bkS/YwNKOCJ7Oha37HscSB0JAWlTuCGY/TtjZzPRB3dXM0L5jRzS8rDLX0nrLRMO iJhp8wx9grttBWDKG1dZGu9ub1H2AU3m4LqcYMrOpvWlpMczQygF9ypWDtq09AAt MKUJFfXzn9OZOWRzXx+aJagwYNEQyGy5R8OCdjjp4QgMabVTahVDst7/rBJMIAIj ApdXjBnNeqKq96N5iWiz5ZN+HVY08L8XTJf049AwnoHo5v2waokkCCZgVjpKCDMZ MbMMa24F57zJAI7KqcPN/cL90+B1Ci18YUldWdSeAStKqOFSdrgfUAf3VJWwnWGb nH0Dnr5UVelqrS8ZvAkeCtb9v4PjP/dALiS5VaWFH5zyc94MnPa21+EOqhNEWGNn kpisSt34LW3Vzi95grEDvusWxL8iPfFCFih2TPd+VCDhixFHFCTo4DxRbrUFDlRx sBvsrEDiHEUJiHoh+hq9cidqkenFh9tGJJ8n50CiHTOc64U1HgMD2lwjTk38d5kE Ags4tYqzoa4NY3rptbRkAcdmBngeujGkEtVc1guW42ko+5wNqGyKM2Wi0Xbs2b87 iJYNrk/MGAF7kGjDDxbrHA39vcIpkc1kE++ZjddKYYFJ2Io68EJ/q1ILuiCypigs pWSusF6uit+fFj2hVW0f =oV6H -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From locutusofborg at debian.org Thu May 12 04:01:31 2016 From: locutusofborg at debian.org (Gianfranco Costamagna) Date: Thu, 12 May 2016 04:01:31 +0000 (UTC) Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: References: Message-ID: <429992963.1289631.1463025691805.JavaMail.yahoo@mail.yahoo.com> Hi Alex I can see it https://packages.qa.debian.org/libb/libbpp-seq.htmlhttps://packages.debian.org/source/unstable/libbpp-seq Did it got removed some when recently? Cheers, Gianfranco Sent from Yahoo Mail on Android On Thu, 12 May, 2016 at 0:03, Alexander Wirt wrote: This package is not even in unstable. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Thu May 12 05:16:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 05:16:54 +0000 Subject: [Debian-med-packaging] Processing of circlator_1.2.1-1~bpo8+1_amd64.changes Message-ID: circlator_1.2.1-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: circlator_1.2.1-1~bpo8+1.dsc circlator_1.2.1-1~bpo8+1.debian.tar.xz circlator_1.2.1-1~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 12 05:19:19 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 05:19:19 +0000 Subject: [Debian-med-packaging] circlator_1.2.1-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 08 May 2016 01:07:27 -0700 Source: circlator Binary: circlator Architecture: source all Version: 1.2.1-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Afif Elghraoui Description: circlator - circularize genome assemblies Changes: circlator (1.2.1-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. . circlator (1.2.1-1) unstable; urgency=medium . * Fix typo in d/upstream/metadata * Add explicit build-dependency on bwa with proper minimum version * Imported Upstream version 1.2.1 * Refresh patches * Don't restrict pysam max version * Update Standards-Version to 3.9.8 Checksums-Sha1: c5a1926efc86df42fafeba0a97ddbf8fdd59a478 2487 circlator_1.2.1-1~bpo8+1.dsc 69456f9f684cd74539b29d2f7c32ab5323cfdeb7 4296 circlator_1.2.1-1~bpo8+1.debian.tar.xz 311989c5c2bf731749836a2172a4c109e8dad0d9 4211834 circlator_1.2.1-1~bpo8+1_all.deb Checksums-Sha256: 9f4652d20bf6bec89a2671e3c3e07933048eb90116ae5664b9ea73f72cdaaf2b 2487 circlator_1.2.1-1~bpo8+1.dsc 2dd99360a5fe7cd3cfe7fa0bb9f7f93844e78cbec48a855c00fd18cb1fa57e8c 4296 circlator_1.2.1-1~bpo8+1.debian.tar.xz 182e36eab0ceb7ecda162e40176408428ef3bbd25f665e4037b4e1eb0a84d2ec 4211834 circlator_1.2.1-1~bpo8+1_all.deb Files: 78dbb0f9c9cf6350c72f0e0ed304570a 2487 science optional circlator_1.2.1-1~bpo8+1.dsc 69a743b4f4465348497ddea869ab9e75 4296 science optional circlator_1.2.1-1~bpo8+1.debian.tar.xz 26d089e3f4cceb6523d6e2122e8409b7 4211834 science optional circlator_1.2.1-1~bpo8+1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXNBF6AAoJEM6uatOv6Cb7qrkP/RHX9AWOBp/aDtgcktW+epac YuXbfZl4FueWY7iDBnrWIEg8veMA1OD4v8HJKHj4a16mDAC0INeI8btWfYWrkCna /mXIFoLWE+CM6z1cNjhT2T6qUvcGn0uA5GNBQ2nvNTJUT8WckKb+lUQ/Ny14VMq7 /rpagJIK2rP0J8Zc1CBlCSuSXol2v+yrywuEFYNWHoUuRnpfVFxfes7DYFpXS0LH 3DHtgLvnSuRMHkPiqakuHvg4IcIhVg9oDPzMjnf8RVcDTv1T6AEp6vLQmDapoaxA CTW5xhpcMldJGciSxOuCBBS34YIKVpupA1ikK18SEWZ6l++intfizWyhwwyoQlQP aTzm23co0KAUBsw6d2zN6qGUd7BcBKdgzkjlG5itQCyHxWQ9InxfGH0299BbiglY A15cwb2JFBUzgt9FjDUMYm4bN18IcgsAe5d/EgTXpPICFHcQrwmnz8AFw3L+AYiJ m73N0m8IygzzJmFDDXwKmD6RhsCxihnOZq2Ow88RFR/ktJDcxpHBD+RH34ltvhlo 1/40H4DyXBzQAVEZvnZOexXCfpuWSdOAvECS6p9lcUjV+25sHLOAuvfINn6Y7xOc KKME71Qltmth8v88hjLBP6Ohup1IoVT+uE6qrjnIsjj4Ljy4qF6Ppfi/kP5tXNLs g6DbppAWQBFUM3SfFOSI =aLW6 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From tille at debian.org Thu May 12 05:51:22 2016 From: tille at debian.org (Andreas Tille) Date: Thu, 12 May 2016 07:51:22 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <429992963.1289631.1463025691805.JavaMail.yahoo@mail.yahoo.com> References: <429992963.1289631.1463025691805.JavaMail.yahoo@mail.yahoo.com> Message-ID: <20160512055122.GA11400@an3as.eu> Hi Alex $ apt-cache policy libbpp-seq-dev libbpp-seq-dev: Installiert: (keine) Installationskandidat: 2.1.0-1 Versionstabelle: 2.2.0-1 0 50 http://ftp.de.debian.org/debian/ unstable/main amd64 Packages 90 http://ftp.de.debian.org/debian/ testing/main amd64 Packages 2.1.0-1 0 500 http://httpredir.debian.org/debian/ jessie/main amd64 Packages Should I reupload to backports? Thanks for maintaining backports Andreas. On Thu, May 12, 2016 at 04:01:31AM +0000, Gianfranco Costamagna wrote: > Hi Alex > I can see it > https://packages.qa.debian.org/libb/libbpp-seq.htmlhttps://packages.debian.org/source/unstable/libbpp-seq > > > Did it got removed some when recently? > Cheers, > Gianfranco > > Sent from Yahoo Mail on Android > > On Thu, 12 May, 2016 at 0:03, Alexander Wirt wrote: > This package is not even in unstable. > > === > > Please feel free to respond to this email if you don't understand why > your files were rejected, or if you upload new files which address our > concerns. > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de From tille at debian.org Thu May 12 06:45:19 2016 From: tille at debian.org (Andreas Tille) Date: Thu, 12 May 2016 08:45:19 +0200 Subject: [Debian-med-packaging] BioConductor interactiveDisplayBase can't connect to bioconductor.org Message-ID: <20160512064519.GC11400@an3as.eu> Hi, I intend to package BioConductor interactiveDisplayBase as a new dependency for biovizBase version 1.20.0 (of BioConductor 3.3) as a Debian package. The Debian packaging process involves loading the package and since the packaging process needs to work on a machine disconnected from the internet it results in the following error: * installing *source* package ?interactiveDisplayBase? ... ** R ** inst ** preparing package for lazy loading Warning in file(filename, "r", encoding = encoding) : unable to connect to 'bioconductor.org' on port 80. Error in file(filename, "r", encoding = encoding) : cannot open the connection Error : unable to load R code in package ?interactiveDisplayBase? ERROR: lazy loading failed for package ?interactiveDisplayBase? I wonder whether there is any chance to make this error non-critical and add a warning to enable passing this step without breaking the build on a disconnected box. BTW, even if I try to do this on a box connected to the internet via proxy the build ends with the same error which is IMHO a real bug inside interactiveDisplayBase since it does not respect the http_proxy variable (and possibly whatever means will be done to set the proxy on non-Linux systems which I did not verified). Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Thu May 12 07:07:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 07:07:17 +0000 Subject: [Debian-med-packaging] Processing of libbpp-seq_2.2.0-1~bpo8+1_amd64.changes Message-ID: libbpp-seq_2.2.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-seq_2.2.0-1~bpo8+1.dsc libbpp-seq_2.2.0-1~bpo8+1.debian.tar.xz libbpp-seq-dev_2.2.0-1~bpo8+1_amd64.deb libbpp-seq9_2.2.0-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 12 07:18:37 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 07:18:37 +0000 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED Message-ID: Signature for changes file was already seen at 2016-05-05 06:18:52.723545. Please refresh the signature of the changes file if you want to upload it again. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From formorer at formorer.de Thu May 12 07:10:58 2016 From: formorer at formorer.de (Alexander Wirt) Date: Thu, 12 May 2016 09:10:58 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160512055122.GA11400@an3as.eu> References: <429992963.1289631.1463025691805.JavaMail.yahoo@mail.yahoo.com> <20160512055122.GA11400@an3as.eu> Message-ID: <20160512071058.GA5174@formorer.de> On Thu, 12 May 2016, Andreas Tille wrote: > Hi Alex > > $ apt-cache policy libbpp-seq-dev > libbpp-seq-dev: > Installiert: (keine) > Installationskandidat: 2.1.0-1 > Versionstabelle: > 2.2.0-1 0 > 50 http://ftp.de.debian.org/debian/ unstable/main amd64 Packages > 90 http://ftp.de.debian.org/debian/ testing/main amd64 Packages > 2.1.0-1 0 > 500 http://httpredir.debian.org/debian/ jessie/main amd64 Packages I have no idea what I exactly saw yesterday. Please reupload and sorry for the inconvenience. Alex From tille at debian.org Thu May 12 07:25:07 2016 From: tille at debian.org (Andreas Tille) Date: Thu, 12 May 2016 09:25:07 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160512055122.GA11400@an3as.eu> References: <429992963.1289631.1463025691805.JavaMail.yahoo@mail.yahoo.com> <20160512055122.GA11400@an3as.eu> Message-ID: <20160512072507.GE11400@an3as.eu> Hi, it seemed evident to me that I need to re-upload since its not inside the queue any more. Another question: I wonder *how exactly* Alex concluded that the packege is neither in testing nor unstable. The thing is: I have also problems to put these packages on the Debian Med tasks pages and I suspect something is actually wrong that the package shows up on some places but don't on others. Kind regards Andreas. On Thu, May 12, 2016 at 07:51:22AM +0200, Andreas Tille wrote: > Hi Alex > > $ apt-cache policy libbpp-seq-dev > libbpp-seq-dev: > Installiert: (keine) > Installationskandidat: 2.1.0-1 > Versionstabelle: > 2.2.0-1 0 > 50 http://ftp.de.debian.org/debian/ unstable/main amd64 Packages > 90 http://ftp.de.debian.org/debian/ testing/main amd64 Packages > 2.1.0-1 0 > 500 http://httpredir.debian.org/debian/ jessie/main amd64 Packages > > Should I reupload to backports? > > Thanks for maintaining backports > > Andreas. > > On Thu, May 12, 2016 at 04:01:31AM +0000, Gianfranco Costamagna wrote: > > Hi Alex > > I can see it > > https://packages.qa.debian.org/libb/libbpp-seq.htmlhttps://packages.debian.org/source/unstable/libbpp-seq > > > > > > Did it got removed some when recently? > > Cheers, > > Gianfranco > > > > Sent from Yahoo Mail on Android > > > > On Thu, 12 May, 2016 at 0:03, Alexander Wirt wrote: > > This package is not even in unstable. > > > > === > > > > Please feel free to respond to this email if you don't understand why > > your files were rejected, or if you upload new files which address our > > concerns. > > > > > > > _______________________________________________ > > Debian-med-packaging mailing list > > Debian-med-packaging at lists.alioth.debian.org > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From tille at debian.org Thu May 12 07:28:12 2016 From: tille at debian.org (Andreas Tille) Date: Thu, 12 May 2016 09:28:12 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160512071058.GA5174@formorer.de> References: <429992963.1289631.1463025691805.JavaMail.yahoo@mail.yahoo.com> <20160512055122.GA11400@an3as.eu> <20160512071058.GA5174@formorer.de> Message-ID: <20160512072812.GF11400@an3as.eu> On Thu, May 12, 2016 at 09:10:58AM +0200, Alexander Wirt wrote: > I have no idea what I exactly saw yesterday. Please reupload and sorry for > the inconvenience. No need to sorry. Your work is highly appreciated and as I wrote in my other mail I suspect that somewhere in our infrastructure might be a hidden glitch. I simply failed to find the time to track this down. Thanks for your work Andreas. PS: There is a series of libbpp-* libs that will follow this package. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Thu May 12 07:52:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 07:52:35 +0000 Subject: [Debian-med-packaging] Processing of libbpp-seq_2.2.0-1~bpo8+1_amd64.changes Message-ID: libbpp-seq_2.2.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-seq_2.2.0-1~bpo8+1.dsc libbpp-seq_2.2.0-1~bpo8+1.debian.tar.xz libbpp-seq-dev_2.2.0-1~bpo8+1_amd64.deb libbpp-seq9_2.2.0-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 12 10:00:30 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 10:00:30 +0000 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes is NEW Message-ID: binary:libbpp-seq-dev is NEW. binary:libbpp-seq9 is NEW. source:libbpp-seq is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 12 10:04:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 10:04:13 +0000 Subject: [Debian-med-packaging] Processing of iva_1.0.6+ds-1_amd64.changes Message-ID: iva_1.0.6+ds-1_amd64.changes uploaded successfully to localhost along with the files: iva_1.0.6+ds-1.dsc iva_1.0.6+ds.orig.tar.xz iva_1.0.6+ds-1.debian.tar.xz iva_1.0.6+ds-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From AbEer.ali9000 at yahoo.com Thu May 12 10:38:51 2016 From: AbEer.ali9000 at yahoo.com (jackieharris) Date: Thu, 12 May 2016 10:38:51 +0000 Subject: [Debian-med-packaging] Hello with love. Message-ID: <622484.64723.bm@smtp103.mail.ir2.yahoo.com> hello dear i wish to know you after see your profile in fb today just want to leave you my comtact as i hope to hear from you for about me hope to hear from you thanks. Jackie Harris. (jackieharris2016 at outlook.com) -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Thu May 12 11:20:56 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 11:20:56 +0000 Subject: [Debian-med-packaging] iva_1.0.6+ds-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 12 May 2016 09:50:41 +0000 Source: iva Binary: iva Architecture: source amd64 Version: 1.0.6+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: iva - iterative virus sequence assembler Changes: iva (1.0.6+ds-1) unstable; urgency=medium . * New upstream release. * Change orig tarball compression. * Add missing repack suffix to package. 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From noreply at release.debian.org Thu May 12 16:39:06 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 12 May 2016 16:39:06 +0000 Subject: [Debian-med-packaging] datatables.js 1.10.11+dfsg-3 MIGRATED to testing Message-ID: FYI: The status of the datatables.js source package in Debian's testing distribution has changed. Previous version: 1.10.11+dfsg-2 Current version: 1.10.11+dfsg-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Thu May 12 16:42:26 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 16:42:26 +0000 Subject: [Debian-med-packaging] Processing of jmodeltest_2.1.10+dfsg-1_amd64.changes Message-ID: jmodeltest_2.1.10+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: jmodeltest_2.1.10+dfsg-1.dsc jmodeltest_2.1.10+dfsg.orig.tar.xz jmodeltest_2.1.10+dfsg-1.debian.tar.xz jmodeltest_2.1.10+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 12 17:24:42 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 17:24:42 +0000 Subject: [Debian-med-packaging] jmodeltest_2.1.10+dfsg-1_amd64.changes is NEW Message-ID: binary:jmodeltest is NEW. source:jmodeltest is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 12 18:12:48 2016 From: ftpmaster at ftp-master.debian.org (Chris Lamb) Date: Thu, 12 May 2016 18:12:48 +0000 Subject: [Debian-med-packaging] Comments regarding jmodeltest_2.1.10+dfsg-1_amd64.changes Message-ID: Some copyrights missing, eg. in src/main/java/es/uvigo/darwin/jmodeltest/io/DocumentOutputStream.java src/main/java/es/uvigo/darwin/jmodeltest/io/TextOutputStream.java src/main/java/es/uvigo/darwin/jmodeltest/utilities/TableMap.java src/main/java/es/uvigo/darwin/jmodeltest/utilities/TableSorter.java (not exhaustive) Please fix on next upload. From ftpmaster at ftp-master.debian.org Thu May 12 18:53:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 18:53:58 +0000 Subject: [Debian-med-packaging] Processing of r-cran-magrittr_1.5-3~bpo8+1_amd64.changes Message-ID: r-cran-magrittr_1.5-3~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: r-cran-magrittr_1.5-3~bpo8+1.dsc r-cran-magrittr_1.5-3~bpo8+1.debian.tar.xz r-cran-magrittr_1.5-3~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 12 19:00:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 19:00:23 +0000 Subject: [Debian-med-packaging] jmodeltest_2.1.10+dfsg-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 12 May 2016 17:09:41 +0200 Source: jmodeltest Binary: jmodeltest Architecture: source all Version: 2.1.10+dfsg-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: jmodeltest - HPC selection of models of nucleotide substitution Closes: 823920 Changes: jmodeltest (2.1.10+dfsg-1) unstable; urgency=low . * Initial release (Closes: #823920) Checksums-Sha1: a13f64b525e09d6ae12db19ead342eff6c00e1a1 2232 jmodeltest_2.1.10+dfsg-1.dsc 37c115e3f4b040b36b83ac3f9c01462bcca765fb 3945412 jmodeltest_2.1.10+dfsg.orig.tar.xz 23996302c223fa534206e0c4aa538de167f51eb7 4472 jmodeltest_2.1.10+dfsg-1.debian.tar.xz 00cc37cf323e4e1312492f6045fe2065542834ed 977732 jmodeltest_2.1.10+dfsg-1_all.deb Checksums-Sha256: f0803f3cb6c47098d06f8cc0e54a103138d71cab46e91a957ac8172581e7a0cc 2232 jmodeltest_2.1.10+dfsg-1.dsc f5595f7efa691cc3b492649f9c9b475f2226891421b1470ae9cce65b572dbbe6 3945412 jmodeltest_2.1.10+dfsg.orig.tar.xz 40eaaf8fac9bef51a37909bf360f13bdd73b2184c61b27de8b983251a0580e3f 4472 jmodeltest_2.1.10+dfsg-1.debian.tar.xz 6380c56e6a45ac6ea2fbc42814ca3e123d86997966de2a48da3dccebd3f3021f 977732 jmodeltest_2.1.10+dfsg-1_all.deb Files: 0f74c0c347125b9cb39c20c9292c62bc 2232 science optional jmodeltest_2.1.10+dfsg-1.dsc 6b03e88b681f7f1e5f555bcb4ca5c0ac 3945412 science optional jmodeltest_2.1.10+dfsg.orig.tar.xz fc77ffa57ab9e849495ea8030deba28d 4472 science optional jmodeltest_2.1.10+dfsg-1.debian.tar.xz 5b8a1ac89a626c467b0ccc5e083eba2b 977732 science optional jmodeltest_2.1.10+dfsg-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXNLF4AAoJEFeKBJTRxkbRXCMP/1SOvRUXF/JmEpiWrLoqRT0x tAlK5HcC/6hwsoHdq3My4yooY9mZOaW7p/8O6Hi45fggN2WTOQsnFwTRH70fWz90 qmNglej3J5bnk/ulvhL1TFXTnJNFshytoRA5ROYvkZGprL6PiNruDVs0j05zg/jN d+Ki/Fm1YTvts9JxXFNG0UnE4Bpn2pUN5991wuSDlqgf5Gx/h5g18NvARes9pYGC Wsnt9ocioMzrd8efpYb7tJfAub3BoxoayDLKD8wNwrF16BCZYlxtGeob3zLujMLs S8noqPagcyJzgPNYQxXaWL2x5wBmPjP/K23rhJu7RqXqpwpV+PYcd2NBU1EDYiIh rsc/XE8njqYke5VVA63tufyV/cRAmH9UqMZRASpa6BBRYiG6/CrsdB5oal/QTPSJ EoswOUvOPmTV0M3/Rre0NPU1CvFNpf6IU7184/7G4qo8+wIuP10QIX94lwdpDu/8 tsdl1hjnO/gFDgchzdwMel0Mt7QkfrEG9TQ/iAZd3NXntvK5GF8AeCj/bbbShnaf pIgcAdbjB9wcFnv3qhxFNtmQ5lIudFsoMMc3ljfdJStfbYo2XP750WOxmrXcHTTv xNh2ortcCSxuVku2gMCuf322h4dzZkFIYbnwRb3UhlWS7/bFsY4m9/z7cmkK66/Y ZVcvR4G4mf2k7MtH7jaa =EjOu -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 12 19:14:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 19:14:04 +0000 Subject: [Debian-med-packaging] Processing of r-cran-stringi_1.0-1-1~bpo8+1_amd64.changes Message-ID: r-cran-stringi_1.0-1-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: r-cran-stringi_1.0-1-1~bpo8+1.dsc r-cran-stringi_1.0-1-1~bpo8+1.debian.tar.xz r-cran-stringi_1.0-1-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 12 19:20:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 19:20:34 +0000 Subject: [Debian-med-packaging] r-cran-magrittr_1.5-3~bpo8+1_amd64.changes is NEW Message-ID: binary:r-cran-magrittr is NEW. source:r-cran-magrittr is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 12 19:20:39 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 12 May 2016 19:20:39 +0000 Subject: [Debian-med-packaging] r-cran-stringi_1.0-1-1~bpo8+1_amd64.changes is NEW Message-ID: binary:r-cran-stringi is NEW. source:r-cran-stringi is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From tille at debian.org Thu May 12 19:57:20 2016 From: tille at debian.org (Andreas Tille) Date: Thu, 12 May 2016 21:57:20 +0200 Subject: [Debian-med-packaging] Comments regarding jmodeltest_2.1.10+dfsg-1_amd64.changes In-Reply-To: References: Message-ID: <20160512195720.GB27879@an3as.eu> Hi Chris, thanks a lot for the superfast processing! (I wonder whether you intend to beat some records ;-)) On Thu, May 12, 2016 at 06:12:48PM +0000, Chris Lamb wrote: > > Some copyrights missing, eg. in > > src/main/java/es/uvigo/darwin/jmodeltest/io/DocumentOutputStream.java > src/main/java/es/uvigo/darwin/jmodeltest/io/TextOutputStream.java > src/main/java/es/uvigo/darwin/jmodeltest/utilities/TableMap.java > src/main/java/es/uvigo/darwin/jmodeltest/utilities/TableSorter.java Fixed in Git. > (not exhaustive) I have greped for further Copyright statements but failed to find any further ones not mentioned yet. May I remind on the r-cran-spdep package. As I said giving a rough estimation about the processing time is perfectly fine but any form or communication would make me really happy. Thanks again for your ftpmaster work Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Fri May 13 11:41:39 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 11:41:39 +0000 Subject: [Debian-med-packaging] Processing of libzeep_3.0.2-4_amd64.changes Message-ID: libzeep_3.0.2-4_amd64.changes uploaded successfully to localhost along with the files: libzeep_3.0.2-4.dsc libzeep_3.0.2-4.debian.tar.xz libzeep-dev_3.0.2-4_amd64.deb libzeep3.0v5_3.0.2-4_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 13 11:49:30 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 11:49:30 +0000 Subject: [Debian-med-packaging] libzeep_3.0.2-4_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 13 May 2016 07:41:01 +0000 Source: libzeep Binary: libzeep-dev libzeep3.0v5 Architecture: source amd64 Version: 3.0.2-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: libzeep-dev - Development files for libzeep libzeep3.0v5 - Library files for libzeep Closes: 824013 Changes: libzeep (3.0.2-4) unstable; urgency=medium . * Team upload. * d/p/libzeep-3.0-g++6-boost1.60.patch: correct compiling with libboost1.60 in combination with g++ Closes: #824013 * d/control: cme fix dpkg-control * d/control: set secure url for repository viewer Checksums-Sha1: d11c040e901b2096149b4e66023c514ccce65a35 2169 libzeep_3.0.2-4.dsc c19db6d1b43b5fccb19c003d1df333cca3c5a81d 5588 libzeep_3.0.2-4.debian.tar.xz 8aa615bbfbc358fc9a5668153f7a48a1dd82e430 117540 libzeep-dev_3.0.2-4_amd64.deb c231bad6ee8ea082d89c83f4ee8b383649f6e6dc 433228 libzeep3.0v5_3.0.2-4_amd64.deb Checksums-Sha256: 9f4afaf58e500c93efa4063e9109370e050ebccbc0d2a820d4d403a803b80e47 2169 libzeep_3.0.2-4.dsc 5499f8aa534e2ade5950bbcc32b5911e1f067bded167a15e5db0b991ff72d44a 5588 libzeep_3.0.2-4.debian.tar.xz 30a14e4853d89b9cfc378e1b747bea5d17883e6e2bb74e9d452403275b7c2473 117540 libzeep-dev_3.0.2-4_amd64.deb 2ce4e6f786c18322501f6e695f84236e0f6837d9a97ce1a2699e5fb7b004e03f 433228 libzeep3.0v5_3.0.2-4_amd64.deb Files: 5e40b66d33c8ac64e61f36fde092641e 2169 libs optional libzeep_3.0.2-4.dsc 8ae87c92b08adf3887d50f863eea4dc2 5588 libs optional libzeep_3.0.2-4.debian.tar.xz 2a1c35bf25c3a59356a9a291187e3281 117540 libdevel optional libzeep-dev_3.0.2-4_amd64.deb 9087957f0a94b7f549b327f09e233aa0 433228 libs optional libzeep3.0v5_3.0.2-4_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXNb0JAAoJEFeKBJTRxkbRJO4P/R7wv9yBWrFVRFh4+rvHItKA 50JS/m3cvtOKkZbm/ZvkMe/mjEOpsBoISZ3t/pHW5VE93PkiIyfPiKZn8IXY0Tw/ rw14irhyZCA4NNPD4+AkRTK8l8JV67j9auhzTR7N728/fKM8Qe1J2lUr5KD6RGbr NmthyIUazYf9evV5gwpqkfKRxCQ7wXkw27m38M7UAQ6QPbYiG/scnj5x+BpB8LHp ITr0N+jr2MpSMS8LB0q77V5ZGKk0IKd/QDwV5SLrCTZzIjC8miObqzWwAo5Q1oNq wtnhIFpT8G0Rhki6z6ehF+3C6aFsDYeIhOBx41lXOGEMvWhLLpaVaMSoTrSncV2G FoN3Rec1DwkOFdzs1907v2iug2sIcn8cZkShMJ3aPwf8Lke2LnOSxojjM4Finetc 4bGlGEV6P30HZQLh3YfPHtmbcVLtPMRKYd0Ew7Dzq3wkDlAQUt+8as1oXO3SNaWD d3J5usqZwWxI6qUccd827B7z7YjfYqpiXpYoNhFNHDy8icwo4tX66f0WIyVq5qDH oKjDxJ2szk2odAnltAN57s80wvFGmdLCxqEH+6Z/D6X3WsezdHWkriGiRTiiWwJm KWMMFQIfhflWiAHy12uZDJZ2AdXNl65D9hpmQ0Cu/puU5DhaTR4SvJzcw64KZu2b 3Gyhqb6AlBtohl33MJH4 =hu1b -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Fri May 13 11:51:08 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 13 May 2016 11:51:08 +0000 Subject: [Debian-med-packaging] Bug#824013: marked as done (libzeep: FTBFS with g++6 and libboost-1.60 also compiled with g++-6) References: <146296160007.29988.16888204778007802937.reportbug@rohan.bai-gerddie.de> Message-ID: Your message dated Fri, 13 May 2016 11:49:30 +0000 with message-id and subject line Bug#824013: fixed in libzeep 3.0.2-4 has caused the Debian Bug report #824013, regarding libzeep: FTBFS with g++6 and libboost-1.60 also compiled with g++-6 to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 824013: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824013 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Gert Wollny Subject: libzeep: FTBFS with g++6 and libboost-1.60 also compiled with g++-6 Date: Wed, 11 May 2016 12:13:20 +0200 Size: 10858 URL: -------------- next part -------------- An embedded message was scrubbed... From: Gert Wollny Subject: Bug#824013: fixed in libzeep 3.0.2-4 Date: Fri, 13 May 2016 11:49:30 +0000 Size: 5687 URL: From ftpmaster at ftp-master.debian.org Fri May 13 12:00:32 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 12:00:32 +0000 Subject: [Debian-med-packaging] mira_4.9.6-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 04 May 2016 11:18:26 -0700 Source: mira Binary: mira-assembler mira-rfam-12s-rrna mira-doc Architecture: source amd64 all Version: 4.9.6-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: mira-assembler - Whole Genome Shotgun and EST Sequence Assembler mira-doc - documentation for the mira assembler mira-rfam-12s-rrna - extract of RFAM 12 rRNA database Changes: mira (4.9.6-1) unstable; urgency=medium . * New upstream release. * dropped all patches except for one spelling fix, as they were incorporated upstream * dropped the -examples package for now, as the minidemo is missing from upstream in this release. * our manpages have been adopted and adapted upstream, so they have been removed * added architecture independent package for rfam 12s rRNA database * enable building docs & rfam packages separately * Standards-Version bump to 3.9.8 * Updated package descriptions to remove tools that upstream no longer provides * minidemo is missing from 4.9.6, commented out -examples package for now * cleaned out unnecessary stanzas from debian/rules Checksums-Sha1: 94b3767a8dcff58785c7dce55fbc04e974824ab9 2497 mira_4.9.6-1.dsc d8c2b4322a7b51409055c5e48ab30dc3c8a45fb0 15006355 mira_4.9.6.orig.tar.bz2 1e19817c18198f9ccea172b81e11eb2f79c1a44b 7944 mira_4.9.6-1.debian.tar.xz b29096f8be2e287cf058b12c4b92a28c8e5d932b 24134264 mira-assembler-dbgsym_4.9.6-1_amd64.deb 9b3aab2be8b12a7f01ed06326c8cae665052e42b 2277610 mira-assembler_4.9.6-1_amd64.deb cd961bf8d4df36155f05a2fa018920c9728b8af9 2800570 mira-doc_4.9.6-1_all.deb 3772b64bbe669c70a60de165942bb60c7be274e5 10442716 mira-rfam-12s-rrna_4.9.6-1_all.deb Checksums-Sha256: d1d6ab8795ffca2a98db36db9db17050ee1621a684c86b0e3f949015c71b6d7b 2497 mira_4.9.6-1.dsc e910479bc5f3f205913ac81cd2a24449cc175a6d1ae1fe3ae33ea0e100435b16 15006355 mira_4.9.6.orig.tar.bz2 66e4459a8d6d3195d2a7b142cbc6c92b8851fb408368f3e8f7cec3dca86b6fc9 7944 mira_4.9.6-1.debian.tar.xz b1eb493f3e6bb4643bef23aa85f74a637e7db4bb1291a680d4ac4d54a1d7995c 24134264 mira-assembler-dbgsym_4.9.6-1_amd64.deb 92b26620fa7dd9bba3e0265d875e3530e4d17dc5647b1fc75ec0682591474a78 2277610 mira-assembler_4.9.6-1_amd64.deb 29225d725d581e602c6f7fb0c459fb363e9f05454a47b0198291287ba8a2ae6f 2800570 mira-doc_4.9.6-1_all.deb efd69aee9ec6267e9537b3ec9c72465880d499939c75363fbc34aedd0cfd0e98 10442716 mira-rfam-12s-rrna_4.9.6-1_all.deb Files: 41c0e02a113acf8e3267a3fd85accf95 2497 science optional mira_4.9.6-1.dsc b0391f9900156aece2dd9bc2ad863e1e 15006355 science optional mira_4.9.6.orig.tar.bz2 7148c177b7e12e059d16514faf86acf3 7944 science optional mira_4.9.6-1.debian.tar.xz 0fdadd57a5e3f8d846183f69cde7cce7 24134264 debug extra mira-assembler-dbgsym_4.9.6-1_amd64.deb 64f29c4dfdff53c9bc481bf50d71e0a9 2277610 science optional mira-assembler_4.9.6-1_amd64.deb 75bbd0f3cf70b4b0cb81f61b9b9bf0be 2800570 doc optional mira-doc_4.9.6-1_all.deb d690a6533d5301eff50bb05b4bdc0100 10442716 science optional mira-rfam-12s-rrna_4.9.6-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXKt8XAAoJEFeKBJTRxkbRvqUP/0qU+m08zazRikK8F2dj8c23 wUlLNFyZDn9zlhV4UVpQ+Y4+Rl2jEYskjx0NV1XxmecEDCIOHnZTvSzX4cofYlmQ 2YfwmzVeJyTe9qDFOFN1sq4gRiF8MdrOSpmOmWHNngNW/4RTpg89Cv+3pM3ZZFJb V1pr5FCtWP/LoeRNk6tOWbgPlhMo0vmAA0gPBLbZxDLGa5751mek1k9NKS+ELAK5 76bo3hupCrXTihUWnDokCMi6IzH6s4E6pLjVSFhbdgW4rYO3t4eK4gAg09zz4fmt VCsbTQJAvSu2hd4CIFJEk86peFNzaH4FlhTTfPg4Bk/G6SCFhL0c0ywSPN/eS8We 70AkGi2nYI4OYbK/BlMNdz8CTYY0/AE2ThLvi9AF7IOCeSGijsA/OUZDJjiOW/9x rGSRvyz2j1l+pi3OBKWaUWrxyOwj7SfyCzoWkEhdNQaw7LRW8vMs9wdYU+YTezx4 sd9gIOogAzrbLM4I6vwmIOlGr6izic5DF5tbLGRKa7JFqBynplaxza6dTWI5P0lv iIfYDZpaciHf9kWFDbtTJnq2Irj+Okl0X3CTAhXqdEl3qrD12By8lxvE/qnnmUab HfsHdsoSs57CkRIX7qjDbgFNjzJpMDn6UfBaSOWU1alY0GOjhAIFYeeB8XhT/KNs nTLs0z0gVBTnQPFAMGJt =vlc7 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 13 13:00:22 2016 From: ftpmaster at ftp-master.debian.org (Thorsten Alteholz) Date: Fri, 13 May 2016 13:00:22 +0000 Subject: [Debian-med-packaging] paml_4.91+dfsg-1_amd64.changes REJECTED Message-ID: Hi Andreas, there is no license information in the software (which should have been for GPL software), there are different information on the website ("It is maintained and distributed for academic use free of charge by Ziheng Yang"). I don't think that one Google post is enough for this software to become part of main. Anyway, GPL means GPL-1+ and not only GPL-3. Thorsten === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Fri May 13 13:00:21 2016 From: ftpmaster at ftp-master.debian.org (Thorsten Alteholz) Date: Fri, 13 May 2016 13:00:21 +0000 Subject: [Debian-med-packaging] fsm-lite_1.0-1_amd64.changes REJECTED Message-ID: Hi Andreas, I just found GPL-3 as license. Where did you find hints for the "+"? Thorsten === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Fri May 13 14:44:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 14:44:23 +0000 Subject: [Debian-med-packaging] Processing of odil_0.6.0-1_source.changes Message-ID: odil_0.6.0-1_source.changes uploaded successfully to localhost along with the files: odil_0.6.0-1.dsc odil_0.6.0.orig.tar.gz odil_0.6.0-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at an3as.eu Fri May 13 15:20:07 2016 From: andreas at an3as.eu (Andreas Tille) Date: Fri, 13 May 2016 17:20:07 +0200 Subject: [Debian-med-packaging] paml_4.91+dfsg-1_amd64.changes REJECTED In-Reply-To: References: Message-ID: <20160513152007.GD15380@an3as.eu> Hi Ziheng, as I was afraid about our ftpmaster wants some more precise explanation and most importantly fixing the homepage. It would be really great if you could do this. Kind regards and thanks for your cooperation Andreas. On Fri, May 13, 2016 at 01:00:22PM +0000, Thorsten Alteholz wrote: > > Hi Andreas, > > there is no license information in the software (which should have been > for GPL software), there are different information on the website ("It is > maintained and distributed for academic use free of charge by Ziheng Yang"). > > I don't think that one Google post is enough for this software to become > part of main. Anyway, GPL means GPL-1+ and not only GPL-3. > > Thorsten > > === > > Please feel free to respond to this email if you don't understand why > your files were rejected, or if you upload new files which address our > concerns. > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From andreas at an3as.eu Fri May 13 15:29:45 2016 From: andreas at an3as.eu (Andreas Tille) Date: Fri, 13 May 2016 17:29:45 +0200 Subject: [Debian-med-packaging] fsm-lite_1.0-1_amd64.changes REJECTED In-Reply-To: References: Message-ID: <20160513152945.GF15380@an3as.eu> On Fri, May 13, 2016 at 01:00:21PM +0000, Thorsten Alteholz wrote: > > Hi Andreas, > > I just found GPL-3 as license. Where did you find hints for the "+"? $ grep -B1 -A1 "any later" LICENSE.md Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the -- the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Sorry, but what do you mean? Isn't "any later version" the "+"? Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Fri May 13 16:29:10 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 16:29:10 +0000 Subject: [Debian-med-packaging] odil_0.6.0-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 12 May 2016 16:58:04 +0200 Source: odil Binary: libodil0 libodil0-dev libodil0-doc python-odil odil Architecture: source Version: 0.6.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Julien Lamy Description: libodil0 - C++11 library for the DICOM standard libodil0-dev - C++11 library for the DICOM standard (development files) libodil0-doc - C++11 library for the DICOM standard (documentation) odil - C++11 library for the DICOM standard (application) python-odil - C++11 library for the DICOM standard (Python wrappers) Changes: odil (0.6.0-1) unstable; urgency=medium . * New upstream release. 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From noreply at release.debian.org Fri May 13 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] ffindex 0.9.9.7-1 MIGRATED to testing Message-ID: FYI: The status of the ffindex source package in Debian's testing distribution has changed. Previous version: 0.9.9.6-2 Current version: 0.9.9.7-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 13 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-bioc-graph 1.50.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-graph source package in Debian's testing distribution has changed. Previous version: 1.48.0-1 Current version: 1.50.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 13 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] pdb2pqr 2.1.1+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the pdb2pqr source package in Debian's testing distribution has changed. Previous version: 2.1.0+dfsg-1 Current version: 2.1.1+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 13 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-bioc-snpstats 1.22.0+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-snpstats source package in Debian's testing distribution has changed. Previous version: 1.20.0+dfsg-1 Current version: 1.22.0+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 13 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-bioc-biocgenerics 0.18.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-biocgenerics source package in Debian's testing distribution has changed. Previous version: 0.16.1-1 Current version: 0.18.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 13 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] mothur 1.37.3-1 MIGRATED to testing Message-ID: FYI: The status of the mothur source package in Debian's testing distribution has changed. Previous version: 1.36.1-1 Current version: 1.37.3-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 13 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-bioc-s4vectors 0.10.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-s4vectors source package in Debian's testing distribution has changed. Previous version: 0.8.11-1 Current version: 0.10.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 13 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-bioc-biobase 2.32.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-biobase source package in Debian's testing distribution has changed. Previous version: 2.30.0-1 Current version: 2.32.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 13 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] r-bioc-biocparallel 1.6.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-biocparallel source package in Debian's testing distribution has changed. Previous version: 1.4.3-1 Current version: 1.6.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 13 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 13 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] pixelmed 20150917-1 MIGRATED to testing Message-ID: FYI: The status of the pixelmed source package in Debian's testing distribution has changed. Previous version: 20140816-1.1 Current version: 20150917-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Fri May 13 16:50:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 16:50:07 +0000 Subject: [Debian-med-packaging] Processing of plip_1.3.1+dfsg-1_amd64.changes Message-ID: plip_1.3.1+dfsg-1_amd64.changes uploaded successfully to ftp-master.debian.org along with the files: plip_1.3.1+dfsg-1.dsc plip_1.3.1+dfsg.orig.tar.xz plip_1.3.1+dfsg-1.debian.tar.xz plip_1.3.1+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host coccia.debian.org) From ftpmaster at ftp-master.debian.org Fri May 13 16:50:22 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 16:50:22 +0000 Subject: [Debian-med-packaging] Processing of plip_1.3.1+dfsg-1_amd64.changes Message-ID: plip_1.3.1+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: plip_1.3.1+dfsg-1.dsc plip_1.3.1+dfsg.orig.tar.xz plip_1.3.1+dfsg-1.debian.tar.xz plip_1.3.1+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From dtenenba at fredhutch.org Fri May 13 17:07:27 2016 From: dtenenba at fredhutch.org (Dan Tenenbaum) Date: Fri, 13 May 2016 10:07:27 -0700 (PDT) Subject: [Debian-med-packaging] [devteam-bioc] BioConductor interactiveDisplayBase can't connect to bioconductor.org In-Reply-To: <20160512064519.GC11400@an3as.eu> References: <20160512064519.GC11400@an3as.eu> Message-ID: <838627098.5708671.1463159247342.JavaMail.zimbra@fredhutch.org> ----- Original Message ----- > From: "maintainer" > To: "Shawn Balcome" , "maintainer" > Cc: "Debian Med Packaging Team" , "Debian Science List" > > Sent: Wednesday, May 11, 2016 11:45:19 PM > Subject: [devteam-bioc] BioConductor interactiveDisplayBase can't connect to bioconductor.org > Hi, > > I intend to package BioConductor interactiveDisplayBase as a new > dependency for biovizBase version 1.20.0 (of BioConductor 3.3) as a > Debian package. The Debian packaging process involves loading the > package and since the packaging process needs to work on a machine > disconnected from the internet it results in the following error: > > > * installing *source* package ?interactiveDisplayBase? ... > ** R > ** inst > ** preparing package for lazy loading > Warning in file(filename, "r", encoding = encoding) : > unable to connect to 'bioconductor.org' on port 80. > Error in file(filename, "r", encoding = encoding) : > cannot open the connection > Error : unable to load R code in package ?interactiveDisplayBase? > ERROR: lazy loading failed for package ?interactiveDisplayBase? > > > I wonder whether there is any chance to make this error non-critical > and add a warning to enable passing this step without breaking the > build on a disconnected box. I have moved the call to source the remote file into the helper function, so it is not executed when the package is loaded. I verified the package can be installed when offline. This is fixed in release (1.10.2) and devel (1.11.2), available via svn now or biocLite() tomorrow. Dan > > BTW, even if I try to do this on a box connected to the internet via > proxy the build ends with the same error which is IMHO a real bug inside > interactiveDisplayBase since it does not respect the http_proxy variable > (and possibly whatever means will be done to set the proxy on non-Linux > systems which I did not verified). > > Kind regards > > Andreas. > > -- > http://fam-tille.de > > ________________________________________________________________________ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc From ftpmaster at ftp-master.debian.org Fri May 13 17:39:59 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 17:39:59 +0000 Subject: [Debian-med-packaging] plip_1.3.1+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 13 May 2016 17:44:04 +0200 Source: plip Binary: plip Architecture: source all Version: 1.3.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Alexandre Mestiashvili Description: plip - fully automated protein-ligand interaction profiler Changes: plip (1.3.1+dfsg-1) unstable; urgency=medium . * Bump Standards-Version * Imported Upstream version 1.3.1+dfsg * Export local python modules, needed for man page generation with help2man Checksums-Sha1: 9cd4b112db38225a6f4a3a51c8abfbd7090de3cb 2061 plip_1.3.1+dfsg-1.dsc abc024e25ba847af7757bf58eb6991e187ceaf4f 56444 plip_1.3.1+dfsg.orig.tar.xz e1d039111656feec3c81819b3cb37bb69922823b 3008 plip_1.3.1+dfsg-1.debian.tar.xz cb5c89a6caa59c720be2a14bd5c7b6b4df027aaf 48330 plip_1.3.1+dfsg-1_all.deb Checksums-Sha256: cd11536ebbfe11493ba281974711b2c32de3b508b01dce2e848e149c6dd1d66d 2061 plip_1.3.1+dfsg-1.dsc b8b2c845514ee174be5b988ff1c050f020b97fd3bde00d9320777af9c764ee5d 56444 plip_1.3.1+dfsg.orig.tar.xz 4b0bdf6c241c84c8dcdb9d48c4a7b8239ed4187a5a79bb62272862b67387b35c 3008 plip_1.3.1+dfsg-1.debian.tar.xz 7b18e7ac8218e031c9c4711c933d464984924afe78c45a74a83ae4a641c0db50 48330 plip_1.3.1+dfsg-1_all.deb Files: 0c352d72c574a939498409d72a23ce1f 2061 python optional plip_1.3.1+dfsg-1.dsc 2778aa6d0f2fcb83c010e9ef6cf04a53 56444 python optional plip_1.3.1+dfsg.orig.tar.xz b3498650d44fd0bde09c0a003b47f5ac 3008 python optional plip_1.3.1+dfsg-1.debian.tar.xz 8ed6d9370b3c655c49e5fbb87b28803d 48330 python optional plip_1.3.1+dfsg-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXNf6CAAoJEBz3khEbUiiwbxUQAKc3s/iztSvL7qAzoy8Xdqge 3W0gtAI6xWqCS6GssMbUAF3MrwwD5Xf2810dxFeW38FqsHYX6yY5/RkxMumSRk73 pyp/8Rl2hn+MRpfIlrXDRwW9hlDhNeQgI27iakwKz/Xy2F7ToenWE9OdZIEZaN9L CFLuykW3GnGm3aAL1N0q500zfpq+Az+nF0ZL4C3xObMqRCkCRDr9I23/bN+Fuyly 20OPHbShAPFNbN/cUmFJSmRhKuLYaXOOw8kdj7kZUhtYMYrsLtTpJkHJssjDC3ya xnL/MJyFnGu2a5bE0UrAkkl9l+vwj4HtFPuuDYGJVwde9/SLupk6j2kXJ90ubt68 /gLTg7MlCu44RI89x4AmdwrHkujwz3MEMiUrstBh17cSqKOAFFSG0yGO3P/6tLTm AnGtfNgq+DH7KIdvlPY2keQdmsQ4TKVLgtVGuHOxk/Go1xd3pIq9UmKDiN1BXb9x ZU9pFVmstoipFFOINj1qVWVD+GV4gHyp4rbOTSmSf510JIzK0GDsP5JHu3JSPCAp 0OOQR2+vpzj76h2D7sZS7ud8oQCMczwzylP5oesvqKdZchnJkXVlr7JfMZhLZB2/ qCotxGL/WTWd/G8OXtzPZY8ZYev5cMpWZJHqAlZo3x8CyEs6fs6HtUXlJq3bpoMx rMPKFp3eJq0gtMLVWt0a =iX8U -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From alteholz at debian.org Fri May 13 17:36:15 2016 From: alteholz at debian.org (Thorsten Alteholz) Date: Fri, 13 May 2016 19:36:15 +0200 (CEST) Subject: [Debian-med-packaging] fsm-lite_1.0-1_amd64.changes REJECTED In-Reply-To: <20160513152945.GF15380@an3as.eu> References: <20160513152945.GF15380@an3as.eu> Message-ID: Hi Andreas, On Fri, 13 May 2016, Andreas Tille wrote: > Sorry, but what do you mean? Isn't "any later version" the "+"? please read some more lines of the license text. The first occurence started with an "if" and the second one ist just an example. Thorsten From ftpmaster at ftp-master.debian.org Fri May 13 18:31:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 18:31:28 +0000 Subject: [Debian-med-packaging] Processing of macs_2.1.1.20160309-1_source.changes Message-ID: macs_2.1.1.20160309-1_source.changes uploaded successfully to localhost along with the files: macs_2.1.1.20160309-1.dsc macs_2.1.1.20160309.orig.tar.gz macs_2.1.1.20160309-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 13 18:31:39 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 18:31:39 +0000 Subject: [Debian-med-packaging] Processing of fsm-lite_1.0-1_amd64.changes Message-ID: fsm-lite_1.0-1_amd64.changes uploaded successfully to localhost along with the files: fsm-lite_1.0-1.dsc fsm-lite_1.0.orig.tar.gz fsm-lite_1.0-1.debian.tar.xz fsm-lite-dbgsym_1.0-1_amd64.deb fsm-lite_1.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From tille at debian.org Fri May 13 18:35:43 2016 From: tille at debian.org (Andreas Tille) Date: Fri, 13 May 2016 20:35:43 +0200 Subject: [Debian-med-packaging] fsm-lite_1.0-1_amd64.changes REJECTED In-Reply-To: References: <20160513152945.GF15380@an3as.eu> Message-ID: <20160513183543.GA3744@an3as.eu> On Fri, May 13, 2016 at 07:36:15PM +0200, Thorsten Alteholz wrote: > Hi Andreas, > > On Fri, 13 May 2016, Andreas Tille wrote: > >Sorry, but what do you mean? Isn't "any later version" the "+"? > > please read some more lines of the license text. The first occurence started > with an "if" and the second one ist just an example. Fixed and uploaded Thanks for checking Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Fri May 13 18:53:09 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 18:53:09 +0000 Subject: [Debian-med-packaging] fsm-lite_1.0-1_amd64.changes is NEW Message-ID: binary:fsm-lite is NEW. source:fsm-lite is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Fri May 13 18:59:24 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 13 May 2016 18:59:24 +0000 Subject: [Debian-med-packaging] macs_2.1.1.20160309-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 13 May 2016 10:49:54 -0700 Source: macs Binary: macs Architecture: source Version: 2.1.1.20160309-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: macs - Model-based Analysis of ChIP-Seq on short reads sequencers Changes: macs (2.1.1.20160309-1) unstable; urgency=medium . * New upstream release. * Bump Standards-Version to 3.9.8 * Refresh & re-submit spelling patch * enable "bindnow" linker flag hardening Checksums-Sha1: 4c3658f02d54e496a7f28383162d3d3806528536 2099 macs_2.1.1.20160309-1.dsc e688fe1a5367274fa4f7bd0d2d7b07b0bb2f0ec6 1627509 macs_2.1.1.20160309.orig.tar.gz ac87fb78c766ed9b77c2725219f996ae60b4709c 7628 macs_2.1.1.20160309-1.debian.tar.xz Checksums-Sha256: 5f66403bdbb36614d872804067ae9bc8670b64ebdc29a99b43865c19ac7cb372 2099 macs_2.1.1.20160309-1.dsc 2008ba838f83f34f8e0fddefe2a3a0159f4a740707c68058f815b31ddad53d26 1627509 macs_2.1.1.20160309.orig.tar.gz fd61794db6ed316a451f4c300b8486fbff0f858849ff3ea34ae22e4b754ea6b1 7628 macs_2.1.1.20160309-1.debian.tar.xz Files: 2de412953364d6af7c0848f8d87571a6 2099 science optional macs_2.1.1.20160309-1.dsc 1cc2fab44b232992060c7ab592bf43fa 1627509 science optional macs_2.1.1.20160309.orig.tar.gz b9a3724591c01522f238968254b30555 7628 science optional macs_2.1.1.20160309-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXNhn6AAoJEDwmdj9sZ+biS3QQALJ0ip2Nil2V/9V+Ho5nxd1K /sPpIZ6ekZOZeLMKEXyvxvugl9T0gfFr+SffoErKSudmZyGW2MAjvfGMCqTeq/5z szABNt1086iePZOvGGgTfW5GoGKAlUo6K9sRAvaKhNJexYrigY+kjKUgx5QL6V1+ leHCfWjVnTZP/J9lVupa7tuvTubpOCxsD+8IYFw2pDHtN/RDzoZM+ZzNo8TWqqYO FXolguCZUANan4dCJO69sLY6aalYpinfSQvo3JcBIRm2U4aGNazDgjY4kIeT9qMY BWGpM4rllvK8B7evcjJYiDhe7736x3otPEO91+d1nW3B4vYw/shHLlq4j0yJVsiI +aH8vafk9QwpqH0adzfhfkFiE4IfA0M8MNNomlywEAfc1f+lj+wpMVclRzosLCuB 0zkGW9BSXE9ygrlxqDXkaEnmTgTNcpxwDc7tyiwpAcFEyg7pSHJQJiiIn1LGhmBi hrQCbIRlpZgvO+hEj0/e0Vn23FsyOcfrASmiQQo1pChjTrekLBGDbjgYDBUt80xQ Lhn40Btmcue2x3XsvRWk5i9/pX9ferr6pL3Hs8XueuRjGz7q5QAUcl7AnDqZI31g z+ST+ageqr9DiuUOB8D8KSIehuK3E8n5FatCGYrqgTbImkGdW3oY/hswdblWuYkn bgR5ynqTa72w4lizH9vl =Jf4y -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From satta at tetrinetsucht.de Fri May 13 21:42:44 2016 From: satta at tetrinetsucht.de (Sascha Steinbiss) Date: Fri, 13 May 2016 22:42:44 +0100 Subject: [Debian-med-packaging] Bug#803550: Bug#803550: rsem: uninstallable on architectures without bowtie In-Reply-To: <20160319143440.32358.92425.reportbug@zam581.zam.kfa-juelich.de> References: <20160319143440.32358.92425.reportbug@zam581.zam.kfa-juelich.de> Message-ID: <9DB5A1BE-3655-4124-84DE-D22F09239A35@tetrinetsucht.de> Hi all, I re-introduced the build dependency on bowtie and also did some minor housekeeping. Committed the fix in git. Cheers Sascha > On 19 Mar 2016, at 14:34, Andreas Beckmann wrote: > > Package: rsem > Followup-For: Bug #803550 > > Hi, > > the > B-D: bowtie | bowtie2 > was dropped in the last upload, causing uninstallable rsem packages > being produced for many architectures, again. > > > Andreas > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging From michael.crusoe at gmail.com Fri May 13 22:00:54 2016 From: michael.crusoe at gmail.com (Michael Crusoe) Date: Sat, 14 May 2016 00:00:54 +0200 Subject: [Debian-med-packaging] Bug#803550: Bug#803550: rsem: uninstallable on architectures without bowtie In-Reply-To: <9DB5A1BE-3655-4124-84DE-D22F09239A35@tetrinetsucht.de> References: <20160319143440.32358.92425.reportbug@zam581.zam.kfa-juelich.de> <9DB5A1BE-3655-4124-84DE-D22F09239A35@tetrinetsucht.de> Message-ID: Thanks Sascha! Pe 13 mai 2016 11:45 p.m., "Sascha Steinbiss" a scris: > Hi all, > > I re-introduced the build dependency on bowtie and also did some minor > housekeeping. Committed the fix in git. > > Cheers > Sascha > > > On 19 Mar 2016, at 14:34, Andreas Beckmann wrote: > > > > Package: rsem > > Followup-For: Bug #803550 > > > > Hi, > > > > the > > B-D: bowtie | bowtie2 > > was dropped in the last upload, causing uninstallable rsem packages > > being produced for many architectures, again. > > > > > > Andreas > > > > _______________________________________________ > > Debian-med-packaging mailing list > > Debian-med-packaging at lists.alioth.debian.org > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From satta at tetrinetsucht.de Fri May 13 22:23:15 2016 From: satta at tetrinetsucht.de (Sascha Steinbiss) Date: Fri, 13 May 2016 23:23:15 +0100 Subject: [Debian-med-packaging] Bug#811827: prank: FTBFS with GCC 6: no match for References: <20160119083624.69041280CCB@dl580gen9-02.hlinux> <20160120022200.GR4951@jirafa.cyrius.com> Message-ID: Hi all, I fixed this in svn and also updated hardening and some other minor things. Cheers Sascha On Tue, 19 Jan 2016 18:22:00 -0800 Martin Michlmayr wrote: > Package: prank > Version: 0.0.150803-1 > Severity: important > User: debian-gcc at lists.debian.org > Usertags: ftbfs-gcc-6 gcc-6-no-match > > This package fails to build with GCC 6. GCC 6 has not been released > yet, but it's expected that GCC 6 will become the default compiler for > stretch. > > Note that only the first error is reported; there might be more. You > can find a snapshot of GCC 6 in experimental. To build with GCC 6, > you can set CC=gcc-6 CXX=g++-6 explicitly. > > You may be able to find out more about this issue at > https://gcc.gnu.org/gcc-6/changes.html > > > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux > ... > > g++ -c -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -pipe -O3 -I. -I/usr/include -o bppancestors.o bppancestors.cpp > > hmmodel.cpp: In member function 'void HMModel::alignmentModel(AncestralNode*)': > > hmmodel.cpp:1513:57: error: no match for 'operator<<' (operand types are 'std::basic_ostream' and 'std::ostream {aka std::basic_ostream}') > > cout<<"HMModel::alignmentModel: impossible 'as'"< > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ > > > > hmmodel.cpp:1513:57: note: candidate: operator<<(int, int) > > hmmodel.cpp:1513:57: note: no known conversion for argument 2 from 'std::ostream {aka std::basic_ostream}' to 'int' > > In file included from /usr/include/c++/6/istream:39:0, > > from /usr/include/c++/6/fstream:38, > > from hmmodel.cpp:24: > > /usr/include/c++/6/ostream:108:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__ostream_type& (*)(std::basic_ostream<_CharT, _Traits>::__ostream_type&)) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] > > operator<<(__ostream_type& (*__pf)(__ostream_type&)) > > ^~~~~~~~ > > > > /usr/include/c++/6/ostream:108:7: note: no known conversion for argument 1 from 'std::ostream {aka std::basic_ostream}' to 'std::basic_ostream::__ostream_type& (*)(std::basic_ostream::__ostream_type&) {aka std::basic_ostream& (*)(std::basic_ostream&)}' > > /usr/include/c++/6/ostream:117:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__ios_type& (*)(std::basic_ostream<_CharT, _Traits>::__ios_type&)) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream; std::basic_ostream<_CharT, _Traits>::__ios_type = std::basic_ios] > > operator<<(__ios_type& (*__pf)(__ios_type&)) > > ^~~~~~~~ > > > > /usr/include/c++/6/ostream:117:7: note: no known conversion for argument 1 from 'std::ostream {aka std::basic_ostream}' to 'std::basic_ostream::__ios_type& (*)(std::basic_ostream::__ios_type&) {aka std::basic_ios& (*)(std::basic_ios&)}' > > /usr/include/c++/6/ostream:127:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(std::ios_base& (*)(std::ios_base&)) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] > > operator<<(ios_base& (*__pf) (ios_base&)) > > ^~~~~~~~ > > > > /usr/include/c++/6/ostream:127:7: note: no known conversion for argument 1 from 'std::ostream {aka std::basic_ostream}' to 'std::ios_base& (*)(std::ios_base&)' > > /usr/include/c++/6/ostream:166:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] > > operator<<(long __n) > > ^~~~~~~~ > > > > /usr/include/c++/6/ostream:166:7: note: no known conversion for argument 1 from 'std::ostream {aka std::basic_ostream}' to 'long int' > > /usr/include/c++/6/ostream:170:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] > > operator<<(unsigned long __n) > > ^~~~~~~~ > > > > /usr/include/c++/6/ostream:170:7: note: no known conversion for argument 1 from 'std::ostream {aka std::basic_ostream}' to 'long unsigned int' > > /usr/include/c++/6/ostream:174:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char; _Traits = std::char_traits; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] > > operator<<(bool __n) > > ^~~~~~~~ > > > > /usr/include/c++/6/ostream:174:7: note: no known conversion for argument 1 from 'std::ostream {aka std::basic_ostream}' to 'bool' From plessy at debian.org Sat May 14 01:13:32 2016 From: plessy at debian.org (Charles Plessy) Date: Sat, 14 May 2016 10:13:32 +0900 Subject: [Debian-med-packaging] Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer) In-Reply-To: <20160511134828.GA15539@bubu.igloo> References: <20160509150152.GH8125@an3as.eu> <20160511134828.GA15539@bubu.igloo> Message-ID: <20160514011332.GD2007@falafel.plessy.net> Le Wed, May 11, 2016 at 10:48:28PM +0900, Charles Plessy a ?crit : > > the source of the problem here is the command AC_INIT("rtracklayer") > in configure.ac. Reported at https://support.bioconductor.org/p/82643/ Have a nice week-end, -- Charles From noreply at release.debian.org Sat May 14 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 14 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] prottest is marked for autoremoval from testing Message-ID: prottest 3.4.1+dfsg-2 is marked for autoremoval from testing on 2016-06-19 It (build-)depends on packages with these RC bugs: 823622: openjfx: CVE-2015-4901 CVE-2015-4906 CVE-2015-4908 CVE-2015-4916 From andreas at an3as.eu Sat May 14 05:12:58 2016 From: andreas at an3as.eu (Andreas Tille) Date: Sat, 14 May 2016 07:12:58 +0200 Subject: [Debian-med-packaging] Bug#811827: prank: FTBFS with GCC 6: no match for In-Reply-To: References: <20160119083624.69041280CCB@dl580gen9-02.hlinux> <20160120022200.GR4951@jirafa.cyrius.com> Message-ID: <20160514051258.GE3744@an3as.eu> On Fri, May 13, 2016 at 11:23:15PM +0100, Sascha Steinbiss wrote: > Hi all, > > I fixed this in svn and also updated hardening and some other minor things. Uploaded, thanks a lot Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sat May 14 05:12:56 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 05:12:56 +0000 Subject: [Debian-med-packaging] Processing of prank_0.0.150803-2_amd64.changes Message-ID: prank_0.0.150803-2_amd64.changes uploaded successfully to localhost along with the files: prank_0.0.150803-2.dsc prank_0.0.150803-2.debian.tar.xz prank-dbgsym_0.0.150803-2_amd64.deb prank_0.0.150803-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 14 05:20:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 05:20:28 +0000 Subject: [Debian-med-packaging] prank_0.0.150803-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 13 May 2016 21:57:42 +0000 Source: prank Binary: prank Architecture: source amd64 Version: 0.0.150803-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: prank - Probabilistic Alignment Kit for DNA, codon and amino-acid sequenc Closes: 811827 Changes: prank (0.0.150803-2) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * New homepage * d/watch: Adapt to new location * d/copyright: Upstream-Contact . [ Sascha Steinbiss ] * Fix building with GCC 6 Closes: #811827 * Enable full hardening. * Bump Standards-Version. * Use secure Vcs-*. 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From andreas at an3as.eu Sat May 14 05:16:39 2016 From: andreas at an3as.eu (Andreas Tille) Date: Sat, 14 May 2016 07:16:39 +0200 Subject: [Debian-med-packaging] Bug#811827: prank: FTBFS with GCC 6: no match for In-Reply-To: <1740004.U7lfUcSdiv@biotek1006> References: <20160119083624.69041280CCB@dl580gen9-02.hlinux> <2228862.PuHjcHxIWk@biotek1006> <20160120104200.GK3873@an3as.eu> <1740004.U7lfUcSdiv@biotek1006> Message-ID: <20160514051639.GF3744@an3as.eu> Hi Ari, Sascha Steinbiss has found a patch for this problem which you can find here: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/prank/trunk/debian/patches/ I'd also recommend to apply the hardening patch. Kind regards Andreas. On Wed, Jan 20, 2016 at 03:10:09PM +0200, Ari L?ytynoja wrote: > Hi, > > I'm using gcc 5.2.1 on Ubuntu 15.10. Is it possible to check the compatibility > with this version of gcc? If not, is there gcc-6 available for Wily? I only > found a repository with gcc-6 for the next Ubuntu release: > https://launchpad.net/~ubuntu-toolchain-r/+archive/ubuntu/test/ > > Regards, Ari > > On Wednesday 20 January 2016 11:42:00 Andreas Tille wrote: > > Hi Ari, > > > > yes, that source tarball from > > http://wasabiapp.org/download/prank/prank.source.150803.tgz > > is used for the packaging. > > > > Thanks a lot for your quick reply > > > > Andreas. > > > > On Wed, Jan 20, 2016 at 12:32:01PM +0200, Ari L?ytynoja wrote: > > > Hi, > > > Which version of PRANK is that? The latest one is here > > > http://wasabiapp.org/download/prank/prank.source.150803.tgz > > > > > > Regards, Ari > > > > > > On Wednesday 20 January 2016 11:04:46 Andreas Tille wrote: > > > > Hi, > > > > > > > > the Debian package for prank failed to build when using gcc version 6 as > > > > you can read below in the bug report. Feel free to contact us via the > > > > bug e-mail address (see To of this mail). > > > > > > > > Kind regards > > > > > > > > Andreas. > > > > > > > > On Tue, Jan 19, 2016 at 06:22:00PM -0800, Martin Michlmayr wrote: > > > > > Package: prank > > > > > Version: 0.0.150803-1 > > > > > Severity: important > > > > > User: debian-gcc at lists.debian.org > > > > > Usertags: ftbfs-gcc-6 gcc-6-no-match > > > > > > > > > > This package fails to build with GCC 6. GCC 6 has not been released > > > > > yet, but it's expected that GCC 6 will become the default compiler for > > > > > stretch. > > > > > > > > > > Note that only the first error is reported; there might be more. You > > > > > can find a snapshot of GCC 6 in experimental. To build with GCC 6, > > > > > you can set CC=gcc-6 CXX=g++-6 explicitly. > > > > > > > > > > You may be able to find out more about this issue at > > > > > https://gcc.gnu.org/gcc-6/changes.html > > > > > > > > > > > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux > > > > > > > > > > ... > > > > > > > > > > > g++ -c -g -O2 -fstack-protector-strong -Wformat > > > > > > -Werror=format-security > > > > > > -pipe -O3 -I. -I/usr/include -o bppancestors.o bppancestors.cpp > > > > > > hmmodel.cpp: In member function 'void > > > > > > HMModel::alignmentModel(AncestralNode*)': hmmodel.cpp:1513:57: > > > > > > error: > > > > > > no match for 'operator<<' (operand types are > > > > > > 'std::basic_ostream' > > > > > > and 'std::ostream {aka std::basic_ostream}')> > > > > > > > > > > > > > cout<<"HMModel::alignmentModel: impossible 'as'"< > > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ > > > > > > > > > > > > hmmodel.cpp:1513:57: note: candidate: operator<<(int, int) > > > > > > > > > > > > hmmodel.cpp:1513:57: note: no known conversion for argument 2 from > > > > > > 'std::ostream {aka std::basic_ostream}' to 'int' In file > > > > > > included > > > > > > from /usr/include/c++/6/istream:39:0, > > > > > > > > > > > > from /usr/include/c++/6/fstream:38, > > > > > > > > > > > > from hmmodel.cpp:24: > > > > > > /usr/include/c++/6/ostream:108:7: note: candidate: > > > > > > std::basic_ostream<_CharT, _Traits>::__ostream_type& > > > > > > std::basic_ostream<_CharT, > > > > > > _Traits>::operator<<(std::basic_ostream<_CharT, > > > > > > _Traits>::__ostream_type& (*)(std::basic_ostream<_CharT, > > > > > > _Traits>::__ostream_type&)) [with _CharT = char; _Traits = > > > > > > std::char_traits; std::basic_ostream<_CharT, > > > > > > _Traits>::__ostream_type = std::basic_ostream]> > > > > > > > > > > > > > operator<<(__ostream_type& (*__pf)(__ostream_type&)) > > > > > > ^~~~~~~~ > > > > > > > > > > > > /usr/include/c++/6/ostream:108:7: note: no known conversion for > > > > > > argument 1 from 'std::ostream {aka std::basic_ostream}' to > > > > > > 'std::basic_ostream::__ostream_type& > > > > > > (*)(std::basic_ostream::__ostream_type&) {aka > > > > > > std::basic_ostream& (*)(std::basic_ostream&)}' > > > > > > /usr/include/c++/6/ostream:117:7: note: candidate: > > > > > > std::basic_ostream<_CharT, _Traits>::__ostream_type& > > > > > > std::basic_ostream<_CharT, > > > > > > _Traits>::operator<<(std::basic_ostream<_CharT, > > > > > > _Traits>::__ios_type& > > > > > > (*)(std::basic_ostream<_CharT, _Traits>::__ios_type&)) [with _CharT > > > > > > = > > > > > > char; _Traits = std::char_traits; std::basic_ostream<_CharT, > > > > > > _Traits>::__ostream_type = std::basic_ostream; > > > > > > std::basic_ostream<_CharT, _Traits>::__ios_type = > > > > > > std::basic_ios]> > > > > > > > > > > > > operator<<(__ios_type& (*__pf)(__ios_type&)) > > > > > > ^~~~~~~~ > > > > > > > > > > > > /usr/include/c++/6/ostream:117:7: note: no known conversion for > > > > > > argument 1 from 'std::ostream {aka std::basic_ostream}' to > > > > > > 'std::basic_ostream::__ios_type& > > > > > > (*)(std::basic_ostream::__ios_type&) {aka > > > > > > std::basic_ios& > > > > > > (*)(std::basic_ios&)}' /usr/include/c++/6/ostream:127:7: note: > > > > > > candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& > > > > > > std::basic_ostream<_CharT, _Traits>::operator<<(std::ios_base& > > > > > > (*)(std::ios_base&)) [with _CharT = char; _Traits = > > > > > > std::char_traits; std::basic_ostream<_CharT, > > > > > > _Traits>::__ostream_type = std::basic_ostream]> > > > > > > > > > > > > > operator<<(ios_base& (*__pf) (ios_base&)) > > > > > > ^~~~~~~~ > > > > > > > > > > > > /usr/include/c++/6/ostream:127:7: note: no known conversion for > > > > > > argument 1 from 'std::ostream {aka std::basic_ostream}' to > > > > > > 'std::ios_base& (*)(std::ios_base&)' > > > > > > /usr/include/c++/6/ostream:166:7: > > > > > > note: candidate: std::basic_ostream<_CharT, > > > > > > _Traits>::__ostream_type& > > > > > > std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with > > > > > > _CharT > > > > > > = char; _Traits = std::char_traits; std::basic_ostream<_CharT, > > > > > > _Traits>::__ostream_type = std::basic_ostream]> > > > > > > > > > > > > > operator<<(long __n) > > > > > > ^~~~~~~~ > > > > > > > > > > > > /usr/include/c++/6/ostream:166:7: note: no known conversion for > > > > > > argument 1 from 'std::ostream {aka std::basic_ostream}' to > > > > > > 'long > > > > > > int' /usr/include/c++/6/ostream:170:7: note: candidate: > > > > > > std::basic_ostream<_CharT, _Traits>::__ostream_type& > > > > > > std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) > > > > > > [with _CharT = char; _Traits = std::char_traits; > > > > > > std::basic_ostream<_CharT, _Traits>::__ostream_type = > > > > > > std::basic_ostream]> > > > > > > > > > > > > > operator<<(unsigned long __n) > > > > > > ^~~~~~~~ > > > > > > > > > > > > /usr/include/c++/6/ostream:170:7: note: no known conversion for > > > > > > argument 1 from 'std::ostream {aka std::basic_ostream}' to > > > > > > 'long > > > > > > unsigned int' /usr/include/c++/6/ostream:174:7: note: candidate: > > > > > > std::basic_ostream<_CharT, _Traits>::__ostream_type& > > > > > > std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = > > > > > > char; _Traits = std::char_traits; std::basic_ostream<_CharT, > > > > > > _Traits>::__ostream_type = std::basic_ostream]> > > > > > > > > > > > > > operator<<(bool __n) > > > > > > ^~~~~~~~ > > > > > > > > > > > > /usr/include/c++/6/ostream:174:7: note: no known conversion for > > > > > > argument 1 from 'std::ostream {aka std::basic_ostream}' to > > > > > > 'bool' > > > > > > In file included from /usr/include/c++/6/ostream:638:0, > > > > > > > > > > > > from /usr/include/c++/6/istream:39, > > > > > > from /usr/include/c++/6/fstream:38, > > > > > > > > > > > from hmmodel.cpp:24: > > > > > _______________________________________________ > > > > > Debian-med-packaging mailing list > > > > > Debian-med-packaging at lists.alioth.debian.org > > > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-pac > > > > > kagi > > > > > ng > > -- > Ari L?ytynoja > Institute of Biotechnology > University of Helsinki, Finland > http://loytynojalab.biocenter.helsinki.fi > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From owner at bugs.debian.org Sat May 14 05:24:09 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sat, 14 May 2016 05:24:09 +0000 Subject: [Debian-med-packaging] Bug#811827: marked as done (prank: FTBFS with GCC 6: no match for) References: <20160120022200.GR4951@jirafa.cyrius.com> Message-ID: Your message dated Sat, 14 May 2016 05:20:28 +0000 with message-id and subject line Bug#811827: fixed in prank 0.0.150803-2 has caused the Debian Bug report #811827, regarding prank: FTBFS with GCC 6: no match for to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 811827: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811827 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Martin Michlmayr Subject: prank: FTBFS with GCC 6: no match for Date: Tue, 19 Jan 2016 18:22:00 -0800 Size: 7312 URL: -------------- next part -------------- An embedded message was scrubbed... From: Sascha Steinbiss Subject: Bug#811827: fixed in prank 0.0.150803-2 Date: Sat, 14 May 2016 05:20:28 +0000 Size: 5690 URL: From ftpmaster at ftp-master.debian.org Sat May 14 06:02:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 06:02:23 +0000 Subject: [Debian-med-packaging] Processing of gmap_2016-05-01-1_amd64.changes Message-ID: gmap_2016-05-01-1_amd64.changes uploaded successfully to ftp-master.debian.org along with the files: gmap_2016-05-01-1.dsc gmap_2016-05-01.orig.tar.gz gmap_2016-05-01-1.debian.tar.xz gmap-dbgsym_2016-05-01-1_amd64.deb gmap_2016-05-01-1_amd64.deb Greetings, Your Debian queue daemon (running on host coccia.debian.org) From ftpmaster at ftp-master.debian.org Sat May 14 06:03:10 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 06:03:10 +0000 Subject: [Debian-med-packaging] Processing of gmap_2016-05-01-1_amd64.changes Message-ID: gmap_2016-05-01-1_amd64.changes uploaded successfully to localhost along with the files: gmap_2016-05-01-1.dsc gmap_2016-05-01.orig.tar.gz gmap_2016-05-01-1.debian.tar.xz gmap-dbgsym_2016-05-01-1_amd64.deb gmap_2016-05-01-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 14 06:19:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 06:19:01 +0000 Subject: [Debian-med-packaging] gmap_2016-05-01-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 27 Apr 2016 13:48:08 +0200 Source: gmap Binary: gmap Architecture: source amd64 Version: 2016-05-01-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Alexandre Mestiashvili Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2016-05-01-1) unstable; urgency=medium . * Imported Upstream version 2016-04-04 * Update copyright years * Imported Upstream version 2016-05-01 * Bump Standards-Version Checksums-Sha1: 7c3f9578c8a52bc6aab6577d2fd87a08c5c3d95b 2065 gmap_2016-05-01-1.dsc 3fcf06e25ce760f6af0c3dad6c5b19e24605344e 4454382 gmap_2016-05-01.orig.tar.gz 8f040fc8ab3c96ae4e2f611b2074d15bd711d70d 6904 gmap_2016-05-01-1.debian.tar.xz 5241e249c03eef6c2e4f43e8d90c7bdb7e5e9f6a 14040374 gmap-dbgsym_2016-05-01-1_amd64.deb a7a21f97866037f69d93ce4daa2ef77168f18d8b 19053504 gmap_2016-05-01-1_amd64.deb Checksums-Sha256: 633a8a2b6a46e988a4a90d1110ccea715778fa5e0b46a1a7fd0e40d3a16fcee5 2065 gmap_2016-05-01-1.dsc ab13a849613c978a6fd584908f758db599143fe5f9e8910e4904c1dea9dfcb8e 4454382 gmap_2016-05-01.orig.tar.gz b2a1f52f4141a9da7750204d45f655ed1251145d78eacdf8919c830d234886dc 6904 gmap_2016-05-01-1.debian.tar.xz cb1deb69a1f2ae9ff26183b5206ebc1f8e86cdf767c773c757c15f4dd349918e 14040374 gmap-dbgsym_2016-05-01-1_amd64.deb a5384848d2caa5503102c1823075945da5a6e3e694705c80e172482fb4e0657d 19053504 gmap_2016-05-01-1_amd64.deb Files: 78a9cc0a8dc67a24f53cb0e459f30ec1 2065 non-free/science optional gmap_2016-05-01-1.dsc e7d007850a741f69e34234b6c67d3ddc 4454382 non-free/science optional gmap_2016-05-01.orig.tar.gz 3aa6442bab19f6614e38fec3d1a92b39 6904 non-free/science optional gmap_2016-05-01-1.debian.tar.xz 53684c583fe872df853d40c0ec784a4a 14040374 non-free/debug extra gmap-dbgsym_2016-05-01-1_amd64.deb e5c2ae13618c977e2ab1f845365af292 19053504 non-free/science optional gmap_2016-05-01-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXNrqMAAoJEBz3khEbUiiwtioP/1S0sP/lxcHciRqtBTAqkUFT tbQOWTUxv62L0aTGqS+74SymmxIDujTfslfJyT0H4tE2CyqyPuaEBzut14gW3Jve nPrDskR9si16cMDY8MHVIORbniXy/7iOq+mlwnHGE6uaeC/RCTiluQxw9FlG4/r6 2rSmvQr2D9h0tPB8e5qK5xYAvXvyuFVX6+ul/iSIgrrjPzgN7fP0YF8waLeuVOMV 8Xr3ElGoGf7wQjKAtRQwPWybUUyeB8vmA27cHhgurnbDyKkTrZQSK5m6521Q2H9F Wuqrkf2qW/RUtsmVIV74OTwKO50FKkaAOIBP5iL8M0ATa5SJrh9NI0VAVazALTJu xSRIB0+MkwJQ8Tf9HB7c+vObiTydGwSG4boKm4PAbde4Q+CvqQLbKfIbyVqXZpFh 2aMWx8MPEXgLZHrNircDeaSyUPhwqacUVU3MyrpIQHVu6VQSStxdacKmuQ0OR6Ul OL5OdTNoxC5nsVJT8Axo0v+rhKqSUtZcoTi/NOpPKBLll7/ufF5p6Ny0V8DzL7t1 LZSv/rj5MIIHoViriyg1PfcOSDBVT18UyJPU3Ijw5EsFe3Otu4ihBJ5U9wVHr50E pxaaobSp4IfZtRy94OYaBH5dPE4S73gNneuvmI+IRhHr7aMtqHQ05hsAn9ht9j+5 gd8Wi/B2YQkLrSqfkh8/ =FAgD -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sat May 14 08:13:49 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 08:13:49 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-genomicfeatures_1.24.1-1_source.changes Message-ID: r-bioc-genomicfeatures_1.24.1-1_source.changes uploaded successfully to localhost along with the files: r-bioc-genomicfeatures_1.24.1-1.dsc r-bioc-genomicfeatures_1.24.1.orig.tar.gz r-bioc-genomicfeatures_1.24.1-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 14 10:04:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 10:04:11 +0000 Subject: [Debian-med-packaging] r-bioc-genomicfeatures_1.24.1-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sat, 14 May 2016 10:07:49 +0200 Source: r-bioc-genomicfeatures Binary: r-bioc-genomicfeatures Architecture: source Version: 1.24.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-genomicfeatures - GNU R tools for making and manipulating transcript centric annota Changes: r-bioc-genomicfeatures (1.24.1-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 2a5d6f9287f41930bc27068b74624e73016b6046 2253 r-bioc-genomicfeatures_1.24.1-1.dsc 7973556ca7de64ae3dee825a074082a4baf063b7 827122 r-bioc-genomicfeatures_1.24.1.orig.tar.gz 68bbc8eb18d25b12b99506933869c7201037d2d5 6316 r-bioc-genomicfeatures_1.24.1-1.debian.tar.xz Checksums-Sha256: 96648c1c83990f21247a4fcd7f025af756d7e7554918e35de9c6811ab55342f9 2253 r-bioc-genomicfeatures_1.24.1-1.dsc ed1cce22048226b878049da1ad6b1048bab3ca3da46e5e1e5aae9d28ce617535 827122 r-bioc-genomicfeatures_1.24.1.orig.tar.gz 1cd9d4a0d6068698c044a9ddd768448198d3c69313d35c5fcb25bbded96c040b 6316 r-bioc-genomicfeatures_1.24.1-1.debian.tar.xz Files: 54c0f31d105480c4c26fff62aa86a695 2253 gnu-r optional r-bioc-genomicfeatures_1.24.1-1.dsc a0bb9fe3fca75bff101f62b83829f98f 827122 gnu-r optional r-bioc-genomicfeatures_1.24.1.orig.tar.gz 43c3f85db7de14ddc661f5c45bc750d8 6316 gnu-r optional r-bioc-genomicfeatures_1.24.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXNt3jAAoJEFeKBJTRxkbR18YQAJulprmaF6udrh2fH0gYY7u2 U/KMon7W/COL1pH8qsdg4CT/qMs0Rqq7XGXOOrbkakIZCg0A0rZhyza7wcpUZC3w QubBeahOPFj5hP4OIuE7AX4mH50TZxDDddvyejn+JbhL8jPKTnU/KKAXJForbTv+ jMhp8Zgoa7k9jnn9nBiP/S0A3+z7IInUVZG9pAgXaI53xhoAkY/LkJExakC7nLse PIbLSoPZDa3qIZi4l8bv+5kJkgalGF/B/BBd1bpecaZKUR/tnRe7D1wc2cKPtGBz onPcniD1GzBDXI7ntcNO4xWrPBVYDfLX2VclMtXvj7XxKgDtVd/aGxy1dlmbNUJ2 VtEN/2HQL4AekdVaHyfhpBHh5XLr0/lX1agHx+Nt4yjSh6DSV4HuSUnpq7wdXPJJ vHua96kE2JkBKdvSDHRhy0y82mDphoJ8PagMWQkBPAfu4NwSeS3skTmcymHiMzIj 0jPcMrI0Ep7qazwsQsn7Ez5Jt5iW2CkK5LWK+V+xl9FhjZrLVO2t76X/cjDmZCT+ sQPOSVZU6DsvN3o7W4Qvvz2FPobOvDDslQk2PSkyNvFBidGSApdU23DiCcob5uRg nCfHTxEUOTQwTdBYXK1UkYtSt+SetuDrgu3hRPSVjxbu0DAr7AMl/bjmhQ42TCHK bZ1lzq6023yiATurM/FX =mw6b -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sat May 14 14:00:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 14:00:17 +0000 Subject: [Debian-med-packaging] fsm-lite_1.0-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 13 Apr 2016 09:39:32 +0200 Source: fsm-lite Binary: fsm-lite Architecture: source amd64 Version: 1.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: fsm-lite - frequency-based string mining (lite) Closes: 820854 Changes: fsm-lite (1.0-1) unstable; urgency=medium . * Initial release (Closes: #820854) Checksums-Sha1: ef0425f98b91e8721e13a353c0947c5c468b98a9 1909 fsm-lite_1.0-1.dsc ea132b307a2fcfdd22538da1f950ef77e8fae892 19599 fsm-lite_1.0.orig.tar.gz 5ce9c542322854133899015146d9cd2d56df8b0a 3248 fsm-lite_1.0-1.debian.tar.xz 42f8771c141855703dfb71c803dc73115a80b552 629106 fsm-lite-dbgsym_1.0-1_amd64.deb 01194d7d51d18810927492e9ebca91692fc3f901 84970 fsm-lite_1.0-1_amd64.deb Checksums-Sha256: f25424064bd6ea0b6e951a195b226ae29ad6f15044ef6a0661544fa3e0eca907 1909 fsm-lite_1.0-1.dsc f781a9fbab5265bd09b3b5b7e1cba904582ec201c3d30baed36e28a03de3ac61 19599 fsm-lite_1.0.orig.tar.gz 8c0e844a5d0ba7801eeb36ceaab7075616f22cd21ef14cc3a13c137d6fb33904 3248 fsm-lite_1.0-1.debian.tar.xz 7e8ae516299b9624bf0ba76d6850e968af3595446a3f2a9e417366ce9f3a1073 629106 fsm-lite-dbgsym_1.0-1_amd64.deb b9d34a5ea2ec2e58931d5b0e920973425e8f7a57381a3ba6c39d439c5976617a 84970 fsm-lite_1.0-1_amd64.deb Files: 43a20e0de63741cf2ebca924acb7cef5 1909 science optional fsm-lite_1.0-1.dsc 2fab374d2477f3a5f55844451c2b1a1f 19599 science optional fsm-lite_1.0.orig.tar.gz 21280dabffcde3b7ed40b81d959d2e74 3248 science optional fsm-lite_1.0-1.debian.tar.xz 6fa72738dc0031816880c838fc35bb6a 629106 debug extra fsm-lite-dbgsym_1.0-1_amd64.deb 5481c09b123bc991af5ad8e94bc3471e 84970 science optional fsm-lite_1.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXNhzMAAoJEFeKBJTRxkbRX9oP/irS2GXg9/AtsWzF2IIjQEDL VGs+doYoBkDKh5x+Na8GZXrTp8llChSYAoZoOQLnKEAdhc54xKqeC97HWemK8ZFX yujYTEYzP5nZB2bhhs9VnkN1HysWnj5/J2qCDza/j0/7U/f13twBhjcWuHngfoK3 7w8deiWaT54W7Aew9rpvswsFY1Xk1aAKizgOcdoLK6D/2Emq2xVYR5LuTx7bDZzG H5yUx1zylAu1j+e5u5JKHz12ovImt+xcKj/trldcfQvE3KJ8u8zLxZHyCF23VOd5 GUUiEMqf9uAyVWB+9HB4IYCa4zSZn+iwpz6PQwWBCYHLwqfhHPGqoZXIHY/KB6hG Kn15/YSFvTdTSAUibskrytIvwkwwD+Bc1G70eNcheClOQdFvs3MrjcUqUGun0M93 jDy4ttSBPajCrM92EKsalTPFUi/GtWIGoesn1JbByLqyNN+fnrqnkQnZNGdqdlQG hLe8mC8QU7/sEE/giIUXmrrcgNAr24ulWN0ydp9nqXzevUSTNVUAQTuKnuYwVuo5 5bUe3Ol+vmQYS3wlZTJeJL6MGy7OcSuT5UIskeNiEbdEedJfTPcxyTv5DUN+zD9J v+BSufvnjateMhWEbT+D//WIFrtZ2oYpgALqUYu999BciUj7l4WkeuhmkM6PscyP MYKYXmqTKCUBtjOobFm/ =Eg4x -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From satta at tetrinetsucht.de Sat May 14 15:43:40 2016 From: satta at tetrinetsucht.de (Sascha Steinbiss) Date: Sat, 14 May 2016 16:43:40 +0100 Subject: [Debian-med-packaging] Bug#811909: parsinsert: FTBFS with GCC 6: invalid conversion References: <20160119051750.EF96E280CC1@dl580gen9-02.hlinux> <20160120033230.GY4951@jirafa.cyrius.com> Message-ID: <400D5F83-460F-4DC1-AF83-7E8D48D789F4@tetrinetsucht.de> Dear all, I have fixed this in SVN and also done the usual housekeeping tasks. Cheers Sascha On Tue, 19 Jan 2016 19:32:30 -0800 Martin Michlmayr wrote: > Package: parsinsert > Version: 1.04-1 > Severity: important > User: debian-gcc at lists.debian.org > Usertags: ftbfs-gcc-6 gcc-6-invalid-convert > > This package fails to build with GCC 6. GCC 6 has not been released > yet, but it's expected that GCC 6 will become the default compiler for > stretch. > > Note that only the first error is reported; there might be more. You > can find a snapshot of GCC 6 in experimental. To build with GCC 6, > you can set CC=gcc-6 CXX=g++-6 explicitly. > > You may be able to find out more about this issue at > https://gcc.gnu.org/gcc-6/changes.html > > > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux > ... > > g++ -g -O3 -c -o ParsInsert.o ParsInsert.cpp > > In file included from ParsInsert.h:29:0, > > from ParsInsert.cpp:34: > > ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': > > ParsimonySet.h:429:35: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > DisplayL("%s [", label); > > ^ > > > > ParsimonySet.h:431:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > DisplayL(" %3d", segCounts[k]); > > ^ > > > > ParsimonySet.h:432:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > DisplayL("]\n"); > > ^ > > > > ParsInsert.cpp: At global scope: > > ParsInsert.cpp:92:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > char *statsName = "PI_Results.log"; > > ^~~~~~~~~~~~~~~~ > > > > ParsInsert.cpp:93:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > char *logFilename = "ParsInsert.log"; > > ^~~~~~~~~~~~~~~~ > > > > ParsInsert.cpp:94:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > char *treeFilename = "PI_Tree.tree"; > > ^~~~~~~~~~~~~~ > > > > ParsInsert.cpp:95:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > char *seqFilename = "PI_Tree.fasta"; > > ^~~~~~~~~~~~~~~ > > > > ParsInsert.cpp:98:42: error: invalid conversion from 'int' to 'char*' [-fpermissive] > > char *files[64] = {64*0}; > > ~~^~ > > -- > Martin Michlmayr > Linux for HPE Helion, Hewlett Packard Enterprise > -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 455 bytes Desc: Message signed with OpenPGP using GPGMail URL: From ftpmaster at ftp-master.debian.org Sat May 14 16:17:00 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 16:17:00 +0000 Subject: [Debian-med-packaging] Processing of parsinsert_1.04-2_amd64.changes Message-ID: parsinsert_1.04-2_amd64.changes uploaded successfully to localhost along with the files: parsinsert_1.04-2.dsc parsinsert_1.04-2.debian.tar.xz parsinsert-dbgsym_1.04-2_amd64.deb parsinsert_1.04-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at an3as.eu Sat May 14 16:19:25 2016 From: andreas at an3as.eu (Andreas Tille) Date: Sat, 14 May 2016 18:19:25 +0200 Subject: [Debian-med-packaging] Bug#811909: parsinsert: FTBFS with GCC 6: invalid conversion In-Reply-To: <400D5F83-460F-4DC1-AF83-7E8D48D789F4@tetrinetsucht.de> References: <20160119051750.EF96E280CC1@dl580gen9-02.hlinux> <20160120033230.GY4951@jirafa.cyrius.com> <400D5F83-460F-4DC1-AF83-7E8D48D789F4@tetrinetsucht.de> Message-ID: <20160514161925.GA4230@an3as.eu> Uploaded, thanks a lot for your effort, Andreas. On Sat, May 14, 2016 at 04:43:40PM +0100, Sascha Steinbiss wrote: > Dear all, > > I have fixed this in SVN and also done the usual housekeeping tasks. > > Cheers > Sascha > > On Tue, 19 Jan 2016 19:32:30 -0800 Martin Michlmayr wrote: > > Package: parsinsert > > Version: 1.04-1 > > Severity: important > > User: debian-gcc at lists.debian.org > > Usertags: ftbfs-gcc-6 gcc-6-invalid-convert > > > > This package fails to build with GCC 6. GCC 6 has not been released > > yet, but it's expected that GCC 6 will become the default compiler for > > stretch. > > > > Note that only the first error is reported; there might be more. You > > can find a snapshot of GCC 6 in experimental. To build with GCC 6, > > you can set CC=gcc-6 CXX=g++-6 explicitly. > > > > You may be able to find out more about this issue at > > https://gcc.gnu.org/gcc-6/changes.html > > > > > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux > > ... > > > g++ -g -O3 -c -o ParsInsert.o ParsInsert.cpp > > > In file included from ParsInsert.h:29:0, > > > from ParsInsert.cpp:34: > > > ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': > > > ParsimonySet.h:429:35: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > > DisplayL("%s [", label); > > > ^ > > > > > > ParsimonySet.h:431:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > > DisplayL(" %3d", segCounts[k]); > > > ^ > > > > > > ParsimonySet.h:432:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > > DisplayL("]\n"); > > > ^ > > > > > > ParsInsert.cpp: At global scope: > > > ParsInsert.cpp:92:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > > char *statsName = "PI_Results.log"; > > > ^~~~~~~~~~~~~~~~ > > > > > > ParsInsert.cpp:93:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > > char *logFilename = "ParsInsert.log"; > > > ^~~~~~~~~~~~~~~~ > > > > > > ParsInsert.cpp:94:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > > char *treeFilename = "PI_Tree.tree"; > > > ^~~~~~~~~~~~~~ > > > > > > ParsInsert.cpp:95:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] > > > char *seqFilename = "PI_Tree.fasta"; > > > ^~~~~~~~~~~~~~~ > > > > > > ParsInsert.cpp:98:42: error: invalid conversion from 'int' to 'char*' [-fpermissive] > > > char *files[64] = {64*0}; > > > ~~^~ > > > > -- > > Martin Michlmayr > > Linux for HPE Helion, Hewlett Packard Enterprise > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sat May 14 16:24:21 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 16:24:21 +0000 Subject: [Debian-med-packaging] parsinsert_1.04-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sat, 14 May 2016 15:26:05 +0000 Source: parsinsert Binary: parsinsert Architecture: source amd64 Version: 1.04-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: parsinsert - Parsimonious Insertion of unclassified sequences into phylogeneti Closes: 811909 Changes: parsinsert (1.04-2) unstable; urgency=medium . * Team upload. * Fix building with GCC 6. Closes: #811909 * Enable full hardening. * Use secure Vcs-*. * Bump Standards-Version. 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From owner at bugs.debian.org Sat May 14 16:27:24 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sat, 14 May 2016 16:27:24 +0000 Subject: [Debian-med-packaging] Bug#811909: marked as done (parsinsert: FTBFS with GCC 6: invalid conversion) References: <20160120033230.GY4951@jirafa.cyrius.com> Message-ID: Your message dated Sat, 14 May 2016 16:24:21 +0000 with message-id and subject line Bug#811909: fixed in parsinsert 1.04-2 has caused the Debian Bug report #811909, regarding parsinsert: FTBFS with GCC 6: invalid conversion to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 811909: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811909 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Martin Michlmayr Subject: parsinsert: FTBFS with GCC 6: invalid conversion Date: Tue, 19 Jan 2016 19:32:30 -0800 Size: 4604 URL: -------------- next part -------------- An embedded message was scrubbed... From: Sascha Steinbiss Subject: Bug#811909: fixed in parsinsert 1.04-2 Date: Sat, 14 May 2016 16:24:21 +0000 Size: 5568 URL: From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-annotate 1.50.0+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-annotate source package in Debian's testing distribution has changed. Previous version: 1.48.0+dfsg-1 Current version: 1.50.0+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-biostrings 2.40.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-biostrings source package in Debian's testing distribution has changed. Previous version: 2.38.4-1 Current version: 2.40.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-summarizedexperiment 1.2.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-summarizedexperiment source package in Debian's testing distribution has changed. Previous version: 1.0.0-1 Current version: 1.2.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-biomart 2.28.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-biomart source package in Debian's testing distribution has changed. Previous version: 2.26.1-1 Current version: 2.28.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-hypergraph 1.44.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-hypergraph source package in Debian's testing distribution has changed. Previous version: 1.42.0-1 Current version: 1.44.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-genomicranges 1.24.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-genomicranges source package in Debian's testing distribution has changed. Previous version: 1.22.4-1 Current version: 1.24.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-makecdfenv 1.48.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-makecdfenv source package in Debian's testing distribution has changed. Previous version: 1.46.0-1 Current version: 1.48.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-iranges 2.6.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-iranges source package in Debian's testing distribution has changed. Previous version: 2.4.7-1 Current version: 2.6.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] samtools 1.3.1-2 MIGRATED to testing Message-ID: FYI: The status of the samtools source package in Debian's testing distribution has changed. Previous version: 1.3.1-1 Current version: 1.3.1-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-biocinstaller 1.22.1-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-biocinstaller source package in Debian's testing distribution has changed. Previous version: 1.20.0-1 Current version: 1.22.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-xvector 0.12.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-xvector source package in Debian's testing distribution has changed. 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From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-genomicalignments 1.8.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-genomicalignments source package in Debian's testing distribution has changed. Previous version: 1.6.3-1 Current version: 1.8.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] r-bioc-affyio 1.42.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-affyio source package in Debian's testing distribution has changed. Previous version: 1.40.0-1 Current version: 1.42.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-rsamtools 1.24.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-rsamtools source package in Debian's testing distribution has changed. Previous version: 1.22.0-2 Current version: 1.24.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-genomeinfodb 1.8.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-genomeinfodb source package in Debian's testing distribution has changed. Previous version: 1.6.0-1 Current version: 1.8.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] r-bioc-altcdfenvs 1:2.34.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-altcdfenvs source package in Debian's testing distribution has changed. Previous version: 1:2.32.0-1 Current version: 1:2.34.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-preprocesscore 1.34.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-preprocesscore source package in Debian's testing distribution has changed. Previous version: 1.32.0-1 Current version: 1.34.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 14 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 14 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-annotationdbi 1.34.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-annotationdbi source package in Debian's testing distribution has changed. Previous version: 1.32.0-1 Current version: 1.34.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From tinaevans25 at hotmail.com Sat May 14 16:59:58 2016 From: tinaevans25 at hotmail.com (Tina evans) Date: Sat, 14 May 2016 16:59:58 +0000 (UTC) Subject: [Debian-med-packaging] HELLO References: <757942256.1977576.1463245198142.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <757942256.1977576.1463245198142.JavaMail.yahoo@mail.yahoo.com> ?Hello Nice to meet you,My name is miss Tina ,i saw your email address on Facebook when I'm browsing in the Internet today and become interested in you, i think we can make it together.can you Reply me in my email for more information okay -------------- next part -------------- An HTML attachment was scrubbed... URL: From satta at tetrinetsucht.de Sat May 14 16:59:49 2016 From: satta at tetrinetsucht.de (Sascha Steinbiss) Date: Sat, 14 May 2016 17:59:49 +0100 Subject: [Debian-med-packaging] Bug#811881: tophat: FTBFS with GCC 6: no matching function for call to References: <20160119174312.8B55A280CB0@dl580gen9-02.hlinux> <20160120025442.GT4951@jirafa.cyrius.com> Message-ID: <683DC2E6-4D2D-4821-B9FB-5FF3E15767DC@tetrinetsucht.de> Hi all, this is now fixed in git. Last GCC 6 bug for the weekend ;) Cheers Sascha On Tue, 19 Jan 2016 18:54:42 -0800 Martin Michlmayr wrote: > Package: tophat > Version: 2.1.0+dfsg-1 > Severity: important > User: debian-gcc at lists.debian.org > Usertags: ftbfs-gcc-6 gcc-6-no-match > > This package fails to build with GCC 6. GCC 6 has not been released > yet, but it's expected that GCC 6 will become the default compiler for > stretch. > > Note that only the first error is reported; there might be more. You > can find a snapshot of GCC 6 in experimental. To build with GCC 6, > you can set CC=gcc-6 CXX=g++-6 explicitly. > > You may be able to find out more about this issue at > https://gcc.gnu.org/gcc-6/changes.html > > > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux > ... > > g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -c -o tophat_reports.o tophat_reports.cpp > > In file included from tophat_reports.cpp:36:0: > > common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)': > > common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable] > > int pre_block_offs=0; //but before this write() > > ^~~~~~~~~~~~~~ > > > > tophat_reports.cpp: In member function 'void ReportWorker::write_singleton_alignments(uint64_t, HitsForRead&, ReadStream&, GBamWriter&, FragmentType, GetReadProc*, QReadData)': > > tophat_reports.cpp:2292:8: warning: variable 'map_code' set but not used [-Wunused-but-set-variable] > > char map_code=0; > > ^~~~~~~~ > > > > tophat_reports.cpp: In function 'void driver(const string&, std::istream&, const std::vector >&, const string&, const std::vector >&, const string&, FILE*, FILE*, FILE*, FILE*)': > > tophat_reports.cpp:2707:128: error: no matching function for call to 'make_pair(Junction, JunctionStats&)' > > gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); > > ^ > > > > In file included from /usr/include/c++/6/bits/stl_algobase.h:64:0, > > from /usr/include/c++/6/vector:60, > > from tophat_reports.cpp:20: > > /usr/include/c++/6/bits/stl_pair.h:406:5: note: candidate: template constexpr std::pair::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) > > make_pair(_T1&& __x, _T2&& __y) > > ^~~~~~~~~ > > > > /usr/include/c++/6/bits/stl_pair.h:406:5: note: template argument deduction/substitution failed: > > tophat_reports.cpp:2707:128: note: cannot convert 'junction_stat' (type 'JunctionStats') to type 'JunctionStats&&' > > gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); > > ^ > > > > Makefile:1453: recipe for target 'tophat_reports.o' failed > > make[3]: *** [tophat_reports.o] Error 1 > > -- > Martin Michlmayr > Linux for HPE Helion, Hewlett Packard Enterprise > > From ftpmaster at ftp-master.debian.org Sat May 14 18:00:17 2016 From: ftpmaster at ftp-master.debian.org (Thorsten Alteholz) Date: Sat, 14 May 2016 18:00:17 +0000 Subject: [Debian-med-packaging] fastqtl_2.184+dfsg-1_amd64.changes REJECTED Message-ID: Hi Dylan, according to the metainfo of FastQTL/doc/img/fastqtl_checks.jpg there is a "Copyright Artifex Software 2011". Can you please check with upstream the license information for this file. Please mention that in your debian/copyright as well. Thanks! Thorsten === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Sat May 14 18:00:17 2016 From: ftpmaster at ftp-master.debian.org (Thorsten Alteholz) Date: Sat, 14 May 2016 18:00:17 +0000 Subject: [Debian-med-packaging] maffilter_1.1.0-1+dfsg-1_amd64.changes REJECTED Message-ID: Hi Andreas, the authors don't have be the Copyright holders. According to the file headers there are some differences: doc/maffilter.texi:Copyright @copyright{} 2014 Julien Y. Dutheil MafFilter/MafFilter.cpp:Copyright or or Copr. CNRS MafFilter/OutputAsFeaturesMafIterator.cpp:Copyright or or Copr. Bio++ Development Team, (2010) MafFilter/OutputAsFeaturesMafIterator.h:Copyright or or Copr. Bio++ Development Team, (2013) Thorsten === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Sat May 14 18:07:52 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 18:07:52 +0000 Subject: [Debian-med-packaging] Processing of spdlog_1.7-1_source.changes Message-ID: spdlog_1.7-1_source.changes uploaded successfully to localhost along with the files: spdlog_1.7-1.dsc spdlog_1.7.orig.tar.gz spdlog_1.7-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 14 18:27:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 18:27:34 +0000 Subject: [Debian-med-packaging] spdlog_1.7-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sat, 14 May 2016 11:06:05 -0700 Source: spdlog Binary: libspdlog-dev Architecture: source Version: 1.7-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: libspdlog-dev - Very fast, header only, C++ logging library Changes: spdlog (1.7-1) unstable; urgency=medium . * new upstream release * Standards-Version: increment to 3.9.8 * Match upstream's switch to cmake Checksums-Sha1: 6fb205f4fa627ed36352711aa7004dcd5dff3486 1917 spdlog_1.7-1.dsc 7c5cce56e67f88faa0d968a9ae804a36fdafcc47 136622 spdlog_1.7.orig.tar.gz 1a9c51af3a705cb37649da1a70d346cec27a439d 3416 spdlog_1.7-1.debian.tar.xz Checksums-Sha256: fd414711ee13508bd25eba07461c3fc764fbc54aa6df988b4c00494a24aa344f 1917 spdlog_1.7-1.dsc 7e122dd2e362de8d8475ddd2bed7314b95ca807380e7b46dc58c09fd7aafca3f 136622 spdlog_1.7.orig.tar.gz 8d4dbf799a97b94ff7c2499611303c21150bc2a6d3eff8556f09ca536154b7ba 3416 spdlog_1.7-1.debian.tar.xz Files: c8bc919788e9627b312db440206d5b6b 1917 libdevel optional spdlog_1.7-1.dsc de66904c617f1cd3093209c5f02c01ee 136622 libdevel optional spdlog_1.7.orig.tar.gz 16c1877a0d0f4c28436606cc446ef5f8 3416 libdevel optional spdlog_1.7-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXN2kiAAoJEDwmdj9sZ+bimKMP/jHlhnxw1u1r9Q8uUsTJOK5e k+a0H5GFSC+YXR7u8X5auajbGl4bqz4/sN94RY3mchSBq10yVhQjEcZEfnVTPaXk bcRsWSsk7s54RfU6V2sKdpz5rDc9oHEQmhOTWXyTIAxwDZcC6gS2+PoHzT/xKjI3 M31cKEelxM3qEJnh2xhXQpwstLL5D4lSXWUcUS8AL9liTcv+CXORndQj1Slfb7Y3 FBjj4kD65griZ/nKl4ZGfZWAFLIPpR2iRjoqegVv5ydDmrLVrdHH2lxqZaGZNhw0 6lleCH5ShARgeiEvpCRdIfkViF69E4NeHaMCysVJM89sRHAJX6HsoKmSmTTU21Es ya4HzyEAaufj6sOtu7dCwJetgc0fn3/Vla+Z7zQRSlBcZiFmItdd+0hi5Iv4kHL+ wPGjF3rJ6J0fxvdIXQKhgtcTKPrpI/3ih4C1UgXuXRgrW9FHX9t2Pk5C85DKVV1S ACAdKnfy4BKZ6A2RGfGghxMiRfLRfq7SJNsd0XmsOUUsVcMS1MF9wSBnr2J5nDFg dhrYdXkqbHTyvz41J2t4D1HQhuFraFqgpWXkef+iUXxRLL2F2+86sPavIoRpLP0s dVvlrUMWBY2axVeOoGuPGoP0+PQTIm21Qt52UuRnEj5fvcXYrgGmEVDS07dKnpRx SvMLqKa+dFL7WD23wtAr =zhMc -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From andreas at fam-tille.de Sat May 14 18:58:49 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Sat, 14 May 2016 20:58:49 +0200 Subject: [Debian-med-packaging] maffilter_1.1.0-1+dfsg-1_amd64.changes REJECTED In-Reply-To: References: Message-ID: <20160514185849.GD4230@an3as.eu> Hi Thorsten, fixed and re-uploaded. Thanks for checking Andreas. On Sat, May 14, 2016 at 06:00:17PM +0000, Thorsten Alteholz wrote: > > Hi Andreas, > > the authors don't have be the Copyright holders. > > According to the file headers there are some differences: > doc/maffilter.texi:Copyright @copyright{} 2014 Julien Y. Dutheil > MafFilter/MafFilter.cpp:Copyright or or Copr. CNRS > MafFilter/OutputAsFeaturesMafIterator.cpp:Copyright or or Copr. Bio++ Development Team, (2010) > MafFilter/OutputAsFeaturesMafIterator.h:Copyright or or Copr. Bio++ Development Team, (2013) > > Thorsten > > > === > > Please feel free to respond to this email if you don't understand why > your files were rejected, or if you upload new files which address our > concerns. > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sat May 14 19:03:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 19:03:35 +0000 Subject: [Debian-med-packaging] Processing of maffilter_1.1.0-1+dfsg-1_amd64.changes Message-ID: maffilter_1.1.0-1+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: maffilter_1.1.0-1+dfsg-1.dsc maffilter_1.1.0-1+dfsg.orig.tar.xz maffilter_1.1.0-1+dfsg-1.debian.tar.xz maffilter-examples_1.1.0-1+dfsg-1_all.deb maffilter_1.1.0-1+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at fam-tille.de Sat May 14 19:06:27 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Sat, 14 May 2016 21:06:27 +0200 Subject: [Debian-med-packaging] fastqtl_2.184+dfsg-1_amd64.changes REJECTED In-Reply-To: References: Message-ID: <20160514190627.GE4230@an3as.eu> Dylan, could you please comment on this? >From my naive point of view this image looks like a result from some experiments and to visualise these some tool from Artifex Software was simply used. I see no sign for any copyright of this company for the image itself. Kind regards Andreas. On Sat, May 14, 2016 at 06:00:17PM +0000, Thorsten Alteholz wrote: > > Hi Dylan, > > according to the metainfo of > FastQTL/doc/img/fastqtl_checks.jpg > there is a "Copyright Artifex Software 2011". Can you please check with > upstream the license information for this file. Please mention that in > your debian/copyright as well. > > Thanks! > Thorsten > > === > > Please feel free to respond to this email if you don't understand why > your files were rejected, or if you upload new files which address our > concerns. > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sat May 14 19:22:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 19:22:28 +0000 Subject: [Debian-med-packaging] maffilter_1.1.0-1+dfsg-1_amd64.changes is NEW Message-ID: binary:maffilter is NEW. binary:maffilter-examples is NEW. source:maffilter is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Sat May 14 21:09:53 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 21:09:53 +0000 Subject: [Debian-med-packaging] Processing of tophat_2.1.1+dfsg-2_source.changes Message-ID: tophat_2.1.1+dfsg-2_source.changes uploaded successfully to localhost along with the files: tophat_2.1.1+dfsg-2.dsc tophat_2.1.1+dfsg-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at fam-tille.de Sat May 14 21:10:14 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Sat, 14 May 2016 23:10:14 +0200 Subject: [Debian-med-packaging] Bug#811881: tophat: FTBFS with GCC 6: no matching function for call to In-Reply-To: <683DC2E6-4D2D-4821-B9FB-5FF3E15767DC@tetrinetsucht.de> References: <20160119174312.8B55A280CB0@dl580gen9-02.hlinux> <20160120025442.GT4951@jirafa.cyrius.com> <683DC2E6-4D2D-4821-B9FB-5FF3E15767DC@tetrinetsucht.de> Message-ID: <20160514211014.GF4230@an3as.eu> Uploaded. On Sat, May 14, 2016 at 05:59:49PM +0100, Sascha Steinbiss wrote: > this is now fixed in git. Last GCC 6 bug for the weekend ;) Thanks a lot as usual and have a nice weekend ;-) Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sat May 14 22:15:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 22:15:06 +0000 Subject: [Debian-med-packaging] Processing of python-pyfaidx_0.4.7.1-1_amd64.changes Message-ID: python-pyfaidx_0.4.7.1-1_amd64.changes uploaded successfully to localhost along with the files: python-pyfaidx_0.4.7.1-1.dsc python-pyfaidx_0.4.7.1.orig.tar.gz python-pyfaidx_0.4.7.1-1.debian.tar.xz python-pyfaidx-examples_0.4.7.1-1_all.deb python-pyfaidx_0.4.7.1-1_all.deb python3-pyfaidx_0.4.7.1-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 14 22:27:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 22:27:04 +0000 Subject: [Debian-med-packaging] python-pyfaidx_0.4.7.1-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sat, 14 May 2016 23:49:10 +0200 Source: python-pyfaidx Binary: python-pyfaidx python3-pyfaidx python-pyfaidx-examples Architecture: source all Version: 0.4.7.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: python-pyfaidx - efficient random access to fasta subsequences for Python python-pyfaidx-examples - example data for efficient random access to fasta subsequences fo python3-pyfaidx - efficient random access to fasta subsequences for Python 3 Changes: python-pyfaidx (0.4.7.1-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: 262414644f8b66787c3f392d8a441191c71dce76 2319 python-pyfaidx_0.4.7.1-1.dsc 8333d46caa9fb8d81feac4e9d115d85f9edd2442 54566 python-pyfaidx_0.4.7.1.orig.tar.gz f319f9c58b05815a0296d66dce0314c7b1413612 3968 python-pyfaidx_0.4.7.1-1.debian.tar.xz 14706ae8a190879cbd3f4108b6922f98b9426d5e 22408 python-pyfaidx-examples_0.4.7.1-1_all.deb 8f831dcc4e9d60de0957f86fb6ea6c881e4a3797 19290 python-pyfaidx_0.4.7.1-1_all.deb 160f7c80e806728cdf068717b3aff62c4dd1bd7f 20786 python3-pyfaidx_0.4.7.1-1_all.deb Checksums-Sha256: 2eae7cceffc94969759dd829f28dfec92c12bc59aceb65cbbdd7d62fd88c7f93 2319 python-pyfaidx_0.4.7.1-1.dsc cd486e50394cc016ed99219eb8df24c3de5bad7297916cebdfe47f4bf2faea3e 54566 python-pyfaidx_0.4.7.1.orig.tar.gz 72ade0ee76dee0715e8769965446e8f011fcb8ec63f89f92a6f0949bcfe9575b 3968 python-pyfaidx_0.4.7.1-1.debian.tar.xz 3878e0eb69893ab2943caca1d5c0ea41174593cca0b2fc32c22565480c0f0654 22408 python-pyfaidx-examples_0.4.7.1-1_all.deb bdeb7ce9471568e8ffad40150ad0681ce45ca7487e57a25f8b79071495b695e3 19290 python-pyfaidx_0.4.7.1-1_all.deb 91e981651126e1dd13a4c3fd2e70fba56c60c3b7d0982a665aaa921d997f58de 20786 python3-pyfaidx_0.4.7.1-1_all.deb Files: 9d4eceb1e3350b20543c02d0b46abffa 2319 python optional python-pyfaidx_0.4.7.1-1.dsc 546d8370cc6f1a7f1f125a8437d203d5 54566 python optional python-pyfaidx_0.4.7.1.orig.tar.gz 249c3f0c864b8de9a8440f4a7a2b661c 3968 python optional python-pyfaidx_0.4.7.1-1.debian.tar.xz a9beddfdec66ec37754dfbd3e31c84a0 22408 python optional python-pyfaidx-examples_0.4.7.1-1_all.deb e52fa8d11a6ab40d2bd16faf3c89e5c4 19290 python optional python-pyfaidx_0.4.7.1-1_all.deb 1e8e4df00013bd69811a4519c88c7aeb 20786 python optional python3-pyfaidx_0.4.7.1-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXN6LnAAoJEFeKBJTRxkbRwuAP/1KfoBqEI28z3xcdf7fxgbom tcYygJwTJXp3c3v5uzBTGQx/+zAQzpJjqdB33LqLV8RFXT6T16eXTLSNc4sh4H8w LdM+jD/zkQ271Aj6t0hRQtrgQbrIwa480ahW1OZryCewhbRCaJtW4MV/w/rHQE13 C8byez41+LfDwrj4CHvqpk8IDPS+YvgYBGH6vJA3ubJkztiok/NuVOZvD6UysBvh vy9nrTtqkwU7AOyqJcZLvMBmRZdeH7Uqep6NT6AR8+zT2wLVYGw9Kq6zPEA1cz2M JnflLcwlw5FTpwBg8x9yXgVG59N9cJGMdXoj0K54gIeQ0AHTdUDSIyQ96rqfkPDH mgsfggEjtZj6UzVAUPY35xS+TGu0Pcl3gS80IO9erSbKm5PJLxbahTO51EnmZGE0 b0AfvpxO46IQA0kQoYxiXF7EuJ7EbK7lZgFRNJvZkytITseWMnnFgBzX4/4OeV1D XHI4c0irpxXDAvBrOKliAMLi+Qn+HiUUI0piTAz9aUVbZzu7FWCJXYHm4VxJWBR4 vjeAhvBe23/oVg3gXbJXQaqX0hnNWWRwtNOIkhCjU7tDzZcUeD/MNspMTxVALF/6 L+VIOsvcXMVbeBiMTUH7HsQLRzyeKWRnesmWcEUfZIpbNEUIGPTnuDsgafd0pQDi n13pG/RtZAPsErKEU/9S =7g0h -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sat May 14 22:27:38 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 14 May 2016 22:27:38 +0000 Subject: [Debian-med-packaging] tophat_2.1.1+dfsg-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sat, 14 May 2016 15:53:10 +0000 Source: tophat Binary: tophat Architecture: source Version: 2.1.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: tophat - fast splice junction mapper for RNA-Seq reads Closes: 811881 Changes: tophat (2.1.1+dfsg-2) unstable; urgency=medium . [ Sascha Steinbiss ] * Team upload. * Fix building with GCC 6. Closes: #811881. . 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From owner at bugs.debian.org Sat May 14 22:30:04 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sat, 14 May 2016 22:30:04 +0000 Subject: [Debian-med-packaging] Bug#811881: marked as done (tophat: FTBFS with GCC 6: no matching function for call to) References: <20160120025442.GT4951@jirafa.cyrius.com> Message-ID: Your message dated Sat, 14 May 2016 22:27:38 +0000 with message-id and subject line Bug#811881: fixed in tophat 2.1.1+dfsg-2 has caused the Debian Bug report #811881, regarding tophat: FTBFS with GCC 6: no matching function for call to to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 811881: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811881 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Martin Michlmayr Subject: tophat: FTBFS with GCC 6: no matching function for call to Date: Tue, 19 Jan 2016 18:54:42 -0800 Size: 5285 URL: -------------- next part -------------- An embedded message was scrubbed... From: Sascha Steinbiss Subject: Bug#811881: fixed in tophat 2.1.1+dfsg-2 Date: Sat, 14 May 2016 22:27:38 +0000 Size: 4981 URL: From tille at debian.org Sat May 14 23:11:07 2016 From: tille at debian.org (Andreas Tille) Date: Sun, 15 May 2016 01:11:07 +0200 Subject: [Debian-med-packaging] Bug#824360: ITP: r-cran-hexbin -- GNU R hexagonal binning routines Message-ID: <20160514231107.16358.44110.reportbug@mail.an3as.eu> Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name : r-cran-hexbin Version : 1.27.1 Upstream Author : Edzer Pebesma * URL : http://cran.r-project.org/web/packages/hexbin/ * License : GPL Programming Lang: GNU R Description : GNU R hexagonal binning routines This GNU R package contains binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods. Remark: This package is needed to enable successful runs of the test suites of some other R packages maintained by the Debian Med team. It will be maintained at svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-hexbin/ From jaroslava.chovancova at partnersgroup.sk Sat May 14 22:43:51 2016 From: jaroslava.chovancova at partnersgroup.sk (=?utf-8?Q?_=C2=A92016_Google_Incorporation=C2=AE?=) Date: Sun, 15 May 2016 00:43:51 +0200 (CEST) Subject: [Debian-med-packaging] Powered By Google In-Reply-To: <2115267584.56725224.1463265449168.JavaMail.zimbra@partnersgroup.sk> References: <954153690.56704617.1463260882527.JavaMail.zimbra@partnersgroup.sk> <819200162.56716797.1463263175034.JavaMail.zimbra@partnersgroup.sk> <661082074.56716984.1463263211673.JavaMail.zimbra@partnersgroup.sk> <1159797684.56717586.1463263331423.JavaMail.zimbra@partnersgroup.sk> <351921245.56721878.1463264354360.JavaMail.zimbra@partnersgroup.sk> <539148006.56724987.1463265366568.JavaMail.zimbra@partnersgroup.sk> <1794821382.56725087.1463265407732.JavaMail.zimbra@partnersgroup.sk> <2115267584.56725224.1463265449168.JavaMail.zimbra@partnersgroup.sk> Message-ID: <1071251869.56726595.1463265831404.JavaMail.zimbra@partnersgroup.sk> Dear Google User, You have been selected as a winner for using Google services. Find attached email with more details. Congratulations, Matt Brittin. CEO Google UK. ?2016 Google Incorporation? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Google UK-1.jpg Type: image/jpeg Size: 768309 bytes Desc: not available URL: From amu at alum.mit.edu Sun May 15 03:23:17 2016 From: amu at alum.mit.edu (Aaron M. Ucko) Date: Sat, 14 May 2016 23:23:17 -0400 Subject: [Debian-med-packaging] Bug#824368: fsm-lite: uses bad CPPFLAGS; always tries to build with -msse4.2 Message-ID: <146328259745.10313.66391586740709546.reportbug@ghostwheel.internal.ucko.debian.net> Source: fsm-lite Version: 1.0-1 Severity: important Justification: fails to build from source Hi, Andreas. Builds of fsm-lite for non-x86 architectures have been failing: g++: error: unrecognized command line option '-msse4.2' : recipe for target 'configuration.o' failed The issue turns out to be with the CPPFLAGS setting in the upstream Makefile, which I found to be problematic in various ways. From most to least severe (at least arguably): * It insists on building with -msse4.2, which is only an option on x86, and even there results in binaries that don't run on older hardware. * It loses any preexisting CPPFLAGS setting, thereby missing the usual -D_FORTIFY_SOURCE=2. * It insists on building with -O3, even in noopt builds. * It pulls in ~/software/include, which could theoretically have bogus content. * It generally contains flags that would be more appropriate for CXXFLAGS. As such, I'd suggest replacing that setting with CPPFLAGS += -DNDEBUG CXXFLAGS += -std=c++11 Also, the depend target should use CPPFLAGS and CXXFLAGS rather than duplicating any of their contents, but that's less of a big deal. Could you please take a look? Thanks! From ftpmaster at ftp-master.debian.org Sun May 15 06:23:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 15 May 2016 06:23:01 +0000 Subject: [Debian-med-packaging] Processing of r-cran-hexbin_1.27.1-1_amd64.changes Message-ID: r-cran-hexbin_1.27.1-1_amd64.changes uploaded successfully to localhost along with the files: r-cran-hexbin_1.27.1-1.dsc r-cran-hexbin_1.27.1.orig.tar.gz r-cran-hexbin_1.27.1-1.debian.tar.xz r-cran-hexbin-dbgsym_1.27.1-1_amd64.deb r-cran-hexbin_1.27.1-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 15 06:34:18 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 15 May 2016 06:34:18 +0000 Subject: [Debian-med-packaging] r-cran-hexbin_1.27.1-1_amd64.changes is NEW Message-ID: binary:r-cran-hexbin is NEW. source:r-cran-hexbin is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Sun May 15 07:53:09 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 15 May 2016 07:53:09 +0000 Subject: [Debian-med-packaging] Processing of fsm-lite_1.0-2_amd64.changes Message-ID: fsm-lite_1.0-2_amd64.changes uploaded successfully to localhost along with the files: fsm-lite_1.0-2.dsc fsm-lite_1.0-2.debian.tar.xz fsm-lite-dbgsym_1.0-2_amd64.deb fsm-lite_1.0-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 15 08:53:50 2016 From: ftpmaster at ftp-master.debian.org (Chris Lamb) Date: Sun, 15 May 2016 08:53:50 +0000 Subject: [Debian-med-packaging] Comments regarding r-cran-hexbin_1.27.1-1_amd64.changes Message-ID: Please recheck R/lattice.R (and others) From ftpmaster at ftp-master.debian.org Sun May 15 09:50:24 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 15 May 2016 09:50:24 +0000 Subject: [Debian-med-packaging] fsm-lite_1.0-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 15 May 2016 09:48:39 +0200 Source: fsm-lite Binary: fsm-lite Architecture: source amd64 Version: 1.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: fsm-lite - frequency-based string mining (lite) Closes: 824368 Changes: fsm-lite (1.0-2) unstable; urgency=medium . * Support more architectures Closes: #824368 Checksums-Sha1: ee44a3c77c37a80f9c7d1ba0f6d71a1eb3d2bd2b 1909 fsm-lite_1.0-2.dsc ef3696ed1105704f15d607cb7f6b1c06a73c07cd 3736 fsm-lite_1.0-2.debian.tar.xz 8a46f4f03e527dabb4f3000505fa94845a2881f8 616118 fsm-lite-dbgsym_1.0-2_amd64.deb 902aa14c852d87644f35622813b075e6ef14a9c7 86396 fsm-lite_1.0-2_amd64.deb Checksums-Sha256: 321648be566299e09bc9753dcbc2775061df14e70d90a432c4f532f9b1f98934 1909 fsm-lite_1.0-2.dsc a613358f86378610dfabb96271bb24d67512a815d836955e562e30183947cb3d 3736 fsm-lite_1.0-2.debian.tar.xz 903cddbe92538e257206b87771087a4010f4b1e396ee25b6473527fbb175a417 616118 fsm-lite-dbgsym_1.0-2_amd64.deb 307d420370ea05766ae8c0736dbb81d5de704c63b286c95b8183605fb9d221bc 86396 fsm-lite_1.0-2_amd64.deb Files: 11f6f96b814bd5a8b96cf377acbfba06 1909 science optional fsm-lite_1.0-2.dsc 31eb74653fef61dd657ac69c6aa06aab 3736 science optional fsm-lite_1.0-2.debian.tar.xz 9f3e1032c76c7c446b6b362c59473a3a 616118 debug extra fsm-lite-dbgsym_1.0-2_amd64.deb 01c29df61b6829b8e9416e3a85e79d04 86396 science optional fsm-lite_1.0-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXOCpKAAoJEFeKBJTRxkbRItcP/08IdWkNZ9jGIt5KdlE3dtl7 LHBlj5EGLmbgDZhXYCxJrRVwtYkx34JUTkhWzRXO1yVCzRdjbDox+LCJn5fVLKcr otpztcrtnrgldYVbb0tiRGT1d/1/l3soYuzitQLYSMUEKcQ0xhLbHzDhl4ByiC5p KYFF/4xY8QxZd5FKwD5R7+m4VsQLOrnn/HbCnZcVg52LQT8V+3wvfCnOw+Dd5yQo P7FZ6jtprGfnEB6E134073a/VYTaQjoUY4F/zKHmNbdUkEgifp5psz+k15AY3xUg Zf3V9tC1h+UvPx0ztdgUcWZJGSgkg3gZuDzH1fvxb4woCynBF0sUkCo37XyhFVY8 Wifd35B3WZyhiLnSNaco0wJvi1TnqaRKlPWuIe7c8Bztx+xPPzczH65xwZvEguOM 6uqgJxYLYO70vAPCM8T3r5HO13hdql+743k7S442hspTOkH+NR3HioxDpCWNLEzm CDJ8kNm4A9lqIROB/7mivTNGt6X0cM3ClW5JnSe7bnsovsJTxvxSAAsue0VEhL2D 3hFYtk6G+4t1FqkwHkz6iw7MrmohPt+us0+ICqGDwd4/Xe9NISQJnGvWjq/LXSy1 0Bb5My85e/QCyO/0VojjYBUtr6jTQoMBOfw0skq6/jXWtnPHya8SpwefIilSrTMY tA36Vikpq84ImncC7o3y =f6uM -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Sun May 15 09:51:23 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sun, 15 May 2016 09:51:23 +0000 Subject: [Debian-med-packaging] Bug#824368: marked as done (fsm-lite: uses bad CPPFLAGS; always tries to build with -msse4.2) References: <146328259745.10313.66391586740709546.reportbug@ghostwheel.internal.ucko.debian.net> Message-ID: Your message dated Sun, 15 May 2016 09:50:24 +0000 with message-id and subject line Bug#824368: fixed in fsm-lite 1.0-2 has caused the Debian Bug report #824368, regarding fsm-lite: uses bad CPPFLAGS; always tries to build with -msse4.2 to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 824368: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824368 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: "Aaron M. Ucko" Subject: fsm-lite: uses bad CPPFLAGS; always tries to build with -msse4.2 Date: Sat, 14 May 2016 23:23:17 -0400 Size: 4825 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#824368: fixed in fsm-lite 1.0-2 Date: Sun, 15 May 2016 09:50:24 +0000 Size: 5338 URL: From tille at debian.org Sun May 15 10:07:08 2016 From: tille at debian.org (Andreas Tille) Date: Sun, 15 May 2016 12:07:08 +0200 Subject: [Debian-med-packaging] Comments regarding r-cran-hexbin_1.27.1-1_amd64.changes In-Reply-To: References: Message-ID: <20160515100708.GD26802@an3as.eu> Hi Chris, fixed in SVN. Thanks for your quick processing Andreas. On Sun, May 15, 2016 at 08:53:50AM +0000, Chris Lamb wrote: > Please recheck R/lattice.R (and others) > > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sun May 15 11:01:05 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 15 May 2016 11:01:05 +0000 Subject: [Debian-med-packaging] r-cran-hexbin_1.27.1-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 15 May 2016 01:01:21 +0200 Source: r-cran-hexbin Binary: r-cran-hexbin Architecture: source amd64 Version: 1.27.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-hexbin - GNU R hexagonal binning routines Closes: 824360 Changes: r-cran-hexbin (1.27.1-1) unstable; urgency=medium . * Initial upload (Closes: #824360) Checksums-Sha1: e91691e9521133936f3c27b2e761268ab19cab8f 2063 r-cran-hexbin_1.27.1-1.dsc 75dc504231965da0cd91498e86bf488fbb7abaae 593621 r-cran-hexbin_1.27.1.orig.tar.gz 2de92d8347b91753dfaecc584aa5c1285823100e 2132 r-cran-hexbin_1.27.1-1.debian.tar.xz 95e5feca6d7355b70173e0a34fc509c3c18bba18 6642 r-cran-hexbin-dbgsym_1.27.1-1_amd64.deb 04278da2b05326a9b42af4e9bb540236bf673d35 762746 r-cran-hexbin_1.27.1-1_amd64.deb Checksums-Sha256: fd50d3c0e4314c553b8dcb1e01b5139340af0bf3daabdce733d2e7d27b1c8f2a 2063 r-cran-hexbin_1.27.1-1.dsc 507a4d94fccbc6aa3a894f0f6046be1faf18f7b0a280ecdc13d66f17dc722676 593621 r-cran-hexbin_1.27.1.orig.tar.gz ba5d44728eb63540191ec18b9584de86eed5bf50e924d0a6f384a839a4bceaaf 2132 r-cran-hexbin_1.27.1-1.debian.tar.xz 8871bc9cebe197e9cd12e314e74678c65ca821cbec3186fd962810e6b2b614ae 6642 r-cran-hexbin-dbgsym_1.27.1-1_amd64.deb e0139979fbfeda831fcda1d23302e3bc4461f3ecdb8b84925cb09952c5fdd673 762746 r-cran-hexbin_1.27.1-1_amd64.deb Files: 9a211487a2d4d6af1676655fffd6e3a3 2063 gnu-r optional r-cran-hexbin_1.27.1-1.dsc 7f380390c6511e97df10a810a3b3bb7c 593621 gnu-r optional r-cran-hexbin_1.27.1.orig.tar.gz 9708ef8b8d8933580b40b47c0476fbf6 2132 gnu-r optional r-cran-hexbin_1.27.1-1.debian.tar.xz 9612a35ee0429c634a60a43453f887f2 6642 debug extra r-cran-hexbin-dbgsym_1.27.1-1_amd64.deb d438e91bfb3065b031ca9fa69435dc6b 762746 gnu-r optional r-cran-hexbin_1.27.1-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXOBSAAAoJEFeKBJTRxkbRcf0QAIS5nF3ufZVR3GCAmzkQdB99 yMKmhnL+doRbswfKy0iRglpBvCup0JOsTj6rKOSCLcUhZtETcQPln5Cmz0DkHJfp 1d96tHHsdX6qHieH1CF0hoEAhC+IyMWpXLSNIf8KAB6K4wAotPBEvmPcbPmbXAq1 ecktnKev5fk0FYUT4igjoryQy+/rTIRQDrqkbx7xnzDmbUWryxX8511wHCaGtAVY 6kezlBtPpMe9Dd4bQVuKmFsmNVpPdEtHtFhHT1qMoDCHetaKJj11NARlbTgy++Pu JXQb0uAsFhUUine29jZt9WGYABiXaFoumf8ipdeUaFD3OB/Kie5AN8cRoowrK5jo OWFR3XBPuILmmfV4eQc3FaCjDt50peNesl5Um7XX7/avyKToCzRmfKwhsH5Q/n8q w/ZzGan4t68dlYcgsHslbl+zwSwbWE+LIz4ptOwYUe8M0M2PgskvzvIXPkvTZ/T1 I5MmAvTLahnKW0B7WuI7eVsaE3blj9hv0TrT9X1axyrh9ubokwF8lQmutItmcRYu PPhrVCqGcGk5u1fpC2OGkTwpmydJ2CoZZ7YmU6rvysr7/EgumJ+Ka6ILdJborW5I anJpyFl9H5rowfcAl06HLsemvVEmDMKUBXfFmnQXrsyz9Jw1fcsND5aXVZ5ZHgGB 7oVY9flI2NzLedETp/EH =n98P -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From andreas at an3as.eu Sun May 15 11:11:33 2016 From: andreas at an3as.eu (Andreas Tille) Date: Sun, 15 May 2016 13:11:33 +0200 Subject: [Debian-med-packaging] [devteam-bioc] BioConductor interactiveDisplayBase can't connect to bioconductor.org In-Reply-To: <838627098.5708671.1463159247342.JavaMail.zimbra@fredhutch.org> References: <20160512064519.GC11400@an3as.eu> <838627098.5708671.1463159247342.JavaMail.zimbra@fredhutch.org> Message-ID: <20160515111133.GG26802@an3as.eu> Hi Dan, thanks for your quick response. On Fri, May 13, 2016 at 10:07:27AM -0700, Dan Tenenbaum wrote: > > > I wonder whether there is any chance to make this error non-critical > > and add a warning to enable passing this step without breaking the > > build on a disconnected box. > > I have moved the call to source the remote file into the helper function, so it is not executed when the package is loaded. I verified the package can be installed when offline. This is fixed in release (1.10.2) and devel (1.11.2), available via svn now or biocLite() tomorrow. Hmmm, I can not find 1.10.2 even today. There was a new version 1.10.1 (compared to the version I was testing which was 1.10.0) but this has the same problem. Is there anything wrong with your latest upload? Kind regards Andreas. -- http://fam-tille.de From g_garcia at muniplibre.gob.pe Sun May 15 11:39:45 2016 From: g_garcia at muniplibre.gob.pe (Chris) Date: Sun, 15 May 2016 17:09:45 +0530 Subject: [Debian-med-packaging] Good New!!! Message-ID: <20160515114040.0A05218E0401@mail.muniplibre.gob.pe> Chris Colin Weir, we are donating eight million five hundred thousand to you. Send NAME*..ADDRESS*..MOBILE*..AGE*..SEX*..COUNTRY. From jana.kiskova at upjs.sk Sun May 15 14:18:46 2016 From: jana.kiskova at upjs.sk (jana) Date: Sun, 15 May 2016 16:18:46 +0200 Subject: [Debian-med-packaging] Bug#824402: sra-toolkit: does not load data from fastq files to directory (and probably more problems) Message-ID: <20160515141846.926.81513.reportbug@jana-laptop> Package: sra-toolkit Version: 2.3.5-2+dfsg-1 Severity: grave Justification: renders package unusable Dear Maintainer, The latf-load binary from sra-toolkit package doesn't load data from fastq files to directory - it will ends up with these errors: $ latf-load -q PHRED_33 -o Desktop/test Desktop/test.fastq 2016-05-15T13:51:17 latf-load.2.3.5 warn: Deprecated argument '-q' may not be supported in future releases. Please use '--quality' instead. 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory within file system module - file="align/align.vschema" 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory within file system module - failed to parse schema file align/align.vschema 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory within file system module - accession="test" errors="0" status="failure" 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory within file system module - load failed It seems the binary doesn't see the necessary vschema files. There is everything fine on the upstream package. The temporary solution is to copy/symlink schema directory from upstream package (latest version) to /usr - this works fine. I think the problem influence other binaries too, but I don't know - didn't try. I tryed this on the clean Debian 8 installation - the problem remains. -- System Information: Debian Release: 8.4 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 3.16.0-4-686-pae (SMP w/1 CPU core) Locale: LANG=sk_SK.UTF-8, LC_CTYPE=sk_SK.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages sra-toolkit depends on: ii libbz2-1.0 1.0.6-7+b3 ii libc6 2.19-18+deb8u4 ii libxml2 2.9.1+dfsg1-5+deb8u1 ii sra-toolkit-libs0 2.3.5-2+dfsg-1 ii zlib1g 1:1.2.8.dfsg-2+b1 sra-toolkit recommends no packages. sra-toolkit suggests no packages. -- no debconf information From ftpmaster at ftp-master.debian.org Sun May 15 16:35:19 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 15 May 2016 16:35:19 +0000 Subject: [Debian-med-packaging] Processing of rsem_1.2.30+dfsg-1_source.changes Message-ID: rsem_1.2.30+dfsg-1_source.changes uploaded successfully to localhost along with the files: rsem_1.2.30+dfsg-1.dsc rsem_1.2.30+dfsg.orig.tar.gz rsem_1.2.30+dfsg-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From noreply at release.debian.org Sun May 15 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 15 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] r-bioc-shortread 1.30.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-shortread source package in Debian's testing distribution has changed. Previous version: 1.28.0-1 Current version: 1.30.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Sun May 15 16:51:57 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 15 May 2016 16:51:57 +0000 Subject: [Debian-med-packaging] rsem_1.2.30+dfsg-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sun, 15 May 2016 03:49:04 -0700 Source: rsem Binary: rsem Architecture: source Version: 1.2.30+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: rsem - RNA-Seq by Expectation-Maximization Changes: rsem (1.2.30+dfsg-1) unstable; urgency=medium . * New upstream release * Use upstream's modified samtools-1.3 as that is required for correct operation * re-enable hardening to match source changes * generate manual pages for rsem-bam2wig & rsem-simulate-reads Checksums-Sha1: 01ebc628466f7e970188f3b0858824b1714db49b 2026 rsem_1.2.30+dfsg-1.dsc 14bd48ae3685a7c8a263973e18d7f3c58d94233e 4882225 rsem_1.2.30+dfsg.orig.tar.gz 89770676a0a9bad5f106ce1b4446829e41306427 5012 rsem_1.2.30+dfsg-1.debian.tar.xz Checksums-Sha256: 7da587406f8c76b21ab7eff5b1916b2253db9e2652c68849e7042562b8554e00 2026 rsem_1.2.30+dfsg-1.dsc 6f1fcd3ce0a523723baadeb188a29f010b69310adabed394f69c6ee5fd1c820d 4882225 rsem_1.2.30+dfsg.orig.tar.gz f765e510fc599103e4e6118aeaf442af9f91e0ae1c0e959d0ad53f22c193708a 5012 rsem_1.2.30+dfsg-1.debian.tar.xz Files: 0d5fb47f3d400117ab894f9ab8b8e274 2026 science extra rsem_1.2.30+dfsg-1.dsc 2fedbfead66b8e0a3823a1b8456f6b45 4882225 science extra rsem_1.2.30+dfsg.orig.tar.gz d988df9ea132c187b204787431e94cf9 5012 science extra rsem_1.2.30+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXOFVWAAoJEDwmdj9sZ+biQWkQAML7IkyohKvrluOK2A4T3JLH iu53HxWeD5W25kIUjfOPmL+u9j7XdmS+SHi5swnrGqvMGmEKygeVZe3OZzHAsUst 6SK4zuNXXSpKn4pz1JKAtMe0yuiCMo0t+cbKCkJjVuLNdgShbcfmL332fVnqgG3g BDZonDVqfakxKRCYk1iEWQyOfWPFVvxJ+m9XaZdOGukTayV710HeregXK3Jvz7AH vEtmeWkPZGyWe52RoMZ4DGa0NVZyg2WjVSjNNzjhJwico4GpqnGnOZqwu0dEyeT2 kjJwTe7+rQpnaN+YEi0t67KZBe5JvJbc2PDevxUZ/2+PMNcRYwiJ4dZOySe+y+/d bGoee3ZAhoAtwyh3O9ty6uPYKu0R9pOX8vBL3diQiJiRUBoWfmycSRNS2G06QxIP tSHcanp2n79grtr0BpiyR0tdIg7rFvx8iIa41Av07JrNBmywuTBGBkivNGzTy8p6 Q55pSJvXDFEwm+fOl10FbWvw23bfstuecPzp5e2lBhsHKsdZXuSCn34e5Em1ujaP ZNv7TGKlU71Nu0ChHqBp18CdxJYFwrI7UmWs6lecY1pn9wClAvPF1hrDTgtsPieF OzJDl+SePh5GSQa4LBixPUQJ9a6hqIRrGFXLhON/8H7RISOMaaVX1+Bal6+piwGz 59QljzLbxEOSscHvAkSD =ksVy -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 15 18:00:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 15 May 2016 18:00:23 +0000 Subject: [Debian-med-packaging] maffilter_1.1.0-1+dfsg-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 27 Apr 2016 15:59:57 +0200 Source: maffilter Binary: maffilter maffilter-examples Architecture: source all amd64 Version: 1.1.0-1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: maffilter - process genome alignment in the Multiple Alignment Format maffilter-examples - process genome alignment in the Multiple Alignment Format (exampl Closes: 822776 Changes: maffilter (1.1.0-1+dfsg-1) unstable; urgency=medium . * Initial release (Closes: #822776) Checksums-Sha1: 38f90246a102f78dd217a1ef0a70cbcef2ab8fdc 2215 maffilter_1.1.0-1+dfsg-1.dsc f1cd91577bcbc3d3b18b76a8c1a29ed6b3ee73c5 5606660 maffilter_1.1.0-1+dfsg.orig.tar.xz 9dbd76e8756a4de1eb1dec38d59a891d5c193c05 3140 maffilter_1.1.0-1+dfsg-1.debian.tar.xz 16d7da81370880e7346d05c16a13559ae99e7297 6177528 maffilter-examples_1.1.0-1+dfsg-1_all.deb 47fbdd7c70fdf22d2cb3fe21b06b48c87c44361d 3494 maffilter_1.1.0-1+dfsg-1_amd64.deb Checksums-Sha256: 28cf3faf6eba9b158389b992256b7f1c53bdd8c1feec8a7d70672bc2f7e106b4 2215 maffilter_1.1.0-1+dfsg-1.dsc 18fe9fb7567bd9645b9797fb7f47259386691c973c1b1ebbda66f4a8834635c1 5606660 maffilter_1.1.0-1+dfsg.orig.tar.xz 272a7757d8a567aea656d7f5b3fbeecb50fb98a5b832e9ad03ba6cb371460983 3140 maffilter_1.1.0-1+dfsg-1.debian.tar.xz 3edbd9d839e94fd176dc3e04f9384c9f5a3b4b52fe989a54624ca823bd6df549 6177528 maffilter-examples_1.1.0-1+dfsg-1_all.deb e135f3fbd3a7774ca77800ce919ba67d2b9791b17ff50271b5c9041a2ec99c64 3494 maffilter_1.1.0-1+dfsg-1_amd64.deb Files: f2cf53950580c17b266549b61c73fc49 2215 science optional maffilter_1.1.0-1+dfsg-1.dsc 261e0764b10f7314eb565f4673da3489 5606660 science optional maffilter_1.1.0-1+dfsg.orig.tar.xz b7d8130464ae3015f40e9683ac18b509 3140 science optional maffilter_1.1.0-1+dfsg-1.debian.tar.xz 007b74f14f9aed17fe5ded775600e58b 6177528 science optional maffilter-examples_1.1.0-1+dfsg-1_all.deb f1ed362a57c8f44f1ac946682f4a9fa7 3494 science optional maffilter_1.1.0-1+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXN3UEAAoJEFeKBJTRxkbRT7sP/R+x2Zk4IrAXjNGAcmx5ohXu Uaznf3ILKU/h+zQdZz75YeK5lrTqjIPLC1G6VUCTrPZUmydKHeD5lPBoo2mVAoFW NzdhKub7hxm9w9slGT0cNm/dwXW/a0q882yp+TwYJG2F6F/gPlFPgckSL4Coe5RI MFB5OzapMlyNNolUVk0NXMhMCMs1mBRWZVtZce9HtwchVbx0NVvWXR5kxYg/kl4X fzUh6CGQSeONUX63riVaTDN/DCPNB4asyjr+/MliP1RYODWIYmAn7HBgs7/Tu7zw +tDkld+FSUFdLAOUlRQ0OMeMnN1AWhh96wxKz26PmOQe197s4xLcExfidmKYtCU7 SmdnrekaEfJHDk3PxzeM0hx9Q/uZldlyyZq16MJ+53XfTJNI07yRhA1DUX5Y2313 iMQITbdtbV/Ha0h+UzidPXavdJMJmkpK9DXB1/aZ9DhsjKLUCu0D3yaE9NADcNhF iRWVyk4lNo9zHxtNld8CGuD4vFsh/ngsmXz17i4cTITqvDGv0Jxebk000V6MovCP TL3gQVhceTKOBaD5o1XNyQIM/V2emoo6Ytw30GVANyiBwCejfajd2GlpdSApQE4R qLnxxXN3tKzot3CKypNrhfFzQXzKc0wWdwpbAYsjoHYQgoktgDTUBqqhDEZ3kfSP VeDl9EZUvmAmWJa5Bcay =DDZJ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From andreas at an3as.eu Sun May 15 20:11:12 2016 From: andreas at an3as.eu (Andreas Tille) Date: Sun, 15 May 2016 22:11:12 +0200 Subject: [Debian-med-packaging] Bug#824402: sra-toolkit: does not load data from fastq files to directory (and probably more problems) In-Reply-To: <20160515141846.926.81513.reportbug@jana-laptop> References: <20160515141846.926.81513.reportbug@jana-laptop> Message-ID: <20160515201112.GA14991@an3as.eu> Hi Jana, thanks for this bug report. I admit that sra-toolkit packaging is lagging behind upstream development. The reason was a new dependency (ngs-sdk) which is packaged now. I tried the latest upstream source but due to the quite unusual build system (the source is using a configure script which is something else than an autoconf created script) the new version does not build as simple. I hope that once we've managed to get the package build there are chances that this problem is fixed - if not we try to contact upstream about this. Any volunteer to fox the build system is more than welcome. Kind regards Andreas. On Sun, May 15, 2016 at 04:18:46PM +0200, jana wrote: > Package: sra-toolkit > Version: 2.3.5-2+dfsg-1 > Severity: grave > Justification: renders package unusable > > Dear Maintainer, > > The latf-load binary from sra-toolkit package doesn't load data from fastq > files to directory - it will ends up with these errors: > > $ latf-load -q PHRED_33 -o Desktop/test Desktop/test.fastq > 2016-05-15T13:51:17 latf-load.2.3.5 warn: Deprecated argument '-q' may not be > supported in future releases. Please use '--quality' instead. > 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory > within file system module - file="align/align.vschema" > 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory > within file system module - failed to parse schema file align/align.vschema > 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory > within file system module - accession="test" errors="0" status="failure" > 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory > within file system module - load failed > > It seems the binary doesn't see the necessary vschema files. There is > everything fine on the upstream package. The temporary solution is to > copy/symlink schema directory from upstream package (latest version) to /usr - > this works fine. I think the problem influence other binaries too, but I don't > know - didn't try. I tryed this on the clean Debian 8 installation - the > problem remains. > > > > -- System Information: > Debian Release: 8.4 > APT prefers stable-updates > APT policy: (500, 'stable-updates'), (500, 'stable') > Architecture: i386 (i686) > > Kernel: Linux 3.16.0-4-686-pae (SMP w/1 CPU core) > Locale: LANG=sk_SK.UTF-8, LC_CTYPE=sk_SK.UTF-8 (charmap=UTF-8) > Shell: /bin/sh linked to /bin/dash > Init: systemd (via /run/systemd/system) > > Versions of packages sra-toolkit depends on: > ii libbz2-1.0 1.0.6-7+b3 > ii libc6 2.19-18+deb8u4 > ii libxml2 2.9.1+dfsg1-5+deb8u1 > ii sra-toolkit-libs0 2.3.5-2+dfsg-1 > ii zlib1g 1:1.2.8.dfsg-2+b1 > > sra-toolkit recommends no packages. > > sra-toolkit suggests no packages. > > -- no debconf information > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From bob.dybian at gmail.com Sun May 15 20:29:33 2016 From: bob.dybian at gmail.com (Dylan) Date: Sun, 15 May 2016 22:29:33 +0200 Subject: [Debian-med-packaging] fastqtl_2.184+dfsg-1_amd64.changes REJECTED In-Reply-To: <20160514190627.GE4230@an3as.eu> References: <20160514190627.GE4230@an3as.eu> Message-ID: Hi Thorsten and Andreas, I agree with Andreas, this image is the result from some experiments and they probably use some tool from Artifex Software to generate it. Best regards, Dylan 2016-05-14 21:06 GMT+02:00 Andreas Tille : > Dylan, could you please comment on this? > > From my naive point of view this image looks like a result from some > experiments and to visualise these some tool from Artifex Software was > simply used. I see no sign for any copyright of this company for the > image itself. > > Kind regards > > Andreas. > > On Sat, May 14, 2016 at 06:00:17PM +0000, Thorsten Alteholz wrote: >> >> Hi Dylan, >> >> according to the metainfo of >> FastQTL/doc/img/fastqtl_checks.jpg >> there is a "Copyright Artifex Software 2011". Can you please check with >> upstream the license information for this file. Please mention that in >> your debian/copyright as well. >> >> Thanks! >> Thorsten >> >> === >> >> Please feel free to respond to this email if you don't understand why >> your files were rejected, or if you upload new files which address our >> concerns. >> >> >> _______________________________________________ >> Debian-med-packaging mailing list >> Debian-med-packaging at lists.alioth.debian.org >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging >> > > -- > http://fam-tille.de From alteholz at debian.org Sun May 15 20:44:37 2016 From: alteholz at debian.org (Thorsten Alteholz) Date: Sun, 15 May 2016 22:44:37 +0200 (CEST) Subject: [Debian-med-packaging] fastqtl_2.184+dfsg-1_amd64.changes REJECTED In-Reply-To: References: <20160514190627.GE4230@an3as.eu> Message-ID: Hi Dylan, On Sun, 15 May 2016, Dylan wrote: > I agree with Andreas, this image is the result from some experiments > and they probably use some tool from Artifex Software to generate it. yes, whatever, this tool obviously puts some own parts into the output file and claims copyright for that. As long as there is no license information for that part, one can not decide whether it is compatible with DFSG. So please clarify this with upstream or Artifex Software. Thanks! Thorsten From bob.dybian at gmail.com Sun May 15 21:31:44 2016 From: bob.dybian at gmail.com (Dylan) Date: Sun, 15 May 2016 23:31:44 +0200 Subject: [Debian-med-packaging] Question about the license of FastQTL for integration into Debian Message-ID: Dear Olivier Delaneau, I'm contacting you on behalf of the Debian Med team, a group within the Debian project that aims to make it the best computing platform for biology and medicine [1]. I have recently created a package to integrate FastQTL in the Debian official repository [2] but it was rejected [3] for a problem about the license of the file FastQTL/doc/img/fastqtl_checks.jpg for which metainfo include a copyright to "Artifex Software 2011". Could you please confirm that "Artifex Software" have really a copyright on this file and what is the license of this file? In the opposite case, could you confirm that this file is under the same license as FastQTL? Merci d'avance. Best regards, Dylan [1] https://www.debian.org/devel/debian-med/ [2] https://anonscm.debian.org/cgit/debian-med/fastqtl.git/ [3] https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-May/042197.html From ppretsch at email.sc.edu Mon May 16 00:24:07 2016 From: ppretsch at email.sc.edu (PRETSCH, PEYTON K) Date: Mon, 16 May 2016 00:24:07 +0000 Subject: [Debian-med-packaging] Ono Pharmaceutical Co, Ltd. Message-ID: We wish to contract you to act as our company's representative and its customers in Canada and United States. Therefore, we need a representative to obtain this cause. Let us know if you can handle this and compensations will be given. Contact us immediately through the email below: EMAIL: onphacompalimited at hotmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Mon May 16 02:42:52 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 16 May 2016 02:42:52 +0000 Subject: [Debian-med-packaging] Processing of python-mne_0.12+dfsg-1_amd64.changes Message-ID: python-mne_0.12+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: python-mne_0.12+dfsg-1.dsc python-mne_0.12+dfsg.orig.tar.gz python-mne_0.12+dfsg-1.debian.tar.xz python-mne_0.12+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 16 03:54:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 16 May 2016 03:54:23 +0000 Subject: [Debian-med-packaging] python-mne_0.12+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 13 May 2016 17:38:17 -0400 Source: python-mne Binary: python-mne Architecture: source all Version: 0.12+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Yaroslav Halchenko Description: python-mne - Python modules for MEG and EEG data analysis Changes: python-mne (0.12+dfsg-1) unstable; urgency=medium . * Fresh upstream release * debian/control - boosted policy to 3.9.8 - suggest python-pycuda Checksums-Sha1: d2420c46e6100f475e2c9f05225c788d2bdf4f02 2364 python-mne_0.12+dfsg-1.dsc 566318c99ef2bed74b8de6c726405373dfc6465d 58843831 python-mne_0.12+dfsg.orig.tar.gz ddfde969a50e753983056fde420750b52ad85575 31740 python-mne_0.12+dfsg-1.debian.tar.xz 4f3afb06d6778845c991b98f4894fe7f8442d59f 4428800 python-mne_0.12+dfsg-1_all.deb Checksums-Sha256: 0fb01a7f0a193b670ee13b50040c43dc2f2474f5aba0e5400c08cafcf2d11540 2364 python-mne_0.12+dfsg-1.dsc 35c44a23fa436b3b40f723b2cb470440ebaf6c8ebbecd5cb3284fc4125f7e2b5 58843831 python-mne_0.12+dfsg.orig.tar.gz 2875da57d02b4afe4cd618ae77bf847ed988eb3cc78aa4eaaeb52b41284c3fce 31740 python-mne_0.12+dfsg-1.debian.tar.xz d633434dad6cd4c2614ad90f65c27b87b2a4a42bb86fc14860a1ed81f4cce70a 4428800 python-mne_0.12+dfsg-1_all.deb Files: 4e3a6dce94d608186cbb96c7aa3e1408 2364 python optional python-mne_0.12+dfsg-1.dsc 05e064e2ea6d710b27569362e0da4b54 58843831 python optional python-mne_0.12+dfsg.orig.tar.gz 37c779780e56ac1588ac04c82bcc6bc3 31740 python optional python-mne_0.12+dfsg-1.debian.tar.xz 75fab927bc2434dd69537ae0c9020860 4428800 python optional python-mne_0.12+dfsg-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXOTOJAAoJEKLeI1Bi2jP61voP/iVDW/Pr80BrjAQA6uLETAYa fUjT55CpCv4tjPYmo2TkNEEpkAUlHI+cmWp1ofZaF3cAFbpCExPqJIyo0KirjNY9 TKE4lNifjW1KWSr85XXvUFn9mXCIw6XkqvvVy7nuRxCyQIR+Af2jBgxCulfZi6ia wZeXlCoNXxHMX5/MCYoX5tvOq1UaIDeJvxoBBADbhbZlj5khbhKkSa6uZamii1A0 zUL/sqM095NAUo22IBfwGI/ys06SVpbS2UrVaZxoX7Vr1vg3mW2ORfc1raea/FrH 4hQ8ZUoivGcwt6twUaV9eIm87l0DhkQzgU/6d3R5XGwdimXiwJ87PHZqwAUfX4Ik bG9Iyho2Pv569HXFalzFMGP30Pk8OTPt1wToefVkuO/SXw5UaA0HtedsfgkR75ay hfFbMEb86Xp6GLf4h7egHDHUzUb6LQ2Ei+6v4mo+GKYMLLJ9Bz626Io9iWocO6LN +lYi2T8+CFlijd+WYlfmKXg4qURg29ZsgtsVJDojMezFCvLLE+Vyq8oMyrEvdPaD RzkmZsEZ17TdNtDxhdhKqRtZBCMwqFnWqI+LWqT8YVY2f409xkNkciVZSu0j734t dQDyrPcACtz7qODu1aOIwm5P4zGJg1k33xRFA1ZuIhEbG0uvvpQd+XyajAdQWLGL W+xczWQqIdveXGVfxaVD =pL6b -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From hpages at fredhutch.org Mon May 16 06:32:18 2016 From: hpages at fredhutch.org (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=) Date: Sun, 15 May 2016 23:32:18 -0700 Subject: [Debian-med-packaging] [devteam-bioc] BioConductor interactiveDisplayBase can't connect to bioconductor.org In-Reply-To: <20160515111133.GG26802@an3as.eu> References: <20160512064519.GC11400@an3as.eu> <838627098.5708671.1463159247342.JavaMail.zimbra@fredhutch.org> <20160515111133.GG26802@an3as.eu> Message-ID: <44641_1463380348_5739697B_44641_15639_1_57396972.1050209@fredhutch.org> Hi Andreas, On 05/15/2016 04:11 AM, Maintainer wrote: > Hi Dan, > > thanks for your quick response. > > On Fri, May 13, 2016 at 10:07:27AM -0700, Dan Tenenbaum wrote: >> >>> I wonder whether there is any chance to make this error non-critical >>> and add a warning to enable passing this step without breaking the >>> build on a disconnected box. >> >> I have moved the call to source the remote file into the helper function, so it is not executed when the package is loaded. I verified the package can be installed when offline. This is fixed in release (1.10.2) and devel (1.11.2), available via svn now or biocLite() tomorrow. > > Hmmm, I can not find 1.10.2 even today. There was a new version 1.10.1 > (compared to the version I was testing which was 1.10.0) but this has > the same problem. Is there anything wrong with your latest upload? Nothing wrong. It's here: https://bioconductor.org/packages/3.3/bioc/html/interactiveDisplayBase.html It can take more than a day for a new version to propagate to our public repositories. Cheers, H. > > Kind regards > > Andreas. > -- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 From tille at debian.org Mon May 16 06:39:13 2016 From: tille at debian.org (Andreas Tille) Date: Mon, 16 May 2016 08:39:13 +0200 Subject: [Debian-med-packaging] Bug#824448: ITP: r-bioc-interactivedisplaybase -- base package for enabling powerful shiny web displays of Bioconductor objects Message-ID: <20160516063913.28716.63692.reportbug@mail.an3as.eu> Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name : r-bioc-interactivedisplaybase Version : 1.10.2 Upstream Author : Shawn Balcome * URL : http://bioconductor.org/packages/release/bioc/html/interactiveDisplayBase.html * License : Artistic-2.0 Programming Lang: GNU R Description : base package for enabling powerful shiny web displays of Bioconductor objects The interactiveDisplayBase package contains the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects. From ftpmaster at ftp-master.debian.org Mon May 16 06:53:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 16 May 2016 06:53:17 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-interactivedisplaybase_1.10.2-1_amd64.changes Message-ID: r-bioc-interactivedisplaybase_1.10.2-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-interactivedisplaybase_1.10.2-1.dsc r-bioc-interactivedisplaybase_1.10.2.orig.tar.gz r-bioc-interactivedisplaybase_1.10.2-1.debian.tar.xz r-bioc-interactivedisplaybase_1.10.2-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 16 07:05:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 16 May 2016 07:05:55 +0000 Subject: [Debian-med-packaging] r-bioc-interactivedisplaybase_1.10.2-1_amd64.changes is NEW Message-ID: binary:r-bioc-interactivedisplaybase is NEW. source:r-bioc-interactivedisplaybase is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From bobbycaldeira at aol.com Mon May 16 08:14:21 2016 From: bobbycaldeira at aol.com (hi) Date: Mon, 16 May 2016 16:14:21 +0800 Subject: [Debian-med-packaging] Hi Message-ID: hi this is very amazing iphone 6s,388euro,samsung s7 adge,400euro,Laptop, TV, bike,camera .... www . slooone .com From andreas at an3as.eu Mon May 16 09:07:43 2016 From: andreas at an3as.eu (Andreas Tille) Date: Mon, 16 May 2016 11:07:43 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack Message-ID: <20160516090743.GA31593@an3as.eu> Hi, as a precondition for some package for Debian Med I intend to package clapack[1]. Despite the discussion on Debian Science about the relation of clapack and lapacke[2] I decided that it is less effort to have clapack in addition since upstream of phast[3] (my final target) does not intend to port the code from clapack to lapacke. I tried to build clapack[1] and it has a nasty format error: /build/clapack-3.2.1/F2CLIBS/libf2c/arithchk.c:125:2: error: format not a string literal and no format arguments [-Werror=format-security] Cray1 = printf(emptyfmt) < 0 ? 0 : 4617762; ^ cc1: some warnings being treated as errors When reading the code it seems to me that actually a test whether this code works or not is intended and thus fixing the format is not in the intention of the authors. So I tried export DEB_BUILD_HARDENING_FORMAT:=0 DPKG_EXPORT_BUILDFLAGS = 1 but the build keeps on failing. Any idea? Kind regards Andreas. [1] https://anonscm.debian.org/git/debian-science/packages/clapack.git [2] https://lists.debian.org/debian-science/2016/04/msg00053.html [3] https://anonscm.debian.org/git/debian-med/phast.git -- http://fam-tille.de From locutusofborg at debian.org Mon May 16 09:14:30 2016 From: locutusofborg at debian.org (Gianfranco Costamagna) Date: Mon, 16 May 2016 09:14:30 +0000 (UTC) Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <20160516090743.GA31593@an3as.eu> References: <20160516090743.GA31593@an3as.eu> Message-ID: <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> Hi, >/build/clapack-3.2.1/F2CLIBS/libf2c/arithchk.c:125:2: error: format not a string literal and no format arguments [-Werror=format-security] > Cray1 = printf(emptyfmt) < 0 ? 0 : 4617762; > ^ >cc1: some warnings being treated as errors I would consider this an RC bug. security wise the printf can be used to inject shell code in the program, so I would avoid having such buggyness in the archive [1] https://en.wikipedia.org/wiki/Uncontrolled_format_string char *emptyfmt = ""; /* avoid possible warning message with printf("") */ printf(emptyfmt); should be replaced with char *emptyfmt = ""; /* avoid possible warning message with printf("") */ printf("%s",emptyfmt); I'm not sure why you don't want to cherry such a simple and safe fix. G. From gw.fossdev at gmail.com Mon May 16 10:02:02 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Mon, 16 May 2016 12:02:02 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> Message-ID: <1463392922.18357.21.camel@gmail.com> Hello,? Am Montag, den 16.05.2016, 09:14 +0000 schrieb Gianfranco Costamagna: > Hi, >? > > /build/clapack-3.2.1/F2CLIBS/libf2c/arithchk.c:125:2: error: format > > not a string literal and no format arguments [-Werror=format- > > security] > > ?Cray1 = printf(emptyfmt) < 0 ? 0 : 4617762; > > ?^ > > cc1: some warnings being treated as errors > > I would consider this an RC bug. > > security wise the printf can be used to inject shell code in the > program, so I would avoid having such buggyness in the archive > [1] https://en.wikipedia.org/wiki/Uncontrolled_format_string I think, since in this case the (empty) format string passed to the printf call is not user generated there is no security problem to be exploited. In addition the source code file in question is part of the "check" target, so this piece of code will will only be using during building and not end up in a library.? > > char *emptyfmt = ""; /* avoid possible warning message with > printf("") */ > printf(emptyfmt); > > should be replaced with > > char *emptyfmt = ""; /* avoid possible warning message with > printf("") */ > printf("%s",emptyfmt); > > I'm not sure why you don't want to cherry such a simple and safe fix. The code seems to be using this call to do some wired checking on what platform it is run, and I would guess that your fix would break this check.? Considering that the variable is called Cray1 I would somehow guess that this test actually finds out whether this code is running on a Cray1 where floating point arithmetic seems to have some differences as compared to IEEE floating point operations.? If Debian doesn't run on such an arch the test could most likely safely be removed, i.e. remove all code from "ccheck" but the "return 0" line.? Apart from that disabling the warning itself can and should be done in the code by using pragmas like this:? #ifdef __GNUC__ # pragma GCC diagnostic push # ifndef __clang__? # ?pragma GCC diagnostic ignored "-Wformat-security" # else # ?pragma clang diagnostic ignored "-Wformat-security" # endif? #endif? /* code that issues warning */ #ifdef __GNUC__ # pragma GCC diagnostic pop #endif? Hope that helps,? Gert? From locutusofborg at debian.org Mon May 16 10:16:29 2016 From: locutusofborg at debian.org (Gianfranco Costamagna) Date: Mon, 16 May 2016 10:16:29 +0000 (UTC) Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <1463392922.18357.21.camel@gmail.com> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> Message-ID: <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> Hi Gert! >I think, since in this case the (empty) format string passed to the printf call is not user generated there is no security problem to be exploited. yes, sure, but disabling this flag has a nasty side-effect, it is disabled in the *whole* build, possibly hiding more serious issues somewhere else. I would prefer disabling that test, rather than disabling a security feature in the whole package. BTW fedora packaged "F2CLIBS" separately from clapack, I'm not sure if worth a try or not, but it should be at least considered. cheers, G. From jwilk at debian.org Mon May 16 10:21:06 2016 From: jwilk at debian.org (Jakub Wilk) Date: Mon, 16 May 2016 12:21:06 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <1463392922.18357.21.camel@gmail.com> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> Message-ID: <20160516102059.GA5603@jwilk.net> * Gert Wollny , 2016-05-16, 12:02: >If Debian doesn't run on such an arch the test could most likely safely >be removed, i.e. remove all code from "ccheck" but the "return 0" >line. This is what I would recommend. It's safe to assume that printf("") always works on Debian. Contrary to what the comment says, the current ccheck() implementation does cause signed integer overflow on 32-bit architectures, which is undefined behavior. So yes, please patch out this code... -- Jakub Wilk From gw.fossdev at gmail.com Mon May 16 10:21:06 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Mon, 16 May 2016 12:21:06 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> Message-ID: <1463394066.18357.24.camel@gmail.com> Am Montag, den 16.05.2016, 10:16 +0000 schrieb Gianfranco Costamagna: > Hi Gert! > > > > > I think, since in this case the (empty) format string passed to the > > printf call is not user generated there is no security problem to > > be exploited. > > yes, sure, but disabling this flag has a nasty side-effect, it is > disabled in the *whole* build, possibly > hiding more serious issues somewhere else. Of course, that's why I gave the #pragma based disabling that can be fitted tightly to the offending code.? Best,? Gert? From ftpmaster at ftp-master.debian.org Mon May 16 10:53:59 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 16 May 2016 10:53:59 +0000 Subject: [Debian-med-packaging] Processing of snp-sites_2.3.2-1_amd64.changes Message-ID: snp-sites_2.3.2-1_amd64.changes uploaded successfully to localhost along with the files: snp-sites_2.3.2-1.dsc snp-sites_2.3.2.orig.tar.gz snp-sites_2.3.2-1.debian.tar.xz libsnp-sites1-dbgsym_2.3.2-1_amd64.deb libsnp-sites1-dev_2.3.2-1_amd64.deb libsnp-sites1_2.3.2-1_amd64.deb snp-sites-dbgsym_2.3.2-1_amd64.deb snp-sites_2.3.2-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 16 11:20:31 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 16 May 2016 11:20:31 +0000 Subject: [Debian-med-packaging] snp-sites_2.3.2-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 16 May 2016 10:39:13 +0000 Source: snp-sites Binary: snp-sites libsnp-sites1 libsnp-sites1-dev Architecture: source amd64 Version: 2.3.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: libsnp-sites1 - Shared libraries of the package snp-sites libsnp-sites1-dev - Static libraries and header files for the package snp-sites snp-sites - Binary code for the package snp-sites Changes: snp-sites (2.3.2-1) unstable; urgency=medium . * New upstream version. * Update upstream metadata. * Bump Standards-Version. 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From debian at danny-edel.de Mon May 16 11:50:39 2016 From: debian at danny-edel.de (Danny Edel) Date: Mon, 16 May 2016 13:50:39 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <20160516090743.GA31593@an3as.eu> References: <20160516090743.GA31593@an3as.eu> Message-ID: <5739B40F.6080005@danny-edel.de> On 05/16/2016 11:07 AM, Andreas Tille wrote: > /build/clapack-3.2.1/F2CLIBS/libf2c/arithchk.c:125:2: error: format not a string literal and no format arguments [-Werror=format-security] > Cray1 = printf(emptyfmt) < 0 ? 0 : 4617762; Hi Andreas, you should have success with changing the type (insted of the value) of emptyfmt, rather than disabling any warnings. Right now it's "char *", which is legal C, but problematic, since character literals are not allowed to be written to anyway and might even be placed in read-only memory[1]. Just the type "readwrite pointer to readwrite character" probably triggers the warning. If you change it to "const char* const", the compiler is assured it's never going to point to anything else and does not emit the warning. Cheers, - Danny [1]: http://en.cppreference.com/w/c/language/string_literal -------------- next part -------------- A non-text attachment was scrubbed... Name: format-security.patch Type: text/x-patch Size: 298 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 473 bytes Desc: OpenPGP digital signature URL: From cid at app.com.br Sun May 15 09:52:11 2016 From: cid at app.com.br (Thomas Manu) Date: Sun, 15 May 2016 02:52:11 -0700 Subject: [Debian-med-packaging] Compliment of the day. Message-ID: <61172d5014571c2a394dafbee63ede5f@app.com.br> -- DEAR SIR/MADAM, MY NAME IS THOMAS MANU, THE DIRECTOR OF OPERATIONS AT THE GHANA NATIONAL PETROLEUM CORPORATION. I APPRECIATE THIS CHANCE TO COMMUNICATE WITH YOU TO MOVE MY INVESTMENT FORWARD AS I VALUE YOUR EXPERTISE IN THE PROCESS. IN MY QUEST TO ESTABLISH A VIABLE INVESTMENT, MY SOLICITOR RECOMMENDED YOU AS A PERSON WITH INNOVATIVE PROGRAMS THAT HAVE SEEN BUSINESSES SUCCEED IN YOUR COUNTRY. FOR THIS REASON, I AM OPTIMISTIC THAT YOU WILL FIND MY PROPOSAL OF $50 MILLION, A GOOD INVESTMENT CAPITAL FOR AN ESTABLISHMENT IN YOUR METROPOLIS WITH HIGH POTENTIAL RETURNS. I WOULD GREATLY APPRECIATE THE CHANCE TO MEET WITH YOU SO WE CAN START NEGOTIATION AND TRANSFER PROCESS. PLEASE ACKNOWLEDGE PROPOSAL SO THAT WE PROCEED WITH DETAILS. SINCERELY, THOMAS MANU DIRECTOR GNPC E-mail: thomasanua at mynet.com From plessy at debian.org Mon May 16 13:02:54 2016 From: plessy at debian.org (Charles Plessy) Date: Mon, 16 May 2016 22:02:54 +0900 Subject: [Debian-med-packaging] fastqtl_2.184+dfsg-1_amd64.changes REJECTED In-Reply-To: References: <20160514190627.GE4230@an3as.eu> Message-ID: <20160516130254.GA5547@bubu.igloo> Le Sun, May 15, 2016 at 10:44:37PM +0200, Thorsten Alteholz a ?crit : > > On Sun, 15 May 2016, Dylan wrote: > >I agree with Andreas, this image is the result from some experiments > >and they probably use some tool from Artifex Software to generate it. > > yes, whatever, this tool obviously puts some own parts into the output file > and claims copyright for that. As long as there is no license information > for that part, one can not decide whether it is compatible with DFSG. So > please clarify this with upstream or Artifex Software. Hi all, I found that the copyright notice is inserted by ghostscript when converting a PDF chart to a JPEG image. Artifex Software, Inc. is one of the copyright holders of Ghostscript. The image in fastqtl looked a lot like a R plot and I verified that R did not create JPEG files with copyright statements in. A search on Internet showed that Artifex commercialises some image converters. A second search gave me a command to convert from PDF to JPEG with ghostscript and voil?! here is how you can similarly copyrighted JPEG files. # Create a PDF file; here I use R to plot random values. Rscript -e 'pdf("foo.pdf");hist(rnorm(50), col="red"); dev.off()' # Convert it to JPEG with Ghostscript. Exit with Ctrl-D. gs -dNOPAUSE -sDEVICE=jpeg -r144 -sOutputFile=foo.jpg foo.pdf # Show the copyright statement: hexdump -C foo.jpg | grep -C3 -i copyr 00000170 20 49 43 43 20 50 72 6f 66 69 6c 65 00 00 00 00 | ICC Profile....| 00000180 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |................| 00000190 00 00 00 00 00 00 00 00 00 00 00 00 00 00 74 65 |..............te| 000001a0 78 74 00 00 00 00 43 6f 70 79 72 69 67 68 74 20 |xt....Copyright | 000001b0 41 72 74 69 66 65 78 20 53 6f 66 74 77 61 72 65 |Artifex Software| 000001c0 20 32 30 31 31 00 58 59 5a 20 00 00 00 00 00 00 | 2011.XYZ ......| 000001d0 f3 51 00 01 00 00 00 01 16 cc 58 59 5a 20 00 00 |.Q........XYZ ..| Indeed, ghostcript ships ICC color profiles and if I undestand well, inserted the "default" one. $ hexdump -C /usr/share/color/icc/ghostscript/default_rgb.icc | grep -C3 -i copyright 00000150 72 6f 66 69 6c 65 00 00 00 00 00 00 00 00 00 00 |rofile..........| 00000160 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |................| 00000170 00 00 00 00 00 00 00 00 74 65 78 74 00 00 00 00 |........text....| 00000180 43 6f 70 79 72 69 67 68 74 20 41 72 74 69 66 65 |Copyright Artife| 00000190 78 20 53 6f 66 74 77 61 72 65 20 32 30 31 31 00 |x Software 2011.| 000001a0 58 59 5a 20 00 00 00 00 00 00 f3 51 00 01 00 00 |XYZ .......Q....| 000001b0 00 01 16 cc 58 59 5a 20 00 00 00 00 00 00 00 00 |....XYZ ........| Ghostscript is distributed in main, but I could not find a clear license statement for the color profiles... Cheers, -- Charles From lamby at debian.org Mon May 16 13:07:39 2016 From: lamby at debian.org (Chris Lamb) Date: Mon, 16 May 2016 14:07:39 +0100 Subject: [Debian-med-packaging] Bug#824475: python-mne: FTBFS: TraitError: The 'input' trait of a QuadricDecimation instance is 'read only'. Message-ID: <1463404059.1017908.609102929.508C056B@webmail.messagingengine.com> Source: python-mne Version: 0.11+dfsg-1 Severity: serious Justification: fails to build from source User: reproducible-builds at lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org Dear Maintainer, python-mne fails to build from source in unstable/amd64: [..] copying mne/time_frequency/__init__.py -> build/lib.linux-x86_64-2.7/mne/time_frequency copying mne/time_frequency/_stockwell.py -> build/lib.linux-x86_64-2.7/mne/time_frequency copying mne/time_frequency/ar.py -> build/lib.linux-x86_64-2.7/mne/time_frequency copying mne/time_frequency/tfr.py -> build/lib.linux-x86_64-2.7/mne/time_frequency copying mne/time_frequency/psd.py -> build/lib.linux-x86_64-2.7/mne/time_frequency copying mne/time_frequency/stft.py -> build/lib.linux-x86_64-2.7/mne/time_frequency copying mne/time_frequency/csd.py -> build/lib.linux-x86_64-2.7/mne/time_frequency copying mne/time_frequency/multitaper.py -> build/lib.linux-x86_64-2.7/mne/time_frequency creating build/lib.linux-x86_64-2.7/mne/time_frequency/tests copying mne/time_frequency/tests/test_psd.py -> build/lib.linux-x86_64-2.7/mne/time_frequency/tests copying mne/time_frequency/tests/__init__.py -> build/lib.linux-x86_64-2.7/mne/time_frequency/tests copying mne/time_frequency/tests/test_stockwell.py -> build/lib.linux-x86_64-2.7/mne/time_frequency/tests copying mne/time_frequency/tests/test_csd.py -> build/lib.linux-x86_64-2.7/mne/time_frequency/tests copying mne/time_frequency/tests/test_multitaper.py -> build/lib.linux-x86_64-2.7/mne/time_frequency/tests copying mne/time_frequency/tests/test_ar.py -> build/lib.linux-x86_64-2.7/mne/time_frequency/tests copying mne/time_frequency/tests/test_stft.py -> build/lib.linux-x86_64-2.7/mne/time_frequency/tests copying mne/time_frequency/tests/test_tfr.py -> build/lib.linux-x86_64-2.7/mne/time_frequency/tests creating build/lib.linux-x86_64-2.7/mne/realtime copying mne/realtime/__init__.py -> build/lib.linux-x86_64-2.7/mne/realtime copying mne/realtime/mockclient.py -> build/lib.linux-x86_64-2.7/mne/realtime copying mne/realtime/epochs.py -> build/lib.linux-x86_64-2.7/mne/realtime copying mne/realtime/stim_server_client.py -> build/lib.linux-x86_64-2.7/mne/realtime copying mne/realtime/fieldtrip_client.py -> build/lib.linux-x86_64-2.7/mne/realtime copying mne/realtime/client.py -> build/lib.linux-x86_64-2.7/mne/realtime creating build/lib.linux-x86_64-2.7/mne/realtime/tests copying mne/realtime/tests/__init__.py -> build/lib.linux-x86_64-2.7/mne/realtime/tests copying mne/realtime/tests/test_fieldtrip_client.py -> build/lib.linux-x86_64-2.7/mne/realtime/tests copying mne/realtime/tests/test_stim_client_server.py -> build/lib.linux-x86_64-2.7/mne/realtime/tests copying mne/realtime/tests/test_mockclient.py -> build/lib.linux-x86_64-2.7/mne/realtime/tests creating build/lib.linux-x86_64-2.7/mne/decoding copying mne/decoding/__init__.py -> build/lib.linux-x86_64-2.7/mne/decoding copying mne/decoding/base.py -> build/lib.linux-x86_64-2.7/mne/decoding copying mne/decoding/time_gen.py -> build/lib.linux-x86_64-2.7/mne/decoding copying mne/decoding/mixin.py -> build/lib.linux-x86_64-2.7/mne/decoding copying mne/decoding/transformer.py -> build/lib.linux-x86_64-2.7/mne/decoding copying mne/decoding/ems.py -> build/lib.linux-x86_64-2.7/mne/decoding copying mne/decoding/csp.py -> build/lib.linux-x86_64-2.7/mne/decoding creating build/lib.linux-x86_64-2.7/mne/decoding/tests copying mne/decoding/tests/__init__.py -> build/lib.linux-x86_64-2.7/mne/decoding/tests copying mne/decoding/tests/test_csp.py -> build/lib.linux-x86_64-2.7/mne/decoding/tests copying mne/decoding/tests/test_ems.py -> build/lib.linux-x86_64-2.7/mne/decoding/tests copying mne/decoding/tests/test_transformer.py -> build/lib.linux-x86_64-2.7/mne/decoding/tests copying mne/decoding/tests/test_time_gen.py -> build/lib.linux-x86_64-2.7/mne/decoding/tests copying mne/commands/utils.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_coreg.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/__init__.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_make_scalp_surfaces.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_browse_raw.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_flash_bem.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_compute_proj_ecg.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_show_fiff.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_watershed_bem.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_surf2bem.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_report.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_maxfilter.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_compute_proj_eog.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_clean_eog_ecg.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_kit2fiff.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_bti2fiff.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_freeview_bem_surfaces.py -> build/lib.linux-x86_64-2.7/mne/commands copying mne/commands/mne_compare_fiff.py -> build/lib.linux-x86_64-2.7/mne/commands creating build/lib.linux-x86_64-2.7/mne/channels copying mne/channels/__init__.py -> build/lib.linux-x86_64-2.7/mne/channels copying mne/channels/layout.py -> build/lib.linux-x86_64-2.7/mne/channels copying mne/channels/channels.py -> build/lib.linux-x86_64-2.7/mne/channels copying mne/channels/montage.py -> build/lib.linux-x86_64-2.7/mne/channels copying mne/channels/interpolation.py -> build/lib.linux-x86_64-2.7/mne/channels creating build/lib.linux-x86_64-2.7/mne/channels/tests copying mne/channels/tests/test_layout.py -> build/lib.linux-x86_64-2.7/mne/channels/tests copying mne/channels/tests/__init__.py -> build/lib.linux-x86_64-2.7/mne/channels/tests copying mne/channels/tests/test_interpolation.py -> build/lib.linux-x86_64-2.7/mne/channels/tests copying mne/channels/tests/test_montage.py -> build/lib.linux-x86_64-2.7/mne/channels/tests copying mne/channels/tests/test_channels.py -> build/lib.linux-x86_64-2.7/mne/channels/tests copying mne/data/mne_analyze.sel -> build/lib.linux-x86_64-2.7/mne/data copying mne/data/icos.fif.gz -> build/lib.linux-x86_64-2.7/mne/data copying mne/data/coil_def.dat -> build/lib.linux-x86_64-2.7/mne/data copying mne/data/coil_def_Elekta.dat -> build/lib.linux-x86_64-2.7/mne/data creating build/lib.linux-x86_64-2.7/mne/data/helmets copying mne/data/helmets/Magnes_3600wh.fif.gz -> build/lib.linux-x86_64-2.7/mne/data/helmets copying mne/data/helmets/306m_rt.fif.gz -> build/lib.linux-x86_64-2.7/mne/data/helmets copying mne/data/helmets/Magnes_2500wh.fif.gz -> build/lib.linux-x86_64-2.7/mne/data/helmets copying mne/data/helmets/122m.fif.gz -> build/lib.linux-x86_64-2.7/mne/data/helmets copying mne/data/helmets/BabySQUID.fif.gz -> build/lib.linux-x86_64-2.7/mne/data/helmets copying mne/data/helmets/KIT.fif.gz -> build/lib.linux-x86_64-2.7/mne/data/helmets copying mne/data/helmets/CTF_275.fif.gz -> build/lib.linux-x86_64-2.7/mne/data/helmets copying mne/data/helmets/306m.fif.gz -> build/lib.linux-x86_64-2.7/mne/data/helmets copying mne/data/FreeSurferColorLUT.txt -> build/lib.linux-x86_64-2.7/mne/data creating build/lib.linux-x86_64-2.7/mne/channels/data creating build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/KIT-AD.lout -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/EGI256.lout -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/Vectorview-mag.lout -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/magnesWH3600.lout -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/Vectorview-all.lout -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/Vectorview-grad.lout -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/CTF-275.lout -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/KIT-157.lout -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/CTF151.lay -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/CTF275.lay -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/EEG1005.lay -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts copying mne/channels/data/layouts/biosemi.lay -> build/lib.linux-x86_64-2.7/mne/channels/data/layouts creating build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/GSN-HydroCel-128.sfp -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/GSN-HydroCel-129.sfp -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/GSN-HydroCel-64_1.0.sfp -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/GSN-HydroCel-257.sfp -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/GSN-HydroCel-32.sfp -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/GSN-HydroCel-65_1.0.sfp -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/GSN-HydroCel-256.sfp -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/biosemi256.txt -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/biosemi64.txt -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/biosemi160.txt -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/biosemi16.txt -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/biosemi32.txt -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/easycap-M10.txt -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/biosemi128.txt -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/easycap-M1.txt -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/standard_alphabetic.elc -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/standard_postfixed.elc -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/standard_prefixed.elc -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/standard_1020.elc -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/standard_1005.elc -> build/lib.linux-x86_64-2.7/mne/channels/data/montages copying mne/channels/data/montages/standard_primed.elc -> build/lib.linux-x86_64-2.7/mne/channels/data/montages creating build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/KIT-157_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/easycap128ch-avg_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/bti248grad_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/neuromag122_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/ctf151_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/ctf275_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/bti248_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/neuromag306mag_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/easycapM14_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/biosemi16_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/biosemi64_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/KIT-208_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/neuromag306planar_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/easycap64ch-avg_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/easycapM11_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/bti148_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/biosemi32_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/easycapM1_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/ctf64_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/easycap32ch-avg_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors copying mne/channels/data/neighbors/easycapM15_neighb.mat -> build/lib.linux-x86_64-2.7/mne/channels/data/neighbors creating build/lib.linux-x86_64-2.7/mne/gui/help copying mne/gui/help/kit2fiff.json -> build/lib.linux-x86_64-2.7/mne/gui/help creating build/lib.linux-x86_64-2.7/mne/html copying mne/html/jquery-ui.min.css -> build/lib.linux-x86_64-2.7/mne/html copying mne/html/bootstrap.min.css -> build/lib.linux-x86_64-2.7/mne/html running build_scripts creating build/scripts.linux-x86_64-2.7 copying and adjusting bin/mne -> build/scripts.linux-x86_64-2.7 changing mode of build/scripts.linux-x86_64-2.7/mne from 644 to 755 yui-compressor debian/JS/bootstrap/bootstrap.js > /home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg/mne/html/bootstrap.min.js echo -e "\n" >> /home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg/mne/html/bootstrap.min.js make[1]: Leaving directory '/home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg' MNE_DONTWRITE_HOME=true MNE_SKIP_SAMPLE_DATASET_TESTS=true MNE_FORCE_SERIAL=true MNE_SKIP_NETWORK_TESTS=1 \ xvfb-run --auto-servernum --server-num=20 -s "-screen 0 1024x768x24 -ac +extension GLX +render -noreset" \ nosetests mne SSSSSSSS.... Normal return from subroutine COBYLA NFVALS = 154 F = 1.313356E-03 MAXCV = 0.000000E+00 X =-2.792911E-03 1.040626E-02 5.626768E-02 9.024506E-02 Normal return from subroutine COBYLA NFVALS = 154 F = 1.313356E-03 MAXCV = 0.000000E+00 X =-2.792911E-03 1.040626E-02 5.626768E-02 9.024506E-02 .................../usr/lib/python2.7/dist-packages/pyface/toolkit.py:43: DeprecationWarning: Default toolkit will change to 'qt4' in PyFace 5.0 DeprecationWarning) S.S.SSS.[Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished .......SS.......................SSSSSSSSS.SSSSSSSSSSSSS....SS................S......SS...SSSSSSS.SSSSSSSSSSSSS.SSS.SSS...........S..........S....SSSSSSSSSSSSSSSSSSSSSSSS/home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg/mne/preprocessing/tests/test_ctps.py:36: DeprecationWarning: This function is deprecated. Please call randint(-150, 150 + 1) instead rand_ints = rng.random_integers(-j_extent, j_extent, n_trials) /home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg/mne/preprocessing/tests/test_ctps.py:36: DeprecationWarning: This function is deprecated. Please call randint(-300, 300 + 1) instead rand_ints = rng.random_integers(-j_extent, j_extent, n_trials) ..S...............SSSSSSSSSSS...[Parallel(n_jobs=1)]: Done 3 out of 3 | elapsed: 0.6s finished ......S...SSSSSSSSSS.............SS..S..SS.............S...SSSSS.................S.SSS.......S.....S.SS...SSS..............SSSSS..S...........S/home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg/mne/utils.py:268: UserWarning: This filename (test.fif) does not conform to MNE naming conventions. All epochs files should end with -epo.fif or -epo.fif.gz '%s' % (fname, filetype, print_endings)) .........[Parallel(n_jobs=1)]: Done 17 tasks | elapsed: 0.0s [Parallel(n_jobs=1)]: Done 71 tasks | elapsed: 0.0s [Parallel(n_jobs=1)]: Done 161 tasks | elapsed: 0.1s [Parallel(n_jobs=1)]: Done 287 tasks | elapsed: 0.2s [Parallel(n_jobs=1)]: Done 449 tasks | elapsed: 0.3s [Parallel(n_jobs=1)]: Done 647 tasks | elapsed: 0.4s [Parallel(n_jobs=1)]: Done 752 out of 752 | elapsed: 0.4s finished ........................................ Normal return from subroutine COBYLA NFVALS = 161 F = 1.310622E-03 MAXCV = 0.000000E+00 X =-2.848050E-03 1.048531E-02 5.620598E-02 9.030976E-02 ...S.....[Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.0s finished .[Parallel(n_jobs=1)]: Done 3 out of 3 | elapsed: 0.0s finished [Parallel(n_jobs=1)]: Done 3 out of 3 | elapsed: 0.0s finished ...................SSSSSSSSSSS..S[Parallel(n_jobs=1)]: Done 7 out of 7 | elapsed: 0.1s finished .[Parallel(n_jobs=1)]: Done 17 tasks | elapsed: 0.0s [Parallel(n_jobs=1)]: Done 71 tasks | elapsed: 0.0s [Parallel(n_jobs=1)]: Done 161 tasks | elapsed: 0.0s [Parallel(n_jobs=1)]: Done 287 tasks | elapsed: 0.1s [Parallel(n_jobs=1)]: Done 376 out of 376 | elapsed: 0.1s finished ....SSS..SS.SSS...SSS..S.SS.SS.SSSS.SSSSSSSSSSSS.S..SSSESS.....S....................S ====================================================================== ERROR: Test triangular surface decimation ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg/mne/utils.py", line 635, in dec return function(*args, **kwargs) File "/home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg/mne/tests/test_surface.py", line 159, in test_decimate_surface _, this_tris = decimate_surface(points, tris, n_tri) File "/home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg/mne/surface.py", line 761, in decimate_surface return _decimate_surface(points, triangles, reduction) File "/home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg/mne/surface.py", line 725, in _decimate_surface decimate = tvtk.QuadricDecimation(input=src, target_reduction=reduction) File "/usr/lib/python2.7/dist-packages/tvtk/tvtk_classes.zip/tvtk_classes/quadric_decimation.py", line 63, in __init__ tvtk_base.TVTKBase.__init__(self, vtk.vtkQuadricDecimation, obj, update, **traits) File "/usr/lib/python2.7/dist-packages/tvtk/tvtk_base.py", line 307, in __init__ super(TVTKBase, self).__init__(**traits) File "/usr/lib/python2.7/dist-packages/traits/trait_handlers.py", line 104, in _read_only name, class_of( object ) ) TraitError: The 'input' trait of a QuadricDecimation instance is 'read only'. ---------------------------------------------------------------------- Ran 561 tests in 320.441s FAILED (SKIP=199, errors=1) debian/rules:19: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 1 make[1]: Leaving directory '/home/lamby/temp/cdt.20160516135655.JhsMkQPWhH.python-mne/python-mne-0.11+dfsg' debian/rules:7: recipe for target 'build' failed make: *** [build] Error 2 [..] The full build log is attached. Regards, -- ,''`. : :' : Chris Lamb `. `'` lamby at debian.org / chris-lamb.co.uk `- -------------- next part -------------- A non-text attachment was scrubbed... Name: python-mne.0.11+dfsg-1.unstable.amd64.log.txt.gz Type: application/octet-stream Size: 27432 bytes Desc: not available URL: From debian at danny-edel.de Mon May 16 14:30:23 2016 From: debian at danny-edel.de (Danny Edel) Date: Mon, 16 May 2016 16:30:23 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <5739B40F.6080005@danny-edel.de> References: <20160516090743.GA31593@an3as.eu> <5739B40F.6080005@danny-edel.de> Message-ID: <5739D97F.3050304@danny-edel.de> On 05/16/2016 01:50 PM, Danny Edel wrote: > If you change it to "const char* const", the compiler is assured it's > never going to point to anything else and does not emit the warning. Sorry for replying to my own email, but after compiling, the test suite crashed on the xeigtstz_* with Segmentation Fault errors. I debugged this a little bit and the reason was these tests use a lot of local (i.e. stack) variables -- so many in fact that they trigger a stack overflow on entry. Disabling stack size limit (mine was 8192 KB) with ulimit -s unlimited before calling dpkg-buildpackage fixed things for me. I hope this avoids someone the half hour I spent in gdb searching for a bug that probably isn't there. - Danny -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 473 bytes Desc: OpenPGP digital signature URL: From andreas at an3as.eu Mon May 16 16:25:47 2016 From: andreas at an3as.eu (Andreas Tille) Date: Mon, 16 May 2016 18:25:47 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <5739D97F.3050304@danny-edel.de> References: <20160516090743.GA31593@an3as.eu> <5739B40F.6080005@danny-edel.de> <5739D97F.3050304@danny-edel.de> Message-ID: <20160516162547.GD31593@an3as.eu> Hi Danny, On Mon, May 16, 2016 at 04:30:23PM +0200, Danny Edel wrote: > Sorry for replying to my own email, but after compiling, the test suite > crashed on the xeigtstz_* with Segmentation Fault errors. No need to sorry, > I debugged this a little bit and the reason was these tests use a lot of > local (i.e. stack) variables -- so many in fact that they trigger a > stack overflow on entry. > > Disabling stack size limit (mine was 8192 KB) with > ulimit -s unlimited > before calling dpkg-buildpackage fixed things for me. > > I hope this avoids someone the half hour I spent in gdb searching for a > bug that probably isn't there. Would you mind commiting to Git what was building for you? Kind regards and thanks for your review Andreas. -- http://fam-tille.de From noreply at release.debian.org Mon May 16 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 16 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] fastml 3.1-3 MIGRATED to testing Message-ID: FYI: The status of the fastml source package in Debian's testing distribution has changed. Previous version: 3.1-2 Current version: 3.1-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 16 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 16 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-rtracklayer 1.32.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-rtracklayer source package in Debian's testing distribution has changed. Previous version: 1.30.1-1 Current version: 1.32.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 16 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 16 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-qvalue 2.4.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-qvalue source package in Debian's testing distribution has changed. Previous version: 2.2.0-1 Current version: 2.4.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 16 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 16 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-bsgenome 1.40.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-bsgenome source package in Debian's testing distribution has changed. Previous version: 1.38.0-2 Current version: 1.40.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 16 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 16 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] roary 3.6.2+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the roary source package in Debian's testing distribution has changed. Previous version: 3.6.1+dfsg-2 Current version: 3.6.2+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From owner at bugs.debian.org Mon May 16 17:18:07 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Mon, 16 May 2016 17:18:07 +0000 Subject: [Debian-med-packaging] Processed: fixed 824475 in python-mne/0.12+dfsg-1 References: <1463418968-1069-bts-debian@onerussian.com> Message-ID: Processing commands for control at bugs.debian.org: > fixed 824475 python-mne/0.12+dfsg-1 Bug #824475 [src:python-mne] python-mne: FTBFS: TraitError: The 'input' trait of a QuadricDecimation instance is 'read only'. Marked as fixed in versions python-mne/0.12+dfsg-1. > thanks Stopping processing here. Please contact me if you need assistance. -- 824475: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824475 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From debian at danny-edel.de Mon May 16 17:23:52 2016 From: debian at danny-edel.de (Danny Edel) Date: Mon, 16 May 2016 19:23:52 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <20160516162547.GD31593@an3as.eu> References: <20160516090743.GA31593@an3as.eu> <5739B40F.6080005@danny-edel.de> <5739D97F.3050304@danny-edel.de> <20160516162547.GD31593@an3as.eu> Message-ID: <573A0228.9080008@danny-edel.de> On 05/16/2016 06:25 PM, Andreas Tille wrote: > > Would you mind commiting to Git what was building for you? > Hi Andreas, I would love to, but I doubt it's possible. I tried something along the lines of "ulimit -s unlimited && dh_auto_test" as an override_dh_auto_test, but depending on the environment (local vs. cowbuilder vs. sbuild) this ulimit call would fail with "Operation not permitted". In case of cowbuilder or sbuild, it only works if I unlimited from the shell I started the builder with, so putting any command inside the debian/ wouldn't do anything. The important question is if a stack-size-limit is active on the buildds or maybe they're already unlimited. I would suggest packing as-is (only with the const-pointer change) and uploading to a debomatic, since I think they're very close to the official buildds. If it actually fails, I'd suggest coordinating with buildd-admins to figure out the best way to communicate this requirement. The tests don't actually need much memory, they just have a very unusual stack-to-heap ratio. Cheers, - Danny -------------- next part -------------- A non-text attachment was scrubbed... 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URL: From ftpmaster at ftp-master.debian.org Tue May 17 07:01:46 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 07:01:46 +0000 Subject: [Debian-med-packaging] Processing of libbpp-seq_2.2.0-1~bpo8+1_amd64.changes Message-ID: libbpp-seq_2.2.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-seq_2.2.0-1~bpo8+1.dsc libbpp-seq_2.2.0-1~bpo8+1.debian.tar.xz libbpp-seq-dev_2.2.0-1~bpo8+1_amd64.deb libbpp-seq9_2.2.0-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 17 07:18:38 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 07:18:38 +0000 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED Message-ID: libbpp-seq_2.2.0-1~bpo8+1.dsc: Does not match file already existing in the pool. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From olivier.delaneau at gmail.com Tue May 17 08:02:58 2016 From: olivier.delaneau at gmail.com (Olivier Delaneau) Date: Tue, 17 May 2016 10:02:58 +0200 Subject: [Debian-med-packaging] Question about the license of FastQTL for integration into Debian In-Reply-To: References: Message-ID: Dear Dylan, Thank you for packaging FastQTL, this is really cool! Concerning the copyright, it got in there because of imagemagick I think. The png was generated with ghostscript so I think there is no copyright. Cheers, -- Olivier DELANEAU Ma?tre assistant D?partement de G?n?tique et D?veloppement (GEDEV) 1, Michel-Servet, CH-1211 Gen?ve 4 +41 (0) 22 379 55 51 2016-05-15 23:31 GMT+02:00 Dylan : > Dear Olivier Delaneau, > I'm contacting you on behalf of the Debian Med team, a group within > the Debian project that aims to make it the best computing platform > for biology and medicine [1]. > > I have recently created a package to integrate FastQTL in the Debian > official repository [2] but it was rejected [3] for a problem about > the license of the file FastQTL/doc/img/fastqtl_checks.jpg for which > metainfo include a copyright to "Artifex Software 2011". > > Could you please confirm that "Artifex Software" have really a > copyright on this file and what is the license of this file? In the > opposite case, could you confirm that this file is under the same > license as FastQTL? > > Merci d'avance. > > Best regards, > Dylan > > [1] https://www.debian.org/devel/debian-med/ > [2] https://anonscm.debian.org/cgit/debian-med/fastqtl.git/ > [3] > https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-May/042197.html > -------------- next part -------------- An HTML attachment was scrubbed... URL: From owner at bugs.debian.org Tue May 17 09:45:04 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 17 May 2016 09:45:04 +0000 Subject: [Debian-med-packaging] Processed (with 1 error): your mail References: Message-ID: Processing commands for control at bugs.debian.org: > archive 803550 Bug #803550 [rsem] rsem: uninstallable on architectures without bowtie Bug 803550 cannot be archived > fixed 803550 1.2.30+dfsg-1 Bug #803550 [rsem] rsem: uninstallable on architectures without bowtie Marked as fixed in versions rsem/1.2.30+dfsg-1. > thanks Stopping processing here. Please contact me if you need assistance. -- 803550: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=803550 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From owner at bugs.debian.org Tue May 17 09:45:08 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 17 May 2016 09:45:08 +0000 Subject: [Debian-med-packaging] Bug#803550: marked as done (rsem: uninstallable on architectures without bowtie) References: <20151031110209.31009.74298.reportbug@zam581.zam.kfa-juelich.de> Message-ID: Your message dated Tue, 17 May 2016 11:41:15 +0200 with message-id and subject line has caused the Debian Bug report #803550, regarding rsem: uninstallable on architectures without bowtie to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 803550: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=803550 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Andreas Beckmann Subject: rsem: uninstallable on architectures without bowtie Date: Sat, 31 Oct 2015 12:02:09 +0100 Size: 2371 URL: -------------- next part -------------- An embedded message was scrubbed... From: Michael Crusoe Subject: Date: Tue, 17 May 2016 11:41:15 +0200 Size: 4867 URL: From ftpmaster at ftp-master.debian.org Tue May 17 09:47:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 09:47:40 +0000 Subject: [Debian-med-packaging] Processing of libbpp-phyl_2.2.0-1~bpo8+1_amd64.changes Message-ID: libbpp-phyl_2.2.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-phyl_2.2.0-1~bpo8+1.dsc libbpp-phyl_2.2.0-1~bpo8+1.debian.tar.xz libbpp-phyl-dev_2.2.0-1~bpo8+1_amd64.deb libbpp-phyl9_2.2.0-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 17 09:52:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 09:52:40 +0000 Subject: [Debian-med-packaging] Processing of spdlog_1.8-1_source.changes Message-ID: spdlog_1.8-1_source.changes uploaded successfully to localhost along with the files: spdlog_1.8-1.dsc spdlog_1.8.orig.tar.gz spdlog_1.8-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 17 10:20:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 10:20:06 +0000 Subject: [Debian-med-packaging] libbpp-phyl_2.2.0-1~bpo8+1_amd64.changes is NEW Message-ID: binary:libbpp-phyl-dev is NEW. binary:libbpp-phyl9 is NEW. source:libbpp-phyl is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Tue May 17 10:24:31 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 10:24:31 +0000 Subject: [Debian-med-packaging] spdlog_1.8-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 17 May 2016 02:52:07 -0700 Source: spdlog Binary: libspdlog-dev Architecture: source Version: 1.8-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: libspdlog-dev - Very fast, header only, C++ logging library Changes: spdlog (1.8-1) unstable; urgency=medium . * new upstream release Checksums-Sha1: d5af3675576c6d16465ddeda0fab6dd7258616e3 1917 spdlog_1.8-1.dsc 291f13382f1248cc5f44c61d91df251b1c9c7a4a 140563 spdlog_1.8.orig.tar.gz 4b21683dc98d8adc0ec5630b06831f31aafb2972 3432 spdlog_1.8-1.debian.tar.xz Checksums-Sha256: 4fed11832037fe8abcc0a05fb30610ada84f700c7121b61c4b8eebd6704631b3 1917 spdlog_1.8-1.dsc 3fd894d409c9efb644ebd9b5ebee86b243beaa3128fec91b4e72d4c97b848aea 140563 spdlog_1.8.orig.tar.gz f519c38fc4d2bfaf9dac3d21464d908d9a1c5530f67fe01bc64f4cd87c5097fb 3432 spdlog_1.8-1.debian.tar.xz Files: 81449af48254914a0ccaba1684cddab5 1917 libdevel optional spdlog_1.8-1.dsc 6f33d93526a42fa4e88a03baedd85720 140563 libdevel optional spdlog_1.8.orig.tar.gz 94138c53666666386e39eaca2fa06e7f 3432 libdevel optional spdlog_1.8-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXOunWAAoJEDwmdj9sZ+biXi0QAJiEwXwS3e2wnh6FIzXiyrFS Lg0LjrsziRtheRIhNrHaP8tTHajlQTXAA2OJFw747iKrPi6kFCJJKHahyduW9a40 Q+nXoLLY1lroSuJNoQm/x0uGWU7rA8e/KbQ5OTZnVZehFjpV7beG2Pa3dvqjeqi5 aaLbosL5KbE1xFDbO132SdKxo2sPtjgLPa3kjnd3LnUJ39ZXTIvVSiCDLcFYo7iJ M0S6KBIdN5ZEmAgK4PAXZD6b8RU9lgds+MRbDW7C1/QkVPDAv1Z2oCVrbvDmS/f3 pzRnpqa75p33HcoAGc8rGCPVdocXi189uyx0E5BGD2wIgIcAaRhXNPq3S3QHsz04 7jQ8VbfEGfZActJSaB2xgyBNgTXFX4dMA+KgXnCx3GfQAk/RE84hft5+agNbTBbF p4LC0LodlULodDFKFyM0EeGvkEQSXhSBizTsTKite5PAI2me/bsvAEQL3XLPP2c5 wuXjMDETwIVnyiav4VUjKM5sfmOWXfkfwMggyqFL7WIq+nWWwAymue+reAQLfrKf Gl+SuUUOq3npMe9wBJuNjFa7w1ohg5uXCHk46eVT0p3DC8idAMEcHgQa8Ab+ztdr WVt1nnoruzvadJrL02U7161rDAq+7avL+QNFeZZQfX89TMyZhMZb0hrukC7bFysd Yr/tswWPuWKAh/vcU9Af =Oohk -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 17 11:52:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 11:52:33 +0000 Subject: [Debian-med-packaging] Bug#824546: Removed package(s) from unstable Message-ID: We believe that the bug you reported is now fixed; the following package(s) have been removed from unstable: rsem | 1.2.26+dfsg-2 | armel, armhf, hurd-i386, i386, kfreebsd-i386, mips, mips64el, mipsel, powerpc, s390x ------------------- Reason ------------------- RoQA; NBS; needs bowtie/bowtie2 ---------------------------------------------- Note that the package(s) have simply been removed from the tag database and may (or may not) still be in the pool; this is not a bug. The package(s) will be physically removed automatically when no suite references them (and in the case of source, when no binary references it). Please also remember that the changes have been done on the master archive and will not propagate to any mirrors until the next dinstall run at the earliest. Packages are usually not removed from testing by hand. Testing tracks unstable and will automatically remove packages which were removed from unstable when removing them from testing causes no dependency problems. The release team can force a removal from testing if it is really needed, please contact them if this should be the case. Bugs which have been reported against this package are not automatically removed from the Bug Tracking System. Please check all open bugs and close them or re-assign them to another package if the removed package was superseded by another one. The version of this package that was in Debian prior to this removal can still be found using http://snapshot.debian.org/. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 824546 at bugs.debian.org. The full log for this bug can be viewed at https://bugs.debian.org/824546 This message was generated automatically; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster at ftp-master.debian.org. Debian distribution maintenance software pp. Scott Kitterman (the ftpmaster behind the curtain) From debian-backports at lists.debian.org Tue May 17 12:02:30 2016 From: debian-backports at lists.debian.org (Alexander Wirt) Date: Tue, 17 May 2016 12:02:30 +0000 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED Message-ID: I can't find that version in DAK: dak ls libbpp-seq9 |grep 2.2.0 libbpp-seq9 | 2.2.0-1~bpo8+1 | backports-new | amd64 === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Tue May 17 12:04:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 12:04:07 +0000 Subject: [Debian-med-packaging] r-cran-magrittr_1.5-3~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 12 May 2016 20:48:43 +0200 Source: r-cran-magrittr Binary: r-cran-magrittr Architecture: source amd64 Version: 1.5-3~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-magrittr - GNU R forward-pipe operator Changes: r-cran-magrittr (1.5-3~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Tue May 17 12:04:08 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 12:04:08 +0000 Subject: [Debian-med-packaging] r-cran-stringi_1.0-1-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 12 May 2016 21:04:09 +0200 Source: r-cran-stringi Binary: r-cran-stringi Architecture: source amd64 Version: 1.0-1-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-stringi - GNU R character string processing facilities Changes: r-cran-stringi (1.0-1-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From andreas at an3as.eu Tue May 17 13:15:27 2016 From: andreas at an3as.eu (Andreas Tille) Date: Tue, 17 May 2016 15:15:27 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: References: Message-ID: <20160517131527.GA13436@an3as.eu> On Tue, May 17, 2016 at 12:02:30PM +0000, Alexander Wirt wrote: > > I can't find that version in DAK: > > dak ls libbpp-seq9 |grep 2.2.0 > libbpp-seq9 | 2.2.0-1~bpo8+1 | backports-new | amd64 Sorry, but how can I safely (and in this specific case quickly since it was wrongly rejected last week where you said it is not in testing) this package into backports? Is re-uploading and pinging you OK? I really need the libbpp-* set in Jessie soon but upon this two times has costed two weeks now. I have no idea what might have went wrong again but I hope if I reupload libbpp-seq again this could be processed quickly. Thanks for your work for backports Andreas. -- http://fam-tille.de From formorer at formorer.de Tue May 17 13:19:05 2016 From: formorer at formorer.de (Alexander Wirt) Date: Tue, 17 May 2016 15:19:05 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160517131527.GA13436@an3as.eu> References: <20160517131527.GA13436@an3as.eu> Message-ID: <20160517131905.GB7172@formorer.de> On Tue, 17 May 2016, Andreas Tille wrote: > On Tue, May 17, 2016 at 12:02:30PM +0000, Alexander Wirt wrote: > > > > I can't find that version in DAK: > > > > dak ls libbpp-seq9 |grep 2.2.0 > > libbpp-seq9 | 2.2.0-1~bpo8+1 | backports-new | amd64 > > Sorry, but how can I safely (and in this specific case quickly since it > was wrongly rejected last week where you said it is not in testing) this > package into backports? Is re-uploading and pinging you OK? I really > need the libbpp-* set in Jessie soon but upon this two times has costed > two weeks now. Ask the ftpmasters why dak on frank doesn't know about that version: dak ls libbpp-seq9 libbpp-seq9 | 2.0.3-1 | oldstable | amd64, armel, armhf, i386, ia64, kfreebsd-amd64, kfreebsd-i386, mips, mipsel, powerpc, s390, s390x, sparc libbpp-seq9 | 2.1.0-1 | stable | amd64, arm64, armel, armhf, i386, mips, mipsel, powerpc, ppc64el, s390x libbpp-seq9 | 2.1.0-1 | stable-kfreebsd | kfreebsd-amd64, kfreebsd-i386 libbpp-seq9 | 2.1.0-1 | unstable | amd64, arm64, armel, armhf, hurd-i386, i386, kfreebsd-amd64, kfreebsd-i386, mips, mips64el, mipsel, powerpc, ppc64el, s390x Alex From costamagnagianfranco at yahoo.it Tue May 17 13:23:42 2016 From: costamagnagianfranco at yahoo.it (Gianfranco Costamagna) Date: Tue, 17 May 2016 13:23:42 +0000 (UTC) Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160517131527.GA13436@an3as.eu> References: <20160517131527.GA13436@an3as.eu> Message-ID: <1861224612.6090935.1463491422767.JavaMail.yahoo@mail.yahoo.com> Hi, Bad dak is bad https://buildd.debian.org/status/package.php?p=libbpp-seq&suite=unstable libbpp-seq9 | 2.0.3-1 | oldstable | amd64, armel, armhf, i386, ia64, kfreebsd-amd64, kfreebsd-i386, mips, mipsel, powerpc, s390, s390x, sparc libbpp-seq9 | 2.1.0-1 | stable | amd64, arm64, armel, armhf, i386, mips, mipsel, powerpc, ppc64el, s390x libbpp-seq9 | 2.1.0-1 | stable-kfreebsd | kfreebsd-amd64, kfreebsd-i386 libbpp-seq9 | 2.1.0-1 | unstable | amd64, arm64, armel, armhf, hurd-i386, i386, kfreebsd-amd64, kfreebsd-i386, mips, mips64el, mipsel, powerpc, ppc64el, s390x dak ls libbpp-seq9v5 libbpp-seq9v5 | 2.2.0-1 | testing | amd64, arm64, armel, armhf, i386, mips, mipsel, powerpc, ppc64el, s390x libbpp-seq9v5 | 2.2.0-1 | unstable | amd64, arm64, armel, armhf, hurd-i386, i386, kfreebsd-amd64, kfreebsd-i386, mips, mips64el, mipsel, powerpc, ppc64el, s390x I guess Andreas is fully correct, the rename is not necessary for backports, right? G. Il Marted? 17 Maggio 2016 15:15, Andreas Tille ha scritto: On Tue, May 17, 2016 at 12:02:30PM +0000, Alexander Wirt wrote: > > I can't find that version in DAK: > > dak ls libbpp-seq9 |grep 2.2.0 > libbpp-seq9 | 2.2.0-1~bpo8+1 | backports-new | amd64 Sorry, but how can I safely (and in this specific case quickly since it was wrongly rejected last week where you said it is not in testing) this package into backports? Is re-uploading and pinging you OK? I really need the libbpp-* set in Jessie soon but upon this two times has costed two weeks now. I have no idea what might have went wrong again but I hope if I reupload libbpp-seq again this could be processed quickly. Thanks for your work for backports Andreas. -- http://fam-tille.de From formorer at formorer.de Tue May 17 13:42:23 2016 From: formorer at formorer.de (Alexander Wirt) Date: Tue, 17 May 2016 15:42:23 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <1861224612.6090935.1463491422767.JavaMail.yahoo@mail.yahoo.com> References: <20160517131527.GA13436@an3as.eu> <1861224612.6090935.1463491422767.JavaMail.yahoo@mail.yahoo.com> Message-ID: <20160517134223.GC7172@formorer.de> On Tue, 17 May 2016, Gianfranco Costamagna wrote: > Hi, > > Bad dak is bad > https://buildd.debian.org/status/package.php?p=libbpp-seq&suite=unstable > libbpp-seq9 | 2.0.3-1 | oldstable | amd64, armel, armhf, i386, ia64, kfreebsd-amd64, kfreebsd-i386, mips, mipsel, powerpc, s390, s390x, sparc > libbpp-seq9 | 2.1.0-1 | stable | amd64, arm64, armel, armhf, i386, mips, mipsel, powerpc, ppc64el, s390x > libbpp-seq9 | 2.1.0-1 | stable-kfreebsd | kfreebsd-amd64, kfreebsd-i386 > libbpp-seq9 | 2.1.0-1 | unstable | amd64, arm64, armel, armhf, hurd-i386, i386, kfreebsd-amd64, kfreebsd-i386, mips, mips64el, mipsel, powerpc, ppc64el, s390x > > > > dak ls libbpp-seq9v5 > libbpp-seq9v5 | 2.2.0-1 | testing | amd64, arm64, armel, armhf, i386, mips, mipsel, powerpc, ppc64el, s390x > libbpp-seq9v5 | 2.2.0-1 | unstable | amd64, arm64, armel, armhf, hurd-i386, i386, kfreebsd-amd64, kfreebsd-i386, mips, mips64el, mipsel, powerpc, ppc64el, s390x > > > I guess Andreas is fully correct, the rename is not necessary for backports, right? I would expect it to follow unstable. I guess the rename had a reason. Alex From locutusofborg at debian.org Tue May 17 13:48:27 2016 From: locutusofborg at debian.org (Gianfranco Costamagna) Date: Tue, 17 May 2016 13:48:27 +0000 (UTC) Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160517134223.GC7172@formorer.de> References: <20160517131527.GA13436@an3as.eu> <1861224612.6090935.1463491422767.JavaMail.yahoo@mail.yahoo.com> <20160517134223.GC7172@formorer.de> Message-ID: <223102053.6033259.1463492907760.JavaMail.yahoo@mail.yahoo.com> Rename was because of gcc-5 transition, that didn't happen in jessie. So the rename has to be reverted for backports, otherwise the library will conflict with the one in jessie, making half of the archive removed if you want to have it installed look e.g. my mistake in llvm-toolchain-3.5 backport, where I didn't rename it https://lists.debian.org/debian-backports/2016/01/msg00113.html (sorry for bothering, I'm not 100% sure about this particular case, I just want to point to a mistake I did in the past, I'm for sure not authoritative at all on the matter, so please don't trust my opinion :) ) Gianfranco Il Marted? 17 Maggio 2016 15:42, Alexander Wirt ha scritto: On Tue, 17 May 2016, Gianfranco Costamagna wrote: > Hi, > > Bad dak is bad > https://buildd.debian.org/status/package.php?p=libbpp-seq&suite=unstable > libbpp-seq9 | 2.0.3-1 | oldstable | amd64, armel, armhf, i386, ia64, kfreebsd-amd64, kfreebsd-i386, mips, mipsel, powerpc, s390, s390x, sparc > libbpp-seq9 | 2.1.0-1 | stable | amd64, arm64, armel, armhf, i386, mips, mipsel, powerpc, ppc64el, s390x > libbpp-seq9 | 2.1.0-1 | stable-kfreebsd | kfreebsd-amd64, kfreebsd-i386 > libbpp-seq9 | 2.1.0-1 | unstable | amd64, arm64, armel, armhf, hurd-i386, i386, kfreebsd-amd64, kfreebsd-i386, mips, mips64el, mipsel, powerpc, ppc64el, s390x > > > > dak ls libbpp-seq9v5 > libbpp-seq9v5 | 2.2.0-1 | testing | amd64, arm64, armel, armhf, i386, mips, mipsel, powerpc, ppc64el, s390x > libbpp-seq9v5 | 2.2.0-1 | unstable | amd64, arm64, armel, armhf, hurd-i386, i386, kfreebsd-amd64, kfreebsd-i386, mips, mips64el, mipsel, powerpc, ppc64el, s390x > > > I guess Andreas is fully correct, the rename is not necessary for backports, right? I would expect it to follow unstable. I guess the rename had a reason. Alex From formorer at formorer.de Tue May 17 13:51:38 2016 From: formorer at formorer.de (Alexander Wirt) Date: Tue, 17 May 2016 15:51:38 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <223102053.6033259.1463492907760.JavaMail.yahoo@mail.yahoo.com> References: <20160517131527.GA13436@an3as.eu> <1861224612.6090935.1463491422767.JavaMail.yahoo@mail.yahoo.com> <20160517134223.GC7172@formorer.de> <223102053.6033259.1463492907760.JavaMail.yahoo@mail.yahoo.com> Message-ID: <20160517135138.GD7172@formorer.de> On Tue, 17 May 2016, Gianfranco Costamagna wrote: > Rename was because of gcc-5 transition, that didn't happen in jessie. > > So the rename has to be reverted for backports, otherwise the library will conflict with > the one in jessie, making half of the archive removed if you want to have it installed > > look e.g. my mistake in llvm-toolchain-3.5 backport, where I didn't rename it > https://lists.debian.org/debian-backports/2016/01/msg00113.html > > (sorry for bothering, I'm not 100% sure about this particular case, I just want to point > to a mistake I did in the past, I'm for sure not authoritative at all on the matter, so > please don't trust my opinion :) ) Ah that may make sense. But if its the case, such things belong into the changelog. Alex From t.glaser at tarent.de Tue May 17 13:51:05 2016 From: t.glaser at tarent.de (Thorsten Glaser) Date: Tue, 17 May 2016 15:51:05 +0200 (CEST) Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160517134223.GC7172@formorer.de> References: <20160517131527.GA13436@an3as.eu> <1861224612.6090935.1463491422767.JavaMail.yahoo@mail.yahoo.com> <20160517134223.GC7172@formorer.de> Message-ID: On Tue, 17 May 2016, Alexander Wirt wrote: > > I guess Andreas is fully correct, the rename is not necessary for backports, right? > I would expect it to follow unstable. I guess the rename had a reason. AFAIK the renaming is positively harmful when done in backports. The reason is that the C++ ABI, provided by the compiler, changes, so unless GCC is also backported, and depended on, this must not be done, IIUC. bye, //mirabilos -- tarent solutions GmbH Rochusstra?e 2-4, D-53123 Bonn ? http://www.tarent.de/ Tel: +49 228 54881-393 ? Fax: +49 228 54881-235 HRB 5168 (AG Bonn) ? USt-ID (VAT): DE122264941 Gesch?ftsf?hrer: Dr. Stefan Barth, Kai Ebenrett, Boris Esser, Alexander Steeg From andreas at an3as.eu Tue May 17 14:00:36 2016 From: andreas at an3as.eu (Andreas Tille) Date: Tue, 17 May 2016 16:00:36 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160517135138.GD7172@formorer.de> References: <20160517131527.GA13436@an3as.eu> <1861224612.6090935.1463491422767.JavaMail.yahoo@mail.yahoo.com> <20160517134223.GC7172@formorer.de> <223102053.6033259.1463492907760.JavaMail.yahoo@mail.yahoo.com> <20160517135138.GD7172@formorer.de> Message-ID: <20160517140036.GB13436@an3as.eu> On Tue, May 17, 2016 at 03:51:38PM +0200, Alexander Wirt wrote: > On Tue, 17 May 2016, Gianfranco Costamagna wrote: > > > Rename was because of gcc-5 transition, that didn't happen in jessie. > > > > So the rename has to be reverted for backports, otherwise the library will conflict with > > the one in jessie, making half of the archive removed if you want to have it installed > > > > look e.g. my mistake in llvm-toolchain-3.5 backport, where I didn't rename it > > https://lists.debian.org/debian-backports/2016/01/msg00113.html > > > > (sorry for bothering, I'm not 100% sure about this particular case, I just want to point > > to a mistake I did in the past, I'm for sure not authoritative at all on the matter, so > > please don't trust my opinion :) ) > Ah that may make sense. But if its the case, such things belong into the > changelog. OK, I missed this in this actual packages changelog. Would it be OK to uploaded with this changelog: libbpp-seq (2.2.0-1~bpo8+1) jessie-backports; urgency=medium * Rebuild for jessie-backports. * Revert v5 name change -- Andreas Tille Tue, 17 May 2016 09:39:02 +0200 and to ping you for fast processing? Sorry for the confusion Andreas. -- http://fam-tille.de From formorer at formorer.de Tue May 17 14:03:43 2016 From: formorer at formorer.de (Alexander Wirt) Date: Tue, 17 May 2016 16:03:43 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160517140036.GB13436@an3as.eu> References: <20160517131527.GA13436@an3as.eu> <1861224612.6090935.1463491422767.JavaMail.yahoo@mail.yahoo.com> <20160517134223.GC7172@formorer.de> <223102053.6033259.1463492907760.JavaMail.yahoo@mail.yahoo.com> <20160517135138.GD7172@formorer.de> <20160517140036.GB13436@an3as.eu> Message-ID: <20160517140343.GE7172@formorer.de> On Tue, 17 May 2016, Andreas Tille wrote: > On Tue, May 17, 2016 at 03:51:38PM +0200, Alexander Wirt wrote: > > On Tue, 17 May 2016, Gianfranco Costamagna wrote: > > > > > Rename was because of gcc-5 transition, that didn't happen in jessie. > > > > > > So the rename has to be reverted for backports, otherwise the library will conflict with > > > the one in jessie, making half of the archive removed if you want to have it installed > > > > > > look e.g. my mistake in llvm-toolchain-3.5 backport, where I didn't rename it > > > https://lists.debian.org/debian-backports/2016/01/msg00113.html > > > > > > (sorry for bothering, I'm not 100% sure about this particular case, I just want to point > > > to a mistake I did in the past, I'm for sure not authoritative at all on the matter, so > > > please don't trust my opinion :) ) > > Ah that may make sense. But if its the case, such things belong into the > > changelog. > > OK, I missed this in this actual packages changelog. Would it be OK to > uploaded with this changelog: > > libbpp-seq (2.2.0-1~bpo8+1) jessie-backports; urgency=medium > > * Rebuild for jessie-backports. > * Revert v5 name change > > -- Andreas Tille Tue, 17 May 2016 09:39:02 +0200 Yes. That way I wouldn't make the error to oversee the change between several other packages I process. Alex From andreas at an3as.eu Tue May 17 14:24:05 2016 From: andreas at an3as.eu (Andreas Tille) Date: Tue, 17 May 2016 16:24:05 +0200 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes REJECTED In-Reply-To: <20160517140343.GE7172@formorer.de> References: <20160517131527.GA13436@an3as.eu> <1861224612.6090935.1463491422767.JavaMail.yahoo@mail.yahoo.com> <20160517134223.GC7172@formorer.de> <223102053.6033259.1463492907760.JavaMail.yahoo@mail.yahoo.com> <20160517135138.GD7172@formorer.de> <20160517140036.GB13436@an3as.eu> <20160517140343.GE7172@formorer.de> Message-ID: <20160517142405.GC13436@an3as.eu> On Tue, May 17, 2016 at 04:03:43PM +0200, Alexander Wirt wrote: > > OK, I missed this in this actual packages changelog. Would it be OK to > > uploaded with this changelog: > > > > libbpp-seq (2.2.0-1~bpo8+1) jessie-backports; urgency=medium > > > > * Rebuild for jessie-backports. > > * Revert v5 name change > > > > -- Andreas Tille Tue, 17 May 2016 09:39:02 +0200 > Yes. That way I wouldn't make the error to oversee the change between several > other packages I process. Just run dput with a fixed changelog. Sorry for this library-backporters beginners mistake Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Tue May 17 14:24:25 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 14:24:25 +0000 Subject: [Debian-med-packaging] Processing of libbpp-seq_2.2.0-1~bpo8+1_amd64.changes Message-ID: libbpp-seq_2.2.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-seq_2.2.0-1~bpo8+1.dsc libbpp-seq_2.2.0-1~bpo8+1.debian.tar.xz libbpp-seq-dev_2.2.0-1~bpo8+1_amd64.deb libbpp-seq9_2.2.0-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 17 16:21:26 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 16:21:26 +0000 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes is NEW Message-ID: binary:libbpp-seq-dev is NEW. binary:libbpp-seq9 is NEW. source:libbpp-seq is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Tue May 17 16:35:02 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 16:35:02 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-xvector_0.12.0-2_source.changes Message-ID: r-bioc-xvector_0.12.0-2_source.changes uploaded successfully to localhost along with the files: r-bioc-xvector_0.12.0-2.dsc r-bioc-xvector_0.12.0-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From noreply at release.debian.org Tue May 17 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 17 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] prottest 3.4.2+dfsg-2 MIGRATED to testing Message-ID: FYI: The status of the prottest source package in Debian's testing distribution has changed. Previous version: 3.4.1+dfsg-2 Current version: 3.4.2+dfsg-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 17 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 17 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] r-bioc-biovizbase 1.18.0-2 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-biovizbase source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 1.18.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 17 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 17 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] r-bioc-variantannotation 1.18.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-variantannotation source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 1.18.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 17 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 17 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] r-bioc-cummerbund 2.12.1-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-cummerbund source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 2.12.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Tue May 17 16:57:57 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 16:57:57 +0000 Subject: [Debian-med-packaging] r-bioc-xvector_0.12.0-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 17 May 2016 17:58:43 +0200 Source: r-bioc-xvector Binary: r-bioc-xvector Architecture: source Version: 0.12.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-xvector - BioConductor representation and manpulation of external sequences Changes: r-bioc-xvector (0.12.0-2) unstable; urgency=medium . * Fix autopkgtest Checksums-Sha1: c3c7fb414e2f7685c2c7b96873011e6147c63303 2116 r-bioc-xvector_0.12.0-2.dsc ab752d2119892a91596f2a79077940a034910ed4 4044 r-bioc-xvector_0.12.0-2.debian.tar.xz Checksums-Sha256: f080d63f4c95cec2e76461a52ef455ab8899a508c4b6f034dc4754a5953bbd56 2116 r-bioc-xvector_0.12.0-2.dsc 04e67c224c4e299fab7396693c96d01df86b01dd0cdd15a90fb36d50acce80df 4044 r-bioc-xvector_0.12.0-2.debian.tar.xz Files: f632751d74d0c4fbb59f03e2f57aea12 2116 gnu-r optional r-bioc-xvector_0.12.0-2.dsc f2866fa551b19e83eaff7cb9698b773b 4044 gnu-r optional r-bioc-xvector_0.12.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXO0LrAAoJEFeKBJTRxkbRqR8P/2Msj92O+he/KAKRYQMpJyTA cMpx/QSEpDC6EzsDGjlJ97fmx6/FNHf9U8pvPVVcHcq6tZP8h4U2+02Y6fZSHXpm vDFPhoLdKTyJRnjd3G4sfXzZrSM67rc8CHrU31YsA3OMlS1Yvc3+kRY3KqvklM9S 7EX9uJxwM0jwjFUG6edeaDb7d72CywsYjbt1T9TSlniPCA3cX5AvuPE7vEURfMzt V5+MSDWeYCthnP6zjquJo56ZEQUarEOMzOAq1dPtQEOb0mNoHH0XcGSdyQ4YPdKT T5Rx1DZ2CDmIsFd9pIK656ikU3HFEs1+YTXa05uO+bSeKfJIZuXS482vEZI9LaI2 11Y6FJE7SDFRsCL13s8Qe0HPiVI9Z4DKBx1UPKsE5YKyE6dsIMTJbeInuRcWRfRH vQvzZ6by94uLlZtEbG96Mt5mULWZZDhNbiIxhv8npUqRVfzpeiF0s8o8rKzzvu+Z hQJFWH/UkwyEpwiDbb8rW2AY3RDFGHE4W/NYh5JxrKXtF5cxnaEJyzvtgF870EjL Oc8Ujp3EWKSdIV0HrNNy23Vv3Osh6/5BTqyEaOJ/qF1Av2LTPZYnZQRUmcGhrlKM TnDMh5IFlLYcHuXa8w9o3D9Q2C/WVzxzTnir8y3FyuTPpvj4/Uub2/sNvXZXEXFh aHv8vVcMpSygwNOVwxK+ =YDfl -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Tue May 17 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 17 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] mpj 0.44+dfsg-2 MIGRATED to testing Message-ID: FYI: The status of the mpj source package in Debian's testing distribution has changed. Previous version: 0.42+dfsg-2 Current version: 0.44+dfsg-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 17 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 17 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] r-bioc-gviz 1.14.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-gviz source package in Debian's testing distribution has changed. Previous version: (not in testing) Current version: 1.14.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Tue May 17 20:01:51 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 20:01:51 +0000 Subject: [Debian-med-packaging] libbpp-seq_2.2.0-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 17 May 2016 09:39:02 +0200 Source: libbpp-seq Binary: libbpp-seq-dev libbpp-seq9 Architecture: source amd64 Version: 2.2.0-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-seq-dev - Bio++ Sequence library development files libbpp-seq9 - Bio++ Sequence library Changes: libbpp-seq (2.2.0-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Revert v5 name change Checksums-Sha1: 5bd515a8d8fcefe743cc9c115ef9811ba9dede4e 2134 libbpp-seq_2.2.0-1~bpo8+1.dsc 5c17c80cec9d2d942524aab94d0e0fcba8f1867a 4816 libbpp-seq_2.2.0-1~bpo8+1.debian.tar.xz 4882ed109d896d4e4979012e08e03a502c53d24e 1117966 libbpp-seq-dev_2.2.0-1~bpo8+1_amd64.deb a773adfc00b21387b870dbb0d5b4749031853ddd 471066 libbpp-seq9_2.2.0-1~bpo8+1_amd64.deb Checksums-Sha256: 0303187609c1f5cd9cef4190eae1219525cb5e682172ed9142fc027cc750132b 2134 libbpp-seq_2.2.0-1~bpo8+1.dsc 98310c44b818189c71ca4c8ab5f9bc6f5630800e0f0fcc4d51c55026b4f31a08 4816 libbpp-seq_2.2.0-1~bpo8+1.debian.tar.xz d9242f02c9c7b0a68c49e07493154f369a0bcf2d5c4c5fb56c3cda97c3427a4f 1117966 libbpp-seq-dev_2.2.0-1~bpo8+1_amd64.deb 15815eff015f79e6c28588bd8aca0bff7c40df7b68cf624c10445f4209869a77 471066 libbpp-seq9_2.2.0-1~bpo8+1_amd64.deb Files: 01c1b07ab8023f4499d322cade8517e9 2134 science optional libbpp-seq_2.2.0-1~bpo8+1.dsc e9525c3b22ec79902233a4fa0577a160 4816 science optional libbpp-seq_2.2.0-1~bpo8+1.debian.tar.xz ca5204a93b67b1e27b76e7764d0458b6 1117966 libdevel optional libbpp-seq-dev_2.2.0-1~bpo8+1_amd64.deb abffc6b93914b54047506a732cac3a8b 471066 libs optional libbpp-seq9_2.2.0-1~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXOySbAAoJEFeKBJTRxkbRArYP/2987D4zCAq7wFuvIcmjWgIH cCJUv7kJ0yh2qxb0B6EKc+UgXrZxby36A3WsTADQtQ2jspONt1bHXJengpud9iRC qot6r7L0IQQNh5etplr6HRStfnOsl6UWbNHODp0GfBOXbSp/SgqkpbDySACTNXhR Vq0KWSAPjvg6rb2hx6RoIX0Pru/XlIYSbbq+SAB1Bm2YpB+XvEqWnMiTg9HCyYck 3a90K93aS+jLcxv7CzxAAQWUzK6vmxJFYsD59tsm2g0KPtrjqJCXzbtsnleVjHO8 3kQ+NffU+9Qv88SSIkBrboQ/52aIm29iRYhslDPKzW64BdPVDEzYo+Y6/8nJ9w/g TSimoLRpwMMxYvTT7l8s9M8W6G38PdujJBRz02TitXrgbuL70457mUzFX0Ke2z6v MbvBD0F7BOUNH/gPnYGVlKaDL4/Fi5kTPi1UQzLtN+JcI8qxtQG46pkEnFgkXmLF trIDG86ncpJoYCluNGMK36FZnryVCGK6nwPupPXA0xgbpunF1x6/Tl3nlcqdRIhr rVqPpLZrHS7AfNAGDl5h02WJwiumFRxp8+G/+V4PRBCMiSC+QWm44rMtx4/5qqhp EslzNItnFPksYCqpn7I+5ZOhZf2+62fiAPjYRmmGpdRcrLFkYkDMYN/XW+gbNDVj VIS3sFulWhjMO6nF4tqF =MS+6 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 17 20:01:49 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 20:01:49 +0000 Subject: [Debian-med-packaging] libbpp-phyl_2.2.0-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 17 May 2016 10:02:30 +0200 Source: libbpp-phyl Binary: libbpp-phyl-dev libbpp-phyl9 Architecture: source amd64 Version: 2.2.0-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-phyl-dev - Bio++ Phylogenetic library development files libbpp-phyl9 - Bio++ Phylogenetic library Changes: libbpp-phyl (2.2.0-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Revert v5 rename of library packages Checksums-Sha1: 1182bcdd7112704e410597038e25bddf31b92c07 2146 libbpp-phyl_2.2.0-1~bpo8+1.dsc adca48fe8552302950e2b5bab4b2d20b261e99f9 4404 libbpp-phyl_2.2.0-1~bpo8+1.debian.tar.xz b3da170498f4932fdb7bd5bf5d3de50bb609696a 3830768 libbpp-phyl-dev_2.2.0-1~bpo8+1_amd64.deb 551beee378e3d381dce25bae4f9241af23dc1725 1459450 libbpp-phyl9_2.2.0-1~bpo8+1_amd64.deb Checksums-Sha256: c37eb8c568b1c5f2c8ade20f2a70d6651d118d4a46814e9a4972f7899646b117 2146 libbpp-phyl_2.2.0-1~bpo8+1.dsc 0836ca9115086e75f845684cb3591595e1d1a2880729b68b78df5fa3f86a8796 4404 libbpp-phyl_2.2.0-1~bpo8+1.debian.tar.xz 5c9831ea697fd5b105900fe2227e9ac4baf0de9fb2b52366f18d3204396a78ec 3830768 libbpp-phyl-dev_2.2.0-1~bpo8+1_amd64.deb cc2228555b3ad173a2c6d8e6096d3019fbdbc9ea2cf100c643c5b8dc8545c8a5 1459450 libbpp-phyl9_2.2.0-1~bpo8+1_amd64.deb Files: 0f5c4cc505d1d07311d6d3b4a5db5848 2146 science optional libbpp-phyl_2.2.0-1~bpo8+1.dsc 59b65eddad584654044e06e1706ee78f 4404 science optional libbpp-phyl_2.2.0-1~bpo8+1.debian.tar.xz 58c4816432c2e3b5f7246d82d0ba8848 3830768 libdevel optional libbpp-phyl-dev_2.2.0-1~bpo8+1_amd64.deb 09841583f10e1bebd0a43d05979b993b 1459450 libs optional libbpp-phyl9_2.2.0-1~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXOudaAAoJEFeKBJTRxkbRT58P/RNydC/mT3HkETVTZC48Z4nL 6f0NwcyYUp5eRYwPQ8Q0/RAg9e0ZXP7SJRVALDxNTyjPtg9mtkYi2176zVdK6co+ NmOiX3OBQA2AXNRYeR3dRv2gJos5vKe5lvYYGGgplO2sur/tW1z7iw2wl0IfgQgk gW6oD5JLGygFWF9FyK5wR92g7eOQq+m9vy813Dohn54WhW6fagRwOtmXZNVdepiD Mpsfmi+DwKsLkpvGu3R2oC7hE2wK3zCSLLw4rRsc/ujDjtKlCf9dxscM7mZ2OKfY Bb2FCwt0Nn81taYP4Eac6Kaa23przZl1EZhAA3sBL/PFm0W8wRtFRuZasJ1G2nqh 1UWGHOM3hejUvywoVSRa2GL3OcEgwpLWhJTmJN6SRGMTNLpF+1+4pLlj++j38GQU GDcncqD9HzeZ9+gWvW+TLMHHnZ8XhxcMgdhTFtCjJrQqGg60wAcXasgfv/kvDxS/ ZuBd4pDwFTzkTflh+CO8SQ2wK7m/NmuR4L3SqOrYtdr8fvEzXeEbmPjjilDnqNgx 7uKNfFkL3F9FHPNQ5Fh2dwih+4I1sffVvvCRkdqPblX6/vEl+pyKTq1bjRPXkzws rY8rnCLOdpefy4ZjdUw8VtiOjCu1da4n4JWWu0WyvnBdyfvdsXLITet/XJ1zOiUO drQsgIYHsdYhF2/x5976 =IG/a -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 17 20:52:46 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 20:52:46 +0000 Subject: [Debian-med-packaging] Processing of prottest_3.4.2+dfsg-2~bpo8+1_amd64.changes Message-ID: prottest_3.4.2+dfsg-2~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: prottest_3.4.2+dfsg-2~bpo8+1.dsc prottest_3.4.2+dfsg-2~bpo8+1.debian.tar.xz prottest_3.4.2+dfsg-2~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 17 21:08:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 21:08:06 +0000 Subject: [Debian-med-packaging] Processing of r-cran-dplyr_0.4.3-6~bpo8+1_amd64.changes Message-ID: r-cran-dplyr_0.4.3-6~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: r-cran-dplyr_0.4.3-6~bpo8+1.dsc r-cran-dplyr_0.4.3-6~bpo8+1.debian.tar.xz r-cran-dplyr_0.4.3-6~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 17 21:38:24 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 21:38:24 +0000 Subject: [Debian-med-packaging] Processing of fis-gtm_6.3-000-2_source.changes Message-ID: fis-gtm_6.3-000-2_source.changes uploaded successfully to localhost along with the files: fis-gtm_6.3-000-2.dsc fis-gtm_6.3-000-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 17 22:20:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 22:20:23 +0000 Subject: [Debian-med-packaging] fis-gtm_6.3-000-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 17 May 2016 09:51:10 -0400 Source: fis-gtm Binary: fis-gtm fis-gtm-6.3-000 Architecture: source Version: 6.3-000-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Amul Shah Description: fis-gtm - metapackage for the latest version of FIS-GT.M database fis-gtm-6.3-000 - package for FIS-GT.M database Changes: fis-gtm (6.3-000-2) unstable; urgency=medium . [ Amul Shah ] * Fix a bug in the installation script . [ Andreas Tille ] * Better hardening * cme fix dpkg-control Checksums-Sha1: 1abba1daef5094841d98cd38af6d608bfb067f87 2390 fis-gtm_6.3-000-2.dsc 540d9e55a3d8bbefdc19c69ee6be845f279ead98 24176 fis-gtm_6.3-000-2.debian.tar.xz Checksums-Sha256: d98e42d36889419f0b5a80300264f583cd62e523e2fbbe496fd11354d8b92a2f 2390 fis-gtm_6.3-000-2.dsc 750e26691c5eb825d1f68750eb7cf7e4dff72863369c37e3f123bbdee23de0b3 24176 fis-gtm_6.3-000-2.debian.tar.xz Files: 38d6efdea8db97cf76bb604a0e77282d 2390 database optional fis-gtm_6.3-000-2.dsc 5d15ec1aff40cc7955092d600daa5cf8 24176 database optional fis-gtm_6.3-000-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXO46gAAoJEFeKBJTRxkbRnUQP/juLJUnZuXIkyskL/ZHP9tX5 cQ8W0fzPzr9wY+OwZSrKikQL5MdFOFVe6y0L2N5e1UKTK/+ETLgXD0Gs3xnsZ2sH sqLLy4pvVZm+KzZFtJplDSjc8e6pPDuF6dbFGuLM++Lafi+kVY9Rcvv/8ln6mucV 2b68mWIBrI7+Htsw0fsBEGi+df0xJOiJfRx7U8pfrWj1xmD8xHvTDMdsvuB8YOL6 7wQIc8aMqghd69P4+SLdYuorhF92/BISRgbf1Uez7NUMEDqKdmoDpD3WGDHlYS7v gCB680cGo+0zhfrUa4w+JUWBCs9x9xAHm3aUOcjjris6vw4IVu1KeDFlrXcYUlIM Y2DQhjjwC0AVjzI+kxn5JRpQtA8oM8VX2NlJCM0NygRiBFIiU0Reu2ioFZG/z6N8 n99+5LqH/bzCFBJUCgJrqywYMV4Ia3km8g1rWDTiiKWeAb4TxAh99bpiWCG9pV+A j2XfTMs7jkgMFLQVxZDqFS32J2WZ1mAHMhrkqGT2oaNcwKrV4UzjvrjTzYuoZmRg aRkZiN7KO/Ns5y1dCG+BQeMq5nHxJeEozTaMNZJqDXr8P2hFswuiy3+0cK2g0Sjf ReyyNPRfsmZu0J2XI5HmEXr6ht0fqOS0XVtruoPWZl4ix22fsNmkNUBhRkJxnLb9 xGT1LfCvOdZo4HmwMfce =ljj7 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 17 22:35:14 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 22:35:14 +0000 Subject: [Debian-med-packaging] prottest_3.4.2+dfsg-2~bpo8+1_amd64.changes is NEW Message-ID: binary:prottest is NEW. source:prottest is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Tue May 17 22:36:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 17 May 2016 22:36:04 +0000 Subject: [Debian-med-packaging] r-cran-dplyr_0.4.3-6~bpo8+1_amd64.changes is NEW Message-ID: binary:r-cran-dplyr is NEW. source:r-cran-dplyr is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Wed May 18 04:25:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 04:25:35 +0000 Subject: [Debian-med-packaging] Processing of libbpp-popgen_2.2.0-1~bpo8+1_amd64.changes Message-ID: libbpp-popgen_2.2.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-popgen_2.2.0-1~bpo8+1.dsc libbpp-popgen_2.2.0-1~bpo8+1.debian.tar.xz libbpp-popgen-dev_2.2.0-1~bpo8+1_amd64.deb libbpp-popgen6_2.2.0-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 04:35:39 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 04:35:39 +0000 Subject: [Debian-med-packaging] Processing of libbpp-qt_2.2.0-1~bpo8+1_amd64.changes Message-ID: libbpp-qt_2.2.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-qt_2.2.0-1~bpo8+1.dsc libbpp-qt_2.2.0-1~bpo8+1.debian.tar.xz libbpp-qt-dev_2.2.0-1~bpo8+1_amd64.deb libbpp-qt1_2.2.0-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 04:40:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 04:40:40 +0000 Subject: [Debian-med-packaging] Processing of libbpp-raa_2.2.0-2~bpo8+1_amd64.changes Message-ID: libbpp-raa_2.2.0-2~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-raa_2.2.0-2~bpo8+1.dsc libbpp-raa_2.2.0-2~bpo8+1.debian.tar.xz libbpp-raa-dev_2.2.0-2~bpo8+1_amd64.deb libbpp-raa1_2.2.0-2~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 04:40:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 04:40:40 +0000 Subject: [Debian-med-packaging] Processing of libbpp-seq-omics_2.2.0-1~bpo8+1_amd64.changes Message-ID: libbpp-seq-omics_2.2.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-seq-omics_2.2.0-1~bpo8+1.dsc libbpp-seq-omics_2.2.0-1~bpo8+1.debian.tar.xz libbpp-seq-omics-dev_2.2.0-1~bpo8+1_amd64.deb libbpp-seq-omics1_2.2.0-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 04:52:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 04:52:07 +0000 Subject: [Debian-med-packaging] libbpp-popgen_2.2.0-1~bpo8+1_amd64.changes is NEW Message-ID: binary:libbpp-popgen-dev is NEW. binary:libbpp-popgen6 is NEW. source:libbpp-popgen is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Wed May 18 04:52:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 04:52:12 +0000 Subject: [Debian-med-packaging] libbpp-qt_2.2.0-1~bpo8+1_amd64.changes is NEW Message-ID: binary:libbpp-qt-dev is NEW. binary:libbpp-qt1 is NEW. source:libbpp-qt is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Wed May 18 04:52:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 04:52:17 +0000 Subject: [Debian-med-packaging] libbpp-raa_2.2.0-2~bpo8+1_amd64.changes is NEW Message-ID: binary:libbpp-raa-dev is NEW. binary:libbpp-raa1 is NEW. source:libbpp-raa is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Wed May 18 04:52:22 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 04:52:22 +0000 Subject: [Debian-med-packaging] libbpp-seq-omics_2.2.0-1~bpo8+1_amd64.changes is NEW Message-ID: binary:libbpp-seq-omics-dev is NEW. binary:libbpp-seq-omics1 is NEW. source:libbpp-seq-omics is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From tille at debian.org Wed May 18 06:45:33 2016 From: tille at debian.org (Andreas Tille) Date: Wed, 18 May 2016 08:45:33 +0200 Subject: [Debian-med-packaging] Bug#777791: [PATCH] ball: ftbfs with GCC-5 In-Reply-To: <20160510171328.GA18647@an3as.eu> References: <56A7A02D.6080501@danny-edel.de> <20160126193150.GD31910@an3as.eu> <570BB9B9.7020408@danny-edel.de> <20160411155403.GE31347@an3as.eu> <20160411155403.GE31347@an3as.eu> <570BE6E7.7060500@danny-edel.de> <20160411184127.GH31347@an3as.eu> <20160504121915.GF20381@an3as.eu> <573200CB.1050700@danny-edel.de> <20160510171328.GA18647@an3as.eu> Message-ID: <20160518064533.GB5019@an3as.eu> Hi Danni, On Tue, May 10, 2016 at 07:13:28PM +0200, Andreas Tille wrote: > > > > I then rebuilt the package on a fresh sid cowbuilder, but now there's a > > new problem (see attachment for the exact error message) near the end of > > the build, involving a static_cast. I can confirm that the current Git repository builds for me. > Thanks a lot. Your work is really appreciated. Please also be bold and > commit to master. I have no time to look the next 2-3 days - but I'd > like to see the changes in master since I see no point in deriving for > this package what we are doing anywhere else. Could you please add your changes to debian/changelog? If you use dch it injects a separate section for your ID. Thanks a lot for your work on this which is really appreciated Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Wed May 18 09:33:52 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 09:33:52 +0000 Subject: [Debian-med-packaging] Processing of transdecoder_2.1.0+dfsg-1_source.changes Message-ID: transdecoder_2.1.0+dfsg-1_source.changes uploaded successfully to localhost along with the files: transdecoder_2.1.0+dfsg-1.dsc transdecoder_2.1.0+dfsg.orig.tar.gz transdecoder_2.1.0+dfsg-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From debian at danny-edel.de Wed May 18 09:56:59 2016 From: debian at danny-edel.de (Danny Edel) Date: Wed, 18 May 2016 11:56:59 +0200 Subject: [Debian-med-packaging] Bug#777791: [PATCH] ball: ftbfs with GCC-5 In-Reply-To: <20160518064533.GB5019@an3as.eu> References: <56A7A02D.6080501@danny-edel.de> <20160126193150.GD31910@an3as.eu> <570BB9B9.7020408@danny-edel.de> <20160411155403.GE31347@an3as.eu> <20160411155403.GE31347@an3as.eu> <570BE6E7.7060500@danny-edel.de> <20160411184127.GH31347@an3as.eu> <20160504121915.GF20381@an3as.eu> <573200CB.1050700@danny-edel.de> <20160510171328.GA18647@an3as.eu> <20160518064533.GB5019@an3as.eu> Message-ID: <573C3C6B.2010004@danny-edel.de> On 05/18/2016 08:45 AM, Andreas Tille wrote: > Could you please add your changes to debian/changelog? If you use > > dch > > it injects a separate section for your ID. Hi Andreas, I updated the changelog with dch and it tagged the changes with my name. The commit is in master. I hope its all right. - Danny From ftpmaster at ftp-master.debian.org Wed May 18 10:41:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 10:41:06 +0000 Subject: [Debian-med-packaging] transdecoder_2.1.0+dfsg-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 18 May 2016 02:28:29 -0700 Source: transdecoder Binary: transdecoder transdecoder-doc Architecture: source Version: 2.1.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: transdecoder - find coding regions within RNA transcript sequences transdecoder-doc - find coding regions within transcripts Changes: transdecoder (2.1.0+dfsg-1) unstable; urgency=medium . * New upstream release * Drop 'reproducible-build' patch, incorprorated upstream Checksums-Sha1: 10860bf60a9f83f401d91753788aca4cd70bec4a 2127 transdecoder_2.1.0+dfsg-1.dsc 996eeec7705521fbebe19f5ecdf620a66f833982 10850939 transdecoder_2.1.0+dfsg.orig.tar.gz 37201e7e4aa57f68c0a0830b87285ba204372d2d 4692 transdecoder_2.1.0+dfsg-1.debian.tar.xz Checksums-Sha256: 69fc79a51cb02bc5219ef03cb38182f411192121fa6d4f3d48ac21ea1d07fedc 2127 transdecoder_2.1.0+dfsg-1.dsc fa934cd93969b1aa0ad60e3d4732fcd5a9dcc879c1f7d8072d373c24fc12a573 10850939 transdecoder_2.1.0+dfsg.orig.tar.gz 36c209596d801e3efac5f7db2987513964eb3839ac40fcadc074c28ffeba2616 4692 transdecoder_2.1.0+dfsg-1.debian.tar.xz Files: f2d204b548b84f1e77832696bf19563f 2127 science optional transdecoder_2.1.0+dfsg-1.dsc d4c641e2ebb760fb027a02663c4635e3 10850939 science optional transdecoder_2.1.0+dfsg.orig.tar.gz 59f7c016f8e899699c97444685537b1e 4692 science optional transdecoder_2.1.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXPDXPAAoJEDwmdj9sZ+bidMUQAK8ZeOgKLQO0eW8SUoPyVqfw hne8wM2l87jaekiy7WLx+MaBWfUgIKaTaSay2BhMVqIwa66vASVlyVf5w5ZkqzyG nYF8KlgrW6Ec/axoJJPkODyMuqn5SUFzyPhL/rvgk0SyGTfm50B4buakmnVJOLf7 6B/zAnubItm70HXWyriNYnvxD3ycZubWSVXDH8rkPRPR3VEc69SjmcMrRV/g4ksX lm5zGik1S/aQyoZbUbAAmZkP9+lJ7PsHcIVd4GBsH8IxweF9DFI9WNvXoKQM7wql HLNUpqDPGzdI/gSe4Q+sWV3fqj4LqxWggj+H3kQ/A88lg6AGruYjlxNHJ2I0ermG HLLPrw0bsqE1lsNU3Atit8W7YVpyXiiCQ1s8ypfrl7UhYRcdmeDHo4ko3iZcbwli jDuAY+Bw56Ahu4x/+Gw1zXo8A/ao0d+1mjHJbW6/m7w06P+wINlDhHfcVmIle5Ak +yzjF2bS5f/54UJJAqlcmcH17thghTJ5qzR+E+N1UuxGlU8rftVMYQ4o+KzkOIg3 y1Ip62kDRDEJgeanDY/7xzoTY4vFwcvzc8yBO/mnQpm8m5jk+HnIPR+ymqMqfYZ/ CDzswDFVkuXwjduX58bE5sYC7M1JhdgwXtP3/l2SmzkT/HtVfOlBnUYVJ2QBMBVD 5/++Vv7LTNg5IFTGZHtO =J1Tp -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 18 11:24:38 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 11:24:38 +0000 Subject: [Debian-med-packaging] Processing of r-cran-epicalc_2.15.1.0-2_amd64.changes Message-ID: r-cran-epicalc_2.15.1.0-2_amd64.changes uploaded successfully to localhost along with the files: r-cran-epicalc_2.15.1.0-2.dsc r-cran-epicalc_2.15.1.0-2.debian.tar.xz r-cran-epicalc_2.15.1.0-2_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 11:30:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 11:30:58 +0000 Subject: [Debian-med-packaging] r-cran-epicalc_2.15.1.0-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 13:04:23 +0200 Source: r-cran-epicalc Binary: r-cran-epicalc Architecture: source all Version: 2.15.1.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-epicalc - GNU R Epidemiological calculator Changes: r-cran-epicalc (2.15.1.0-2) unstable; urgency=medium . * Epicalc is not actively maintained any more and was moved to the CRAN archive * cme fix dpkg-control Checksums-Sha1: e6812a85cb8ebfa87cd6249b68679c6f2fc2d7b4 2121 r-cran-epicalc_2.15.1.0-2.dsc cb78ae4a09b98a61735dc8b8f1e1fefa0857e289 2668 r-cran-epicalc_2.15.1.0-2.debian.tar.xz d9da9142662f2d1629b3e1de7df82326135e014c 446458 r-cran-epicalc_2.15.1.0-2_all.deb Checksums-Sha256: ed141e94db4b5b06475db103c1c64e2ff1c99d1b129ec174e8bb9b8711372abb 2121 r-cran-epicalc_2.15.1.0-2.dsc f35ac5bfb48bdb66fb6f13c9b8059c3bdb171cc10faed28f314e7bf259780c1f 2668 r-cran-epicalc_2.15.1.0-2.debian.tar.xz e1ce0bf28e290976e9ec6669b78d67963072e3a191bcda4e096f1d24383a02b9 446458 r-cran-epicalc_2.15.1.0-2_all.deb Files: 7ff2c885b1ff2c2d5d0a3d5769737643 2121 gnu-r optional r-cran-epicalc_2.15.1.0-2.dsc 242f27f6adb31fbe3807e095c2e4ce3c 2668 gnu-r optional r-cran-epicalc_2.15.1.0-2.debian.tar.xz 05e34b6bec89cb5e2087af0b2dbb970b 446458 gnu-r optional r-cran-epicalc_2.15.1.0-2_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPE/EAAoJEFeKBJTRxkbRVH0QAIqB3bVR2QnHsTR8rVncaNdO tydi4ea0OK4FG/ojJktBT3wdZ0QeJNWnts02YwOj7sbxe+jxktt8L4M39/AZLMn9 VJ4Xt9ghqAixpwIy4c73Prs0pLVZtea6disju+RWLwWn8vqNebKaAhui8MrYSVW6 ynuIOHZ2lNq+s1naLXGhZNPEeFg49FsEMIy9oD2ULC3Bbl/WTc6rN2csy6U9ZAH2 MjzWzJOm8ppzixXcPLV32iQJKRyJpzciEZzgosy9wlUsJM2Hp7d+m4PWVbNRI3cU Irw5gMvT2CWKDWimVmadQRnBw2kx9TNGF7eMeS2nBIPKQlbTxQR1o3XU5Bf1S0Wu 6RG2J+qr3Nw3wTZcbGLO++/kgyV/sAGoU77PTgzfqZWqy3YmhFv/3Z5xZpEKt2qE oEfmEhQkwfaTPtkrdxxxLIPSSNftr0FFjyyaMh5WBo4OYw6vH4SvdNHXOkZpy4lb iynXpIrFpP7Yx1es7jtL3eLk3ISXZGHGePNLxJEP/FUm0l64OQOxl1b9eilu/6uP Bucey9RzU00WWESwqn7xKYkOAioyuaTYrckMnLCdz3qX6Txtv6NGWvOKYsAaeT6O WxGmpMjV6Uhzd5kJC6grFKarGOv3BT0Fu5b9Bm5l8zaXf0VgjgYX/kIYh8noPibw MkEyuwwUCLY7usLmLTuB =/DJz -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 18 12:02:49 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 12:02:49 +0000 Subject: [Debian-med-packaging] prottest_3.4.2+dfsg-2~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 17 May 2016 22:17:15 +0200 Source: prottest Binary: prottest Architecture: source all Version: 3.4.2+dfsg-2~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: prottest - selection of best-fit models of protein evolution Changes: prottest (3.4.2+dfsg-2~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Versioned Depends from mpj is not a Build-Depends Checksums-Sha1: 1ed5e62fe5939350dcadee18d5878ad9f815e769 2088 prottest_3.4.2+dfsg-2~bpo8+1.dsc 72affde8caa4443db3194a52cd2a6562e019b0db 5336 prottest_3.4.2+dfsg-2~bpo8+1.debian.tar.xz bf9e91845b9ea465357f376358bc563f191d9bd9 346486 prottest_3.4.2+dfsg-2~bpo8+1_all.deb Checksums-Sha256: fa3fbba8ecd6eff905f0e79d164703db588c829d3f8491b5c6096c90fedae021 2088 prottest_3.4.2+dfsg-2~bpo8+1.dsc 69b7e284146cb54bf2d35818ddcd177ad26b2a16ff3bf2c6c4826b977f7fe436 5336 prottest_3.4.2+dfsg-2~bpo8+1.debian.tar.xz f99b302eff12d3fb3dee60099863bb8c0c709474f6573b32c6c790a6ea65c26f 346486 prottest_3.4.2+dfsg-2~bpo8+1_all.deb Files: ef6bbc220bf7a0c47ed1f98f3fa09459 2088 science optional prottest_3.4.2+dfsg-2~bpo8+1.dsc 24f794b9d4b29ee7dab0855dd1659f75 5336 science optional prottest_3.4.2+dfsg-2~bpo8+1.debian.tar.xz 3491a7e5ca79b64364214b4ef521bef4 346486 science optional prottest_3.4.2+dfsg-2~bpo8+1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXO4NpAAoJEFeKBJTRxkbR7hwP/0IBioPWxMmhoTqjYNK+qpgH GxmFNUValJl9FXIPC6J4OgTjFzxmToRLg1LLQGSJhM1Wdj8xG5vmCqG6LqRwy3kw pSw3Dc1/IpgkSDSClGrjE/CKzHXH8F7JpSkHmtCyMQiKSCzbdnWbCyNQm5JVJGXK n43WApHTuAPe+qtBJbsKbSr/faKRE+fREs41ua8FYquswBpAOW4y1HTiwELk9x2i eshe5YNHfJ+kxlvuaVnDtTg1HyBKOWXxN4xz0dUmwDUsEBlt2e4Navo22TXrRrve QuFFD3zc0oPKnHCQeXTX+SPWDZt9IKz6sEf0Q0xMTSmf6yAQU6WMagQufUr7tS6h 2YIYJbWgHSy3rQTYtyzwGT09oUtjujxP6y+CvfzWJluU0ozpQJNK+F80EUcohuDS AdcdLj2e644gOQ6ZVboL1p/Myr11weezSiX9WXp0r3sGeDp64TcKIqf7aZ5y+2O7 xue8piIXM8TXDIR+m7+dqFAjJ8fAFvL4sdcHbQSKgg3/T0N+pJCEFUGCMY1WxMWL 24T+w+cUXL55FiIErKHH5leq8OlVNv/3y0RkCRVlUg0O3dOusixIz+n6+yQRTzZ1 kxqiN3xfTL+W5kWWpUaz4jABQfNAi0My4/8TBMYWwcylDCl43C27TjZO/V5F7PPw v98wPNaYZ/hF5BBv828X =QqJg -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 18 12:02:50 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 12:02:50 +0000 Subject: [Debian-med-packaging] r-cran-dplyr_0.4.3-6~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 12 May 2016 20:47:02 +0200 Source: r-cran-dplyr Binary: r-cran-dplyr Architecture: source amd64 Version: 0.4.3-6~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-dplyr - GNU R grammar of data manipulation Changes: r-cran-dplyr (0.4.3-6~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Drop versioned Build-Depends for libboost-dev * Set versioned Build-Depends for r-base and rcpp Checksums-Sha1: 62f0a203bf70070b5aaa212fae421d74d457a6d0 2194 r-cran-dplyr_0.4.3-6~bpo8+1.dsc ea7a98821777694cbf36c62f42003de3272a4603 3676 r-cran-dplyr_0.4.3-6~bpo8+1.debian.tar.xz 5fe6a301362325e164e9983ca9ce173aa9ef3f84 1281038 r-cran-dplyr_0.4.3-6~bpo8+1_amd64.deb Checksums-Sha256: b38b3d43af3ddddf52e3cd11b4c5622b93dc9f8036f77d21f2dd1cd6b7e96cbe 2194 r-cran-dplyr_0.4.3-6~bpo8+1.dsc 126af8d83fad8e3fe77e381c599defe186bb9a2f0a225d1db39fe02758c63efa 3676 r-cran-dplyr_0.4.3-6~bpo8+1.debian.tar.xz 8955a8c09b4bcb02cddee1c8b4c8255ab4f8edb193ccfd277287706123e5398f 1281038 r-cran-dplyr_0.4.3-6~bpo8+1_amd64.deb Files: bd1b105eecb80546a46267f7d5c9cd64 2194 gnu-r optional r-cran-dplyr_0.4.3-6~bpo8+1.dsc c840b8b7a31e7d44ced2058f1933c5ab 3676 gnu-r optional r-cran-dplyr_0.4.3-6~bpo8+1.debian.tar.xz 78694c15527c7b2c91cc589f2ad9c0a9 1281038 gnu-r optional r-cran-dplyr_0.4.3-6~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXO4b2AAoJEFeKBJTRxkbRf6oQAJByG4K3bbv9DPFm0RnC5SqY oTaswfpQNIDmHo565pfur/JMr5pre1+hktpJ6Lvu3sQcwWvuVNUT8aPmGsKBsuWW QHfqLNY3GQjejbLoq6AUOfK0E5mm3FGXXe3IfhTWs7yxhKqmkV8IgM+WoEnSPWZB B5rJGDqxkhuF6WqAflqCpIQ60msXY978hP/4MDmDB7aucYrtBLm5kVJqAt0ClmiY XN5uZcBX/AtQWJzmEkGiga0kZN8rCr5rj9UutCxrFtp/ixWmgUEvSgQ3JuFIer37 lTodtKoTcx9VU2g/o2nLfTZCMzYn4gKHJo8+SYdcBsTh4rh15KeOPqjaN+SX79w5 2Q9EfiKsWGEpNeto0cwazfGXyKNHVjcCEvKKuXpdMBdyG4VTC8U2esqVbXs2STpO 1vGBCJwxTicnUJZfqiXsGMUZJDDj8yenmFD8uCEPFmta3Cg815NDOAwlJU2I2W08 e0my5lfLKSRCIeVF466Z+xdffMZLE8ZnS2bLDYc9WyxH5MNjVZkexMqLUQSkMKtU pP5XTN6Y+EyPyuhqQ4JIiTD/uI4ZGH4NgnNqmKjtQy7fWQsTcuBCjWFiZYDBdMZM 4NG+tt11ivaa32HVt2X3z5vchqOgUjbGUHrfOcANpvSxcdeG7pgi93h3QB1h66Hr 9fJ4aJUNQWOc3INdvNyQ =UXMF -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 18 12:15:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 12:15:28 +0000 Subject: [Debian-med-packaging] Processing of exonerate_2.4.0-2_source.changes Message-ID: exonerate_2.4.0-2_source.changes uploaded successfully to localhost along with the files: exonerate_2.4.0-2.dsc exonerate_2.4.0-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 12:18:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 12:18:58 +0000 Subject: [Debian-med-packaging] exonerate_2.4.0-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 14:11:15 +0200 Source: exonerate Binary: exonerate Architecture: source Version: 2.4.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Canberk Ko? Description: exonerate - generic tool for pairwise sequence comparison Changes: exonerate (2.4.0-2) unstable; urgency=medium . [ Canberk Ko? ] * Team upload * debian/tests: added testsuite * debian/rules: changes for testing . [ Andreas Tille ] * cme fix dpkg-control Checksums-Sha1: efe576b4d5f91de9dba36149c9ea00ccaf99e099 2114 exonerate_2.4.0-2.dsc f9e476a4c8621db0c4b15ffaa3d9c8318ff3ed05 8252 exonerate_2.4.0-2.debian.tar.xz Checksums-Sha256: 67f7c9dbfc4e2872cf380214561b4f6459d03fff6af54cf4c3a245b2c5feaf49 2114 exonerate_2.4.0-2.dsc 39b0813fd8e9176592ed1e76b40fa7e4f077ad577f3c4e21905a27778c48c284 8252 exonerate_2.4.0-2.debian.tar.xz Files: 7e97e086cb00e58fc047cb8e01318d41 2114 science optional exonerate_2.4.0-2.dsc 90232e013eca7c96e364ef8c46c82d59 8252 science optional exonerate_2.4.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPFxAAAoJEFeKBJTRxkbR4YYP/Rzuu0+gC5lF/R2VkqF3Y2pZ uYOk9JLv7LqGC0ZT/warwV+6KggDX9PQI6MZuuyBphcrffkyfetc5IBd8tdKF2z0 TI3+QhQgccSjzfScJIhDInTU6zT1Js5Wq981OVVz2li5W1eEQ6Kj07nO6DEJ613n DSBws9pgIGZiNG7RzI0xF8jCYnG4a/UhzGZXeCFQX2RqhVj3rRLhGJD4/snL+8u/ /+v+XDyqpfPtVEmgzdv5csTPy0ROqfYwUOYAqn4WRTrfUEul9ICNCPsLONrMIFPS gvrgUw6/cNAkZUCHznl/QpUdn5CxcDZVCtRwUkwpk0/XQ5+OPtjmW4Vb9HpDi0c4 5z1KntG8q6C1/uwP7ZC4kHgn6JJNH4nc7er1G/BS/ec9Eedizvt5t5C/u/XEDG4C 6qYrvh12bbzRBQ06n78UFGLlfq9qiOF6D55acRJctkGXKMbbPG1W/pRamn6dj04z o+Mi/S/AeajJObOj4LP6+Bwnk0OeUBy2o/on7bOIPJ9usTQKSPR3fFK/Q4J83sYp eFzanrMD30srj1wXbCJ4MmwRoqpVcIVYIbn5uhnLXjBUN0iP1LBGW9FTK2/n0BwS nPevIsI7OSlibQTbJFzkbLiC41hOmK/n5GEkhErHGG9rwY2X9UUQ3hdz3ZsE6GGv y2b9qoPaV9LfMUKMlYGF =v90f -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From andreas at an3as.eu Wed May 18 12:54:50 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 18 May 2016 14:54:50 +0200 Subject: [Debian-med-packaging] Bug#777791: [PATCH] ball: ftbfs with GCC-5 In-Reply-To: <573C3C6B.2010004@danny-edel.de> References: <570BB9B9.7020408@danny-edel.de> <20160411155403.GE31347@an3as.eu> <20160411155403.GE31347@an3as.eu> <570BE6E7.7060500@danny-edel.de> <20160411184127.GH31347@an3as.eu> <20160504121915.GF20381@an3as.eu> <573200CB.1050700@danny-edel.de> <20160510171328.GA18647@an3as.eu> <20160518064533.GB5019@an3as.eu> <573C3C6B.2010004@danny-edel.de> Message-ID: <20160518125450.GG5019@an3as.eu> Hi Danny, On Wed, May 18, 2016 at 11:56:59AM +0200, Danny Edel wrote: > > I updated the changelog with dch and it tagged the changes with my name. > The commit is in master. > > I hope its all right. Its perfect. Your input was extremely helpful to get the ball package back in shape and is very well percived. I'm just building the final status to upload to unstable. Thanks a lot Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Wed May 18 13:00:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 13:00:58 +0000 Subject: [Debian-med-packaging] Processing of ball_1.4.3~beta1-1_source.changes Message-ID: ball_1.4.3~beta1-1_source.changes uploaded successfully to localhost along with the files: ball_1.4.3~beta1-1.dsc ball_1.4.3~beta1.orig.tar.gz ball_1.4.3~beta1-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 13:18:59 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 13:18:59 +0000 Subject: [Debian-med-packaging] ball_1.4.3~beta1-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 14:49:09 +0200 Source: ball Binary: libball1.4-data libball1.4 libball1.4-dev libballview1.4 libballview1.4-dev python-ball python-ballview ballview libball1.4-doc Architecture: source Version: 1.4.3~beta1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: ballview - free molecular modeling and molecular graphics tool libball1.4 - Biochemical Algorithms Library libball1.4-data - Biochemical Algorithms Library (data files) libball1.4-dev - Header files for the Biochemical Algorithms Library libball1.4-doc - documentation for the BALL library libballview1.4 - Biochemical Algorithms Library, VIEW framework libballview1.4-dev - Header files for the VIEW part of the Biochemical Algorithms Libr python-ball - Python bindings for the Biochemical Algorithms Library python-ballview - Python bindings for VIEW-parts of the Biochemical Algorithms Libr Closes: 777791 787888 Changes: ball (1.4.3~beta1-1) unstable; urgency=medium . [ Andreas Tille ] * New upstream version Closes: #777791 * New homepage * Moved to Github * Adapt watch file to Github * Cherry-pick from upstream "Use c++11 on Clang" * Andreas Hildebrandt does not work on the packaging any more * cme fix dpkg-control * debian/rules: use dh Closes: #787888 * debian/control: Drop *-dbg package since this is created automatically now * delete debian/menu * polish d/copyright * better hardening * cme fix dpkg-control * do not install empty directories for docs * do not repeat section field in d/control * doc package can be installed without main package -> only suggests main package * Use libjs-jquery instead of local copy pf jquery.js * DEP5 fixes * Use python-helper properly * Enhance long description of dev package * Use Breaks where Conflicts is to strong * Remove extra license file * Add lintian override for false positive package-contains-empty-directory . [ Danny Edel ] * d/rules: Enable building and execution of unittests * Drop patch gcc5.diff (fixed upstream) * Backport patches from upstream git to fix FTBFS on recent sid: * b3679aa Fix: String failed to compile with newer GCC * 029fd2b Fix building PoseClustering with recent Boost * 3170b28 Fix compilation of BinaryFingerprintMethods_test * 7bb0166 Fixed PoseClustering test to account for changes in boost * 8ff1d1b FingerPrintSim: Fix build under clang 3.6 (also needed on gcc) * 38a955a Fix Python bindings for Box * f646875 Increased sleeping time on Socket_test * Add patches: * disable-assign-positions-from-template.patch (binary was only built, but not shipped previously, and fails to build with libeigen3-dev 3.3~beta1) * adjust-poseClustering_Test-boost-1.58.patch Checksums-Sha1: 72920502037d42a063d9a11ea4d7d92b8ab9f43f 2973 ball_1.4.3~beta1-1.dsc 05cc6905d255162934687a7f80f747cf72d074cb 56995375 ball_1.4.3~beta1.orig.tar.gz 2a398b2cacf92af8e5d4aafd92c59531b09248bd 16772 ball_1.4.3~beta1-1.debian.tar.xz Checksums-Sha256: 30bd628f001bfaae48791f58e71019f467d3cae811ad2653d2dd7946be92d1b6 2973 ball_1.4.3~beta1-1.dsc 85caeef007f54a147f9d484d47003b4240683f6d1a753babdb6797025a7de385 56995375 ball_1.4.3~beta1.orig.tar.gz a6605369e6bf0ba7842fbf46968ed47e0b9a928008e6224347a429c0d76d5fab 16772 ball_1.4.3~beta1-1.debian.tar.xz Files: ee5d396b2be773d252af24abed49c003 2973 science optional ball_1.4.3~beta1-1.dsc f8d5765bb790c70b9c1d5063ea82772b 56995375 science optional ball_1.4.3~beta1.orig.tar.gz ad613ea5e2504156cbc2b2b959762874 16772 science optional ball_1.4.3~beta1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPGbWAAoJEFeKBJTRxkbRcM0P/3rT/nIPvZfRZ2TvCN3f4m5h 8ervUKspfH+4ENHIJ8/R1kfk1ZAlxqK1XbKlkuqgJyqzOtg5poMuruSSc2RIcp0a 0ov/cXRuseHzGmn4fzRlbozLiyNg4bx7nT8rMV5f0nbzmn6K0x0rOryp6kT79R9U OfN+i35umAChcL0SBQebBRoNlY6itXa+fzmTWwXV9Tt1yldjehfb+i39SGbfMhrf Nf2U8Esz0wWQsQwiX75Yr6tM/liAUpntYUQrhLmvpsb7Z2dX8q8fOYPlOuODYJoM TVAuFJjp5Cmf7/6A5jL3ds8ZzNZgxI686K3ITghRAMrvc+UByZ7YWD+rPdZ+zRxd rA+wN2ED8rdVzLvovN8jeGJ+T5QuovnVVC6TFgvltM5/GQkh6ATBMJHGyeWTjap3 UZf98ZondyzEycted/BqLFhDt96wIAftlkoSCwGn5ZHN+o9+fFk8SsWzPYltm1dr ryv0wi9cBFEh929B0+HUf72lK05rrWRnbqGVt+m/TQlrAutak21cP1YMwwSawAjv tw/MwecTFwthPxwv5fg7ZLj5ix+eZ8FR+6/tIvEQgzEoNUqbCgPBqMAMqS8E/dYI cak9xfVwPz28LJvYuH6mTOFSycvHWFiuTgV6QMRJULLjyTXINXXUQv3vRq/cdzX0 21d2ELCQu/ZsDJdF6PZg =ojEf -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Wed May 18 13:21:16 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Wed, 18 May 2016 13:21:16 +0000 Subject: [Debian-med-packaging] Bug#777791: marked as done (ball: ftbfs with GCC-5) References: Message-ID: Your message dated Wed, 18 May 2016 13:18:59 +0000 with message-id and subject line Bug#777791: fixed in ball 1.4.3~beta1-1 has caused the Debian Bug report #777791, regarding ball: ftbfs with GCC-5 to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 777791: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=777791 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Matthias Klose Subject: ball: ftbfs with GCC-5 Date: Thu, 12 Feb 2015 10:30:09 +0000 Size: 7213 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#777791: fixed in ball 1.4.3~beta1-1 Date: Wed, 18 May 2016 13:18:59 +0000 Size: 7602 URL: From owner at bugs.debian.org Wed May 18 13:21:22 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Wed, 18 May 2016 13:21:22 +0000 Subject: [Debian-med-packaging] Bug#787888: marked as done (Minor improvements) References: <20150605235656.8291.7990.reportbug@luna.lisandropm.com.ar> Message-ID: Your message dated Wed, 18 May 2016 13:18:59 +0000 with message-id and subject line Bug#787888: fixed in ball 1.4.3~beta1-1 has caused the Debian Bug report #787888, regarding Minor improvements to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 787888: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=787888 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: =?utf-8?q?Lisandro_Dami=C3=A1n_Nicanor_P=C3=A9rez_Meyer?= Subject: Minor improvements Date: Fri, 05 Jun 2015 20:56:56 -0300 Size: 2202 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#787888: fixed in ball 1.4.3~beta1-1 Date: Wed, 18 May 2016 13:18:59 +0000 Size: 7626 URL: From tamara18 at superdon.net Wed May 18 13:59:15 2016 From: tamara18 at superdon.net (tamara18 at superdon.net) Date: Wed, 18 May 2016 13:59:15 +0000 Subject: [Debian-med-packaging] HI Message-ID: <423614.36426.qm@smtp105.biz.mail.gq1.yahoo.com> Hi. My name is Nancy Edwards. I am a soldier working as United Nations peace keeping. It's my pleasure to contact you after going through your profile it really interest me to have communication with you as a new friend, you can also write me through email (sgtnancyedwards at hotmail.com) to enable a fast reply, i will be waiting to hear from you soon. please don't forget to contact me by mail , I have very important something to discuss with you. Email (sgtnancyedwards at hotmail.com) From ftpmaster at ftp-master.debian.org Wed May 18 16:15:25 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 16:15:25 +0000 Subject: [Debian-med-packaging] Processing of mafft_7.294-1_amd64.changes Message-ID: mafft_7.294-1_amd64.changes uploaded successfully to localhost along with the files: mafft_7.294-1.dsc mafft_7.294.orig.tar.gz mafft_7.294-1.debian.tar.xz mafft_7.294-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 16:20:27 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 16:20:27 +0000 Subject: [Debian-med-packaging] Processing of last-align_737-1_amd64.changes Message-ID: last-align_737-1_amd64.changes uploaded successfully to localhost along with the files: last-align_737-1.dsc last-align_737.orig.tar.xz last-align_737-1.debian.tar.xz last-align-dbgsym_737-1_amd64.deb last-align_737-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 16:23:57 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 16:23:57 +0000 Subject: [Debian-med-packaging] mafft_7.294-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 17:59:56 +0200 Source: mafft Binary: mafft Architecture: source amd64 Version: 7.294-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: mafft - Multiple alignment program for amino acid or nucleotide sequences Changes: mafft (7.294-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * /usr/bin/mafft-sparsecore.rb is non-zero - remove the test in debian/rules * Better hardening Checksums-Sha1: 4aaf411662fafb7a8421f7bdd50f741ab4846cf6 1975 mafft_7.294-1.dsc 20edcf0d02dce4ecb9b0da3bbc1a85bfc5f7fe00 464238 mafft_7.294.orig.tar.gz aa0bacdba1d0b5e452ef26ad681300d48eb0e562 6584 mafft_7.294-1.debian.tar.xz 75dd8a7f9d523e07bcc6ed79386595b283890609 894960 mafft_7.294-1_amd64.deb Checksums-Sha256: 328ead1021345e164d230f16f08de60235a6690b00bccfc4d0a37485af9bd1eb 1975 mafft_7.294-1.dsc 2b35600f2b0814cbaa3385b35f66a0ee1535a5db40b7376f8bf552a15ab12b68 464238 mafft_7.294.orig.tar.gz e86660407d5fada8f7ef0ebfdd00d5f65d22d835827f57d111e17ba5e9d2b485 6584 mafft_7.294-1.debian.tar.xz e399ce8d5578c80b2cf9774decd2b546adb1483a45b12020362a202d86507585 894960 mafft_7.294-1_amd64.deb Files: 1d75ed0666a71271e038ee659005fec8 1975 science optional mafft_7.294-1.dsc 490b389cf039e3d1f0b43e65dcc6c6e8 464238 science optional mafft_7.294.orig.tar.gz 7b69da387680963240b89b8a6c6de742 6584 science optional mafft_7.294-1.debian.tar.xz ace4e3092700d6ea0772d4fdcb375ea8 894960 science optional mafft_7.294-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPJT6AAoJEFeKBJTRxkbRpfIP/Rp4nBKY3Np2sh/0Xf+lFEy+ xjTBAaQYpkfEhnoaUCD7O8GUEwQo5xd9eZyOn0/unK3svSkNN8ZWHT4Lh0x9Hr+5 Vz0j5iBZj+pRYyNHRF9KwblZLvTqO5VPGZE2qZSNWhU9SqOffLlIfz/HuEQQlvQ7 XYuHsWAe0EzNcZ+pn+g7vvS1PYBGnfZWL2yLw8YyYp5EBsg6YrzS5b6Xiqz6TDV9 5bRH26hKtOjnWNoe4cPMsOZTXqzKyQh8G78jmqVBphx7Mg16tH1HboFJ7jaZoNT/ U35dzoAmQwUUQ21Uu6hU9N6coIdcmc1ocSTbjOEUKhzP4kbGmRQ64h6nhLZzVhoB fKaRTQKVqDs2sevQzI/e/fndmUKhddC/BJh5eIcyz0N/u4EpwvBGX0VI3OUoN8U5 W7Z2R2t8wSq2x4SVxsH3mM4NW1/GpFv/YaAPZPYom2cfvKOYK6xAEpRUvtfE/014 896DDYqzDvxMdszS2bAanngpaMAsNEHaqIk8z/E1+GNhaPA10AuTUqj0VxFVrMnb AUnCSe1aemEkA80HTZpGdHI0Ij200ZMAxBTT0uqNbYTR6FNLxTfnJXCVD5VMVAcB 74BygUK5U42aHeOApZYb950T+nOQJAonT7ZyNOsYsPH4Za/OupQZXgAT8vk2buq3 7qyHYPlayCIWN3uO+/V1 =Gvav -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 18 16:30:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 16:30:28 +0000 Subject: [Debian-med-packaging] Processing of king-probe_2.13.110909-2_amd64.changes Message-ID: king-probe_2.13.110909-2_amd64.changes uploaded successfully to localhost along with the files: king-probe_2.13.110909-2.dsc king-probe_2.13.110909-2.debian.tar.xz king-probe-dbgsym_2.13.110909-2_amd64.deb king-probe_2.13.110909-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 17:21:45 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 17:21:45 +0000 Subject: [Debian-med-packaging] king-probe_2.13.110909-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 18:26:27 +0200 Source: king-probe Binary: king-probe Architecture: source amd64 Version: 2.13.110909-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: king-probe - Evaluate and visualize protein interatomic packing Changes: king-probe (2.13.110909-2) unstable; urgency=medium . * Fix watch file * cme fix dpkg-control * Better hardening Checksums-Sha1: 77b536151aa64b659471be9bdb65bcb5e8dd3471 2073 king-probe_2.13.110909-2.dsc 2e7a4350f7224d3f4e07f816f4fe79438f94a769 6692 king-probe_2.13.110909-2.debian.tar.xz f7a24d653531e8d7dc757a4039d4cc7fc4e4bfda 108054 king-probe-dbgsym_2.13.110909-2_amd64.deb 149888ed369e6dfee633963204376ff222cd3ff4 86522 king-probe_2.13.110909-2_amd64.deb Checksums-Sha256: 65e0cf28ba80d424b45d03d2217532f89c61939f1c8d355900924c1f1fa95850 2073 king-probe_2.13.110909-2.dsc c02f7f1e6c5ef440c9ad4d4ec35fcba80def445e62a9384c392b23dd68bd43f6 6692 king-probe_2.13.110909-2.debian.tar.xz de5017673556b1c10d95421aa131b714a649eb876f6b5f370d1853eb4157a147 108054 king-probe-dbgsym_2.13.110909-2_amd64.deb f2077fc27a0b11b126171725e1d114ff197b84e64d369aa7d53de51ef668b029 86522 king-probe_2.13.110909-2_amd64.deb Files: 671105e306c06a170c17df6718a37211 2073 science optional king-probe_2.13.110909-2.dsc f7a357bc4644fae7205a1f0b05c7b952 6692 science optional king-probe_2.13.110909-2.debian.tar.xz c9403b296ec0bb8f1c2fcd108fad15f3 108054 debug extra king-probe-dbgsym_2.13.110909-2_amd64.deb 76700b9686ff43de814643c1b52a2fe7 86522 science optional king-probe_2.13.110909-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPJhmAAoJEFeKBJTRxkbRJ2YP/25VMlKobQRahRX2UuLK/PY0 5+mRku+QhGqksaA5lfMFzoDd2odN3KG7iur8jgKX97LR5C49tYOmbBdGCR+mxcLk MgAlQECXYm93ZqFtr8AH5671ZP3d9LIRY1SbmN0MYtjiujESIqTWArhGwC90F2GY bz/gGJJI85kyy3h+yap5cnBS4iM0ZRt36lrzGIQ7FCKxATJdsH3PhzW+tcVrOueJ eq/59OnGjriAslBH8J2B2TyAl7Sa7rhzCJ+P77gSAOQKwBsteSs/vx1fesYHq9ue 36dDlwRClMH0nPb49nWU0F8x/ENe2C1WrJAc6ECuYU9OmgaBBR5U0H1VWYKZ01Pz fVyNLsAxSPuWnpIRNL71vVVMc/JrejMw/PrxWwUf2jefNLUgsuGYaVGoIznskjZN DEWi83S/QpQMTxzUYmBAM4gqaPkmkKB8gSJiYvCkYsppPMpuM4jcbTBx7SZJsKEU zuC705P9h92XT7x+MksPi4Whj/XERk7eoywP/hW1oJVNYUonmxdhDBQLsqrN7OB1 +3P0pWummCYS3QZCwkJXezeDthKzDsjaXV6UOTT7V5V0rqfwlk/vArg+jcthu+Dk ZZJ9EXVh6fapReGYMkkXAQNEuyay+oGLB+yZOhMK0igRSEzPsPREw/TGdNkxS28F 1dM2BKcVW+JcUOlGXyb7 =CQsI -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 18 17:22:05 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 17:22:05 +0000 Subject: [Debian-med-packaging] last-align_737-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 18:08:29 +0200 Source: last-align Binary: last-align Architecture: source amd64 Version: 737-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: last-align - genome-scale comparison of biological sequences Changes: last-align (737-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * better hardening Checksums-Sha1: bf9d0a42bb8a872167ebf114c89549ba868bfc5a 1967 last-align_737-1.dsc 44fa0ea7354566c15e3ff67894d0507c83547fac 372580 last-align_737.orig.tar.xz a750fe90aea04b597688bb2d48dc8e20fec9d56b 8364 last-align_737-1.debian.tar.xz 34ef868cc484075c19ac4b62cea9df1a485df23f 4201298 last-align-dbgsym_737-1_amd64.deb c6f16046fce9b4df06bf9e64d73a2ac757c7c1cc 645778 last-align_737-1_amd64.deb Checksums-Sha256: 06f223a177e87471df441d292d6037b1c4ff5524d527ccfd08c6a77721a205b5 1967 last-align_737-1.dsc 63994d0386a10fe9d9c94a7937ab2683dbc20ecd554916085f20777e10b55904 372580 last-align_737.orig.tar.xz d81a7a5eee3089be06f0d2def9cf47c8f06193f4760695a1badb5d54797a7b2b 8364 last-align_737-1.debian.tar.xz 9112dd089376b7697aad65239be064e4791baea540e7b7f13cd1e39d00525967 4201298 last-align-dbgsym_737-1_amd64.deb 3bac83b24b7026df681f3600cab1423e9ef688c859010e739ad9e1fae3cf8e36 645778 last-align_737-1_amd64.deb Files: 14206e407f9c9863e26420cad6f501f4 1967 science optional last-align_737-1.dsc c46812977095586cf940645d735878d6 372580 science optional last-align_737.orig.tar.xz 39692727e12ff86a7ffdb4175b18df20 8364 science optional last-align_737-1.debian.tar.xz 2760abb8252c3b715beb8e43440b3373 4201298 debug extra last-align-dbgsym_737-1_amd64.deb 6a6b8cc42386f1c0c110e6dd763296a8 645778 science optional last-align_737-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPJV8AAoJEFeKBJTRxkbRIGwP/2FXb6vLDqJ49X5ecnjWE35W LRaOVy67v3OlgQfhViQVRybOCTdjteU4xGbA8o7akqM6y8aFWHJiXpi9iBP22l0b RTejPuInYat+aEmGedhfv6YR2dSMkRu/QpFcsWO1/GpaOGpXA02WBC15VpuxY+CI gh9aqZYbL9Hy/gpsHXiKAGeHaIYoOBTz4xYxNhmVAvaXpiXirfrF6u/gpcTfZlf9 1QsxtSCnB3g0zig/DWv98F1t1ECYuFd8XI52fkI1dX1yZlwfJpEIhn4mGYA8RwnD bdTlBA4qpL4j+W4nFUHywGZo3B7hNmrKBocZ7Wy1hMNedoTcz4kOZDEFagS9jk0Y NPJO41qh0JMyS627hCv14/a7yKQOeqeBNJ9TKmhTjKAj/qkftxCaJKGPjoh+nMFs 8xIQt/HHh+k9A6wxI7dHCapZv1g1hG1OMeHKEYi6zrgj4Dmy3RoNLzoi9DrhTpzP oE0uPuqSBlzaaafZEumb6kXS5ADLXLJD3OATtQDpTT12QWAmTDbExQ5w1KvmSxMp LnMeOyGsp/Rh5Gggz2/hxS0u/IIvVA8Tg5EO+CUkDk2TuFvgKCQ3XZayHhZ+zz5Q C2Zu7PMNkZlKFv18nRgLmbhJpMhGAYBKWul1JfhtGlceXsjj46ESQBqOV7AZ3CBe JU9j7FSnC/WwEWVX832J =wqi/ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From arunavam at andrew.cmu.edu Wed May 18 17:49:40 2016 From: arunavam at andrew.cmu.edu (Andrea Lynn Grieco) Date: Wed, 18 May 2016 20:49:40 +0300 Subject: [Debian-med-packaging] that's cool Message-ID: <0000a762c1f1$a167ab37$b89b57a4$@andrew.cmu.edu> Hi, Have you seen this? You've got to take a look, that's really cool, read more here Typos courtesy of my iPhone, Andrea Lynn Grieco -------------- next part -------------- An HTML attachment was scrubbed... URL: From vbaderks at gmail.com Wed May 18 20:23:10 2016 From: vbaderks at gmail.com (Victor Derks) Date: Wed, 18 May 2016 22:23:10 +0200 Subject: [Debian-med-packaging] Bug#816607: http://charls.codeplex.com/workitem/10742 In-Reply-To: References: Message-ID: Hi Sjors and Mathieu, I found the problem why the output of the decoded image by the original loco implementation and charls were not identical. This issue was caused by a defect in the charls test applications that creates the .pnm file. With the repaired test application the imaged can be encoded and decoded identical to the original input file. The charls library itself was ok after the initial fix. I have tagged the branches as 1.1.0 and 2.0.0. Victor On Wed, Apr 27, 2016 at 2:43 PM, Mathieu Malaterre wrote: > Hi Victor, > > On Wed, Mar 30, 2016 at 11:53 PM, Victor Derks wrote: > > Hi Sjors, > > > > I pushed the fix to the master and 1.x-master branch on github. > > > > The sample file can now be encoded to JPEG-LS and back to the .pnm > format. > > If I decode it back with CharLS the image is however not 100% identical. > If > > I decode it back with the ITU LOCO exe, the original and the > encoded\decoded > > files are identical. > > So the encoding to JPEG-LS seems to be ok, but there seems another issue > in > > the charls decoding process (maybe the fact the width is odd of this > sample > > image?). > > > > Will keep you posted > > Hum your patch make the attached DICOM file works. So indeed it does > solve some issues. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Wed May 18 22:04:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 22:04:12 +0000 Subject: [Debian-med-packaging] Processing of r-cran-tidyr_0.4.1-1~bpo8+1_amd64.changes Message-ID: r-cran-tidyr_0.4.1-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: r-cran-tidyr_0.4.1-1~bpo8+1.dsc r-cran-tidyr_0.4.1-1~bpo8+1.debian.tar.xz r-cran-tidyr_0.4.1-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 22:49:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 22:49:40 +0000 Subject: [Debian-med-packaging] Processing of staden-io-lib_1.14.8-1_amd64.changes Message-ID: staden-io-lib_1.14.8-1_amd64.changes uploaded successfully to localhost along with the files: staden-io-lib_1.14.8-1.dsc staden-io-lib_1.14.8.orig.tar.gz staden-io-lib_1.14.8-1.debian.tar.xz libstaden-read-dev_1.14.8-1_amd64.deb libstaden-read11-dbgsym_1.14.8-1_amd64.deb libstaden-read11_1.14.8-1_amd64.deb staden-io-lib-examples_1.14.8-1_all.deb staden-io-lib-utils-dbgsym_1.14.8-1_amd64.deb staden-io-lib-utils_1.14.8-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 22:49:41 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 22:49:41 +0000 Subject: [Debian-med-packaging] Processing of ray_2.3.1-4_amd64.changes Message-ID: ray_2.3.1-4_amd64.changes uploaded successfully to localhost along with the files: ray_2.3.1-4.dsc ray_2.3.1-4.debian.tar.xz ray-dbgsym_2.3.1-4_amd64.deb ray-doc_2.3.1-4_all.deb ray-extra_2.3.1-4_all.deb ray_2.3.1-4_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Wed May 18 23:27:59 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 23:27:59 +0000 Subject: [Debian-med-packaging] r-cran-tidyr_0.4.1-1~bpo8+1_amd64.changes is NEW Message-ID: binary:r-cran-tidyr is NEW. source:r-cran-tidyr is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Wed May 18 23:28:10 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 23:28:10 +0000 Subject: [Debian-med-packaging] ray_2.3.1-4_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 21:06:31 +0000 Source: ray Binary: ray ray-doc ray-extra Architecture: source amd64 all Version: 2.3.1-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: ray - de novo genome assemblies of next-gen sequencing data ray-doc - focumentation for ray parallel de novo genome assembler ray-extra - Scripts and XSL sheets for post-processing for ray Changes: ray (2.3.1-4) unstable; urgency=medium . * Team upload. * Enforce stable sort order for linking to make build reproducible. * Fix hardening by using CPPFLAGS etc. Checksums-Sha1: 08db5436195e89fcabf895725be40ba1c410f13e 2059 ray_2.3.1-4.dsc 318a4058a83430a01aff4367603908903c96cc4c 9396 ray_2.3.1-4.debian.tar.xz 704eca43d25bd4e5991cd9c4f3963121c4734bd7 13529632 ray-dbgsym_2.3.1-4_amd64.deb a44d22bf7d347c095e69b0e0fdbedd71d4f4c011 45156 ray-doc_2.3.1-4_all.deb 99ebdef7ff9c3a311be73b34126d9189ffda00b5 12036 ray-extra_2.3.1-4_all.deb 2d1f00b93b83b51e3992ed576ffc802e83be8048 622290 ray_2.3.1-4_amd64.deb Checksums-Sha256: 4886d6741b5313c50e335288292a2bf0d284ff23c4c51b1c3e141c0707be3dfd 2059 ray_2.3.1-4.dsc dd406fe3f7d9bbe4931307102a59b27c3c5b958d2855fb154a7408fd434450d7 9396 ray_2.3.1-4.debian.tar.xz 40316ae4fe9f23d80b3a3c968d5dfd48ff58197b96238b896c36ac4d4ace3d88 13529632 ray-dbgsym_2.3.1-4_amd64.deb a2377a713f9a616d911b4d177f15107380987a432c29b7c4d61468eac3fbe661 45156 ray-doc_2.3.1-4_all.deb 900f9b311c1af2b8776b69536604cb2d7cefbfe6d80a0bfb71093a1e6eaa8843 12036 ray-extra_2.3.1-4_all.deb 119875d468c19b7755f2f740f1a77be1de4391899adceff56bdd26e243ca56d2 622290 ray_2.3.1-4_amd64.deb Files: bf0f1d5b2c7493652a9f707762bb540c 2059 science optional ray_2.3.1-4.dsc 767a363d211ed7b7b576d423d1c2b492 9396 science optional ray_2.3.1-4.debian.tar.xz 8f37fd424d0760a14ac530e50ad2e96f 13529632 debug extra ray-dbgsym_2.3.1-4_amd64.deb 0bce25d09ec4a62966058a8fe48fe754 45156 doc optional ray-doc_2.3.1-4_all.deb 5771392170fbeef95ca3a1d34503dce9 12036 science optional ray-extra_2.3.1-4_all.deb eba12fe72c5209c00691bb5300d64fb0 622290 science optional ray_2.3.1-4_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPO3EAAoJEFeKBJTRxkbRjA8P/10WPWBJ3ZOA+h2LsBet7iFr zF11WQcbSjn8PUen9uV1eVWEGaYI1UVAouRM52bOzrbtbAvfD4xAvgq7SpiHYT0n Cl5Of5bmO56XS5nizxX0Dr+Y6tX2YkEvam5CLNIDfdV6ZaHYuZ7ilfsQ3ArUCVF5 h9AvmiZZ/xbZWIHrJlqi/P+CA9IKKZtO1OsL+5ULd/8QKmQFa/F0NPp3aNloXLmf Xh+sxt1sLwy5VN1k3+v5nNZyvcA+TSnzo9f1gxCloJ+6gAQFGKsw8zw8mZiPXEzH CzgN8zWyBA9j44Hpq9BI4LREz78VfkMung94Uiv6fVqTpkTax260k0PxrP763BzJ 86B1c8983d+7QnQSGtHUTMAwA+zwXGiRaxcpKBB8EelLm72iR8Ia0LkRBeDjCrWg mQSIz8H9h2bVxU7CJ+nMRZ6rQAmiHGmlSDSTQQH67zyFzRXQ0YQbJNsii04Cvspo s5bZD/1B/zQAUmmLiyzxlEXzwlAlsdlx+77m8jbtPckCxDthPlF2LTLrN4QrclyQ 0J1hkfysVfy1Lc+BjN5S/ncizy3K+PjAkcVy3je1cV19mytXreVj99i5oJrTKBBg 8Dgrzj8B9tQlID/3WmMRmSaOPCz7Eozo3mGQX8tlsfT9Ee1jf0VPpgOELEDfmBcA bZ3XIbVl+h+KS5hLTnE2 =+a/J -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Wed May 18 23:30:30 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 18 May 2016 23:30:30 +0000 Subject: [Debian-med-packaging] staden-io-lib_1.14.8-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 00:38:22 +0200 Source: staden-io-lib Binary: staden-io-lib-utils libstaden-read-dev libstaden-read11 staden-io-lib-examples Architecture: source amd64 all Version: 1.14.8-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libstaden-read-dev - development files for libstaden-read libstaden-read11 - Staden library for reading and writing DNA sequencing results staden-io-lib-examples - programs for maniuplating DNA sequencing files (usage examples) staden-io-lib-utils - programs for maniuplating DNA sequencing files Changes: staden-io-lib (1.14.8-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * Better hardening Checksums-Sha1: aae6ff45eacf3212272118fb0c0f65196ab447c9 2408 staden-io-lib_1.14.8-1.dsc 342f8b6cdb00ac297eb3be333bcc944c5bf91003 2217122 staden-io-lib_1.14.8.orig.tar.gz bd7c8b277a77976982e19d2c71fcede61d5b0ca5 9112 staden-io-lib_1.14.8-1.debian.tar.xz 412c2c4ae54cbd35e951418d4253573853b2cf29 390332 libstaden-read-dev_1.14.8-1_amd64.deb 96306fe426514de4377b091dba3b23c694afa586 472068 libstaden-read11-dbgsym_1.14.8-1_amd64.deb f126785746b192ecdbfa9018b80770502ee017ac 311466 libstaden-read11_1.14.8-1_amd64.deb d1916f5af2298c158b754e062a0c0e4d3d7f3b34 1308728 staden-io-lib-examples_1.14.8-1_all.deb b31509c618d3c03b670d507fb1cee3d4359f2e62 328490 staden-io-lib-utils-dbgsym_1.14.8-1_amd64.deb 6083eb8c8b50fe4c32269572d9a145876c6ed813 250366 staden-io-lib-utils_1.14.8-1_amd64.deb Checksums-Sha256: 9d134d8b7c76d8532ae6b94505a23a42748dccb62010febd1d612d80e34f6b2d 2408 staden-io-lib_1.14.8-1.dsc 3bd560309fd6d70b14bbb8230e1baf8706b804eb6201220bb6c3d6db72003d1b 2217122 staden-io-lib_1.14.8.orig.tar.gz 8159c1fdf0e31ad3d00664e5bdd6ba7e92bf55512335a1e78e8878488db8c759 9112 staden-io-lib_1.14.8-1.debian.tar.xz 781bb6302ca8fb47968a92a47a41d298c8df0321467e44b24ec4a66638ad2b46 390332 libstaden-read-dev_1.14.8-1_amd64.deb 7baa636832effecd6734cf77d980b3a0e1e477096bb8a1a2ff2cfcea84d4b981 472068 libstaden-read11-dbgsym_1.14.8-1_amd64.deb 4d0a71501789679f79827cc2e9256c073e19b721d5a07a7a0842f12a552cb704 311466 libstaden-read11_1.14.8-1_amd64.deb b428a2be87f7ce1b22467f6c08e5155bbca89be0d46bf962f231f29282e9e585 1308728 staden-io-lib-examples_1.14.8-1_all.deb 746c1bc3ce388c0f7a6f78ae29e4c18db924e4afe934b9e83d785801c5089abc 328490 staden-io-lib-utils-dbgsym_1.14.8-1_amd64.deb 63c3fa9ea8d335470c3e9a1291782e80cfdcf5d5a446d77a6c2cd9ff9a8dd706 250366 staden-io-lib-utils_1.14.8-1_amd64.deb Files: 6c7fc548ba39a57c5a84da5edd517491 2408 science optional staden-io-lib_1.14.8-1.dsc fe5ee6aaec8111a5bc3ac584a0c0c0c7 2217122 science optional staden-io-lib_1.14.8.orig.tar.gz 0b7572695d7539a6263445f35dafd74f 9112 science optional staden-io-lib_1.14.8-1.debian.tar.xz 20ecc172ad8913269154b07e92464382 390332 libdevel optional libstaden-read-dev_1.14.8-1_amd64.deb ec8d5a014377a5b36aed0f6cd163bd15 472068 debug extra libstaden-read11-dbgsym_1.14.8-1_amd64.deb 35a0bf0b26ed3e7b560b8362e52bc6d4 311466 libs optional libstaden-read11_1.14.8-1_amd64.deb 62d4e5a9dc53358e2f1a70b2fb2984d8 1308728 science optional staden-io-lib-examples_1.14.8-1_all.deb 3abdf97cd7e8568a516721f3acc422b0 328490 debug extra staden-io-lib-utils-dbgsym_1.14.8-1_amd64.deb 032fb2580c4f4f7063a96dfad2fb3a50 250366 science optional staden-io-lib-utils_1.14.8-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPPBXAAoJEFeKBJTRxkbRd+AQAIcHeugpXpkp+1VcF8L6sOHD osENc160oZtE0iiiIH/ZqErhAVuRAFAa1LHvqITMLxMbCQr33XWv9CFX2AfB0tsl hXtjNNZFXtr5xxFwo9fiH6GcLXqGUcnkfDo7jhBGSV5YWD1Pi+lZsgl35SG7AT9S NDMBXm8ODrIQQOG18PmamENS20zUh0sgkhstUrZwpC3kZOMN6TVA5I6VSxW7/FwX FXo+CF5mnP0BgHL/UdJr0s8P2YaucdIrL5u5txZa7IbO80+ApWJBSOOwT2B08mnH 66mP7QQy2VKJBnvzR6zIexZDofSoWQfRPBkWg2Ex2VDV9pB5FBMHzg0rvDagtfDv rf6vNR9ZiasEkaDi2G+DcE7Bm3aYHL0Xn7pvWZK9/pzCjDEwS2a6rEyiEH2CUw65 supzA4udWiosDbejXmdVY2+sXOmqrVm0Cwt4yQjl2QtxF7qiXo3YABV0T7/FdICS A1G8uq5OnS87/BpHFx/we11qTt6Bbgt4nE90KJAa2Jjn5TcLyC86HT00TBUn4daP /HT/XudTHJ8b5mnkHcaGltsyjABX69o8sK0/iSu5IV40dv68gxKVAMLnBnZCQMEw 2M0SXXDShgYqZQA/f1Twf3/9eo8IFmhZlq7iy7/gn5IankMqLq2181InkIiYNDbt BzoCc21fC3k3yPoqgLwv =u/sQ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Thu May 19 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Thu, 19 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] mobyle-tutorials is marked for autoremoval from testing Message-ID: mobyle-tutorials 1.5.0-2 is marked for autoremoval from testing on 2016-06-24 It (build-)depends on packages with these RC bugs: 824048: python-biopython: FTBFS: AssertionError: 10 != 1 From noreply at release.debian.org Thu May 19 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Thu, 19 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] python-biopython is marked for autoremoval from testing Message-ID: python-biopython 1.66+dfsg-2 is marked for autoremoval from testing on 2016-06-24 It is affected by these RC bugs: 824048: python-biopython: FTBFS: AssertionError: 10 != 1 From noreply at release.debian.org Thu May 19 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Thu, 19 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] mobyle-programs is marked for autoremoval from testing Message-ID: mobyle-programs 5.1.2-1 is marked for autoremoval from testing on 2016-06-24 It (build-)depends on packages with these RC bugs: 824048: python-biopython: FTBFS: AssertionError: 10 != 1 From noreply at release.debian.org Thu May 19 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Thu, 19 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] mobyle is marked for autoremoval from testing Message-ID: mobyle 1.5.3+dfsg-3 is marked for autoremoval from testing on 2016-06-24 It (build-)depends on packages with these RC bugs: 824048: python-biopython: FTBFS: AssertionError: 10 != 1 From noreply at release.debian.org Thu May 19 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Thu, 19 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] gubbins is marked for autoremoval from testing Message-ID: gubbins 1.4.9-1 is marked for autoremoval from testing on 2016-06-24 It (build-)depends on packages with these RC bugs: 824048: python-biopython: FTBFS: AssertionError: 10 != 1 From owner at bugs.debian.org Thu May 19 07:00:05 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Thu, 19 May 2016 07:00:05 +0000 Subject: [Debian-med-packaging] Processed: your mail References: Message-ID: Processing commands for control at bugs.debian.org: > tags 822785 = upstream Bug #822785 [src:dcmtk] dcmjpls: Big Endian Transfer Syntax not handlled correctly Removed tag(s) fixed-upstream, patch, and confirmed. > forwarded 822785 bugs at dcmtk.org Bug #822785 [src:dcmtk] dcmjpls: Big Endian Transfer Syntax not handlled correctly Set Bug forwarded-to-address to 'bugs at dcmtk.org'. > End of message, stopping processing here. Please contact me if you need assistance. -- 822785: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822785 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From owner at bugs.debian.org Thu May 19 07:03:06 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Thu, 19 May 2016 07:03:06 +0000 Subject: [Debian-med-packaging] Processed: your mail References: Message-ID: Processing commands for control at bugs.debian.org: > retitle 822785 dcmcjpls: Private GE Transfer Syntax not handlled correctly Bug #822785 [src:dcmtk] dcmjpls: Big Endian Transfer Syntax not handlled correctly Changed Bug title to 'dcmcjpls: Private GE Transfer Syntax not handlled correctly' from 'dcmjpls: Big Endian Transfer Syntax not handlled correctly'. > End of message, stopping processing here. Please contact me if you need assistance. -- 822785: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822785 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From malat at debian.org Thu May 19 07:14:42 2016 From: malat at debian.org (Mathieu Malaterre) Date: Thu, 19 May 2016 09:14:42 +0200 Subject: [Debian-med-packaging] Bug#824721: CharLS: 1.1.0 is out Message-ID: Package: src:charls CharLS 1.1.0 is out. It does include the recent fix done in Debian on 1.0.0: https://github.com/team-charls/charls/releases/tag/1.1.0 CharLS 2.0.0 has a different API (AFAIK), so it may be risky to update to it at this time for Debian. ---------- Forwarded message ---------- From: Victor Derks <> Date: Wed, May 18, 2016 at 10:23 PM Subject: Re: http://charls.codeplex.com/workitem/10742 Hi Sjors and Mathieu, I found the problem why the output of the decoded image by the original loco implementation and charls were not identical. This issue was caused by a defect in the charls test applications that creates the .pnm file. With the repaired test application the imaged can be encoded and decoded identical to the original input file. The charls library itself was ok after the initial fix. I have tagged the branches as 1.1.0 and 2.0.0. Victor From andreas at fam-tille.de Thu May 19 09:49:54 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Thu, 19 May 2016 11:49:54 +0200 Subject: [Debian-med-packaging] Bug#824048: Any change in blastp? (Was: Bug#824048: python-biopython: FTBFS: AssertionError: 10 != 1) In-Reply-To: <20160511200849.GA28855@an3as.eu> References: <1462984527.2366877.604901465.716271DC@webmail.messagingengine.com> <20160511200849.GA28855@an3as.eu> Message-ID: <20160519094954.GO5019@an3as.eu> Hi Peter, since some time the blastp test fails when building the Debian BioPython package. I've got no answer what might be wrong here. Do you have any idea which is better than deactivating this specific test for the monent which would be the only poor idea I'd have? Please let me know if you need more information. Kind regards Andreas. On Wed, May 11, 2016 at 10:08:49PM +0200, Andreas Tille wrote: > On Wed, May 11, 2016 at 05:35:27PM +0100, Chris Lamb wrote: > > ... > > Bio.PDB.Selection docstring test ... ok > > ====================================================================== > > FAIL: test_blastp (test_NCBI_BLAST_tools.Pairwise) > > Pairwise BLASTP search > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_NCBI_BLAST_tools.py", line 103, in test_blastp > > self.assertEqual(10, stdoutdata.count("Query= ")) > > AssertionError: 10 != 1 > > > > ---------------------------------------------------------------------- > > Ran 228 tests in 101.627 seconds > > > > FAILED (failures = 1) > > Does any body know about a recent change in blastp? > > Kind regards > > Andreas. > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Thu May 19 10:58:47 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 10:58:47 +0000 Subject: [Debian-med-packaging] Processing of vsearch_1.11.1-1_amd64.changes Message-ID: vsearch_1.11.1-1_amd64.changes uploaded successfully to localhost along with the files: vsearch_1.11.1-1.dsc vsearch_1.11.1.orig.tar.gz vsearch_1.11.1-1.debian.tar.xz vsearch-dbgsym_1.11.1-1_amd64.deb vsearch_1.11.1-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 11:22:38 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 11:22:38 +0000 Subject: [Debian-med-packaging] vsearch_1.11.1-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 12:50:51 +0200 Source: vsearch Binary: vsearch Architecture: source amd64 Version: 1.11.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: vsearch - tool for processing metagenomic sequences Changes: vsearch (1.11.1-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * Drop unused lintian override * Better hardening Checksums-Sha1: e73ea0d1406a3a5ea4e90856a9b2eeb99f86e9ef 2083 vsearch_1.11.1-1.dsc f51aa45658c6380b2561b6676933a437755abbfb 186057 vsearch_1.11.1.orig.tar.gz 000326f71905719eb822eae1ffc4bd14a08f7454 5540 vsearch_1.11.1-1.debian.tar.xz d8468d3e8fff0490cc49ffd225c3e7ea54f6d6dc 266046 vsearch-dbgsym_1.11.1-1_amd64.deb 3dc3dc2ed1c2a342095de663f3068c50d9ddf94e 242888 vsearch_1.11.1-1_amd64.deb Checksums-Sha256: 95a05e8d15d1b1b8d26187d1a01291ab856ba806d5722cf7ab0008ea06e03d0e 2083 vsearch_1.11.1-1.dsc 8715c4dfdff3b5d77397c96d33c3f8c12dc05e921e10e17dfe033f69ffa8bbdd 186057 vsearch_1.11.1.orig.tar.gz 6bf04fa332570e9b6730cda778c95238aa7e60b84f867d715b934b12324b8958 5540 vsearch_1.11.1-1.debian.tar.xz 40b6ada05f8c0d2ff75aca6dd418964724a924c6b2e35ca4ffe149741c6984b9 266046 vsearch-dbgsym_1.11.1-1_amd64.deb 5adef67936c0c2a588849ebef16599d415db6f93c5f34d086ad382893d781098 242888 vsearch_1.11.1-1_amd64.deb Files: 3ab33fa497a7d892ef2a7575f41ca312 2083 science optional vsearch_1.11.1-1.dsc 837969e390846fa10c5672f74a0e716a 186057 science optional vsearch_1.11.1.orig.tar.gz d1267c216ad3a1389e6cf893ad942f41 5540 science optional vsearch_1.11.1-1.debian.tar.xz 47ec36349d5904631da46c66750d1e23 266046 debug extra vsearch-dbgsym_1.11.1-1_amd64.deb c92569ab6b09320d6ede2b54c8516092 242888 science optional vsearch_1.11.1-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPZvtAAoJEFeKBJTRxkbRhQ8P/RBni0tQQO3I4QEyKlE4tkIg QwrdNFGfj793M/rK6EW0x5mTwbOOxpbEVMqnvj6+yJPuwCf3JNcqq3AcxRwuFVlQ 4chDY/9XQ6uRztfXhYVw+2QNJ0w9yqLMEDuN/l0ANzMuP1MhL1yRhGyOEjcTJkeJ e3aWG7Q46XRznSEg8LsKt7jzME+FWN87oGysXUyQDtICDBXpdCaN9oK5PKMzTRQ5 tgQvjTXB6WdMg2WCXdpcwCKOvOe1E8kwESk+isVLKcZhgvbVGg7vDYfTR/geqF+f IbzR7ZwnItMp9qfsllRjojgwE9FP591vimk6z3KB9lFg0IsVTXM/WnsM/4YLfaab kmYQxwZlueFuvXYXtmYKyKOaLG0eIZyzaVwOTfEKE2qE32A1yvhbFIfgRTVF5evg 8SVutU/jVgC32j58kvzfmQd9xPqA3O+yZ/ViCfa3nqg9m+UEWNGDzVEHa6uQqMTR rUJWG2TZS0GKETHu/a3lWkONiF8RoldFfcFJ/NlrWJCCF4uocX46Gh9BPL/lVq7D nJjxZa3zBh+KBEoXul0KaSPDwTJKxPTN0hrzxyMYYnxb8j/Xjmadk8NnTrmXFFpp q6MgNv39PbliI3F9vngY8XAD65ieCGqfHq79FI+TUS/JaODxyBFBtJd1ly8G2WXU Ug96RAb/wHHdeZwopVzr =m4M1 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 11:23:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 11:23:58 +0000 Subject: [Debian-med-packaging] Processing of sumaclust_1.0.20-1_amd64.changes Message-ID: sumaclust_1.0.20-1_amd64.changes uploaded successfully to localhost along with the files: sumaclust_1.0.20-1.dsc sumaclust_1.0.20.orig.tar.gz sumaclust_1.0.20-1.debian.tar.xz sumaclust-dbgsym_1.0.20-1_amd64.deb sumaclust_1.0.20-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 11:34:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 11:34:07 +0000 Subject: [Debian-med-packaging] Processing of stacks_1.40-1_amd64.changes Message-ID: stacks_1.40-1_amd64.changes uploaded successfully to localhost along with the files: stacks_1.40-1.dsc stacks_1.40.orig.tar.gz stacks_1.40-1.debian.tar.xz stacks-dbgsym_1.40-1_amd64.deb stacks-web_1.40-1_all.deb stacks_1.40-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 11:35:46 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 11:35:46 +0000 Subject: [Debian-med-packaging] sumaclust_1.0.20-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 13:02:05 +0200 Source: sumaclust Binary: sumaclust Architecture: source amd64 Version: 1.0.20-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: sumaclust - fast and exact clustering of genomic sequences Changes: sumaclust (1.0.20-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: cc986bb549234ffaf99b29b8dbabc5ff790d9239 1991 sumaclust_1.0.20-1.dsc 06d70475b2893d6e6f32818cf699b3511c278edf 153140 sumaclust_1.0.20.orig.tar.gz ed90704a336ced2bffbfe40c4fae5971315c0fd7 9916 sumaclust_1.0.20-1.debian.tar.xz ee35ecba1dfea98d09f90bc2e4e459a743da0562 4770 sumaclust-dbgsym_1.0.20-1_amd64.deb f0c486c3d14e6e9c0bb8e7d7151fe6a999ab5a61 113326 sumaclust_1.0.20-1_amd64.deb Checksums-Sha256: 67601a434aab12adf0d91ceb5b18a7478246b2c13c6cafa93429a574abaff318 1991 sumaclust_1.0.20-1.dsc b697495f9a2b93fe069ecdb3bc6bba75b07ec3ef9f01ed66c4dd69587a40cfc1 153140 sumaclust_1.0.20.orig.tar.gz 53a61ebf48d2717b633261488119251415f573a19fcbe06a6e6352103bd10b38 9916 sumaclust_1.0.20-1.debian.tar.xz 5c5ffd0b91b2e2a12e2878bf3adc5e71967c94e9213b4368b30bd386c390fce4 4770 sumaclust-dbgsym_1.0.20-1_amd64.deb 3886aef72131602a9609d6b832c4ef99ad36aea968e96c268ba6327771493189 113326 sumaclust_1.0.20-1_amd64.deb Files: 61e89ffce59ad9e848bf1ea910267838 1991 science optional sumaclust_1.0.20-1.dsc 31c7583fbe2e3345d5fe3e9431d9b30c 153140 science optional sumaclust_1.0.20.orig.tar.gz e6456f40e9ba67ba6802f57462bc0ad0 9916 science optional sumaclust_1.0.20-1.debian.tar.xz 8a1260a602aab365e53fcea384201969 4770 debug extra sumaclust-dbgsym_1.0.20-1_amd64.deb c50269d9648d94c39cf71d990a7606a0 113326 science optional sumaclust_1.0.20-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPaH4AAoJEFeKBJTRxkbR/t8P/i45QIiVr/f4pYLSoavzXvyb YmlSGdc1YI09V5Ci6/mbnMNEOYziAHhV8G89dju0Pd8m6DO8/oWfZlfIguujy0WL LNIIYyeaNqGHc+1p89gBIaMcKNgYmZ2ZrMuUqiWWl73KYTWfn5qiJ7cD+PLm2mMG edbq/mwNyz32d/9alTemLSJJe2Y8Xbtek3u4Bj7RXvhP9rl8OIMIMEnuyDO9geyI CF1cjpCjEFUnw2+WYFmhLc7IXJPewd4xIsvz2YUti6vlYrbs/HOJTi5AJFHK6cZG 7vgSNfKSJZQhIhLmWZ+8ORUmeJUcwaIpWOxhki1xgAzrCXm2Yx5TXnZgD31wThpw G68bUe416RHNwMZ/iOvgt3RCnd6XLB3CxiFcTB3qTrPisciCsy1na+9Ewryn8lH4 LtuIH1xeewNOWYoqXr+WjHv9fp2MmW4a4Ccgf6WUSXmsHyzE2leMBUERo+67odDR 0x/er0Q55M0fYKWd2KKoMm1+gamdoRw7a+5P80xc9TH4FUfODLbTbUy1cfiPnQjy e3jmDERz+V0bNIZKNLGALFccJVdHqazjDZD5oKfkZp/DfcBKIaYBg6awzqhZpS0k OGmELvlUWj+DiE3CF8c5BEs2yPm5Ewch6Iprbdbwz5TEu1fPFNSwX3h325QJje0n drWrU0tKhqaNiyotXl6E =EEGK -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 11:49:44 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 11:49:44 +0000 Subject: [Debian-med-packaging] stacks_1.40-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 12:55:47 +0200 Source: stacks Binary: stacks stacks-web Architecture: source amd64 all Version: 1.40-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: stacks - pipeline for building loci from short-read DNA sequences stacks-web - web interface for displaying loci from short-read sequences Changes: stacks (1.40-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * Build-Depends: samtools to ensure that package builds only on those architectures where samtools is available Checksums-Sha1: 20568b221d99f0614849f4e3dc77f97c33ba8509 2042 stacks_1.40-1.dsc b9c1a7a67f567058dc2acdaea37923bd0306a6c8 531543 stacks_1.40.orig.tar.gz 1d4329316f10217cf5f757dbcf33f14193b4f442 8064 stacks_1.40-1.debian.tar.xz e38f1b487bec630161cea110777158228b4619f9 12831070 stacks-dbgsym_1.40-1_amd64.deb 213e47a9807c3eadc9aa2450ce41e68e874e0fc7 83852 stacks-web_1.40-1_all.deb 9b0007d1f732d0860b3be01cbd446216f25bbe2b 848364 stacks_1.40-1_amd64.deb Checksums-Sha256: 73d114cc479067dd0ec5a698e0aa7ff867275129d86362664cddc5070060af7a 2042 stacks_1.40-1.dsc bf2304ba4ec44991db327ea77eb0f8c58de6d665162abf72470f5cd9dfb71493 531543 stacks_1.40.orig.tar.gz 39837ab55eae841ee5db8ab8f775eefdc110bf91cd6e97481564d2446d21df13 8064 stacks_1.40-1.debian.tar.xz d05adda9279e5424b41e403445cb6d4f902e7d929434c5d6c2d6a94103c7aae4 12831070 stacks-dbgsym_1.40-1_amd64.deb aaf2990e3957366e34a08059bcdef8d1d4e2a7c37aaa4a0def7d87a742a216f0 83852 stacks-web_1.40-1_all.deb 28da42ceb3163530b5b6f5463df2f94e834b52bbb10b64a8be0b7bcb5fc98aca 848364 stacks_1.40-1_amd64.deb Files: 222e252ae8145adcab511fa31971f948 2042 science optional stacks_1.40-1.dsc 6e37053d3a5fcbbe2b421be9624b19fa 531543 science optional stacks_1.40.orig.tar.gz 7f8e5ea4050708560e2bf6c1b548254f 8064 science optional stacks_1.40-1.debian.tar.xz 7dc5f61042d9a69c3a3e606f29b57188 12831070 debug extra stacks-dbgsym_1.40-1_amd64.deb 460fa3d8a2871b9a753268144a447a9d 83852 science optional stacks-web_1.40-1_all.deb 4b9ffbf9bcb49ebd3266698b042162d0 848364 science optional stacks_1.40-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPaRLAAoJEFeKBJTRxkbRDfwP/j6kP0lt0oR9sleaaMbbJxWc oY5T4pgoHbh4cDJ0/bScgZ2WOS33Q2tt8eYBbzGiY13CcOgR0jEXpsVQP1XwMWlf qoAypVuDP7xqg7bO0DjEKaaZAEt4rAXZi9wdiNpBxdqGNIzR/tH3E6wZcsDtLF11 7jsg+L9NNaTcepOLRMRWrn9JZ+UoF2cKUqD4B7bNfbDJY0zT4eOll0PEIicLURAd qqqN7fgBklVFrZW2+0sqmUBB2rU5DY6yMlln2817xBB2hZjcRa0AgDZr25/7tRX3 ITCj60729LNkXpQHUwBbk36n4HlmQBRe5A6yCeK085Dde40l9VtpEwsz3MIHMoxQ U+psULiDs3hIKlpcsYlVfsixZva51YLuqTQhl+tN/1CLTT9zwynIi0N0OJ9y/3rf umo8mjtVYZDX/JAaqQ3Do1pSU+57sGIP4KeOONaSjbGDq6wF69JFdjS1QdVxZdU0 KG77Zh4XRt5XXTl3dVkj4/FQ6jaJcgwCGIRYrjmON2FJt7OJEFlHqi914avmkaPn lNaRBYg77QUyHwtwQFooKjmJECo1UKG1ihk/3ozk/rg1usPVPSPK7p9HrmKgBtSC WURaNV/cgyst4VxxbIjWaA0+/og5xFIO7f9GdBKcrOtGcYPDWxvnSO+0+qOdEse3 X4HhA0fQPfmQ5KHbAmDL =+5hh -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 12:02:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 12:02:54 +0000 Subject: [Debian-med-packaging] libbpp-popgen_2.2.0-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 06:17:36 +0200 Source: libbpp-popgen Binary: libbpp-popgen-dev libbpp-popgen6 Architecture: source amd64 Version: 2.2.0-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-popgen-dev - Bio++ Population Genetics library development files libbpp-popgen6 - Bio++ Population Genetics library Changes: libbpp-popgen (2.2.0-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Revert v5 rename of library packages Checksums-Sha1: 73828e7450c7bdb5e020580aeffda1d7596fe944 2200 libbpp-popgen_2.2.0-1~bpo8+1.dsc fd2e76a30f2fc86754025d335ab788c7478f7bb7 3948 libbpp-popgen_2.2.0-1~bpo8+1.debian.tar.xz 2babbd99c581e04b9c3d2c9b725bf5ae5bdd497a 454774 libbpp-popgen-dev_2.2.0-1~bpo8+1_amd64.deb 28130d54304ee3d078d193b1e02f682596c0a4a3 291980 libbpp-popgen6_2.2.0-1~bpo8+1_amd64.deb Checksums-Sha256: 24af5b16f4e04b381e5aa4266ac73fa79f9a41cb142b33a13deee11ba8fbe769 2200 libbpp-popgen_2.2.0-1~bpo8+1.dsc e64fdceda7e56bb521580bd0a0f9d557139da176d35c2051d271e9e707ef077f 3948 libbpp-popgen_2.2.0-1~bpo8+1.debian.tar.xz eb925deffe255b6f8335641d8f54cbbd2ab25843b1bd8819e76c7a053a6c3736 454774 libbpp-popgen-dev_2.2.0-1~bpo8+1_amd64.deb f753626c62ab7b6a604d9bd1430bc56c7c3ce8554851386ab407ebbd09adf08e 291980 libbpp-popgen6_2.2.0-1~bpo8+1_amd64.deb Files: 605c61e24fe07b687c43ffe8f19e2a21 2200 science optional libbpp-popgen_2.2.0-1~bpo8+1.dsc 837bf015a37c011520b714c0ff967921 3948 science optional libbpp-popgen_2.2.0-1~bpo8+1.debian.tar.xz 6ef2a562e554397933c662c85fcf1932 454774 libdevel optional libbpp-popgen-dev_2.2.0-1~bpo8+1_amd64.deb 011dd651075e95c25f3f9134bfb8d424 291980 libs optional libbpp-popgen6_2.2.0-1~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXO+2nAAoJEFeKBJTRxkbRaRgP/ifl/442/5obxXUthHuOYBB7 gK8Q9hy940yzXbVeeFBX/QE1aFW1BPZs2BchWFRCbodXwVcGve0Fgt2p1ipYmh/U 3kl+2yQ0Q+3p+V2zb2PsFZPcXxMPedPxsdZOlk8HG1sVWmt05dwvYMFRtJ4xLdjH ypwp135aW2epoVOE7tlgPrRaV9qtI+ebeo26ffVXYTg8QBKbp/MnBD7d5hDA052k q7z4Om1S5/6e0wAUqqlZu92VwDaVVev1CbaNBLmQrdpvjAZyIl2YbgXFcUUuZNPA 9a0wQq+MMggomtYc3MZmRrFeLTm4uSyz0JJX84mBmPZZMTUgbKNJJg3nws5SnLRI K4EENCUXxzRbh26TfZ81EjdTPSAl81Xam9AYwQ4c7qd9ydEcobB0PVsBzD0t2BGr 5Rm04U5cBkRBs3e8URowI8sv+CKZ5AqXLtI2VE/NMq6mcYxlfeo5yw2lsc60gGKt o2+Om6MsHuE63bcYGMBAAs9xKCYmpy3Rgm3qqockssnRf6bTO5pGjMfrKSQqur0j bVDEhy4LZveKD2OW323XumKcgjq2SYPy0H/xwk2UnqH5+h8Zgz6tWDl6sspRukWg zwdHbbA9GXcYFOnIXYqa3zyOziSf0IXbIwhzBX4riYmHoqRJbCcBrtxhxu1EkdLe NWMzjdj6jwMLhuwTPk3W =fC3L -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 12:02:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 12:02:55 +0000 Subject: [Debian-med-packaging] libbpp-qt_2.2.0-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 06:23:31 +0200 Source: libbpp-qt Binary: libbpp-qt-dev libbpp-qt1 Architecture: source amd64 Version: 2.2.0-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-qt-dev - Bio++ Qt Graphic classes library development files libbpp-qt1 - Bio++ Qt Graphic classes library Changes: libbpp-qt (2.2.0-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Revert v5 rename of library packages Checksums-Sha1: 9451ec7430653c9ad36e37f70683dd2473cc4969 2141 libbpp-qt_2.2.0-1~bpo8+1.dsc e3d637b87192123ea2f7d134c92c2662e45f01df 3772 libbpp-qt_2.2.0-1~bpo8+1.debian.tar.xz 8714522c3d1b0d86da12cb75d4977532282ca7c5 88366 libbpp-qt-dev_2.2.0-1~bpo8+1_amd64.deb 3101217c27e7def4d2721d1f2a4f28c7fe388321 65928 libbpp-qt1_2.2.0-1~bpo8+1_amd64.deb Checksums-Sha256: 5885f920fe89f91a4b56aa3b4aaf008cfed8f0d62541bbf781b14e6b77a913ca 2141 libbpp-qt_2.2.0-1~bpo8+1.dsc 6320072322f216c291ad100332f5676779c7c79e3ef36d304ccb0999e4b27222 3772 libbpp-qt_2.2.0-1~bpo8+1.debian.tar.xz cbd8dcf54577ba3aa11c2c111487b653b4dad4ed6276b3c4c9c9fd2ef6a9b757 88366 libbpp-qt-dev_2.2.0-1~bpo8+1_amd64.deb 2a0a50f847bf6fbd36e997ef84a305c0e04aa0037af43ff481d89fb3da4043b4 65928 libbpp-qt1_2.2.0-1~bpo8+1_amd64.deb Files: 6da6ea2c696d8e1036fac06fc08faba1 2141 science optional libbpp-qt_2.2.0-1~bpo8+1.dsc 2866986fa8cde75968f2372a75060008 3772 science optional libbpp-qt_2.2.0-1~bpo8+1.debian.tar.xz d7548d12b7ac6af3aa9ab76d5c0c5499 88366 libdevel optional libbpp-qt-dev_2.2.0-1~bpo8+1_amd64.deb 5bc2ccb6a0d32d4358771a19effc7fa6 65928 libs optional libbpp-qt1_2.2.0-1~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXO/BhAAoJEFeKBJTRxkbRSqYP/RhLFP6ZIoCez1ukcgxi4/Kq 1te+6lxjlwYQK6jPSYJLqxP3lu19PBPcCHQI9AGUIZ3O8IUhwerfMhvYbCUq+QCg NGIV+CKtb2omKUKMJxX34AtO+b9l39fS5Zw5L+LMTVBrXToETHvov/ZTdb//Tlev K6neNeNqzRyGa+6NkBNfhhFI90K7rOHexIDvpHRs7BAzaAiBKaTLaSDnJedJKoWy kP/yrTqVxh2TtmrkcD7dFI5+1peXOo0BvdIpYncU1ncQNn7aoz/f0v3wSMGFdvIS GlLYpCrZza/OJJKN7XeCo76uhw3j1DtsBWfo/iAaSycNQLLqtRMTu7fVPp0b0Cv1 J0Yb4l63tGyCgJKtXEErLbmN6I3x+KC6hhkNYuBwF/IkdiXXeiKG75RI/2/pHQgd R67c8zuYUr14MvynqM7SrQoKi+8pDozj0u79ICYgs9H0yoz9O/Z9bNMohhtcz5sV dG85FMNDb5Z8m6lm3xfQntJQTzIgKsLXj3YkI1WEnuhGiiFYqEv5gZdMwtc2pjAa La4IYr2nlTqQq6qwAyPtN0GMxez+1vVCR1rP9fnqVx7pWTXm7O0gCv7RaECK1+2V gOQEY/ERoZ2AGS9Mn1ylphfeoHGQPOZXKLU6sQtQWFXnKTvzjI57ZD1xxoMcD9uE q4hb61X/OnWNTApcNmGq =+1ow -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 12:02:56 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 12:02:56 +0000 Subject: [Debian-med-packaging] libbpp-seq-omics_2.2.0-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 17 May 2016 11:50:50 +0200 Source: libbpp-seq-omics Binary: libbpp-seq-omics-dev libbpp-seq-omics1 Architecture: source amd64 Version: 2.2.0-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-seq-omics-dev - Bio++ Sequence library: genomics components (development files) libbpp-seq-omics1 - Bio++ Sequence library: genomics components Changes: libbpp-seq-omics (2.2.0-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Revert v5 rename of library packages Checksums-Sha1: 2975b80c1d01812e0414539e31b2057584c97700 2211 libbpp-seq-omics_2.2.0-1~bpo8+1.dsc 5744abb406b67df11a721b6b0b632c73f0376222 4144 libbpp-seq-omics_2.2.0-1~bpo8+1.debian.tar.xz ff6f7c6a8bd645937b8bf9886eb940554d51b54e 556130 libbpp-seq-omics-dev_2.2.0-1~bpo8+1_amd64.deb 13f0da551e3b371ffcdcbe8894388c06c0ba9f01 243496 libbpp-seq-omics1_2.2.0-1~bpo8+1_amd64.deb Checksums-Sha256: d174788bf2ad8c20488790c9c4ba30493a0285daea858430f917ed55dd11f666 2211 libbpp-seq-omics_2.2.0-1~bpo8+1.dsc fa2b6db80013c823c263d44332d938a6b9248710d5264d010d4f94ffad8cbabd 4144 libbpp-seq-omics_2.2.0-1~bpo8+1.debian.tar.xz 808b7a88ce05a950dca61e9057e63176d562342b59f252aba2a38c92dbed508e 556130 libbpp-seq-omics-dev_2.2.0-1~bpo8+1_amd64.deb b838cc6b14ccd19761f6943fb69dc49138d399404fd5f5c3efe8b793f13a66f4 243496 libbpp-seq-omics1_2.2.0-1~bpo8+1_amd64.deb Files: 164a3a9969079413a8b98042e3f17a88 2211 science optional libbpp-seq-omics_2.2.0-1~bpo8+1.dsc 60f39c3132f2aeee65b192ca8619249e 4144 science optional libbpp-seq-omics_2.2.0-1~bpo8+1.debian.tar.xz 327ec4fd5f9341c02aaf54ead08def56 556130 libdevel optional libbpp-seq-omics-dev_2.2.0-1~bpo8+1_amd64.deb 82abba93c6ac0c1db4349620e6897d9f 243496 libs optional libbpp-seq-omics1_2.2.0-1~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXO/GIAAoJEFeKBJTRxkbRY7IP/R0EJlrxeZF14MqnyMjc6F0p Lh7UfmccukES0Xhl+zrzVWN7nZO2yz3yNY9OYaOhZQwriyAjr2idU4UisdmsXnlI FMxO7COb/IjjRrOIe31myZ9sdHefrBj49p12fJ3YeFUWRbLSIiStGxdK54NDrTK9 lK1NPkPOES85s2VKVThJwRmfy8FQMV6CZ3fxrXL+ktf46LJZFRmP+9dQwQcAjg/3 K1ra99kRmHwdNNatPNwbY/lotBt24kcMVJgAG81Ayzwr0KkMno9fwwNfpORYTtdX duMsgDZI7H61B8m8Nc4pqnaeX2CtHMFw12bEBhS48Cur9O7eobQEP7HM2BsjB9UE QD/9EHak2N2vYpQPxBVUxPVO76XflQ9bas9DjoU7bnTu23ibJEzoFUFaxj0tpE/d z3hOYbtKhDuhjZM6d6PMsx963vsp7ehzcakCq0JAnjcJgjBIv6HAeuTiF7V6+JrS vaMsYm/htQknvmrn+XaCTwbAmqCh+HerYItjanR6G9KaGHGFl83vF979npqFQ7xw DvhTm07qEU02oaENJ80gyZ7xfs/BQuY1iMrV9HhHvHDEMNOzwVOjh1QYqPGAK7YH zkzVXXLubUUO+rid+4kk+3i+AowC9+sk+zFDzmRPVpbBtb18vWS70di/VjiPCVoB n9+mjLirzwzAmNHmCdR5 =1HOn -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 12:02:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 12:02:55 +0000 Subject: [Debian-med-packaging] libbpp-raa_2.2.0-2~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 18 May 2016 06:33:40 +0200 Source: libbpp-raa Binary: libbpp-raa-dev libbpp-raa1 Architecture: source amd64 Version: 2.2.0-2~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-raa-dev - Bio++ Remote Acnuc Access library development files libbpp-raa1 - Bio++ Remote Acnuc Access library Changes: libbpp-raa (2.2.0-2~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Revert v5 rename of library packages Checksums-Sha1: 1206c295b6451276478aaf0819496f212c9f64fa 2142 libbpp-raa_2.2.0-2~bpo8+1.dsc 9934d204a2df7e3267e06645be5ff77785effee0 3776 libbpp-raa_2.2.0-2~bpo8+1.debian.tar.xz db63cd2bd1321cf0ad5be276537cdc4227dd4bc3 59556 libbpp-raa-dev_2.2.0-2~bpo8+1_amd64.deb 9db7af2792c4d36e53bd760fc3857246166188d8 47714 libbpp-raa1_2.2.0-2~bpo8+1_amd64.deb Checksums-Sha256: 024610566e9c1ed828380ce34701d94151bc0f2e652b6b86a6c9ad23a9d191a6 2142 libbpp-raa_2.2.0-2~bpo8+1.dsc f6f606152f74aabf1c63370c35bccd0af136b7fa9464d90c58796455ddd6adf6 3776 libbpp-raa_2.2.0-2~bpo8+1.debian.tar.xz ad7ab5fae2875d32cdfe0a243b22df5b0531d75e3148f90f742c6f5523e996ce 59556 libbpp-raa-dev_2.2.0-2~bpo8+1_amd64.deb 3f4c5ba3d55cfebcdc5fa6916752570cfe84797d23fd4a489ec41146d440f1ba 47714 libbpp-raa1_2.2.0-2~bpo8+1_amd64.deb Files: 48804810321ea27e33bf260821355f5e 2142 science optional libbpp-raa_2.2.0-2~bpo8+1.dsc 03f263d0c5e0c4a54251e44b02c1346c 3776 science optional libbpp-raa_2.2.0-2~bpo8+1.debian.tar.xz 60bde677305764e07322ab770c01ca5d 59556 libdevel optional libbpp-raa-dev_2.2.0-2~bpo8+1_amd64.deb 0bbb3cfc8fca78d711df5a05a82052e9 47714 libs optional libbpp-raa1_2.2.0-2~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXO/FiAAoJEFeKBJTRxkbR0MgP/RzhSRdDGRZI/iGfHwrMplrP tazSfR60iW1FfcnNQ4i/pDchEt1r6kCLo6FtOEIOcb79hKYgZIyBb7OCnUvcOrfu PeTIQX36fdgMN9iUCod7Xs6Tm/3+TjygJ6K1i+v7I6tvGs9WIdNxDkCGF/z539ot UMnWS561LQxt/N84A2Jq/1YRPnNk3DwydEKbn/cUlFkUN0i7MFCb/XA0KRuk6NQy g9BgUTUSOtWA2+UPechpCw5UuG2gpavc0u3T+rP3lOxtyLorWUB4n9jx4P5nxVdg O/oENlJPTcH6FlCRqAEucxDee1IdD87WJg3lghzrJzY3ieVKBiMqxH9x4d5lcE/G exuHikt/+OuY0hdG6dkgOXBkpMNjoCunOC60T3Bim6f+liEjh3yHA+2SqEJKaTab pbCO3NdBr5MfSNL5RdVwuDe8ngOwM68IsdozqtYxUPyL9I7B/FymTWTOZqRvbg06 nkQ41TpUMIQNlt6Q5W1ejX8QB7tmAhgcsrWDbZg0gSOvTX8ziSf5FAsGIMp28xmr NyMf/dAdrx+VPCiqTRzd7tlrafa92Ff7U0bzgy6Vmqi4n2XaOAqh/TrwdbisO3Wa KuUnEzMGx0O7RxHDWptLDYW6pS6n5B5VOmp0aaTQ4MQtFqgOzpLEZO1qU/JVLrUf KHVGl3AnIW+XP0uQgFyg =2Dur -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 12:02:59 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 12:02:59 +0000 Subject: [Debian-med-packaging] r-cran-tidyr_0.4.1-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 12 May 2016 21:03:05 +0200 Source: r-cran-tidyr Binary: r-cran-tidyr Architecture: source amd64 Version: 0.4.1-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-tidyr - GNU R package to easily tidy data Changes: r-cran-tidyr (0.4.1-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From andreas at fam-tille.de Thu May 19 12:11:54 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Thu, 19 May 2016 14:11:54 +0200 Subject: [Debian-med-packaging] Bug#824048: Any change in blastp? (Was: Bug#824048: python-biopython: FTBFS: AssertionError: 10 != 1) In-Reply-To: References: <1462984527.2366877.604901465.716271DC@webmail.messagingengine.com> <20160511200849.GA28855@an3as.eu> <20160519094954.GO5019@an3as.eu> Message-ID: <20160519121154.GP5019@an3as.eu> Hi Peter On Thu, May 19, 2016 at 12:32:17PM +0100, Peter Cock wrote: > Thanks Andreas, Thanks for your very quick response. > Ah, https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824048 > > It looks like yet another minor change to the plain text human > readable output with the latest NCBI BLAST+ v2.3.0 release is to > blame, > > $ ~/ncbi_blast/2.2.31+/blastp -query Fasta/rose.pro -evalue 1 -subject > GenBank/NC_005816.faa | grep "Query= " > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > $ ~/ncbi_blast/2.3.0+/blastp -query Fasta/rose.pro -evalue 1 -subject > GenBank/NC_005816.faa | grep "Query= " > Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING > > The Biopython test was expecting 10 lines with this pattern, but there > is now only 1. This may or may not break the parser - I've not yet > checked: > > https://github.com/biopython/biopython/issues/827 This sounds like a very probable explanation for the effect. It would be great if you could come up with a patch (or a new release) so I could update the Debian package. Thanks a lot for the perfect cooperation Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Thu May 19 12:39:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 12:39:33 +0000 Subject: [Debian-med-packaging] Processing of trimmomatic_0.36+dfsg-1_amd64.changes Message-ID: trimmomatic_0.36+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: trimmomatic_0.36+dfsg-1.dsc trimmomatic_0.36+dfsg.orig.tar.xz trimmomatic_0.36+dfsg-1.debian.tar.xz trimmomatic_0.36+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 12:49:08 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 12:49:08 +0000 Subject: [Debian-med-packaging] trimmomatic_0.36+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 13:46:49 +0200 Source: trimmomatic Binary: trimmomatic Architecture: source all Version: 0.36+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: trimmomatic - flexible read trimming tool for Illumina NGS data Changes: trimmomatic (0.36+dfsg-1) unstable; urgency=medium . [ Steffen Moeller ] * Introduced EDAM ontology information to debian/upstream/edam * Added patch to find adapters in /usr/share/trimmomatic . 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From tille at debian.org Thu May 19 12:49:22 2016 From: tille at debian.org (Andreas Tille) Date: Thu, 19 May 2016 14:49:22 +0200 Subject: [Debian-med-packaging] Bug#824754: ITP: r-cran-princurve -- fit a principal curve in arbitrary dimension Message-ID: <20160519124922.25819.41434.reportbug@mail.an3as.eu> Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name : r-cran-princurve Version : 1.1-12-1 Upstream Author : Andreas Weingessel * URL : http://cran.r-project.org/web/packages/princurve/ * License : GPL Programming Lang: GNU R Description : fit a principal curve in arbitrary dimension GNU R package to fit a principal curve to a data matrix in arbitrary dimensions. Remark: This package is used in the test suite of r-bioc-aroma.light and will be maintained by the Debian Med team at svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-princurve/trunk/ From ftpmaster at ftp-master.debian.org Thu May 19 12:54:36 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 12:54:36 +0000 Subject: [Debian-med-packaging] Processing of r-cran-matrixstats_0.50.2-1_amd64.changes Message-ID: r-cran-matrixstats_0.50.2-1_amd64.changes uploaded successfully to localhost along with the files: r-cran-matrixstats_0.50.2-1.dsc r-cran-matrixstats_0.50.2.orig.tar.gz r-cran-matrixstats_0.50.2-1.debian.tar.xz r-cran-matrixstats-dbgsym_0.50.2-1_amd64.deb r-cran-matrixstats_0.50.2-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 13:04:43 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 13:04:43 +0000 Subject: [Debian-med-packaging] Processing of r-cran-princurve_1.1-12-1_amd64.changes Message-ID: r-cran-princurve_1.1-12-1_amd64.changes uploaded successfully to localhost along with the files: r-cran-princurve_1.1-12-1.dsc r-cran-princurve_1.1-12.orig.tar.gz r-cran-princurve_1.1-12-1.debian.tar.xz r-cran-princurve-dbgsym_1.1-12-1_amd64.deb r-cran-princurve_1.1-12-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From aws15904 at uga.edu Thu May 19 13:08:54 2016 From: aws15904 at uga.edu (Alexander Smith) Date: Thu, 19 May 2016 13:08:54 +0000 Subject: [Debian-med-packaging] Are you there Message-ID: I am a widow from Syrian Damascus my family and I was affected by the chemical weapon in Syrian which has led to the death of my husband and children.. I need an honest and a trust worthy person like you to help me retrieve my family treasure amounting to USD7.2 Million I will be glad if you can assist me -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Thu May 19 13:24:09 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 13:24:09 +0000 Subject: [Debian-med-packaging] r-cran-matrixstats_0.50.2-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 14:43:50 +0200 Source: r-cran-matrixstats Binary: r-cran-matrixstats Architecture: source amd64 Version: 0.50.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-matrixstats - GNU R methods that apply to rows and columns of a matrix Changes: r-cran-matrixstats (0.50.2-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: b130a4e6aa62580729f94bfc2874e4ca07077bb2 2140 r-cran-matrixstats_0.50.2-1.dsc 5527f4edb119d84190b7f1994c0cb3a767680b56 167570 r-cran-matrixstats_0.50.2.orig.tar.gz b2c13ce7aa2c098caa2b9813a2e085a308d9a02c 3620 r-cran-matrixstats_0.50.2-1.debian.tar.xz d460531cbf080e6bea9b7c8fc9f2c3de74edef78 1334402 r-cran-matrixstats-dbgsym_0.50.2-1_amd64.deb e3292c14b9810c6f4901b90852054109307502e5 677212 r-cran-matrixstats_0.50.2-1_amd64.deb Checksums-Sha256: 1abe02ed2e1dbb5b2a8c6c6a6d12a90bcbfbdf765f5fdcdc4075801e902c0ac7 2140 r-cran-matrixstats_0.50.2-1.dsc 72d1aa0e92c79c4878e0285c2c1cbac83c9c27a0e3119b4dc0d9b3d47b3f427e 167570 r-cran-matrixstats_0.50.2.orig.tar.gz c04be18d9549e7be398b13327cd5529097082cb2fbd4d2425e5f7e9b4f0c8ae5 3620 r-cran-matrixstats_0.50.2-1.debian.tar.xz 6da64425dd76e55ed37027a05bddd9b06fd445daecc7d4a2e534e1f7295034d6 1334402 r-cran-matrixstats-dbgsym_0.50.2-1_amd64.deb 90ebb7ceb0f9dec81ce2f77fe908b6a5b4d647e8bcfbd65ae3e5f03b8350e0d4 677212 r-cran-matrixstats_0.50.2-1_amd64.deb Files: 6b53ab48b914996e31eca943a8b4edf5 2140 gnu-r optional r-cran-matrixstats_0.50.2-1.dsc 6e583514dfcbe468d1be6a60ef3bbb9d 167570 gnu-r optional r-cran-matrixstats_0.50.2.orig.tar.gz 91d845ccaca64d3b13b49cdf2094d081 3620 gnu-r optional r-cran-matrixstats_0.50.2-1.debian.tar.xz f6bed47336e1d1affb9c8bb595e1aa3a 1334402 debug extra r-cran-matrixstats-dbgsym_0.50.2-1_amd64.deb 7d6b2b6078f28deca9e415741ce24692 677212 gnu-r optional r-cran-matrixstats_0.50.2-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPbczAAoJEFeKBJTRxkbRTloQAJuvKbMgaiRolpDx3e9ri4PS 8PKT+hy7BBHZrnMhe4OrEUwMyFA6/FyV9NfJAA5VXHS8eXUctw8kckO/BcfySxdJ hkyY7UCDKxpo4McZ79Jt71zaQFAKEmV6k3zjo8ybbT6rvH5Oi5ip6dKraDT0+XS5 vr1N08SExKwn7gH70U6/0ErbXOs9BYPUK7omNhuoTjzHdRE7r0uownsWdk7cFeE1 TAg20XR9QzUNJKW5ryzlJ4W6r8OQny/U7PQt7+V77gsxYysEJ75WBhObye1B56fd 8ZbFKhuuD35ypb+Vyg2BMRgzcBrNUl/3wMBwshQU5wR3OALoAz7gqwBdxy0PR4s/ WhzpBLWDre7X0K4elR9hmIRf5ohl4HnJAur7t/o+1Cf0Bzxf/egiglOPhYBG84lm FKIvk3ryA6L7kEKuAz05OEInoOG+v/u7IzveGnmaSVbN1POaK5mKIE6wi273dfot BZfIiXYUCuiGqFrQCSCvL3IL1gK2PKEbKKffQlwmiEFqImzxzlEwWii4iSqNYIAo hLYar2W3VrDrWfcvHVZZkEWu5VDFvK7H7+kSbcTBEHczEMNGbC2RrH0MYjlO4nCN ir1dtVoutuBkntZen3Je2+JN6tsOWhs645Ib79RipB6ewvVP+myAkdtgMDG1CuWe nPvpcY4K49zWtCXpiX2V =/+c3 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 13:24:16 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 13:24:16 +0000 Subject: [Debian-med-packaging] r-cran-princurve_1.1-12-1_amd64.changes is NEW Message-ID: binary:r-cran-princurve is NEW. source:r-cran-princurve is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 19 14:25:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 14:25:23 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-aroma.light_3.2.0-1_amd64.changes Message-ID: r-bioc-aroma.light_3.2.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-aroma.light_3.2.0-1.dsc r-bioc-aroma.light_3.2.0.orig.tar.gz r-bioc-aroma.light_3.2.0-1.debian.tar.xz r-bioc-aroma.light_3.2.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From p.j.a.cock at googlemail.com Thu May 19 14:31:59 2016 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 19 May 2016 15:31:59 +0100 Subject: [Debian-med-packaging] Bug#824048: Any change in blastp? (Was: Bug#824048: python-biopython: FTBFS: AssertionError: 10 != 1) In-Reply-To: <20160519121154.GP5019@an3as.eu> References: <1462984527.2366877.604901465.716271DC@webmail.messagingengine.com> <20160511200849.GA28855@an3as.eu> <20160519094954.GO5019@an3as.eu> <20160519121154.GP5019@an3as.eu> Message-ID: RE: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824048 I've committed this as "fix", https://github.com/biopython/biopython/commit/cb5b8f7cf16dfa9aada8d3c71ab8d588ebf0693f This was a sanity test which failed due to a change in the NCBI output. We don't currently try to parse the plain text output in this test (the NCBI discourage parsing the plain text output, and we'd like to drop our plain text BLAST parser anyway). If it is easier, you could just comment out or remote this for the Biopython 1.66 Debian package? Thanks for letting us know, Peter From ftpmaster at ftp-master.debian.org Thu May 19 15:21:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 15:21:07 +0000 Subject: [Debian-med-packaging] Processing of python-biopython_1.66+dfsg-3_amd64.changes Message-ID: python-biopython_1.66+dfsg-3_amd64.changes uploaded successfully to localhost along with the files: python-biopython_1.66+dfsg-3.dsc python-biopython_1.66+dfsg-3.debian.tar.xz python-biopython-dbgsym_1.66+dfsg-3_amd64.deb python-biopython-doc_1.66+dfsg-3_all.deb python-biopython-sql_1.66+dfsg-3_all.deb python-biopython_1.66+dfsg-3_amd64.deb python3-biopython-dbgsym_1.66+dfsg-3_amd64.deb python3-biopython-sql_1.66+dfsg-3_all.deb python3-biopython_1.66+dfsg-3_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at fam-tille.de Thu May 19 15:20:01 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Thu, 19 May 2016 17:20:01 +0200 Subject: [Debian-med-packaging] Bug#824048: Any change in blastp? (Was: Bug#824048: python-biopython: FTBFS: AssertionError: 10 != 1) In-Reply-To: References: <1462984527.2366877.604901465.716271DC@webmail.messagingengine.com> <20160511200849.GA28855@an3as.eu> <20160519094954.GO5019@an3as.eu> <20160519121154.GP5019@an3as.eu> Message-ID: <20160519152001.GQ5019@an3as.eu> Hi Peter, I've just uploaded a package featuring the patch. Thanks a lot for the quick and helpful response Andreas. On Thu, May 19, 2016 at 03:31:59PM +0100, Peter Cock wrote: > RE: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824048 > > I've committed this as "fix", > > https://github.com/biopython/biopython/commit/cb5b8f7cf16dfa9aada8d3c71ab8d588ebf0693f > > This was a sanity test which failed due to a change in the NCBI output. > > We don't currently try to parse the plain text output in this test > (the NCBI discourage parsing the plain text output, and we'd like > to drop our plain text BLAST parser anyway). > > If it is easier, you could just comment out or remote this for > the Biopython 1.66 Debian package? > > Thanks for letting us know, > > Peter > -- http://fam-tille.de From tille at debian.org Thu May 19 15:50:07 2016 From: tille at debian.org (Andreas Tille) Date: Thu, 19 May 2016 17:50:07 +0200 Subject: [Debian-med-packaging] Bug#824721: CharLS: 1.1.0 is out In-Reply-To: References: Message-ID: <20160519155007.GS5019@an3as.eu> Hi Mathieu, following my principle to move those packages to Git that are featuring a somehow changed download source I moved charls to Git[1]. I injected version 1.1.0 and tried to apply quilt patches. It seems the code patches not dealing with cmake build system are applied upstream. I noticed that none of the cmake patches apply to the new version. If you are interested in a soonish upload it would be great if you would adapt all those patches created by you previously to the new version. Thanks for your cooperation Andreas. [1] https://anonscm.debian.org/git/debian-med/charls.git On Thu, May 19, 2016 at 09:14:42AM +0200, Mathieu Malaterre wrote: > Package: src:charls > > CharLS 1.1.0 is out. It does include the recent fix done in Debian on 1.0.0: > > https://github.com/team-charls/charls/releases/tag/1.1.0 > > CharLS 2.0.0 has a different API (AFAIK), so it may be risky to update > to it at this time for Debian. > > ---------- Forwarded message ---------- > From: Victor Derks <> > Date: Wed, May 18, 2016 at 10:23 PM > Subject: Re: http://charls.codeplex.com/workitem/10742 > > > Hi Sjors and Mathieu, > > I found the problem why the output of the decoded image by the > original loco implementation and charls were not identical. This issue > was caused by a defect in the charls test applications that creates > the .pnm file. With the repaired test application the imaged can be > encoded and decoded identical to the original input file. The charls > library itself was ok after the initial fix. > > I have tagged the branches as 1.1.0 and 2.0.0. > > Victor > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Thu May 19 16:06:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 16:06:13 +0000 Subject: [Debian-med-packaging] Processing of scrm_1.7.2-1_amd64.changes Message-ID: scrm_1.7.2-1_amd64.changes uploaded successfully to localhost along with the files: scrm_1.7.2-1.dsc scrm_1.7.2.orig.tar.gz scrm_1.7.2-1.debian.tar.xz scrm-dbgsym_1.7.2-1_amd64.deb scrm_1.7.2-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 16:16:15 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 16:16:15 +0000 Subject: [Debian-med-packaging] Processing of rna-star_2.5.2a+dfsg-1_amd64.changes Message-ID: rna-star_2.5.2a+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: rna-star_2.5.2a+dfsg-1.dsc rna-star_2.5.2a+dfsg.orig.tar.xz rna-star_2.5.2a+dfsg-1.debian.tar.xz rna-star-dbgsym_2.5.2a+dfsg-1_amd64.deb rna-star_2.5.2a+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 16:29:20 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 16:29:20 +0000 Subject: [Debian-med-packaging] python-biopython_1.66+dfsg-3_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 16:48:15 +0200 Source: python-biopython Binary: python-biopython python3-biopython python-biopython-doc python-biopython-sql python3-biopython-sql Architecture: source amd64 all Version: 1.66+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: python-biopython - Python library for bioinformatics (implemented in Python 2) python-biopython-doc - Documentation for the Biopython library python-biopython-sql - Biopython support for the BioSQL database schema (Python 2) python3-biopython - Python library for bioinformatics (implemented in Python 3) python3-biopython-sql - Biopython support for the BioSQL database schema (Python 3) Closes: 824048 Changes: python-biopython (1.66+dfsg-3) unstable; 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From ftpmaster at ftp-master.debian.org Thu May 19 16:30:00 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 16:30:00 +0000 Subject: [Debian-med-packaging] r-bioc-aroma.light_3.2.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 16:11:47 +0200 Source: r-bioc-aroma.light Binary: r-bioc-aroma.light Architecture: source all Version: 3.2.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-aroma.light - BioConductor methods normalization and visualization of microarra Changes: r-bioc-aroma.light (3.2.0-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * Bump versioned (Build-)Depends: r-cran-matrixstats (>= 0.50.1) Checksums-Sha1: b3ae9576adfddd014e855b6d5a05b4193309f6d6 2197 r-bioc-aroma.light_3.2.0-1.dsc 10b379ea1aefb3435a4c16ef65555d84c4b1ab0b 392062 r-bioc-aroma.light_3.2.0.orig.tar.gz f074a42ca67e41112bf3b979f4ed268ea3dd7558 5016 r-bioc-aroma.light_3.2.0-1.debian.tar.xz c974ffe5644a1318f628ca78767d7fc76a815ac8 495300 r-bioc-aroma.light_3.2.0-1_all.deb Checksums-Sha256: afaa10a7de3f45a00d94dad3d42db4e93dc1d75f777a92ec554224e13e59f9cc 2197 r-bioc-aroma.light_3.2.0-1.dsc 95e4675400cf94e3786ff357d92246add76ed3dc7d843478c9b6d08760af557a 392062 r-bioc-aroma.light_3.2.0.orig.tar.gz 75afc397def08963434439425ce16e2f2e78ce23ed584ce9b446e0c478507e55 5016 r-bioc-aroma.light_3.2.0-1.debian.tar.xz 0a3a347868a0a1dd58b02a89248fb7ee3ade767dfeda8cba6064955b6ca78b84 495300 r-bioc-aroma.light_3.2.0-1_all.deb Files: 50d6c45663107f1b781279234e89282f 2197 gnu-r optional r-bioc-aroma.light_3.2.0-1.dsc 100423e650584f1332c1b474e66f753e 392062 gnu-r optional r-bioc-aroma.light_3.2.0.orig.tar.gz fc14f78ee43f59de4af31ab31505ddf3 5016 gnu-r optional r-bioc-aroma.light_3.2.0-1.debian.tar.xz 5f3963691437bccdb533d9cb11361b18 495300 gnu-r optional r-bioc-aroma.light_3.2.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPcwbAAoJEFeKBJTRxkbReTsP/idz0EYMWqH97/w9MwaMeLit m0RvH1Hix+WsFMmDfIQjkrXX1z0S0VlccbQbKBtCKL5COwWUDr0VuvaxwsAeMkKq 2+82tPaCoeRQ5thmCOkr6wwpR4wx8pzBfFX+xYL5WoyBsrxaW5FLo5ESdT/bycKl jXpbgKwvzWP++G9SRtsmZ4+GdYPsQIHlYwQf+VfN4pc0CcqOnbIfBHhtsjW669Eo Wx/KpXhHv2OZ3bnayklwapy04klzaMOJYMH3hzORQsfQtzSFmarX7/JeFfAZYq1E N8crZkRcQti2jww6DxksSIltrtekldxRHzXjNvFrhwzhoL2kxiD8Pbg8FsQahLq+ bnAk/S1zm+Rc0E1G/ToH+z9ToB99HyN46Z+fCxYlt1yJRl2EEoA+g5aZsBkgBzeJ gmS5IvkHxCDe39gXSxZ/AvFxmdn66WC+mfTLOg28rLVSiRvCUAhObRNhVMRYUC55 MO31KFmGn31Wk6g4gko9p4WjKK/j/Y8fu0ogW5ZA9BlTxBpgnaxIsumFvST7151w VAAU+Tim1R5EB1X7w9Byg/jRnG0RffMCUehvn1Tdb31RXTzsI2/kwjAwyHHf5+92 /BgHogHaczOY0JGFpS2hCr9DDUeW2qrRM4ocQlR5gAQyMltHgBFM+MUis0jGplWk IR0qbjwdLH/Jq69IhGmW =Ij0q -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 16:30:08 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 16:30:08 +0000 Subject: [Debian-med-packaging] rna-star_2.5.2a+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 18:12:59 +0200 Source: rna-star Binary: rna-star Architecture: source amd64 Version: 2.5.2a+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.5.2a+dfsg-1) unstable; urgency=medium . * New upstream version * Use xz compression option in d/watch * cme fix dpkg-control * Fix homepage * Better hardening Checksums-Sha1: 6bdb0c5a37a4f444aebf3abfda54349202c380f2 2027 rna-star_2.5.2a+dfsg-1.dsc b0157315dbb50b7694bf7dd94232d784a10bed82 320520 rna-star_2.5.2a+dfsg.orig.tar.xz 9f1cca60a100b89dd04bcb2691229da06f578e7e 6012 rna-star_2.5.2a+dfsg-1.debian.tar.xz 9e33f60936c640604451e21cb5ed248a4e5dce45 1034064 rna-star-dbgsym_2.5.2a+dfsg-1_amd64.deb f56ac34f16e42835394926aacbb25182969581b1 363822 rna-star_2.5.2a+dfsg-1_amd64.deb Checksums-Sha256: c26593bf53c14362a82c4dc07f97f0364221b96aa18abdc699ed188d736a9edc 2027 rna-star_2.5.2a+dfsg-1.dsc e2c79a4f01ee0487c930e888debe5e94dbc8bbfc84e0fcdeacd6301dbadf8087 320520 rna-star_2.5.2a+dfsg.orig.tar.xz 02313d5ffc938d083fad95460276ecdeef08a36b0b4ae638179a764686c621c4 6012 rna-star_2.5.2a+dfsg-1.debian.tar.xz 810ec9a520fd81aa437dddf1ad1276a1d5085d187bea5eb63d39332e230a0318 1034064 rna-star-dbgsym_2.5.2a+dfsg-1_amd64.deb c8dfc648d32d071d691c1726935ff672cf8437ff95a923736ec2cf2a9f2d2e87 363822 rna-star_2.5.2a+dfsg-1_amd64.deb Files: f389fa1aaae5bc66eaec1e7c76e11265 2027 science optional rna-star_2.5.2a+dfsg-1.dsc 093fa897b4ee68809986625d84209ebd 320520 science optional rna-star_2.5.2a+dfsg.orig.tar.xz ff9d1f040f0eb6a8479e03b2c1a08406 6012 science optional rna-star_2.5.2a+dfsg-1.debian.tar.xz f2cd5314a6c16e4b2d0adfe22ade652c 1034064 debug extra rna-star-dbgsym_2.5.2a+dfsg-1_amd64.deb 74565520cc3cdd57afd47b90a0efeb44 363822 science optional rna-star_2.5.2a+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPeahAAoJEFeKBJTRxkbR7esP/05yx4zINd+yCMAgNU6z177Z SJ5Qnow6tmomb/6B6S4oQJXSfgdM7Wjtq6ZqThO+yP3zg/3MaK9bO7TCunMxD9y+ BMHjWN1nFZHavOST5MFxz67XrZDSmcUD+BHgo+5g8vMmGpFY+QhZ2DAjybFyF8RY cU/zE7gV1P0L/HfGRW+8BiFI3xy/8xJcStbfokuwK11Qo97fA8vM2FpDps6ZPOhx 2zla2z3DovlQp2xHRv4VhDH0JOcVcb/2vOtHaEZPMW8MbPSOe5Z4ckB6t/T88TzE vSMvMoDaNKqiyUmTECJf0qf+ZLdA5xWS5ieLM4Rxx4xXVwFGLxUb5hGv0UscrWUA n/zrsDoS7ai6lGMW+G0HgTupHBSd3PCPTtUIeh6uxaaAp3w/8tDD23vLw/jn/dfM wglxj18xn7dfRmaGDzhmcGNaXMkpjBHYGIM3UpDaS2vBy7TtfLSg0v70YMiiVnhm S6C7vAeI4oHG0NV230JDPyuXFfeq1Ww9frprMk8TUfQlTJu3FCAqTdvtucrSj9WB LkGeQE+N3u7SrzON699VOL8PmsDIU7xbfCJp5ge5FZyPbIVJLkNGh8MEzUpftYuL YXM7xkjfE0hg/GBIGfp2NEmpmGEjD4LznMU+MoBmphYzULMkL2s8qkVo9BYZLSSf PPT5mkj9yDY70m3wvBDj =cWG8 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From p.j.a.cock at googlemail.com Thu May 19 16:27:22 2016 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 19 May 2016 17:27:22 +0100 Subject: [Debian-med-packaging] Bug#824048: Any change in blastp? (Was: Bug#824048: python-biopython: FTBFS: AssertionError: 10 != 1) In-Reply-To: <20160519152001.GQ5019@an3as.eu> References: <1462984527.2366877.604901465.716271DC@webmail.messagingengine.com> <20160511200849.GA28855@an3as.eu> <20160519094954.GO5019@an3as.eu> <20160519121154.GP5019@an3as.eu> <20160519152001.GQ5019@an3as.eu> Message-ID: Great - I'm glad that made sense, my email had more typos than usual as I was in a hurry to leave the office earlier. Thanks, Peter On Thu, May 19, 2016 at 4:20 PM, Andreas Tille wrote: > Hi Peter, > > I've just uploaded a package featuring the patch. > > Thanks a lot for the quick and helpful response > > Andreas. > > On Thu, May 19, 2016 at 03:31:59PM +0100, Peter Cock wrote: >> RE: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824048 >> >> I've committed this as "fix", >> >> https://github.com/biopython/biopython/commit/cb5b8f7cf16dfa9aada8d3c71ab8d588ebf0693f >> >> This was a sanity test which failed due to a change in the NCBI output. >> >> We don't currently try to parse the plain text output in this test >> (the NCBI discourage parsing the plain text output, and we'd like >> to drop our plain text BLAST parser anyway). >> >> If it is easier, you could just comment out or remote this for >> the Biopython 1.66 Debian package? >> >> Thanks for letting us know, >> >> Peter >> > > -- > http://fam-tille.de From ftpmaster at ftp-master.debian.org Thu May 19 16:30:59 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 16:30:59 +0000 Subject: [Debian-med-packaging] scrm_1.7.2-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 17:55:10 +0200 Source: scrm Binary: scrm Architecture: source amd64 Version: 1.7.2-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Changed-By: Andreas Tille Description: scrm - simulator of evolution of genetic sequences Changes: scrm (1.7.2-1) unstable; urgency=low . * Team upload . [ Kevin Murray ] * New upstream release (fixes bug) * Debian med is maintainer * Fix vcs git url . 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From ftpmaster at ftp-master.debian.org Thu May 19 16:31:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 16:31:17 +0000 Subject: [Debian-med-packaging] Processing of raxml_8.2.8+dfsg-1_amd64.changes Message-ID: raxml_8.2.8+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: raxml_8.2.8+dfsg-1.dsc raxml_8.2.8+dfsg.orig.tar.xz raxml_8.2.8+dfsg-1.debian.tar.xz raxml-dbgsym_8.2.8+dfsg-1_amd64.deb raxml_8.2.8+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From owner at bugs.debian.org Thu May 19 16:33:11 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Thu, 19 May 2016 16:33:11 +0000 Subject: [Debian-med-packaging] Bug#824048: marked as done (python-biopython: FTBFS: AssertionError: 10 != 1) References: <1462984527.2366877.604901465.716271DC@webmail.messagingengine.com> Message-ID: Your message dated Thu, 19 May 2016 16:29:20 +0000 with message-id and subject line Bug#824048: fixed in python-biopython 1.66+dfsg-3 has caused the Debian Bug report #824048, regarding python-biopython: FTBFS: AssertionError: 10 != 1 to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 824048: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824048 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Chris Lamb Subject: python-biopython: FTBFS: AssertionError: 10 != 1 Date: Wed, 11 May 2016 17:35:27 +0100 Size: 52281 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#824048: fixed in python-biopython 1.66+dfsg-3 Date: Thu, 19 May 2016 16:29:20 +0000 Size: 7607 URL: From noreply at release.debian.org Thu May 19 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 19 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] mira 4.9.6-1 MIGRATED to testing Message-ID: FYI: The status of the mira source package in Debian's testing distribution has changed. Previous version: 4.9.5-6 Current version: 4.9.6-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Thu May 19 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 19 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] plip 1.3.1+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the plip source package in Debian's testing distribution has changed. Previous version: 1.3.0a+dfsg-1 Current version: 1.3.1+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Thu May 19 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 19 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] odil 0.6.0-1 MIGRATED to testing Message-ID: FYI: The status of the odil source package in Debian's testing distribution has changed. Previous version: 0.5.0-3 Current version: 0.6.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Thu May 19 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 19 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] macs 2.1.1.20160309-1 MIGRATED to testing Message-ID: FYI: The status of the macs source package in Debian's testing distribution has changed. Previous version: 2.1.1.20160226-1 Current version: 2.1.1.20160309-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Thu May 19 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 19 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] prank 0.0.150803-2 MIGRATED to testing Message-ID: FYI: The status of the prank source package in Debian's testing distribution has changed. Previous version: 0.0.150803-1 Current version: 0.0.150803-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Thu May 19 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 19 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] libzeep 3.0.2-4 MIGRATED to testing Message-ID: FYI: The status of the libzeep source package in Debian's testing distribution has changed. Previous version: 3.0.2-3 Current version: 3.0.2-4 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Thu May 19 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Thu, 19 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] gmap 2016-05-01-1 MIGRATED to testing Message-ID: FYI: The status of the gmap source package in Debian's testing distribution has changed. Previous version: 2015-12-31.v9-1 Current version: 2016-05-01-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Thu May 19 17:11:30 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 17:11:30 +0000 Subject: [Debian-med-packaging] Processing of libbpp-phyl-omics_2.2.0-2~bpo8+1_amd64.changes Message-ID: libbpp-phyl-omics_2.2.0-2~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: libbpp-phyl-omics_2.2.0-2~bpo8+1.dsc libbpp-phyl-omics_2.2.0-2~bpo8+1.debian.tar.xz libbpp-phyl-omics-dev_2.2.0-2~bpo8+1_amd64.deb libbpp-phyl-omics1_2.2.0-2~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 17:16:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 17:16:33 +0000 Subject: [Debian-med-packaging] Processing of r-cran-stringr_1.0.0-1~bpo8+1_amd64.changes Message-ID: r-cran-stringr_1.0.0-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: r-cran-stringr_1.0.0-1~bpo8+1.dsc r-cran-stringr_1.0.0-1~bpo8+1.debian.tar.xz r-cran-stringr_1.0.0-1~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 17:20:36 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 17:20:36 +0000 Subject: [Debian-med-packaging] libbpp-phyl-omics_2.2.0-2~bpo8+1_amd64.changes is NEW Message-ID: binary:libbpp-phyl-omics-dev is NEW. binary:libbpp-phyl-omics1 is NEW. source:libbpp-phyl-omics is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 19 17:21:39 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 17:21:39 +0000 Subject: [Debian-med-packaging] r-cran-stringr_1.0.0-1~bpo8+1_amd64.changes is NEW Message-ID: binary:r-cran-stringr is NEW. source:r-cran-stringr is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 19 17:21:49 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 17:21:49 +0000 Subject: [Debian-med-packaging] raxml_8.2.8+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 18:09:31 +0200 Source: raxml Binary: raxml Architecture: source amd64 Version: 8.2.8+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: raxml - Randomized Axelerated Maximum Likelihood of phylogenetic trees Changes: raxml (8.2.8+dfsg-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: bab54f31ac47ee86c6f1c33e8e1d1a4f6b49e4a2 1989 raxml_8.2.8+dfsg-1.dsc 82148a15faee1aea36dc7608842f3190f7754f4b 940664 raxml_8.2.8+dfsg.orig.tar.xz 79071197c6024f0568ad153b3a8073089e6cd2bc 4412 raxml_8.2.8+dfsg-1.debian.tar.xz c5dfbb60b8b7173a8fd477e98806994dcea37ba1 22532 raxml-dbgsym_8.2.8+dfsg-1_amd64.deb 3e058a40a735429f08e7c09547d988c7302e9c56 1278974 raxml_8.2.8+dfsg-1_amd64.deb Checksums-Sha256: 686c419e5dc47ab40817479901fb7b6ec26ed171066be4dd6addb31939d52d2a 1989 raxml_8.2.8+dfsg-1.dsc 532ac1a4457f98d65874b7dcc0eede3aa8edaa1e7f7ede7c4a3c08759ca23803 940664 raxml_8.2.8+dfsg.orig.tar.xz 23c8902847ccd5e9a9662b6846dac4eaf5689e32a1633c346265fee455badc5a 4412 raxml_8.2.8+dfsg-1.debian.tar.xz 4ec99325a92ce5b8e4d4a9ac3e016f1cc996cca74e68800765557ff3b0f8003e 22532 raxml-dbgsym_8.2.8+dfsg-1_amd64.deb f885b2f21f91866f4a890a18ecbfb5e9749c7a811e316b7ecf523d5bffcf6e4d 1278974 raxml_8.2.8+dfsg-1_amd64.deb Files: 609e775f1b4ff70dbd4a1e4efb2ef33d 1989 science optional raxml_8.2.8+dfsg-1.dsc aef65bf18474594eeb465384fb77252b 940664 science optional raxml_8.2.8+dfsg.orig.tar.xz d072f5ce759c8d3767bf87df8206a07f 4412 science optional raxml_8.2.8+dfsg-1.debian.tar.xz 1ca42511bd9e3e2e9af373602b2d9783 22532 debug extra raxml-dbgsym_8.2.8+dfsg-1_amd64.deb 6ac0ddd8643717e26114c25c1100a57c 1278974 science optional raxml_8.2.8+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPem2AAoJEFeKBJTRxkbRe28P/1Fs+e7PkaytE+LT1INPj4n8 nd0hpAuBD4pZDY8OEEdZrzYi9wL2SkJ6Q2VXLbHtGunKET4IxkF3ygQQogX3vilE OhJq32WSv2OYnVw8DhgxpRXRz7JJg10zYC9527VbcUwNoYOUyZs/mmuPYwr8xbo2 Mffm7sbOuLtoiNXzabwD1vebWnV/qc8KflfUodp2XFHsrzmpoQ57PTY16JF8VgBU CCjjVxxeRBMBBwdf3BjDIn4N3K1pRgT1dttiRhZ7Hp1F1GSbhf+xAXJZsQmJDK1O 9lw/tT53trsSiL0jT8Ss4gvZnyNBOeqBxr80igvUrLw2W8dP+5zP381GidLg6Kbv DK9nmHBY9VwgFLlY0FL+Z6gpXLCwk9S+tq0LzW0Ss44ymrKJF87O7CdvGMQZKMie KxCJy8sIkaLc1jlMBnBuAwruGbQhiUapXCiymtlzmr0Rs0bqVT8vr+CrGhat3LS4 Vg5V4YJANkiUWzfQF8kl2CankrU6V1/94/DejMXOUHdO+wAWOHf2AeKcd5PMqWvb 5HEoVFJV0Ig4m+eXSwkcoGLXU3Sf82HY1Cq/LVD1QuByFUNclwrcoEBLfQJduJlI FEFj3ccQCzU4+R4xPUJNvuswB/Omtx+/jXxUZ4axLMbiMBlNA7fu8DspxNsENf0j Np4CdDMpGMlNVOafY70D =Jbhp -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 21:34:53 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 21:34:53 +0000 Subject: [Debian-med-packaging] Processing of r-cran-vegan_2.3-5-1_amd64.changes Message-ID: r-cran-vegan_2.3-5-1_amd64.changes uploaded successfully to localhost along with the files: r-cran-vegan_2.3-5-1.dsc r-cran-vegan_2.3-5.orig.tar.gz r-cran-vegan_2.3-5-1.debian.tar.xz r-cran-vegan-dbgsym_2.3-5-1_amd64.deb r-cran-vegan_2.3-5-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 21:44:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 21:44:55 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-limma_3.28.4+dfsg-1_amd64.changes Message-ID: r-bioc-limma_3.28.4+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-limma_3.28.4+dfsg-1.dsc r-bioc-limma_3.28.4+dfsg.orig.tar.xz r-bioc-limma_3.28.4+dfsg-1.debian.tar.xz r-bioc-limma-dbgsym_3.28.4+dfsg-1_amd64.deb r-bioc-limma_3.28.4+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 22:04:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 22:04:58 +0000 Subject: [Debian-med-packaging] Processing of pcalendar_3.4.1-1_amd64.changes Message-ID: pcalendar_3.4.1-1_amd64.changes uploaded successfully to localhost along with the files: pcalendar_3.4.1-1.dsc pcalendar_3.4.1.orig.tar.xz pcalendar_3.4.1-1.debian.tar.bz2 pcalendar_3.4.1-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From tille at debian.org Thu May 19 22:09:39 2016 From: tille at debian.org (Andreas Tille) Date: Fri, 20 May 2016 00:09:39 +0200 Subject: [Debian-med-packaging] Bug#824805: ITP: r-bioc-go.db -- annotation maps describing the entire Gene Ontology Message-ID: <20160519220939.10809.25315.reportbug@mail.an3as.eu> Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name : r-bioc-go.db Version : 3.3.0 Upstream Author : Marc Carlson * URL : http://bioconductor.org/packages/release/data/annotation/html/GO.db.html * License : Artistic-2.0 Programming Lang: GNU R Description : annotation maps describing the entire Gene Ontology This package is part of BioConductor and provides a set of annotation maps describing the entire Gene Ontology assembled using data from GO. Remark: This package is needed for some unit tests of BioConductor packages. It will be maintained by the Debian Med team at svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-go.db/trunk/ From ftpmaster at ftp-master.debian.org Thu May 19 22:30:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 22:30:01 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-ebseq_1.12.0-1_amd64.changes Message-ID: r-bioc-ebseq_1.12.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-ebseq_1.12.0-1.dsc r-bioc-ebseq_1.12.0.orig.tar.gz r-bioc-ebseq_1.12.0-1.debian.tar.xz r-bioc-ebseq_1.12.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 22:54:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 22:54:33 +0000 Subject: [Debian-med-packaging] pcalendar_3.4.1-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 19 May 2016 23:31:10 +0200 Source: pcalendar Binary: pcalendar Architecture: source all Version: 3.4.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Miriam Ruiz Description: pcalendar - track menstrual cycles and predict fertility periods Changes: pcalendar (3.4.1-1) unstable; urgency=medium . * New upstream version * Upgraded Standards-Version from 3.9.5 to 3.9.8 * Removed the menu file from the package * debian/pcalendar.desktop: Added %f to 'Exec' Checksums-Sha1: 7e4415f3e7718a3c9fa5bc54307a9d5e3fba6bd8 2057 pcalendar_3.4.1-1.dsc c54e61326dece6fadbbbb4d2f652e408f9a2d4ce 379776 pcalendar_3.4.1.orig.tar.xz 71ecac6a7c2723d265503409f6c00aa6b40977a0 15946 pcalendar_3.4.1-1.debian.tar.bz2 1bfa39fad62409e40a9fec887c84768c428611b6 540266 pcalendar_3.4.1-1_all.deb Checksums-Sha256: 67981ad953f5de95c8c77411ba2d364ab00a4a28b004ebea7d0952e058a95857 2057 pcalendar_3.4.1-1.dsc 0719fea66d624e0c762092345cdf1f4190a0eeef655939f5b8ad1bd3e1bf6d77 379776 pcalendar_3.4.1.orig.tar.xz bb53b15ff78aa2f75776c2125bb83a8fe8b075561c510f009f8e132fb85b550d 15946 pcalendar_3.4.1-1.debian.tar.bz2 d24f9949ee0227f3daef52a1fa8cae7268527bb6c4611b4c79939d12f29057a8 540266 pcalendar_3.4.1-1_all.deb Files: 7be6e32b43ce0db2450054c6b03e9bcf 2057 utils optional pcalendar_3.4.1-1.dsc e771c4522aaeab4c2b1dc5e6c1916667 379776 utils optional pcalendar_3.4.1.orig.tar.xz bdf7890b1a2bdf7118c4b4d0e6aa961a 15946 utils optional pcalendar_3.4.1-1.debian.tar.bz2 e122bce480b2b4691a7d45d851c2bf38 540266 utils optional pcalendar_3.4.1-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXPjcrAAoJEF+Oa+CSj/r6BEcP/RW9hSGwr/2Aj5V4FFQgueE0 1GPNRiHiOaWn9Y04VSA/agIpxRCZJ9+cxUOMkdWUGG5mAKmRr/800HJJJiYwOTdo p4VZqmdgWSLz7M8Md7bSDPpFuIQIPVls8CVhB8Yzt34lr95Q8eXXFKG7o8QiOXPz XAM1ZCO4z6dJtcDMBECQZSRPF96ngzQSIOhmCd8/ULR2NOR4Tppb4rYtaU/K6Uq5 r6xn78MA0EFTb0Oyxu0Ogfx9T63fut4Q032/GddV9Pj7dxDA+9T5+YTVvBYGknwS mFo679cQHZO+bIpfjbF0FWreQDHOK4yXy08LMHsXpKotexc+/mbzryDssRKSKXZC ttt0rLY77eI3TYlsa1NAdeB7X1RxIwFGvuH1rkxjoSDKzCKERXgUUWA/2blzlZhl uQ808+eGi5eMOf0bMdkgyWY5r+RzvRXDmnLrfU8WFuMBcCQPWwVZozSNX8u+dbj8 7Q3IlbZXS/Wpxm4jtSShpXuzHAr6h1efgc7ES7PlcA/xotOeCVwZG8GNVCrHbIOn i8yJjILvWYSCGl5S1d9sKh+HUrUimeMyOACslKWmlR4sHe/8t7WJr24dpPlui77D 8i+qiXqi0/fW/614ucz1wGEQPEXSn38Xgp7rUhOwgYp6xoXlBcTzwUNt01gKhEFi HraMJ8Fa0ZezFi8f0HLY =8MSJ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 23:00:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 23:00:06 +0000 Subject: [Debian-med-packaging] Processing of t-coffee_11.00.8cbe486-3_source.changes Message-ID: t-coffee_11.00.8cbe486-3_source.changes uploaded successfully to localhost along with the files: t-coffee_11.00.8cbe486-3.dsc t-coffee_11.00.8cbe486-3.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 23:00:09 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 23:00:09 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-go.db_3.3.0-1_amd64.changes Message-ID: r-bioc-go.db_3.3.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-go.db_3.3.0-1.dsc r-bioc-go.db_3.3.0.orig.tar.gz r-bioc-go.db_3.3.0-1.debian.tar.xz r-bioc-go.db_3.3.0-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 23:00:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 23:00:11 +0000 Subject: [Debian-med-packaging] r-bioc-limma_3.28.4+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 23:38:13 +0200 Source: r-bioc-limma Binary: r-bioc-limma Architecture: source amd64 Version: 3.28.4+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-limma - linear models for microarray data Changes: r-bioc-limma (3.28.4+dfsg-1) unstable; urgency=medium . * New upstream version * Use xz compression per d/watch file * cme fix dpkg-control Checksums-Sha1: c1dcce5eef33afe15efc8ddad91026f2ec0d5f70 2034 r-bioc-limma_3.28.4+dfsg-1.dsc fb8d1862e0ca8b2890ade58b12a19e73f7f821dc 290808 r-bioc-limma_3.28.4+dfsg.orig.tar.xz c526683a3d9a52236bf3c39bc7a64be97dfdf137 6040 r-bioc-limma_3.28.4+dfsg-1.debian.tar.xz 8f616c2513a28c38f11bf7d10c1f3dffbe2a4103 13458 r-bioc-limma-dbgsym_3.28.4+dfsg-1_amd64.deb 20592214e1dd10801d450d36be4fca35f04cc403 1020182 r-bioc-limma_3.28.4+dfsg-1_amd64.deb Checksums-Sha256: df857f8b9cf67bb58e3e3fcea9ca9416bdf6d48dcea1a76529c48bc12ea382bd 2034 r-bioc-limma_3.28.4+dfsg-1.dsc 551ff8d5ae90b54bf67577575c05b4185272eeeed0305ddd5433fc1b466fe6e0 290808 r-bioc-limma_3.28.4+dfsg.orig.tar.xz 225c3b9e282e5ac39a5e331f75662600026b0aaf6c07b11018d4fa94502053a2 6040 r-bioc-limma_3.28.4+dfsg-1.debian.tar.xz d491f8e66827c3104e1f5212487660b7dd4567214ef6cf42d74f6e6e575899e3 13458 r-bioc-limma-dbgsym_3.28.4+dfsg-1_amd64.deb f72d321fde5c45ae478b2a6c9eb77d1d37b186a43f72fdb78e25d24a15bb5238 1020182 r-bioc-limma_3.28.4+dfsg-1_amd64.deb Files: cd00a582d108f0650e387529c3b5dc6f 2034 gnu-r optional r-bioc-limma_3.28.4+dfsg-1.dsc 33edd869fedd55e0727f15d5645acbac 290808 gnu-r optional r-bioc-limma_3.28.4+dfsg.orig.tar.xz 8a6fc42efb24b7acb4c8be5c2d987408 6040 gnu-r optional r-bioc-limma_3.28.4+dfsg-1.debian.tar.xz 84623e71ab26eec586455d3d4b4c0443 13458 debug extra r-bioc-limma-dbgsym_3.28.4+dfsg-1_amd64.deb 3c6cc0565aeab81730345cd7ce71d766 1020182 gnu-r optional r-bioc-limma_3.28.4+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPjLEAAoJEFeKBJTRxkbRuO0P/iFhTVeMjAXJtiPlKPO0Mozk 0dTCHo7fhpCIxU6eWo7kJIhHgsjMUMbkpR40FDSlyf1gO4AIQ9maOV7KDHmKo9Y5 C2at9lb6iXu/U1Q+1w4jE6jOOtmegm3QTl0CSaA+7RTZ2OGvP4osHY04LZs/VI8k yTPjL5gZy3CEY+pFA0FNPS1kn++RxCzH9eKa8Z/UImvV7e85ShFkrLhxYR56JGd8 NpSG6F4gX2mOav2PuGYWV1SJWO1qvSerl2EgjAKpw7a7wEifrSdTdjf2Cou+2kVt Fl8+o/xHH1cL+I5Q/tAEmyCfevCktRvYNPotF9HyT8KTJW3u6OOiP7ebR18VXY0D ZmXpUZD1Wgpa18o5g50JLSGJ+XkTBqfOA7fB+QBrP/4rgJfP14RyswELctZ5u7Qx RTaePjqqRIUjTd3cayGVys9/0a8XEzf3C11WN1GYxFnCgx3ndlE72jucRf2+SiPN jYkPucTHm3XgiIgojZ/TKsMrLNdl/w3zdceC2n1++NI6wP1P9bWRZT/Z3DeYsXE3 rGzRZ5pVv/jUVImT92lbD0sFqCkHztFSDyYjsAK4ChQWk+SQYT1J7PeO/ygyfwU5 F8tJXTqu+p7uwqeseqJATlvMivi8cBKJc2bOn9GSW6p9dOXqUat7dve4hulkI1Dy v1eU7ge5cBlc+VMA1Pa6 =7mX0 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 23:00:43 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 23:00:43 +0000 Subject: [Debian-med-packaging] r-cran-vegan_2.3-5-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 23:21:26 +0200 Source: r-cran-vegan Binary: r-cran-vegan Architecture: source amd64 Version: 2.3-5-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-vegan - Community Ecology Package for R Changes: r-cran-vegan (2.3-5-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control * Remove copyright information of removed file Checksums-Sha1: 1d6590523d29856c48f30e655c012fffa055912e 2083 r-cran-vegan_2.3-5-1.dsc 517340bbfe4bf48c5ff7b6bc74dbef30e8434752 1867599 r-cran-vegan_2.3-5.orig.tar.gz d6c63052f29c44ffa88d27a956fa60707bb6d153 3904 r-cran-vegan_2.3-5-1.debian.tar.xz a6aeb45bf77bab2fb00b8798ecdc53742b40e284 42730 r-cran-vegan-dbgsym_2.3-5-1_amd64.deb a537a11005beba7bd33dce6a6e54b62870b36482 2554216 r-cran-vegan_2.3-5-1_amd64.deb Checksums-Sha256: 3feb2a92d544b166fc4abc2ade9714d90687720a71b51441e8a9dfb4669e1e43 2083 r-cran-vegan_2.3-5-1.dsc 9cb6415071aa6ae4cb07b29f2d6e0af71f1fc1de5bad6cd565056b09c2c67b01 1867599 r-cran-vegan_2.3-5.orig.tar.gz c628cdf823412d7648e483440603776f6ed2996c895be40fa8a540f040395046 3904 r-cran-vegan_2.3-5-1.debian.tar.xz 2e931e52efc3d68b832b03325520bfacfa023cdbb6370b47c65f376803177a6b 42730 r-cran-vegan-dbgsym_2.3-5-1_amd64.deb e336394d75ccaaf15f1127d0bbb476e7acfb4b04eccd266cdcd5c86bb562fd7d 2554216 r-cran-vegan_2.3-5-1_amd64.deb Files: b04f3c123dca834b5ad4e286b19f2c8d 2083 gnu-r optional r-cran-vegan_2.3-5-1.dsc f101d5e9f886417e8c9484dd17a96f9e 1867599 gnu-r optional r-cran-vegan_2.3-5.orig.tar.gz 102df2865695956d0e24258916ea3f1b 3904 gnu-r optional r-cran-vegan_2.3-5-1.debian.tar.xz 5616f65d5e30deab8391bad8e010adbd 42730 debug extra r-cran-vegan-dbgsym_2.3-5-1_amd64.deb 7ba5fd81c277884272300bc74b712d72 2554216 gnu-r optional r-cran-vegan_2.3-5-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPjDEAAoJEFeKBJTRxkbRy2IP/RTpebBh5El0ZD8wOQe4umcs Xl2VQaE6EEe5BCDGNMUHjQa8s8cJYKs5SLf1E4ATE4oXn299LsxSs1SLraomDTUQ YYNPNg422SRFWg985lJtp1UGi9XaC5TAWCaghJqZKPvtcDC2/aB5mA8UPffSo8AP aWFa8FhL0EMiG92DW8RQ1EOkgpmR+NKJQhqlRyIKf/atOQPnktXa3McC6AEX3SNg HbJXz6kWxQok9loHNssZhvh2jv7T40OEcvRzWWWBGL4LcVkUWeC59S5MjHtZBFIG w16BjZ+y+ob0heGlQsq50Rh1VC2Yq3qyNL34Euj+6wckZeQRWFwSBwNnZ6PBJvue NCpL21SpEC8X83p6fqHy5pGSHsZjAkcb8jSj0xUuceHyu4c3Lj1PS6j4Olrx1CoJ VH+0hRuMcvvuABWCmjyczBg2DWJA+UYeNkqDYjzD/lHc1YW3g3K/HknzyPVcYOkw vzze9zxks+MW9FlQ0WSdVXovP/aLBJ4soGuBFkygkH2QrN+2W0hBY9/TzNeZM0C3 NxfNLhi8MADMcN+8ABv7oIXWV1/ce1dfycmZKtzuhWTllL/xLr8ki/7tTq9nrE9x xte+7Le6KlaZi3MUKHhCRXT4Fq9v/jGvSuafwv/2XoLL09D4T660aSdhjuf9+AqV GQZDwuXu7xe5N/W/pkQz =h8tg -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 23:10:14 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 23:10:14 +0000 Subject: [Debian-med-packaging] Processing of wise_2.4.1-18_source.changes Message-ID: wise_2.4.1-18_source.changes uploaded successfully to localhost along with the files: wise_2.4.1-18.dsc wise_2.4.1-18.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 19 23:41:44 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 23:41:44 +0000 Subject: [Debian-med-packaging] r-bioc-ebseq_1.12.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 00:11:23 +0200 Source: r-bioc-ebseq Binary: r-bioc-ebseq Architecture: source all Version: 1.12.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-ebseq - R package for RNA-Seq Differential Expression Analysis Changes: r-bioc-ebseq (1.12.0-1) unstable; urgency=medium . * New upstream version * Add Vcs fields * cme fix dpkg-control Checksums-Sha1: 09287514b502ad700664e3f75dc9f32b1ea49690 2106 r-bioc-ebseq_1.12.0-1.dsc a00853d91ba26fa8db826a85c52e74adaf084f24 1062036 r-bioc-ebseq_1.12.0.orig.tar.gz a34482e9a8b74eac184b1fc930b2aacd7b014e22 4132 r-bioc-ebseq_1.12.0-1.debian.tar.xz 3424e7fac29fec5a08fb0c4a1bac9ed82737dbd6 1104520 r-bioc-ebseq_1.12.0-1_all.deb Checksums-Sha256: 0d28de66ad14e4497f7ad29764d9c9ec4ae0ce6ce44b8abcbe3852697d62758e 2106 r-bioc-ebseq_1.12.0-1.dsc d723702601bb9ce8b772b730840813ec1ea2c0328fdf1b9445b4a2d397ca197b 1062036 r-bioc-ebseq_1.12.0.orig.tar.gz 503848d5e215192db5cc4553ed054ffbb3061fa335532fd6c370539ef877419d 4132 r-bioc-ebseq_1.12.0-1.debian.tar.xz 4e4a5f389aad79bb77f11609ddfd0a68cea26ca29008359281b5314cd79520a7 1104520 r-bioc-ebseq_1.12.0-1_all.deb Files: 079f347c9c04cb0c02d392a7ead66138 2106 gnu-r optional r-bioc-ebseq_1.12.0-1.dsc 8d3aa1ef92ab87f20da41627110ffec1 1062036 gnu-r optional r-bioc-ebseq_1.12.0.orig.tar.gz 7ef9ad05203fe9347fb706af4dac092f 4132 gnu-r optional r-bioc-ebseq_1.12.0-1.debian.tar.xz efc2d8a294380479baaa8b156fce0ec6 1104520 gnu-r optional r-bioc-ebseq_1.12.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPjp5AAoJEFeKBJTRxkbRhpEP/RNMKOj7I1vfcrdJ9rqg5FI5 +BkU277X6ShD+d/fzqYMBFzV4KnR93iVUZHckcjkqtyLVVzKlchG4dvgqlHq8O64 ODLM15LssmOdpMhqEjqRMafQPRIYuPIRH/YgAWqN5Zew2fi1I+UPB7sGvxLp5rcS LflgJ2Ra2AD13FthDzDMirECJvSSJASNeqedsMO1Phap6rmY6Mf2NLVpQf186XsL 3G7UdGm1eYGwd8poHcqG/o18j5L4iyJ6T8Y+qtIaUBiH/Z+dMwFW+vJlAVaXcxtR TGw9TchK5g7oyINb5t7XhOFPiml6O4TgP33fxsjMfYRvIxwvhKjtxmwRbWLvXeTm Jmi0OBlB/S5XnIMbSjAvAXfkvKz44t+8vZUtMkNiprDDvwbc87h+/GaRqvKuST5a PwB4UjS4YBctOOEY2wTZrau4h9tLi/sk/udVtIIlD7SnowTZvo2HI9qS29H5IwS8 hnvFngB6T8iXwtJGCZHb1hEhrNVU0kIH506YSTk5ZrBazM7EW2xUow5U8TwZRU7b Yt6ysexM/JLYLyt2vUAPIuygH84u464yuA9FS2SFgDYVRmf6wx3r/WK/5xWsco9g N21YPbCqs2IzHi1oQ/lu6KEGD+sc3ZxwEeUeDDYbz1rE+JEWF+ulzzM7AW5nvPXe ZmPtdY6HR4Vu7ziYvVDz =1P4b -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Thu May 19 23:41:56 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 23:41:56 +0000 Subject: [Debian-med-packaging] r-bioc-go.db_3.3.0-1_amd64.changes is NEW Message-ID: binary:r-bioc-go.db is NEW. source:r-bioc-go.db is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Thu May 19 23:42:51 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 23:42:51 +0000 Subject: [Debian-med-packaging] t-coffee_11.00.8cbe486-3_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 20:52:28 +0000 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: source Version: 11.00.8cbe486-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Changes: t-coffee (11.00.8cbe486-3) unstable; urgency=medium . * Team upload. * Force stable linking order to make build reproducible. * Bump Standards-Version. * Enable full hardening. * Use secure Vcs-Browser. 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From ftpmaster at ftp-master.debian.org Thu May 19 23:43:24 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 19 May 2016 23:43:24 +0000 Subject: [Debian-med-packaging] wise_2.4.1-18_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 21:53:30 +0000 Source: wise Binary: wise wise-doc wise-data Architecture: source Version: 2.4.1-18 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: wise - comparison of biopolymers, like DNA and protein sequences wise-data - data files for the wise package wise-doc - documentation for the wise package Changes: wise (2.4.1-18) unstable; urgency=medium . * Team upload. * Make build reproducible. - Fix dates in manual .tex files. - Use stable order for API inputs. * Bump Standards-Version. * Enable full hardening. * Use secure Vcs-Browser. 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From malat at debian.org Fri May 20 06:01:35 2016 From: malat at debian.org (Mathieu Malaterre) Date: Fri, 20 May 2016 08:01:35 +0200 Subject: [Debian-med-packaging] Bug#824818: CharLS: One JPEG-LS not handled Message-ID: Package: src:charls Version: 1.0-7 I recently discover that at least one instance of a JPEG-LS codestream is not handled by CharLS: http://gdcm.sourceforge.net/thingies/JPEG_LS_InvalidEscapeSequence_COM_padding.dcm I've tried to simplify it: - Remove COM marker, - Change the recommended DICOM padding with a simplier mechanism (a traliing 0) but CharLS still reject that file again: http://gdcm.sourceforge.net/thingies/JPEG_LS_InvalidEscapeSequence.dcm I've not tested yet with 1.1.0 or 2.0.0 yet. From malat at debian.org Fri May 20 06:11:56 2016 From: malat at debian.org (Mathieu Malaterre) Date: Fri, 20 May 2016 08:11:56 +0200 Subject: [Debian-med-packaging] Bug#824721: CharLS: 1.1.0 is out In-Reply-To: <20160519155007.GS5019@an3as.eu> References: <20160519155007.GS5019@an3as.eu> Message-ID: Hi, On Thu, May 19, 2016 at 5:50 PM, Andreas Tille wrote: [...] > noticed that none of the cmake patches apply to the new version. If you > are interested in a soonish upload it would be great if you would adapt > all those patches created by you previously to the new version. Ok. This will depend on what I found out from #824818. -M From malat at debian.org Fri May 20 06:14:05 2016 From: malat at debian.org (Mathieu Malaterre) Date: Fri, 20 May 2016 08:14:05 +0200 Subject: [Debian-med-packaging] Bug#824819: debian/watch Message-ID: Package: src:charls Version: 1.0-7 This is not tested, but since upstream decided to move away from codeplex to github, this means we can have a working debian/watch file ! -M From ftpmaster at ftp-master.debian.org Fri May 20 07:49:45 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 07:49:45 +0000 Subject: [Debian-med-packaging] Processing of transdecoder_3.0.0+dfsg-1_source.changes Message-ID: transdecoder_3.0.0+dfsg-1_source.changes uploaded successfully to localhost along with the files: transdecoder_3.0.0+dfsg-1.dsc transdecoder_3.0.0+dfsg.orig.tar.gz transdecoder_3.0.0+dfsg-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 20 08:00:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 08:00:13 +0000 Subject: [Debian-med-packaging] Processing of dicom3tools_1.00~20160516104835-1_source.changes Message-ID: dicom3tools_1.00~20160516104835-1_source.changes uploaded successfully to localhost along with the files: dicom3tools_1.00~20160516104835-1.dsc dicom3tools_1.00~20160516104835.orig.tar.bz2 dicom3tools_1.00~20160516104835-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From tille at debian.org Fri May 20 08:11:12 2016 From: tille at debian.org (Andreas Tille) Date: Fri, 20 May 2016 10:11:12 +0200 Subject: [Debian-med-packaging] Bug#824819: debian/watch In-Reply-To: References: Message-ID: <20160520081112.GX5019@an3as.eu> On Fri, May 20, 2016 at 08:14:05AM +0200, Mathieu Malaterre wrote: > Package: src:charls > Version: 1.0-7 > > This is not tested, but since upstream decided to move away from > codeplex to github, this means we can have a working debian/watch file This was done in Git yesterday. Please make sure you clone the Git repository. Kind regards Andreas. -- http://fam-tille.de From tille at debian.org Fri May 20 08:11:12 2016 From: tille at debian.org (Andreas Tille) Date: Fri, 20 May 2016 10:11:12 +0200 Subject: [Debian-med-packaging] Bug#824819: debian/watch In-Reply-To: References: Message-ID: <20160520081112.GX5019@an3as.eu> On Fri, May 20, 2016 at 08:14:05AM +0200, Mathieu Malaterre wrote: > Package: src:charls > Version: 1.0-7 > > This is not tested, but since upstream decided to move away from > codeplex to github, this means we can have a working debian/watch file This was done in Git yesterday. Please make sure you clone the Git repository. Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Fri May 20 08:56:00 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 08:56:00 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-hilbertvis_1.30.0-1_amd64.changes Message-ID: r-bioc-hilbertvis_1.30.0-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-hilbertvis_1.30.0-1.dsc r-bioc-hilbertvis_1.30.0.orig.tar.gz r-bioc-hilbertvis_1.30.0-1.debian.tar.xz r-bioc-hilbertvis-dbgsym_1.30.0-1_amd64.deb r-bioc-hilbertvis_1.30.0-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at an3as.eu Fri May 20 09:51:05 2016 From: andreas at an3as.eu (Andreas Tille) Date: Fri, 20 May 2016 11:51:05 +0200 Subject: [Debian-med-packaging] Trying to update htsjdk but some tests are failing Message-ID: <20160520095105.GZ5019@an3as.eu> Hi, I tried to upgrade htsjdk to the latest upstream version but some tests are failing. Vincent (or anybody else) could you please have a look at the current state in Git? Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Fri May 20 10:21:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 10:21:35 +0000 Subject: [Debian-med-packaging] dicom3tools_1.00~20160516104835-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 07:18:04 +0000 Source: dicom3tools Binary: dicom3tools Architecture: source Version: 1.00~20160516104835-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: dicom3tools - DICOM medical image files manipulation and conversion tools Changes: dicom3tools (1.00~20160516104835-1) unstable; urgency=medium . * Imported Upstream version 1.00~20160516104835 * d/control: cme fix dpkg-control Checksums-Sha1: d69835ee8ae250e7f03af049bb8043cd523b04c2 1819 dicom3tools_1.00~20160516104835-1.dsc 8185fc843e936e676e21b12238d3b3773325905b 958071 dicom3tools_1.00~20160516104835.orig.tar.bz2 9d87107d49ce74c77bd02ff8ee3e7f057dce9c6d 10672 dicom3tools_1.00~20160516104835-1.debian.tar.xz Checksums-Sha256: b5ba86727cd784fc71e8c09996c1249acd3a6fcfa60b0c9d4a74e598664b4032 1819 dicom3tools_1.00~20160516104835-1.dsc aa4a0d324a4d422ba36fcaabecfe694dd57d0ffbdca8997a84a645e65aceb148 958071 dicom3tools_1.00~20160516104835.orig.tar.bz2 5d0178138c9d9cf33f93f46debb0984a735992a75c7863e1d35b2aed0c20226f 10672 dicom3tools_1.00~20160516104835-1.debian.tar.xz Files: 492faeff568a6d881bb98d9f85f064d4 1819 graphics optional dicom3tools_1.00~20160516104835-1.dsc 3e565e815e2b96cc0bfbbdc59a99e55e 958071 graphics optional dicom3tools_1.00~20160516104835.orig.tar.bz2 cf5132d0455b111a8ec2f9dbb73af04d 10672 graphics optional dicom3tools_1.00~20160516104835-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXPr/eAAoJEPgeNoubJquYgFUIAKFuFBDuJ7taNgO+aNtEXc/z c1MFGsuaHw0FnWZZPSVtpcXeTZjq7iH7VvXAUzuqltekhLJSlXosyEJFTbJTC2Hy RgDq3M5b4GWqJkajlr1vb4dMoiWiEepr/lSJvKaugQzt8KXTB+ChhqUMEc9wRKA5 K+40uwt9ywlI+7qOTrNSQLXSBu8vXbc7Q5uyBB6TjlMMSaKp5NKPu0eha99Gl0dt nPVEJ8FdknWiqIPBzytfy8/RtAD1hQIXncIjGx/cvT3SkHr3W/OEicKJOwiBwNhc kfC5KC/M+WNIotsaVZArez1lLJrzC9BtK4wzrjjn35vmCWewHXMjkniCTg3ZnI8= =Za0Y -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 20 10:37:14 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 10:37:14 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-edger_3.14.0+dfsg-1_amd64.changes Message-ID: r-bioc-edger_3.14.0+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-edger_3.14.0+dfsg-1.dsc r-bioc-edger_3.14.0+dfsg.orig.tar.xz r-bioc-edger_3.14.0+dfsg-1.debian.tar.xz r-bioc-edger-dbgsym_3.14.0+dfsg-1_amd64.deb r-bioc-edger_3.14.0+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 20 10:39:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 10:39:01 +0000 Subject: [Debian-med-packaging] r-bioc-hilbertvis_1.30.0-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 10:36:58 +0200 Source: r-bioc-hilbertvis Binary: r-bioc-hilbertvis Architecture: source amd64 Version: 1.30.0-1 Distribution: unstable Urgency: medium Maintainer: Debian-Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-hilbertvis - GNU R package to visualise long vector data Changes: r-bioc-hilbertvis (1.30.0-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 91c05fde0e90b6beee3f3f30df72d722053ddb11 2152 r-bioc-hilbertvis_1.30.0-1.dsc 7b533288d378933ac44257ca24c048992d68aa7a 1045717 r-bioc-hilbertvis_1.30.0.orig.tar.gz 9812002f15c83c6c0012890008f8813c6fd45316 3520 r-bioc-hilbertvis_1.30.0-1.debian.tar.xz ad01a2fc9a600ce3894a3d28926c4669535b0c00 7110 r-bioc-hilbertvis-dbgsym_1.30.0-1_amd64.deb 89a7a045562922a64d85da9c078049b8a28577d7 971070 r-bioc-hilbertvis_1.30.0-1_amd64.deb Checksums-Sha256: 8bd9b1140121e4dd82ba0a859dbd8ecfd8ce50ee564392e8fe6637dc2ef3f6e6 2152 r-bioc-hilbertvis_1.30.0-1.dsc 4a34d20a72b444b4cd8afca87ad56d27fe20082cc25460396444e36ffcd63f5f 1045717 r-bioc-hilbertvis_1.30.0.orig.tar.gz 4f9d989a5482e55ea422aa773c4b83036ae07b5d9eb1986e9c434f9a5dd4dccc 3520 r-bioc-hilbertvis_1.30.0-1.debian.tar.xz 443f8e2506b9d21d16a68ce903804fe6ac07624b5b43f776354adc0744193304 7110 r-bioc-hilbertvis-dbgsym_1.30.0-1_amd64.deb bb643ab24b763c691270fd85aeed87e7e9109de4f0906464e1ff5d431f214931 971070 r-bioc-hilbertvis_1.30.0-1_amd64.deb Files: a045b550143183e13206ecf0a3075d6b 2152 math optional r-bioc-hilbertvis_1.30.0-1.dsc 95fa59d5101318ef401b4ef7ed75d1aa 1045717 math optional r-bioc-hilbertvis_1.30.0.orig.tar.gz c74f88ac47904a7e1eb4b4c031bfe9c9 3520 math optional r-bioc-hilbertvis_1.30.0-1.debian.tar.xz 61b64485692d5a7593d0cd3da6cf4393 7110 debug extra r-bioc-hilbertvis-dbgsym_1.30.0-1_amd64.deb c9ea003cbfcab37837d8081a7841ca57 971070 math optional r-bioc-hilbertvis_1.30.0-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPtCuAAoJEFeKBJTRxkbRVVUP/2ctqVzORGclVdsWl/ag0XYx 6AXBdsrFgRIsPgLF19FucBLH5nK2eTm752p/P/xxTuvxOiJMuKc+/AAukqhVbWIb 9c3CX0Sphchk2mflqDJeCJ7BjP+oD55cnM4xhRqIJeohqmtuBKf73kChlw0byy9f nZit3U1vG6v5i9bMU/zOY56P8wZO3sZuadtQgKtzjZvglJqh/mRL4dPqKrr0bzL3 O0tuJx5nV0efXqwT+ftaXwTRyp0xetQYflJJuLpfLLqyLU2sf7DVVYOsAirps1jo mdB42eKd6HKXbAQ5SsUdx83gKEnLhpxt8u9KtdeIjBue5aSZX8P3k80CnTjQO02I 9fWoxMs4xoPfnRmWaxEhSy8KFeVi6z9jbpM7TVS4brqqM8qH3c/aBjVXPZg011Xo kj8dVutA+Awdhhg5x6dXyiZWI09bcaR4I4Bh57OeDLjQIvSBGEmlA6zeJcRVBdzo 3ej5G8V1Fk06OJ0i0rViiMBREb1iY5ddEnXrSMGr0KUNa21TWHdhI5bBHz85++lC PYSeuiUyPARQ7r85GgStkhhCUgv8HjwKeNa//DsmSIsoBOAO/dffh2OSdG1/CNs/ poD3p4dXlSdX2m0zuNiytrXY/AsHfbHvLHYDIUXFbAdJktloRgf1IfzViZer2MFZ uVlslSqsSRbIzoA92Vzt =6XFX -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 20 10:40:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 10:40:01 +0000 Subject: [Debian-med-packaging] transdecoder_3.0.0+dfsg-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 18 May 2016 03:03:30 -0700 Source: transdecoder Binary: transdecoder transdecoder-doc Architecture: source Version: 3.0.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: transdecoder - find coding regions within RNA transcript sequences transdecoder-doc - find coding regions within transcripts Changes: transdecoder (3.0.0+dfsg-1) unstable; urgency=medium . * new upstream release Checksums-Sha1: 471b152492d5181c3bdaa77cf82c4d931eca09d6 2127 transdecoder_3.0.0+dfsg-1.dsc d6b0b7c76a5fb9bf8270fc7df220427809c09783 11083893 transdecoder_3.0.0+dfsg.orig.tar.gz 9bcbcbae87f84bf5557c36459284a1da341884e5 4724 transdecoder_3.0.0+dfsg-1.debian.tar.xz Checksums-Sha256: d6fe273800e2fee9c506f54f7feeb3b4d64ecfd2ace8174a52a609a64f7bb8aa 2127 transdecoder_3.0.0+dfsg-1.dsc eb4064d536bb7799c9e07d48f3c332e78c730ed3f56e400926d3f54f7d56984e 11083893 transdecoder_3.0.0+dfsg.orig.tar.gz a70ef1de5956de01207a81c9cb6b07d46945a496742c6cfa3950f05653be2d86 4724 transdecoder_3.0.0+dfsg-1.debian.tar.xz Files: 872f3eab4ef70e883b3aef9a9299bc4c 2127 science optional transdecoder_3.0.0+dfsg-1.dsc d30a9cab810cc008763e84052bcc6a1b 11083893 science optional transdecoder_3.0.0+dfsg.orig.tar.gz bdf6806b15181ea5a68fa6e1564d1184 4724 science optional transdecoder_3.0.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXPFvbAAoJEDwmdj9sZ+biYnMP/RMZXPg2nev23CHW8beD9kaT suJKeE4pr1pQGVi4ZCghPrFbKGnIvlofJZpyYHQrjNMJzuAnkJwSzLdXq//qD6v1 VDZtAg+0607UXT+QNapSvT/PhYVlXrvI56dKdFMlO4XRYUQhQv3oZDhbFeritYMI Z30XI4kOX4WFVvtcgATslbjQbg+4LNXQhbxrILwn3t9XJb4khpIyso8YUmG1faCT sRwcW8mKz6ILkGRkEkTUmLUQ5wPeuZyHBiGYxBHxDDHdOfx1Hz4MEfTJZiO3ewcZ UnncBeYQfqwQBdPIz67rfr29MSfohwvg47s8YXzaYVIOnABuGjZbciYZCCZhtC3H uq+dJ6Mdb7iP5kmZ3wRUgc9m/ukzRXWJBdWUIxVD+NHhi1IhZJdWfQCaTP5M6gRc s7LWVLs/13oua3AVKVRbt4NivDtmXu5owcsX1gW/kOlm34p2ZHw9IKrNBYKiOa3I 5biiT8UhmNYAZ0DlDhMq49YQjGdNCSU3La5CyLyAITYEqrfAht1myz+Kke08XyOr y1i3iz61Wbazq68Fx07exjRi4jAxydnOUTvmu34sQ0glK3P08yxyUxkczpdiObud mWbDEYagPOHOb9eI89MHKab4vdP7EJsngMc4NfwS/hhkEUkmOQyOl6ULHmaB9GLm XgT4LH0wIwdPSrtHXZhV =Pw3M -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 20 11:34:37 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 11:34:37 +0000 Subject: [Debian-med-packaging] r-bioc-edger_3.14.0+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 12:00:13 +0200 Source: r-bioc-edger Binary: r-bioc-edger Architecture: source amd64 Version: 3.14.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-edger - Empirical analysis of digital gene expression data in R Changes: r-bioc-edger (3.14.0+dfsg-1) unstable; urgency=medium . * New upstream version * Use xz option in watch file * cme fix dpkg-control Checksums-Sha1: 6519b86ea77e91ef96ed1442faeab4fc42c9f228 2091 r-bioc-edger_3.14.0+dfsg-1.dsc 06dad0bf3d2e5b53b33bfefc770a8cd949641de5 174436 r-bioc-edger_3.14.0+dfsg.orig.tar.xz 2f8af76e6ed8727e94f0787188e5ff06779b166e 5592 r-bioc-edger_3.14.0+dfsg-1.debian.tar.xz 60097d48ab7e55a9a4931d9af93cd9e256737aa1 188262 r-bioc-edger-dbgsym_3.14.0+dfsg-1_amd64.deb 75b9a11bd27fb8d9cac17b9436c0ce3f889ed6e2 543354 r-bioc-edger_3.14.0+dfsg-1_amd64.deb Checksums-Sha256: 5b338b387649982db2ba64c423e03dd71bf6dc92d4561f0eef5c9ab99e7e42d4 2091 r-bioc-edger_3.14.0+dfsg-1.dsc 53a4bb24565223894d3b40e7492060e8244aa2a89464b188a2dc51e694e8f16d 174436 r-bioc-edger_3.14.0+dfsg.orig.tar.xz 18eef18b15b37d88a8d2ca2701e7318be208cd0cbd36e6d45c7eee6a4f1d9520 5592 r-bioc-edger_3.14.0+dfsg-1.debian.tar.xz efdb00681bdcba71f041780088c6060175ec3d90b52813630c6585f8fdc85a0b 188262 r-bioc-edger-dbgsym_3.14.0+dfsg-1_amd64.deb d0aa371a90e32a51cb418ce47acfffff4ae91a2399c3768cb660618c19c362ea 543354 r-bioc-edger_3.14.0+dfsg-1_amd64.deb Files: 4996d191ba439475314c153a84f4cb63 2091 gnu-r optional r-bioc-edger_3.14.0+dfsg-1.dsc 3f1b3802f12a613bb4af9741db257ead 174436 gnu-r optional r-bioc-edger_3.14.0+dfsg.orig.tar.xz 97000e290b3b3352ddc67cb6b74879f9 5592 gnu-r optional r-bioc-edger_3.14.0+dfsg-1.debian.tar.xz 0e45a39d6195bb577e1a19ede851980a 188262 debug extra r-bioc-edger-dbgsym_3.14.0+dfsg-1_amd64.deb 9cb919e8765441b5a045fa3888e6a6e0 543354 gnu-r optional r-bioc-edger_3.14.0+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPuDlAAoJEFeKBJTRxkbRqhMP/1bKNusOUWS8ePoyZybanbAJ BbdbrKPn7v5k0rH/cdijYqyYLykaTB8x7Ys1EssdKc2D1GFA/b0C20avN5vVRnGR jN9xHY5csp7dH4XJR7OME+pqlm4KL+v8VTQQsSpXcFBa2fsgCPipn5uRNGJTGo/T RPms2OSw5BlKHB2BvfN3ryY4plshRhTwsXcmXUVlFcYtBKR0PQcj205JjUliuB6c sQyLwsOBmQ/VVAUTtWrIiGGCshe5bYsUS9StgNn98plnRl7KuWeOhVk+hjkG0b9J yAu3SVmHiM6jZKFAaJIIzTlUVgE+32m6FWqoaJUZecBZmv7SwVjWvQTNfx/duZki 11bjgbXDe5sU1YXV0UwOvYtw2O5ZgpsvTKfsYzs0icDoJSOrrvDDI5qKL8xcndT/ 01VjQipGlaHBMjLFJPdimdFlTn9fnzMaYhH57xfIEaOdqkU5Bvprjj8EanePO0sV +VNuav6LAylhNk/eGbO7BT2/Pjj0FZ6CL068TsJVpeL+JwKHXQW6FrrFiKY5C//a 7V9lyc8PtypF/LTKtWdBZsW1Eg2FM4pmW+w+ySm2Nlq40vhFsvtfc3be0dDRV9ag f9D0rvwKenf1UHYVp5gl7Bf+PvNynmQGpsSXKK2B7mqLBeaRTcsEwzrcum3fNCwc QEDGubrseAAqF77W5dkt =Epac -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 20 12:01:20 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 12:01:20 +0000 Subject: [Debian-med-packaging] r-cran-princurve_1.1-12-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 14:57:03 +0200 Source: r-cran-princurve Binary: r-cran-princurve Architecture: source amd64 Version: 1.1-12-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-princurve - fit a principal curve in arbitrary dimension Closes: 824754 Changes: r-cran-princurve (1.1-12-1) unstable; urgency=low . * Initial release (closes: #824754). 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From ftpmaster at ftp-master.debian.org Fri May 20 12:03:32 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 12:03:32 +0000 Subject: [Debian-med-packaging] libbpp-phyl-omics_2.2.0-2~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 17 May 2016 11:48:31 +0200 Source: libbpp-phyl-omics Binary: libbpp-phyl-omics-dev libbpp-phyl-omics1 Architecture: source amd64 Version: 2.2.0-2~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-phyl-omics-dev - Bio++ Phylogenetics library: genomics components (development fil libbpp-phyl-omics1 - Bio++ Phylogenetics library: genomics components Changes: libbpp-phyl-omics (2.2.0-2~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * Revert v5 rename of library packages Checksums-Sha1: ec51b5737ff00782af58d2263afebe75ee75ca87 2255 libbpp-phyl-omics_2.2.0-2~bpo8+1.dsc fdc6299cf43eac68a32649ec72fcfd15f1cbcbef 3788 libbpp-phyl-omics_2.2.0-2~bpo8+1.debian.tar.xz bd2d3f333c9968c94f1bdc7fcec7d124f3ad5908 123042 libbpp-phyl-omics-dev_2.2.0-2~bpo8+1_amd64.deb 5df1cfb530dddb88489bd02d8c22d3ea692ccc76 66524 libbpp-phyl-omics1_2.2.0-2~bpo8+1_amd64.deb Checksums-Sha256: e8ce7c004c03423c19cbe950c292c6b625e14913ba868b542f5f7ed0ef9cffc1 2255 libbpp-phyl-omics_2.2.0-2~bpo8+1.dsc 5863790d4d3e77be6db919c14d532b8890aba2c57e9233bb88d85a9d4dddb136 3788 libbpp-phyl-omics_2.2.0-2~bpo8+1.debian.tar.xz 2bbc2d65e8d3842d60685e63d005f09cd441d5113876f0e1bd12e49e4b378d59 123042 libbpp-phyl-omics-dev_2.2.0-2~bpo8+1_amd64.deb bf8ad10871c36aca1bbd655983defdd67a97a3ff3ec30f477fa77696e89c4aef 66524 libbpp-phyl-omics1_2.2.0-2~bpo8+1_amd64.deb Files: ed236a45f70a4f7bb04033bcf718a6a6 2255 science optional libbpp-phyl-omics_2.2.0-2~bpo8+1.dsc 4c68e690a0000b43a68ded0f68fd42ec 3788 science optional libbpp-phyl-omics_2.2.0-2~bpo8+1.debian.tar.xz 206227ca6b1cf5a95d39afe0bb3d904a 123042 libdevel optional libbpp-phyl-omics-dev_2.2.0-2~bpo8+1_amd64.deb 84649b47f8e7287e808b21c4944e7fa4 66524 libs optional libbpp-phyl-omics1_2.2.0-2~bpo8+1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPfJrAAoJEFeKBJTRxkbRC3AP/3Q/BWlN57ZIlLTrzxE4F1q3 0gf5uxlS7rk8MP9fCl3Dd1leAe5xZM6umLLrnSeBQe62sOlifu8MzbAH10biGgb5 E5CTSGmPhlPRrZENNSphZNZpq/ug2EG4WvQ/H4DCfSh6Axg5Sq97uZb8Nh5qdxeJ e63N3E2l6VydJQrwkpBjNIm8Y5KdPw7B1wMD3yQ1hVJ+z8PzKGnPBrpoF/WNtpT0 IZqUU3CdsIOmanYLbCucl6wIJNd4MR/uFElAwytOYUd+YJ0saV145AIojjZewJIp KkPanOAJnwAet3kEKRckeNi41DCuwCJbQWbZsEenJdO4KcHK6PK2ziyZcAfxbdq5 COsgg+eVXP9Gif0XGWwjMvkZpEf5YxJQn123sxO7EAIv2j9h10QqHSrhw3A76G5Q CSY2D8fK1O3oIoJ8vmvxYbtd+fYge1BpP2p14Sx/J0MY8N1AhW9o5WDn/BvmsuEn C7MLY8hsdd0NsmnwNcrvtcWd+VMCyBxuiM90MihpijmgOfDH5XYT4m4Xnhp0p8EF bDpwCrvEytf5tC0KdLwy8wxAFBpHetqAiRGjTxCLWhPYVMes7ZORiirT8RLnTzsL oE5Ydwnnk/R+iou3NkMuo4AKx9DByAcMYTR5IfHT/re9jkKLiBwarOPV6R2rLNzI wEA+fFzJHBtSRlQGR0nh =+aWb -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 20 12:03:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 12:03:55 +0000 Subject: [Debian-med-packaging] r-cran-stringr_1.0.0-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 May 2016 19:12:07 +0200 Source: r-cran-stringr Binary: r-cran-stringr Architecture: source all Version: 1.0.0-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-stringr - Make it easier to work with strings Changes: r-cran-stringr (1.0.0-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From owner at bugs.debian.org Fri May 20 12:21:17 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 20 May 2016 12:21:17 +0000 Subject: [Debian-med-packaging] Processed: your mail References: Message-ID: Processing commands for control at bugs.debian.org: > tags 824819 pending Bug #824819 [src:charls] debian/watch Added tag(s) pending. > End of message, stopping processing here. Please contact me if you need assistance. -- 824819: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824819 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Fri May 20 12:59:20 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 12:59:20 +0000 Subject: [Debian-med-packaging] Processing of circos_0.69.2+dfsg-1_amd64.changes Message-ID: circos_0.69.2+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: circos_0.69.2+dfsg-1.dsc circos_0.69.2+dfsg.orig.tar.xz circos_0.69.2+dfsg-1.debian.tar.xz circos_0.69.2+dfsg-1_all.deb fonts-circos-symbols_0.69.2+dfsg-1_all.deb otf-symbols-circos_0.69.2+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From malat at debian.org Fri May 20 13:01:21 2016 From: malat at debian.org (Mathieu Malaterre) Date: Fri, 20 May 2016 15:01:21 +0200 Subject: [Debian-med-packaging] Bug#824818: 1.1.0 works Message-ID: block 824818 by 824721 thanks I am not clear what changed in the 1.1.0 release but this works now: mathieu at debian:~/charls-1.1.0$ ./charlstest -decodetopnm JPEG_LS_InvalidEscapeSequence.jls JPEG_LS_InvalidEscapeSequence.pgm mathieu at debian:~/charls-1.1.0$ md5sum JPEG_LS_InvalidEscapeSequence.pgm 596da5bc228ea42784f9780517e071d3 JPEG_LS_InvalidEscapeSequence.pgm From owner at bugs.debian.org Fri May 20 13:03:20 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 20 May 2016 13:03:20 +0000 Subject: [Debian-med-packaging] Processed: 1.1.0 works References: Message-ID: Processing commands for control at bugs.debian.org: > block 824818 by 824721 Bug #824818 [src:charls] CharLS: One JPEG-LS not handled 824818 was not blocked by any bugs. 824818 was not blocking any bugs. Added blocking bug(s) of 824818: 824721 > thanks Stopping processing here. Please contact me if you need assistance. -- 824818: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824818 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From owner at bugs.debian.org Fri May 20 13:09:04 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 20 May 2016 13:09:04 +0000 Subject: [Debian-med-packaging] Processed: your mail References: Message-ID: Processing commands for control at bugs.debian.org: > tags 824818 fixed-upstream Bug #824818 [src:charls] CharLS: One JPEG-LS not handled Added tag(s) fixed-upstream. > End of message, stopping processing here. Please contact me if you need assistance. -- 824818: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824818 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Fri May 20 13:14:27 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 13:14:27 +0000 Subject: [Debian-med-packaging] Processing of andi_0.10-1_amd64.changes Message-ID: andi_0.10-1_amd64.changes uploaded successfully to localhost along with the files: andi_0.10-1.dsc andi_0.10.orig.tar.gz andi_0.10-1.debian.tar.xz andi-dbgsym_0.10-1_amd64.deb andi_0.10-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 20 13:20:32 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 13:20:32 +0000 Subject: [Debian-med-packaging] andi_0.10-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 15:03:38 +0200 Source: andi Binary: andi Architecture: source amd64 Version: 0.10-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: andi - Efficient Estimation of Evolutionary Distances Changes: andi (0.10-1) unstable; urgency=medium . * Team upload * New upstream version * cme fix dpkg-control * Better hardening Checksums-Sha1: 38ce919760fb966990a0fba7d15c10dcc6e3521f 1944 andi_0.10-1.dsc 692b4a034e65e89debeadc33a184bca4c0f5f416 535066 andi_0.10.orig.tar.gz 5b63c94d688451cdcb00a8192cf43d4518cdd13d 8200 andi_0.10-1.debian.tar.xz 97b7675beca7c0a13039ae88d3656a96d5b78b58 36188 andi-dbgsym_0.10-1_amd64.deb 70e32f04eeb6d85ae3fd42966ca28bb9acf1de86 466166 andi_0.10-1_amd64.deb Checksums-Sha256: 44c675dfed102c5728d9c95a80666e6486b4bf96fd209641b3d9ad8299776f53 1944 andi_0.10-1.dsc 1ff371de0b6db4080e402ded2687947dc2d6913e28626edec21dcf5149489ee8 535066 andi_0.10.orig.tar.gz bb22c7b593b61e5613a11aff1d41c3b0ebce28c0dcc71a5d1e60103e7341ab38 8200 andi_0.10-1.debian.tar.xz 26a059090d761a07ac0299db8115f84005d9daab507de888b49469bc5bcf0287 36188 andi-dbgsym_0.10-1_amd64.deb 587cd3df3b6e80ce03a5833690151d51c32437f1ffaa1b64c4040b7dd366bc94 466166 andi_0.10-1_amd64.deb Files: f6965bf9cb10a55119725f3c7e085dba 1944 science optional andi_0.10-1.dsc 3aaba7961798bb4aaa546baa44e469d8 535066 science optional andi_0.10.orig.tar.gz 7cd0c8c80071b3a20ca7936586bdbc58 8200 science optional andi_0.10-1.debian.tar.xz f6ec240f2f04bcb93f98c47f3c5d63eb 36188 debug extra andi-dbgsym_0.10-1_amd64.deb 8867e9e6445032abfdd8cd54f6177e6a 466166 science optional andi_0.10-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPw1PAAoJEFeKBJTRxkbRc0UP/1ufuVyLkIr/oTaveAyQN0go 6TV6YHcTWkaHP1Hb2y1apsYtz2xrVPXLzqoM1NoHRUjJ58h2pMxa74+j7HJCRAKl FYdX4DtZTl32kBgGqb8tFtuQZ0Iovz4HfJmE/CV2XvIWFXGztT/p0h10Se5yoliB z2qIxcVdUVC7ewQZ+/WqOtmYNi+a2EF5aOXJz/w0tBibmY4d/CxMpZHalX/2RgAk CljVlx9h4ymoxJUk5Kmpcux4XQrOtuNnxCSyThZDDVmWo2pvwQz52XNru2QzfnWt q0StXlcXseVpU4nwaoHRWYt1DiEM1TLihJPiDHzdRy8VWaYTHnEf1pXyfxxZQRFK XpQw3W97/oaW1WVb0H58iUqyGKaH7SFUaiZ1Hi0Tutquyfo8G3ZyBJjMofao3as0 gEUnJMfbht2zyFUCAqmM5Bo9LNzoJkYwDR/gFtIUZQtw4bJUH9Frnsq2W5B3DMjF Gy/qsn8VWdGoHkpefbtP09wXxGGidLGiwKC3nto3hCS8g1UlEvTqE+dHRUqGBl7u whP3/eLjcds8JqrI7BCvj50FwK1A6iVVq1CG/EVf6whyNmRyteHVsAeTmbMcEsur 601ecs0hBlgJ1u1ETi1BUJirMPr+siuCdtBl881VJ8cWVkR0Wos4c2d/batQ8kXk oB0GB01KPvu4yPrh9sSD =OX9U -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 20 13:20:51 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 13:20:51 +0000 Subject: [Debian-med-packaging] circos_0.69.2+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 14:39:44 +0200 Source: circos Binary: circos otf-symbols-circos fonts-circos-symbols Architecture: source all Version: 0.69.2+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: circos - plotter for visualizing data fonts-circos-symbols - plotter for visualizing data - standard fonts otf-symbols-circos - transitional dummy package Changes: circos (0.69.2+dfsg-1) unstable; urgency=medium . * New upstream version * Move packaging from SVN to Git * cme fix dpkg-control * Remove unneeded binaries from upstream source * Fix pod syntax Checksums-Sha1: 92979d3cae69da0944a0d06342bea7d79f4b5dd6 2119 circos_0.69.2+dfsg-1.dsc 9b8ce294f1fb65266a708398ef205c6e3484f773 16031780 circos_0.69.2+dfsg.orig.tar.xz c77904ef32fab64450fb1b303389cc59fae12f05 7260 circos_0.69.2+dfsg-1.debian.tar.xz 8950c67706c8cb2416ca34ae5a9d5970c3e05dbf 22238048 circos_0.69.2+dfsg-1_all.deb 44c576a5048f37f79ed1ddb22321007e5286d3bb 46432 fonts-circos-symbols_0.69.2+dfsg-1_all.deb 9e075f87d815a78d111bde55301196465d23e4a2 19730 otf-symbols-circos_0.69.2+dfsg-1_all.deb Checksums-Sha256: 5d7299815fe6e3a0fe6ce1811df9842ee37382c016b6a13f44514fb04f14f685 2119 circos_0.69.2+dfsg-1.dsc 67d63bffa8fc366ba57c198b8331551d46696e8ad240a4195d70197c89390741 16031780 circos_0.69.2+dfsg.orig.tar.xz b21daf2ab3027749917ff233f35c33dc4b9cde2162a232f06713396b7e5a8162 7260 circos_0.69.2+dfsg-1.debian.tar.xz bb449f017101c4afe58b2327608d3c952c02591ca9115d4bc32b67c46a73a64e 22238048 circos_0.69.2+dfsg-1_all.deb 60a0704ce439ff42c5cbeac4720fb5a6c021eb6f259d9b627bb7834eb1d610e4 46432 fonts-circos-symbols_0.69.2+dfsg-1_all.deb 98fa26f2b8699779c963deda36327b20ec6779f02c426fb574dc7b52100cb58e 19730 otf-symbols-circos_0.69.2+dfsg-1_all.deb Files: 78acabc87545103820e31d9aed1f12a1 2119 science optional circos_0.69.2+dfsg-1.dsc 6ab2f9ab5642814aeae40f711f819abe 16031780 science optional circos_0.69.2+dfsg.orig.tar.xz 68220c1c1ef31e4f9115a49582162fe9 7260 science optional circos_0.69.2+dfsg-1.debian.tar.xz 24bc1c048032af74a7c45adde96d32d2 22238048 science optional circos_0.69.2+dfsg-1_all.deb 4a726d50e1e5cc55e4f9f994b5d97fcf 46432 fonts optional fonts-circos-symbols_0.69.2+dfsg-1_all.deb 0a6ab3d00825c2fe059b4acc2a7948cd 19730 oldlibs extra otf-symbols-circos_0.69.2+dfsg-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPwYaAAoJEFeKBJTRxkbRqUIP/2UpowYJzxVy4AwnFBptID3a wzlxT8eGf+ac926okG85whcE3CLgQHymcGTDCY5Xg9b05mOuuoSGX9G3gcyC9mLv 2eLGxt4WIDRC/lhICnWjKWCOtPUGCMt3/KQlcDKi0VFqMDb43lsd4HTNVKC0oVJE geKpfeBv+hlsg6z1CWgNOaJIlrV/fyfgnLU60y9VzKopyLgCXTVNxSbR6QNdbjJW vxy4BNpDIUETtUSQzR2Vy93G9HpYfH5UuJM3NLgYAh7kmVnDNRke5FGzjA9jjiAF ZDyIff+x1TSzgxd0OOPxHkG4iIlEQNUue0WYmTEM0Z1pypnrf8Zf3njUA7bRUOL/ vyZnegY9YAIZInUMVnjPlp9v6+3OmduuwDJAQ4Ev6Xde/qsFwOV02Zx/ZJaHHOQ2 VGSZFf9df31chP4LSKzmR+2SouSM740N7fm6LKdB1205nOuure9L+5tPsmZtCO4J zhls/d7MO2FBhjYAOI34fru9EKIA3tJ/wx2rYCuy8sQ21gU0qADzKjdpflOi1at3 O7t7ZRk412T1pH6y1h7d/1O43Mnv5s81MfHCN3G0a5xsLCvyg7QIzhPDM5zkEmcR tOwiSGxkU7yvXnNB0DJUZRpN6EbgqqdBhAPZ1lPGKXo9WQfqraDzBAHcOTVArY6i HL08vAYgAJGILZwJS3yj =a2oL -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 20 13:34:37 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 13:34:37 +0000 Subject: [Debian-med-packaging] Processing of andi_0.10-2_amd64.changes Message-ID: andi_0.10-2_amd64.changes uploaded successfully to localhost along with the files: andi_0.10-2.dsc andi_0.10-2.debian.tar.xz andi-dbgsym_0.10-2_amd64.deb andi_0.10-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 20 13:48:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 13:48:40 +0000 Subject: [Debian-med-packaging] andi_0.10-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 15:23:18 +0200 Source: andi Binary: andi Architecture: source amd64 Version: 0.10-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Fabian Kl?tzl Description: andi - Efficient Estimation of Evolutionary Distances Changes: andi (0.10-2) unstable; urgency=medium . * Add EDAM file Checksums-Sha1: 39e2e5f600e6c19771aa3d812a98ff5eda3c64cf 1944 andi_0.10-2.dsc ccb1fccab3810fe8d37ae4abafdd3d93fe6c575d 8344 andi_0.10-2.debian.tar.xz d017eb00d6d880b2c41b9d2aa8cd895972219bd1 36188 andi-dbgsym_0.10-2_amd64.deb aa7fb674b0e49771abdb676077d6c1685d039662 466176 andi_0.10-2_amd64.deb Checksums-Sha256: 816f7c8a9ca371576d44d608d0d8ede0ed50cda1fe2150bad54a3fb0e8cca738 1944 andi_0.10-2.dsc 6155f13a612f93a944d6ec21dc698c6691866be2612617f1a04163724d5171a5 8344 andi_0.10-2.debian.tar.xz 3e9909153f664c17976fc169b6b7e391d1a5a962f6f4d69c5a0269a5faaad299 36188 andi-dbgsym_0.10-2_amd64.deb fed6f9439b88df3769bae4f444da2f239751bbf341273c0b71f1374b8d75a53f 466176 andi_0.10-2_amd64.deb Files: 0a8e5d364fbd79892368a6b0bdbb2205 1944 science optional andi_0.10-2.dsc 4e2ed7e65aef3c5117e0a85ae59282e7 8344 science optional andi_0.10-2.debian.tar.xz bcb79f6d9ff2e2176229289807248b3d 36188 debug extra andi-dbgsym_0.10-2_amd64.deb 2e6d1f1e5005cb7ffe5602ed969d4000 466176 science optional andi_0.10-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPxF7AAoJEFeKBJTRxkbRS0UP/j2d0CtwoPfsainiujYGoJBR tAK+8+cruaQR8WdYCrhNQgqsUzo+iO1kC720+TJJjIS52RbenX3BRvyll5OQSFJh ssyPle7aKTprOnaRBkph/Qv47vd4OmWSwZQB55AnvSCCxqzbgOONlz7MT8AXBVNe jUfdNJTc+BnbEjejZpblcl72ubxGou93+7+gP3VyJNBPZMi72eEAEABSiT3ZHpeG GSdK9h7kdzFYnPv5vyAzmKdyqO4CKmFAQiWsgy319ry7R4dH3hl6SZvbs8GKRk8H B7JLMWZ8yXYVa1K6tnB1Onx6xZA+u7GVJIThpBB9Ehn/SLznt15Toi6+4ZrBxpJ2 eDL9oxi7xjdqyZ/FbOi34DyePnAsZMWVLmjCJpQL0pX2ge8kEZJZnWJermQuDPzE ZNERBDaBtYpwTX2vzPz4o0SXJ6DJjuvIXO5r3oCSc/xQ52pwtmPFoRx4UPU+34h0 RCX0A13iXX1m5BhvxLsozhFXvR6/NQ8Eg4eZmVPfDBkmziN1fdTEZ/OcyAEMIhZ9 4X9o8vbzUKHESeLA45qcV/DxMN3pLKv6Mk2ppAcIRSU1X6mD6RX1dwGh2xKHHNok ahyf/WvQ8NV4xRv0r3FzhaDdbXw5qYKt+45rJa3nAbPusy0pKzrnIhPF+qW6YsYG 1Wr7SHrPOjWMu26CIqFc =EbmY -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From malat at debian.org Fri May 20 13:55:02 2016 From: malat at debian.org (Mathieu Malaterre) Date: Fri, 20 May 2016 15:55:02 +0200 Subject: [Debian-med-packaging] Bug#824721: CharLS: 1.1.0 is out In-Reply-To: References: <20160519155007.GS5019@an3as.eu> Message-ID: On Fri, May 20, 2016 at 8:11 AM, Mathieu Malaterre wrote: > Hi, > > On Thu, May 19, 2016 at 5:50 PM, Andreas Tille wrote: > [...] >> noticed that none of the cmake patches apply to the new version. If you >> are interested in a soonish upload it would be great if you would adapt >> all those patches created by you previously to the new version. > > Ok. This will depend on what I found out from #824818. I've cleaned up the old 1.0 patches, nothing really big, except the 3 new C++ symbols. Whoever uploads it, will need to close both 824721 & 824818. So clearly 1.1.0 do make sense for stretch. Thanks. From kloetzl at evolbio.mpg.de Fri May 20 13:57:30 2016 From: kloetzl at evolbio.mpg.de (=?UTF-8?Q?Fabian_Kl=c3=b6tzl?=) Date: Fri, 20 May 2016 15:57:30 +0200 Subject: [Debian-med-packaging] andi_0.10-2_amd64.changes ACCEPTED into unstable In-Reply-To: References: Message-ID: <573F17CA.60705@evolbio.mpg.de> Hi Andreas, Thank you for uploading the latest version. I would have done that as soon as I get debian running on my laptop again. (It is proving difficult because of proprietary wifi, yada yada) Same goes for the MUMmer patches I promised. Thanks again, Fabian From owner at bugs.debian.org Fri May 20 14:15:12 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 20 May 2016 14:15:12 +0000 Subject: [Debian-med-packaging] Processed: your mail References: Message-ID: Processing commands for control at bugs.debian.org: > tags 824818 upstream Bug #824818 [src:charls] CharLS: One JPEG-LS not handled Added tag(s) upstream. > affects 824818 src:gdcm Bug #824818 [src:charls] CharLS: One JPEG-LS not handled Added indication that 824818 affects src:gdcm > affects 824818 src:dcmtk Bug #824818 [src:charls] CharLS: One JPEG-LS not handled Added indication that 824818 affects src:dcmtk > End of message, stopping processing here. Please contact me if you need assistance. -- 824818: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824818 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From noreply at release.debian.org Fri May 20 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 20 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-bioc-genomicfeatures 1.24.1-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-genomicfeatures source package in Debian's testing distribution has changed. Previous version: 1.22.4-1 Current version: 1.24.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 20 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 20 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] parsinsert 1.04-2 MIGRATED to testing Message-ID: FYI: The status of the parsinsert source package in Debian's testing distribution has changed. Previous version: 1.04-1 Current version: 1.04-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 20 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 20 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] tophat 2.1.1+dfsg-2 MIGRATED to testing Message-ID: FYI: The status of the tophat source package in Debian's testing distribution has changed. Previous version: 2.1.1+dfsg-1 Current version: 2.1.1+dfsg-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 20 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 20 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] python-pyfaidx 0.4.7.1-1 MIGRATED to testing Message-ID: FYI: The status of the python-pyfaidx source package in Debian's testing distribution has changed. Previous version: 0.4.5.2-1 Current version: 0.4.7.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From andreas at an3as.eu Fri May 20 18:36:39 2016 From: andreas at an3as.eu (Andreas Tille) Date: Fri, 20 May 2016 20:36:39 +0200 Subject: [Debian-med-packaging] andi_0.10-2_amd64.changes ACCEPTED into unstable In-Reply-To: <573F17CA.60705@evolbio.mpg.de> References: <573F17CA.60705@evolbio.mpg.de> Message-ID: <20160520183639.GC5019@an3as.eu> On Fri, May 20, 2016 at 03:57:30PM +0200, Fabian Kl?tzl wrote: > Thank you for uploading the latest version. Good to hear that you are happy after I messed up your latest changes since I forgit to git pull in the first place. I've done a lot of upgrades on the CWL hackathon in Paris. > I would have done that as > soon as I get debian running on my laptop again. (It is proving > difficult because of proprietary wifi, yada yada) I've made good experiences with seeking on wiki.d.o for specific hardware parameters I've found via lspci. More detailed help is great?ly provided by debian-user-german at lists.debian.org. > Same goes for the > MUMmer patches I promised. Fine. Kind regards Andreas. -- http://fam-tille.de From vdanjean.ml at free.fr Fri May 20 19:18:09 2016 From: vdanjean.ml at free.fr (Vincent Danjean) Date: Fri, 20 May 2016 21:18:09 +0200 Subject: [Debian-med-packaging] Trying to update htsjdk but some tests are failing In-Reply-To: <20160520095105.GZ5019@an3as.eu> References: <20160520095105.GZ5019@an3as.eu> Message-ID: <573F62F1.80103@free.fr> Le 20/05/2016 11:51, Andreas Tille a ?crit : > Hi, > > I tried to upgrade htsjdk to the latest upstream version but some tests are failing. > Vincent (or anybody else) could you please have a look at the current state in Git? The error in the tests seems to come from a (local) zip lib that is not used. The comments in src/java/htsjdk/samtools/util/zip/DeflaterFactory.java seems to show that - this is not a big issue (at most, it will be a little slower) - this is uneeded with JDK8 (and it seems we are using it now): "Note that this class will no longer be necessary once Java 8 is required, because[...]" So, I tried a very small patch to remove this test in the testsuite: --- a/src/tests/java/htsjdk/samtools/util/IntelDeflaterTest.java +++ b/src/tests/java/htsjdk/samtools/util/IntelDeflaterTest.java @@ -86,9 +86,13 @@ outputFile.deleteOnExit(); - Assert.assertTrue(DeflaterFactory.usingIntelDeflater(), "IntelDeflater is not loaded."); - log.info("IntelDeflater is loaded"); - + //Assert.assertTrue(DeflaterFactory.usingIntelDeflater(), "IntelDeflater is not loaded."); + //log.info("IntelDeflater is loaded"); + if (DeflaterFactory.usingIntelDeflater()) { + log.info("IntelDeflater is loaded"); + } else { + log.info("IntelDeflater is not loaded."); + } SamReaderFactory readerFactory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); if (eagerlyDecode) { And it seems to build correctly (all other tests passed on my machine) I'm not sure if the right fix is in the test suite (as I propose) or in the DeflaterFactory class. So, I did not commit anything for now. Regards, Vincent PS: thank to put me in CC: even if I'm subscribed, I do not read d-med-packaging regularly. > Kind regards > > Andreas. > From ftpmaster at ftp-master.debian.org Fri May 20 21:24:02 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 21:24:02 +0000 Subject: [Debian-med-packaging] Processing of mobyle_1.5.5+dfsg-1_amd64.changes Message-ID: mobyle_1.5.5+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: mobyle_1.5.5+dfsg-1.dsc mobyle_1.5.5+dfsg.orig.tar.xz mobyle_1.5.5+dfsg-1.debian.tar.xz mobyle-utils-dbgsym_1.5.5+dfsg-1_amd64.deb mobyle-utils_1.5.5+dfsg-1_amd64.deb mobyle_1.5.5+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 20 21:39:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 21:39:06 +0000 Subject: [Debian-med-packaging] Processing of charls_1.1.0+dfsg-1_amd64.changes Message-ID: charls_1.1.0+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: charls_1.1.0+dfsg-1.dsc charls_1.1.0+dfsg.orig.tar.xz charls_1.1.0+dfsg-1.debian.tar.xz libcharls-dev_1.1.0+dfsg-1_amd64.deb libcharls1-dbgsym_1.1.0+dfsg-1_amd64.deb libcharls1_1.1.0+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at fam-tille.de Fri May 20 21:50:35 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Fri, 20 May 2016 23:50:35 +0200 Subject: [Debian-med-packaging] Trying to update htsjdk but some tests are failing In-Reply-To: <573F62F1.80103@free.fr> References: <20160520095105.GZ5019@an3as.eu> <573F62F1.80103@free.fr> Message-ID: <20160520215035.GI5019@an3as.eu> Hi Vincent, On Fri, May 20, 2016 at 09:18:09PM +0200, Vincent Danjean wrote: > > I tried to upgrade htsjdk to the latest upstream version but some tests are failing. > > Vincent (or anybody else) could you please have a look at the current state in Git? > > The error in the tests seems to come from a (local) zip lib that is not used. > The comments in src/java/htsjdk/samtools/util/zip/DeflaterFactory.java > seems to show that > - this is not a big issue (at most, it will be a little slower) > - this is uneeded with JDK8 (and it seems we are using it now): > "Note that this class will no longer be necessary once Java 8 is > required, because[...]" Thanks for checking. We should probably add a versioned Depends since if we backport to Jessie this becomes important. > So, I tried a very small patch to remove this test in the testsuite: > --- a/src/tests/java/htsjdk/samtools/util/IntelDeflaterTest.java > +++ b/src/tests/java/htsjdk/samtools/util/IntelDeflaterTest.java > @@ -86,9 +86,13 @@ > outputFile.deleteOnExit(); > > > - Assert.assertTrue(DeflaterFactory.usingIntelDeflater(), "IntelDeflater is not loaded."); > - log.info("IntelDeflater is loaded"); > - > + //Assert.assertTrue(DeflaterFactory.usingIntelDeflater(), "IntelDeflater is not loaded."); > + //log.info("IntelDeflater is loaded"); > + if (DeflaterFactory.usingIntelDeflater()) { > + log.info("IntelDeflater is loaded"); > + } else { > + log.info("IntelDeflater is not loaded."); > + } > > SamReaderFactory readerFactory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); > if (eagerlyDecode) { > > And it seems to build correctly (all other tests passed on my machine) > > I'm not sure if the right fix is in the test suite (as I propose) > or in the DeflaterFactory class. So, I did not commit anything for > now. Please be so kind to commit. Thanks. > PS: thank to put me in CC: even if I'm subscribed, I do not read > d-med-packaging regularly. I think I'm somehow aware of this - at least when I wrote the mail today I was vaguely remembering. Thanks for refreshing. ;-) Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Fri May 20 21:59:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 21:59:12 +0000 Subject: [Debian-med-packaging] Processing of maffilter_1.1.0-1+dfsg-1~bpo8+1_amd64.changes Message-ID: maffilter_1.1.0-1+dfsg-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: maffilter_1.1.0-1+dfsg-1~bpo8+1.dsc maffilter_1.1.0-1+dfsg-1~bpo8+1.debian.tar.xz maffilter_1.1.0-1+dfsg-1~bpo8+1_amd64.deb maffilter-examples_1.1.0-1+dfsg-1~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 20 21:59:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 21:59:11 +0000 Subject: [Debian-med-packaging] Processing of r-cran-rnexml_2.0.6-1~bpo8+1_amd64.changes Message-ID: r-cran-rnexml_2.0.6-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: r-cran-rnexml_2.0.6-1~bpo8+1.dsc r-cran-rnexml_2.0.6-1~bpo8+1.debian.tar.xz r-cran-rnexml_2.0.6-1~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 20 22:37:45 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 22:37:45 +0000 Subject: [Debian-med-packaging] charls_1.1.0+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 23:29:00 +0200 Source: charls Binary: libcharls-dev libcharls1 Architecture: source amd64 Version: 1.1.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libcharls-dev - Implementation of the JPEG-LS standard (development libraries) libcharls1 - Implementation of the JPEG-LS standard Closes: 824721 824818 824819 Changes: charls (1.1.0+dfsg-1) unstable; urgency=medium . * New upstream version (use Files-Excluded) Closes: #824721, #824818 * CharLS moved to Github * Packaging moved from SVN to Git * d/watch pointing to Github Closes: #824819 * Better hardening Checksums-Sha1: 4402b65d1e79cf30fd375f1fde2e10b82a8a01f2 2035 charls_1.1.0+dfsg-1.dsc 93ba44b5d113eeff3c01154ee6ec0873c60347b4 35060 charls_1.1.0+dfsg.orig.tar.xz 25e9f433e5721f81f04d68db90f94aebd0407eca 4992 charls_1.1.0+dfsg-1.debian.tar.xz 26b83e6578b20bc0cee677ac4ba50281ee374a26 21512 libcharls-dev_1.1.0+dfsg-1_amd64.deb 55e69bfa102ff948cdc4a4afa8bccdbd8827f607 391412 libcharls1-dbgsym_1.1.0+dfsg-1_amd64.deb 7d4b7ae33f9c405a1f4fe3742690843d83980c39 55968 libcharls1_1.1.0+dfsg-1_amd64.deb Checksums-Sha256: 2efe3a04f696737189c4c6034bee952a7b3cc8031d9496658c5c0bd283302a16 2035 charls_1.1.0+dfsg-1.dsc e41475961f7c40c4c56fe4163873eb7751544b1ee120fb2fb26e7aa72927c40b 35060 charls_1.1.0+dfsg.orig.tar.xz a0bcda5fc1418fc8b56ac94428ac3f64e9664213357174ed85f125c80383c2ea 4992 charls_1.1.0+dfsg-1.debian.tar.xz f01b7b3edf73346f4c4d5716dd5859a8ec8f99a5fb9803220dd9592d6e7e1e7a 21512 libcharls-dev_1.1.0+dfsg-1_amd64.deb 5aad628bea7da73f76d22494c42e2bb7c56b441ce165a47f012277be7c406bf1 391412 libcharls1-dbgsym_1.1.0+dfsg-1_amd64.deb d5ee28021d3cdc5a81a0d06aacdc1d703959f3d4afa0c2f3e54b2ee001cf390c 55968 libcharls1_1.1.0+dfsg-1_amd64.deb Files: 2a7f1bee6ea5ae4e51931f38b36c4248 2035 libs optional charls_1.1.0+dfsg-1.dsc d1408abbe9a41580f246e5a3d2d1ef08 35060 libs optional charls_1.1.0+dfsg.orig.tar.xz c305411542873b241b5568817864f997 4992 libs optional charls_1.1.0+dfsg-1.debian.tar.xz 258b99f2a6aaf66d2ec03d0509fe3e86 21512 libdevel optional libcharls-dev_1.1.0+dfsg-1_amd64.deb 5ba826b62534a8767344f3fbae5eeaa6 391412 debug extra libcharls1-dbgsym_1.1.0+dfsg-1_amd64.deb 9bf803e2654826f0655216a16e0ab866 55968 libs optional libcharls1_1.1.0+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXP4LiAAoJEFeKBJTRxkbRfiUQAJKb8B/dwxBnIdH46JWlDDS5 9Ot6tzVZiiBAbZz/Mp1omaMC5sVDgwQ90D2NqUWMSjxkq7TuxDtd9iW6TbLyonJl JmSJnRw6SvbJm7grv9/cY3Lb3icKx3a+0sJTsszdEnlUywCNtwtXd3tlartpxn+5 +iu2eenQspn9N4n2ww3Ay2CWs3zuuGP+Jk19JECewYm1otsgQB50XgeWr2rDZ5rk nAcPnVq/Ggaa0UvQz7Phdo1q0E7cZilLf2v6N+TixZwGGRqekvCF+Y9zCiOnvucR LriXIMvLtQfMDETQc2vw+7tIWTSKAg76qX+EYwVWhHfVYkl82HGicFVclntx4uwd kwhGhL1FURj7VET0x4zpk9hCDRpBKOMBCCsoKs6p/UCaaGytdORr/RpLil5q+VfH jPQhjMbKHLoin/epwsv9Uol+D/Xt6mY17WsjUe+2naMZh4T7+QKRgBpiTOyjluZY p1I+LRgV1eXXWkcU+P9fjjzSzz6kGoY7ActrXz7glWKOe9gLKRJHKicASJwW6ruN iZP2YgUaIsnw2QUMEu8nqEWfdAwYcqwslQrjKOY7+ts7k4PEYq1E92KGdPsCYBuE HydObP1oK4RsWCAv4SEfvU1p7MsaRN+VGQos4WosoO0rI8+4l5HwiBrv4xfqVz6s 1gkQpKq5YnjC0D5DJKcd =3VXb -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Fri May 20 22:39:07 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 20 May 2016 22:39:07 +0000 Subject: [Debian-med-packaging] Bug#824721: marked as done (CharLS: 1.1.0 is out) References: Message-ID: Your message dated Fri, 20 May 2016 22:37:45 +0000 with message-id and subject line Bug#824721: fixed in charls 1.1.0+dfsg-1 has caused the Debian Bug report #824721, regarding CharLS: 1.1.0 is out to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 824721: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824721 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Mathieu Malaterre Subject: CharLS: 1.1.0 is out Date: Thu, 19 May 2016 09:14:42 +0200 Size: 3970 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#824721: fixed in charls 1.1.0+dfsg-1 Date: Fri, 20 May 2016 22:37:45 +0000 Size: 6268 URL: From owner at bugs.debian.org Fri May 20 22:39:10 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 20 May 2016 22:39:10 +0000 Subject: [Debian-med-packaging] Bug#824818: marked as done (CharLS: One JPEG-LS not handled) References: Message-ID: Your message dated Fri, 20 May 2016 22:37:45 +0000 with message-id and subject line Bug#824818: fixed in charls 1.1.0+dfsg-1 has caused the Debian Bug report #824818, regarding CharLS: One JPEG-LS not handled to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 824818: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824818 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Mathieu Malaterre Subject: CharLS: One JPEG-LS not handled Date: Fri, 20 May 2016 08:01:35 +0200 Size: 3604 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#824818: fixed in charls 1.1.0+dfsg-1 Date: Fri, 20 May 2016 22:37:45 +0000 Size: 6244 URL: From owner at bugs.debian.org Fri May 20 22:39:13 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 20 May 2016 22:39:13 +0000 Subject: [Debian-med-packaging] Bug#824819: marked as done (debian/watch) References: Message-ID: Your message dated Fri, 20 May 2016 22:37:45 +0000 with message-id and subject line Bug#824819: fixed in charls 1.1.0+dfsg-1 has caused the Debian Bug report #824819, regarding debian/watch to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 824819: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824819 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Mathieu Malaterre Subject: debian/watch Date: Fri, 20 May 2016 08:14:05 +0200 Size: 3289 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#824819: fixed in charls 1.1.0+dfsg-1 Date: Fri, 20 May 2016 22:37:45 +0000 Size: 6266 URL: From ftpmaster at ftp-master.debian.org Fri May 20 22:46:56 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 22:46:56 +0000 Subject: [Debian-med-packaging] maffilter_1.1.0-1+dfsg-1~bpo8+1_amd64.changes is NEW Message-ID: binary:maffilter is NEW. binary:maffilter-examples is NEW. source:maffilter is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Fri May 20 22:47:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 22:47:12 +0000 Subject: [Debian-med-packaging] mobyle_1.5.5+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 23:14:19 +0200 Source: mobyle Binary: mobyle mobyle-utils Architecture: source amd64 all Version: 1.5.5+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: mobyle - Web portal that provides web forms for command-line software mobyle-utils - binary tools used by Mobyle Changes: mobyle (1.5.5+dfsg-1) unstable; urgency=medium . * New upstream version * Move packaging from SVN to Git * Use xz compression in watch file and remove get-orig-source * cme fix dpkg-control * Better hardening Checksums-Sha1: 7cfb09801e6fced76db65c3f2301c3623313283e 2152 mobyle_1.5.5+dfsg-1.dsc f20ed4ba156a0d16fd5a109df13230aa634397c3 4676748 mobyle_1.5.5+dfsg.orig.tar.xz 574b8b016394a801e8adbb6e3873674d63acba7c 14916 mobyle_1.5.5+dfsg-1.debian.tar.xz cbb8d935a27fbd92bba253f1d87c61ccdf39e18b 2250 mobyle-utils-dbgsym_1.5.5+dfsg-1_amd64.deb 8cec5dbc89b9a9f1c5e41231bc5af53e8af33b1c 11822 mobyle-utils_1.5.5+dfsg-1_amd64.deb 0d29e2d72fb0188bdd97a628794e66eb25903816 4546702 mobyle_1.5.5+dfsg-1_all.deb Checksums-Sha256: d776222f25e0d877febce280c31290db4ba5286245c57d28f828fecc7bf04363 2152 mobyle_1.5.5+dfsg-1.dsc bf8d738f55c2594d63496cf4c61ff296d7b6da5993094224b5598b4dc295c379 4676748 mobyle_1.5.5+dfsg.orig.tar.xz 0cca93efac963a32fa22b05d84bc2442cc84434115d126816e7e1072ee6b327f 14916 mobyle_1.5.5+dfsg-1.debian.tar.xz cf6eb76f0e07e484b848384113d5eac25a804494e54d4ac92fb56f438686c31c 2250 mobyle-utils-dbgsym_1.5.5+dfsg-1_amd64.deb 1b9f82933caec8a8b9ef785d07ed76d1a04222d78f1a77375a5b57409d689fb0 11822 mobyle-utils_1.5.5+dfsg-1_amd64.deb 68986d0c0968506975e3f01b84fddc42940ef466c7cf622a0d8f6e5cc3167a9b 4546702 mobyle_1.5.5+dfsg-1_all.deb Files: c2711eb04f8cbd018fb59c964e10b795 2152 science optional mobyle_1.5.5+dfsg-1.dsc 10af8b77d7ef056f509fc47fb06df510 4676748 science optional mobyle_1.5.5+dfsg.orig.tar.xz c0ea558d1e137f2c8b747f62988bc649 14916 science optional mobyle_1.5.5+dfsg-1.debian.tar.xz e2240925a6f0d43758c2baf526e4e605 2250 debug extra mobyle-utils-dbgsym_1.5.5+dfsg-1_amd64.deb cea2a86a5e5d43a7a6860d3d7c737d8e 11822 science optional mobyle-utils_1.5.5+dfsg-1_amd64.deb 31e2182a4e26de640ff55e34fce2eef0 4546702 science optional mobyle_1.5.5+dfsg-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXP39HAAoJEFeKBJTRxkbRZWAP/i4vVm2lD7hKCt8nK3Sr2T2A fk39nAaXcrNqTOP8DVB2/90yrv+jjJAjBglZWNlXPpEAbrVHievp4iO11UjZ9ZwV Dojy7gw7tzlGMbFSm1KLBQSqj8McBKAEOIgDKG5cXIh4sDDVHXBSU92A2aQ6AHXG +9WzPZSFGKNSMqiAYA5gm9NU2+ekOw6OzO+OuNv9DkcIFqM3zJ2VONMBx01QJacw 4nVOSLIlrY/2AYOqdAxyNlL5P9whwv2kl9MIBtF2Ch2vKex7dowmaOFlryEUlSTI zHWoB3Lio06h1O3YGV5ceW+qebTULRmkUDlyWeURJyJhmdgG4+U+URX6y/WhMdwF sCuIJPvGWXUBqzVzfzIoWQe2q5K3ePLh9gf+0Jbdp796SuUwYM3jNPzcHtuRrC4g 9dJOlNwx2SA4YyqfhCzYE8C4sjU5NBOKGUNiHi+tqioM/kVh3kBORMCmuiDIZcXe 53x/PQQp4ZxKHEYI9GqGAskPd6TPBbJ+J8fyX+7wmuI/i2ZXYvJxBo6mtz35Q6l7 LV6+A1UKr42b+V5mf70L4oDzB/sPtS41am/nOKWwyNN6ZY2DshJqEKm4fFakuXQA Ulkrz4bt9fEe9rzkaw00y2jtoSnWijQ0bsj4FBSbIclQ2VhixBjruRJoyHycYLdQ Df6EeBNfPh+Ci8BoABDK =+Y2M -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 20 22:48:27 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 20 May 2016 22:48:27 +0000 Subject: [Debian-med-packaging] r-cran-rnexml_2.0.6-1~bpo8+1_amd64.changes is NEW Message-ID: binary:r-cran-rnexml is NEW. source:r-cran-rnexml is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From andreas at an3as.eu Sat May 21 11:34:23 2016 From: andreas at an3as.eu (Andreas Tille) Date: Sat, 21 May 2016 13:34:23 +0200 Subject: [Debian-med-packaging] Problems to find classes that should be in itext1.jar Message-ID: <20160521113423.GM5019@an3as.eu> Hi, I need help with another Java package of the Debian Med team which you can find in git[1]. I have stripped all JARs from the mesquite source tarball and tried to work down the list of missing classes. I'm stumbling upon classes which should be found in itext1.jar but the build process can't finde these. It would be great if some kind soul could have a look. Kind regards Andreas. [1] https://anonscm.debian.org/git/debian-med/mesquite.git -- http://fam-tille.de From matheusfbraz1 at aol.com Sat May 21 13:55:10 2016 From: matheusfbraz1 at aol.com (hi) Date: Sat, 21 May 2016 21:55:10 +0800 Subject: [Debian-med-packaging] salve Message-ID: <64902A181D51464878AA2F71550BC961@eacmgkwqt> bom dia laptop, tv, dj, guitarra, bicicleta .... podemos oferecer 50% de desconto iphone 6s,388euro site: slooone .com From andreas at fam-tille.de Sat May 21 15:53:46 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Sat, 21 May 2016 17:53:46 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <1463394066.18357.24.camel@gmail.com> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> Message-ID: <20160521155346.GR5019@an3as.eu> Hi again, after the build issues in clapack[1] were solved and I was even able to create shared libraries I wonder how I can properly set a sensible SONAME. I tried to do this via SET_TARGET_PROPERTIES but failed. Another question is how I could link against the Debian packaged f2c rather than building the one that comes with clapack upstream. Any help would be welcome Andreas. [1] https://anonscm.debian.org/git/debian-science/packages/clapack.git On Mon, May 16, 2016 at 12:21:06PM +0200, Gert Wollny wrote: > Am Montag, den 16.05.2016, 10:16 +0000 schrieb Gianfranco Costamagna: > > Hi Gert! > > > > > > > > I think, since in this case the (empty) format string passed to the > > > printf call is not user generated there is no security problem to > > > be exploited. > > > > yes, sure, but disabling this flag has a nasty side-effect, it is > > disabled in the *whole* build, possibly > > hiding more serious issues somewhere else. > > Of course, that's why I gave the #pragma based disabling that can be > fitted tightly to the offending code.? > > Best,? > Gert? > > > -- http://fam-tille.de From noreply at release.debian.org Sat May 21 16:39:14 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 21 May 2016 16:39:14 +0000 Subject: [Debian-med-packaging] rsem 1.2.30+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the rsem source package in Debian's testing distribution has changed. Previous version: 1.2.26+dfsg-1 Current version: 1.2.30+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 21 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 21 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] python-mne 0.12+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the python-mne source package in Debian's testing distribution has changed. Previous version: 0.11+dfsg-1 Current version: 0.12+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ebourg at apache.org Sat May 21 20:28:50 2016 From: ebourg at apache.org (Emmanuel Bourg) Date: Sat, 21 May 2016 22:28:50 +0200 Subject: [Debian-med-packaging] Problems to find classes that should be in itext1.jar In-Reply-To: <20160521113423.GM5019@an3as.eu> References: <20160521113423.GM5019@an3as.eu> Message-ID: <983252db-edfc-1d8f-0e29-8a11b7d55258@apache.org> Le 21/05/2016 ? 13:34, Andreas Tille a ?crit : > I'm > stumbling upon classes which should be found in itext1.jar but the build > process can't finde these. What are the missing classes? Emmanuel Bourg From vdanjean.ml at free.fr Sat May 21 21:40:11 2016 From: vdanjean.ml at free.fr (Vincent Danjean) Date: Sat, 21 May 2016 23:40:11 +0200 Subject: [Debian-med-packaging] Trying to update htsjdk but some tests are failing In-Reply-To: <20160520215035.GI5019@an3as.eu> References: <20160520095105.GZ5019@an3as.eu> <573F62F1.80103@free.fr> <20160520215035.GI5019@an3as.eu> Message-ID: <5740D5BB.1090501@free.fr> Le 20/05/2016 23:50, Andreas Tille a ?crit : > On Fri, May 20, 2016 at 09:18:09PM +0200, Vincent Danjean wrote: >> I'm not sure if the right fix is in the test suite (as I propose) >> or in the DeflaterFactory class. So, I did not commit anything for >> now. > > Please be so kind to commit. Thanks. Done Regards Vincent From noreply at release.debian.org Sun May 22 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sun, 22 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] mrs is marked for autoremoval from testing Message-ID: mrs 6.0.5+dfsg-1 is marked for autoremoval from testing on 2016-05-26 It is affected by these RC bugs: 822466: mrs: FTBFS: error: 'log' was not declared in this scope 816569: mrs: FTBFS with GCC 6: was not declared in this scope From noreply at release.debian.org Sun May 22 04:39:02 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sun, 22 May 2016 04:39:02 +0000 Subject: [Debian-med-packaging] concavity is marked for autoremoval from testing Message-ID: concavity 0.1+dfsg-1 is marked for autoremoval from testing on 2016-05-23 It is affected by these RC bugs: 822382: concavity: non-free files (NC) From costamagnagianfranco at yahoo.it Sun May 22 06:48:36 2016 From: costamagnagianfranco at yahoo.it (Gianfranco Costamagna) Date: Sun, 22 May 2016 06:48:36 +0000 (UTC) Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <20160521155346.GR5019@an3as.eu> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> <20160521155346.GR5019@an3as.eu> Message-ID: <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> Hi, >after the build issues in clapack[1] were solved and I was even able to >create shared libraries I wonder how I can properly set a sensible >SONAME. I tried to do this via SET_TARGET_PROPERTIES but failed. this is what I did on ettercap https://sources.debian.net/src/ettercap/1:0.8.2-2/src/CMakeLists.txt/#L213 it works, as long as you create the library with add_library I guess >Another question is how I could link against the Debian packaged f2c >rather than building the one that comes with clapack upstream. I would say: remove the add_subdirectory (line 21) and then: 1) create a "FindF2C.cmake" file and use it as helper (that would be the best and upstreamable choice you can find some examples in "ettercap/cmake/Modules/Find*" 2) just include_directories for helping it to find the .h file (if not in standard directory) and target_link_libraries of the .so file. G. [1] https://anonscm.debian.org/git/debian-science/packages/clapack.git On Mon, May 16, 2016 at 12:21:06PM +0200, Gert Wollny wrote: > Am Montag, den 16.05.2016, 10:16 +0000 schrieb Gianfranco Costamagna: > > Hi Gert! > > > > > > > > I think, since in this case the (empty) format string passed to the > > > printf call is not user generated there is no security problem to > > > be exploited. > > > > yes, sure, but disabling this flag has a nasty side-effect, it is > > disabled in the *whole* build, possibly > > hiding more serious issues somewhere else. > > Of course, that's why I gave the #pragma based disabling that can be > fitted tightly to the offending code. > > Best, > Gert > > > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sun May 22 09:02:48 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 09:02:48 +0000 Subject: [Debian-med-packaging] Processing of smalt_0.7.6-5_amd64.changes Message-ID: smalt_0.7.6-5_amd64.changes uploaded successfully to localhost along with the files: smalt_0.7.6-5.dsc smalt_0.7.6-5.debian.tar.xz smalt-dbgsym_0.7.6-5_amd64.deb smalt-examples_0.7.6-5_all.deb smalt_0.7.6-5_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 22 09:08:03 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 09:08:03 +0000 Subject: [Debian-med-packaging] Processing of bowtie2_2.2.9-2_amd64.changes Message-ID: bowtie2_2.2.9-2_amd64.changes uploaded successfully to localhost along with the files: bowtie2_2.2.9-2.dsc bowtie2_2.2.9-2.debian.tar.xz bowtie2-dbgsym_2.2.9-2_amd64.deb bowtie2-examples_2.2.9-2_all.deb bowtie2_2.2.9-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 22 09:28:24 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 09:28:24 +0000 Subject: [Debian-med-packaging] Processing of rna-star_2.5.2a+dfsg-2_amd64.changes Message-ID: rna-star_2.5.2a+dfsg-2_amd64.changes uploaded successfully to localhost along with the files: rna-star_2.5.2a+dfsg-2.dsc rna-star_2.5.2a+dfsg-2.debian.tar.xz rna-star-dbgsym_2.5.2a+dfsg-2_amd64.deb rna-star_2.5.2a+dfsg-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From sascha at steinbiss.name Sun May 22 09:35:17 2016 From: sascha at steinbiss.name (Sascha Steinbiss) Date: Sun, 22 May 2016 09:35:17 +0000 Subject: [Debian-med-packaging] Bug#824997: rna-star: FTBFS on non-64bit archs Message-ID: <146390971757.16212.7054713307531536455.reportbug@vagrant-debian.vagrantup.com> Package: rna-star Version: 2.5.2a+dfsg-1 Severity: normal Dear Maintainer, rna-star >= 2.5.0 fails to build on 32-bit architectures (armel, *i386, mipsel, m68k, sh4), mostly due to the missing __uint128_t type, which is apparently not available on these platforms. Indeed, in their README file upstream explicitly lists x86_64 as a requirement. I propose to remove the failing ones from the list of supported architectures in d/control. Any comments? Thanks Sascha From ftpmaster at ftp-master.debian.org Sun May 22 10:19:45 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 10:19:45 +0000 Subject: [Debian-med-packaging] bowtie2_2.2.9-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sat, 21 May 2016 17:18:25 +0000 Source: bowtie2 Binary: bowtie2 bowtie2-examples Architecture: source amd64 all Version: 2.2.9-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: bowtie2 - ultrafast memory-efficient short read aligner bowtie2-examples - Examples for bowtie2 Changes: bowtie2 (2.2.9-2) unstable; urgency=medium . * Team upload. * Make build reproducible. - Remove embedding of build hostname, time and compiler. - Fix help2man wrapper heredoc. - Sort wildcard expansions in Makefile. - Pin down language settings. 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From ftpmaster at ftp-master.debian.org Sun May 22 10:30:00 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 10:30:00 +0000 Subject: [Debian-med-packaging] rna-star_2.5.2a+dfsg-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sat, 21 May 2016 20:53:28 +0000 Source: rna-star Binary: rna-star Architecture: source amd64 Version: 2.5.2a+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.5.2a+dfsg-2) unstable; urgency=medium . * Team upload. * Make build reproducible. - Stop recording build environment in binary. * Enable full hardening. 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From ftpmaster at ftp-master.debian.org Sun May 22 10:30:56 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 10:30:56 +0000 Subject: [Debian-med-packaging] smalt_0.7.6-5_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sat, 21 May 2016 11:05:08 +0000 Source: smalt Binary: smalt smalt-examples Architecture: source amd64 all Version: 0.7.6-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: smalt - Sequence Mapping and Alignment Tool smalt-examples - Sequence Mapping and Alignment Tool (examples) Changes: smalt (0.7.6-5) unstable; urgency=medium . * Team upload. * Make build reproducible. - set CONFIG_SHELL to fixed /bin/bash. * Bump Standards-Version. * Update Homepage entry. * Reword long package description. * Use secure Vcs-Browser. * Add Lintian overrides for timestamped example gzips. * Enable full hardening. 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From andreas at an3as.eu Sun May 22 11:20:27 2016 From: andreas at an3as.eu (Andreas Tille) Date: Sun, 22 May 2016 13:20:27 +0200 Subject: [Debian-med-packaging] Bug#824997: rna-star: FTBFS on non-64bit archs In-Reply-To: <146390971757.16212.7054713307531536455.reportbug@vagrant-debian.vagrantup.com> References: <146390971757.16212.7054713307531536455.reportbug@vagrant-debian.vagrantup.com> Message-ID: <20160522112027.GA9131@an3as.eu> On Sun, May 22, 2016 at 09:35:17AM +0000, Sascha Steinbiss wrote: > I propose to remove the failing ones from the list of supported architectures in > d/control. Any comments? Fine. Feel free to ask ftpmaster for removal of these architectures. Thanks for noticing Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sun May 22 11:54:22 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 11:54:22 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-genefilter_1.54.2-1_amd64.changes Message-ID: r-bioc-genefilter_1.54.2-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-genefilter_1.54.2-1.dsc r-bioc-genefilter_1.54.2.orig.tar.gz r-bioc-genefilter_1.54.2-1.debian.tar.xz r-bioc-genefilter-dbgsym_1.54.2-1_amd64.deb r-bioc-genefilter_1.54.2-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 22 11:59:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 11:59:28 +0000 Subject: [Debian-med-packaging] Processing of charls_1.1.0+dfsg-1_amd64.changes Message-ID: charls_1.1.0+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: charls_1.1.0+dfsg-1.dsc charls_1.1.0+dfsg.orig.tar.xz charls_1.1.0+dfsg-1.debian.tar.xz libcharls-dev_1.1.0+dfsg-1_amd64.deb libcharls1-dbgsym_1.1.0+dfsg-1_amd64.deb libcharls1_1.1.0+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 22 12:18:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 12:18:55 +0000 Subject: [Debian-med-packaging] charls_1.1.0+dfsg-1_amd64.changes REJECTED Message-ID: Version check failed: Your upload included the source package charls, version 1.1.0+dfsg-1, however unstable already has version 1.1.0+dfsg-1. Uploads to unstable must have a higher version than present in unstable. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Sun May 22 12:21:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 12:21:28 +0000 Subject: [Debian-med-packaging] r-bioc-genefilter_1.54.2-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 22 May 2016 13:42:10 +0200 Source: r-bioc-genefilter Binary: r-bioc-genefilter Architecture: source amd64 Version: 1.54.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-genefilter - methods for filtering genes from microarray experiments Changes: r-bioc-genefilter (1.54.2-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: a31898717c4a81745021535c3d1126f534ed387c 2183 r-bioc-genefilter_1.54.2-1.dsc 47a8995b25a13eef56b3e29cb956c86e936ad8d3 1412073 r-bioc-genefilter_1.54.2.orig.tar.gz 7bdc61246251968b8ed1437d41db4bbf46a5bdb9 3716 r-bioc-genefilter_1.54.2-1.debian.tar.xz 60c9af037b1318cc0fc8780bda6ffa382ff53744 37670 r-bioc-genefilter-dbgsym_1.54.2-1_amd64.deb c54cadd17664b75d920abddfeec240c5df5eddd5 1539136 r-bioc-genefilter_1.54.2-1_amd64.deb Checksums-Sha256: 3ae8947d66e7efdb33e19296bba607ebb02110d57c75e2a96de11d8258a5c8b4 2183 r-bioc-genefilter_1.54.2-1.dsc 653ba9046e7410680ad9789abb9bdbd85acabc1467d6b75ad6794b0bb432bfc2 1412073 r-bioc-genefilter_1.54.2.orig.tar.gz f85562d1839cfc6ec6ecde15ade4bed88e75627cca28586ce34a6dbb8d48b937 3716 r-bioc-genefilter_1.54.2-1.debian.tar.xz 8a36ccfde4485ef4b0a2897b15c8b7001ececd255b3832248ca6a97ed618ebc2 37670 r-bioc-genefilter-dbgsym_1.54.2-1_amd64.deb ee01503aa58ee9b38aa87590001d801af56606760508cb164b6f3ebd787476bf 1539136 r-bioc-genefilter_1.54.2-1_amd64.deb Files: 8b0bc5539e05e873da0727cdd431b69f 2183 gnu-r optional r-bioc-genefilter_1.54.2-1.dsc 2c34e32bdfa498eac9ffb0304df5df12 1412073 gnu-r optional r-bioc-genefilter_1.54.2.orig.tar.gz dbdba46d176d62408ac5ac0f9e3a7327 3716 gnu-r optional r-bioc-genefilter_1.54.2-1.debian.tar.xz 6ac3c087d61259795d2c875a5890eef1 37670 debug extra r-bioc-genefilter-dbgsym_1.54.2-1_amd64.deb a3326b6565dec3217f8407d87d15de20 1539136 gnu-r optional r-bioc-genefilter_1.54.2-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXQZ1jAAoJEFeKBJTRxkbR110P/1ojP365pE6x2lnbs5C1dwSc GK+y7iBNz616HtSjkHXtukxQNumz9HJC8AYF89ZF3xEeEDNmv2UUQSfJUfo9+7Q3 8hk/NZK90wa73DMkxL5NHUcIOmFj7r4D0+8dZnqZfvdlDTK6p7CyxlUPsO2oLdI4 dxAX9bzV9uFLCqoKvida7Cdz6Q+fgfwbo8Xzdnn/i7kggCj35GyfKuXM2U14RkHv 7lMJI21BO160PxxKrbU1u33h5E6jgj6odaOk0YIyFG8k+wIUQeN4cBAIdqMzXGnC xJL6o3BZwu0DC8wMS5gnn9tmtfr83+YPbd5lKMISpdx+fcfB2vBSx3by1mJYvqwj Z1QCtFeFmSpxGTOX0vvb/3ufR5L1eksiT8FSkNFfQwrh9ifwFYM9hDsuFSs7/Hjc IEvNVMTww7gpheQWJ+3A3krN4vYW7GOcCBOM/SY6vw0XDlZCG0QhtVZBkq922kOM 3WE+zR5kPHGUUxEl5yABT2bcEfPeOt7gMwSXJ7L9F9pwFKfN+5SXAe+uUpjOyiVy TqTQksau8VwLYGvzARkKAaTDWZkh5kMtmMfUINVybt4hjjqMbu1fm3q+f0pLdvf/ LieonGALGA9Rzy8QXgqgZT52bqme/+HGxd5QfDEoKfRm2w6AmoNzaisBEfVOBg4j 48eZRml72a0J62yCvi46 =KlYg -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From satta at tetrinetsucht.de Sun May 22 13:50:19 2016 From: satta at tetrinetsucht.de (Sascha Steinbiss) Date: Sun, 22 May 2016 14:50:19 +0100 Subject: [Debian-med-packaging] Bug#824997: Bug#824997: rna-star: FTBFS on non-64bit archs In-Reply-To: <20160522112027.GA9131@an3as.eu> References: <146390971757.16212.7054713307531536455.reportbug@vagrant-debian.vagrantup.com> <20160522112027.GA9131@an3as.eu> Message-ID: <64B8AA08-1D59-4EFD-AB42-C01602516FC3@tetrinetsucht.de> Hi Andreas, thanks for the quick reply. >> I propose to remove the failing ones from the list of supported architectures in >> d/control. Any comments? > > Fine. Feel free to ask ftpmaster for removal of these architectures. Ok, will do later. I?m quite inclined to just put in *amd64 as upstream does not say anything about supporting arm64, ppc64el, mips64el and the like. An alternative would be to add a quick build time test for those arch, but if these fail I would need to request their removal anyway as they are currently built untested. Any preferences? Cheers Sascha From andreas at an3as.eu Sun May 22 14:04:45 2016 From: andreas at an3as.eu (Andreas Tille) Date: Sun, 22 May 2016 16:04:45 +0200 Subject: [Debian-med-packaging] Bug#824997: Bug#824997: rna-star: FTBFS on non-64bit archs In-Reply-To: <64B8AA08-1D59-4EFD-AB42-C01602516FC3@tetrinetsucht.de> References: <146390971757.16212.7054713307531536455.reportbug@vagrant-debian.vagrantup.com> <20160522112027.GA9131@an3as.eu> <64B8AA08-1D59-4EFD-AB42-C01602516FC3@tetrinetsucht.de> Message-ID: <20160522140445.GE9131@an3as.eu> On Sun, May 22, 2016 at 02:50:19PM +0100, Sascha Steinbiss wrote: > > > > Fine. Feel free to ask ftpmaster for removal of these architectures. > > Ok, will do later. I?m quite inclined to just put in *amd64 as upstream does not say anything about supporting arm64, ppc64el, mips64el and the like. Only very few upstreams are explicitly specifying these architectures. The default procedure is to upload for all architectures a package builds without problems (porters are even providing patches for *building* - without knowing whether a package really runs as expected). Since we do not have reasons to assume that a package does not run on an "not so common" architecture before somebody files a bug report we assume that everything works as expected. > An alternative would be to add a quick build time test for those arch, but if these fail I would need to request their removal anyway as they are currently built untested. Any preferences? I confirm that providing build time tests is a good idea for any of our packages - so also for this. Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sun May 22 14:21:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 14:21:12 +0000 Subject: [Debian-med-packaging] Processing of charls_1.1.0+dfsg-2_amd64.changes Message-ID: charls_1.1.0+dfsg-2_amd64.changes uploaded successfully to localhost along with the files: charls_1.1.0+dfsg-2.dsc charls_1.1.0+dfsg-2.debian.tar.xz libcharls-dev_1.1.0+dfsg-2_amd64.deb libcharls1-dbgsym_1.1.0+dfsg-2_amd64.deb libcharls1_1.1.0+dfsg-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From noreply at release.debian.org Sun May 22 16:39:14 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 22 May 2016 16:39:14 +0000 Subject: [Debian-med-packaging] snp-sites 2.3.2-1 MIGRATED to testing Message-ID: FYI: The status of the snp-sites source package in Debian's testing distribution has changed. Previous version: 2.3.1-1 Current version: 2.3.2-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Sun May 22 16:49:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 16:49:58 +0000 Subject: [Debian-med-packaging] charls_1.1.0+dfsg-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 22 May 2016 16:11:53 +0200 Source: charls Binary: libcharls-dev libcharls1 Architecture: source amd64 Version: 1.1.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libcharls-dev - Implementation of the JPEG-LS standard (development libraries) libcharls1 - Implementation of the JPEG-LS standard Changes: charls (1.1.0+dfsg-2) unstable; urgency=medium . [ Mathieu Malaterre ] * Adjust symbols . [ Andreas Tille ] * Check whether we can use d-shlibs but no static lib is build. Leave the code for documentation Checksums-Sha1: b19e2ca79684df56bf232fb230dae3e44fc64d03 2057 charls_1.1.0+dfsg-2.dsc d3aef7ae396c2a9699f97965f2dfdfa173c09580 5172 charls_1.1.0+dfsg-2.debian.tar.xz 3984d41ab92183228f1465048540861faf434e72 21596 libcharls-dev_1.1.0+dfsg-2_amd64.deb 678c43a02039c44632193f1cb9f0fa439a46e67f 391512 libcharls1-dbgsym_1.1.0+dfsg-2_amd64.deb 62976fdc31e892973e55f44bce6979053fc3759e 56042 libcharls1_1.1.0+dfsg-2_amd64.deb Checksums-Sha256: 50016f859c4b1fb6df77b4af533c6df246eb48f2bf31af6583ff9d988dbf0747 2057 charls_1.1.0+dfsg-2.dsc 391ff96bb5e7c096caed443441c1ca477b54ce07e726adf66bb5f92dc4201b05 5172 charls_1.1.0+dfsg-2.debian.tar.xz ad7381d1468ea331338146298ecc514b184eff6736eba000ed68375e0735def5 21596 libcharls-dev_1.1.0+dfsg-2_amd64.deb 79037e64caa8389e819846915374d8506a270289a5497da4179aadca08bfe88d 391512 libcharls1-dbgsym_1.1.0+dfsg-2_amd64.deb a1acb4c81d1d97c422deafc10fe0ba79650c7633a5910730b0b01f02a4d54414 56042 libcharls1_1.1.0+dfsg-2_amd64.deb Files: 0e8b1f453a6ea4b7d44e8443f2b02db2 2057 science optional charls_1.1.0+dfsg-2.dsc bdb8d2c095b53e5f748965956c4126db 5172 science optional charls_1.1.0+dfsg-2.debian.tar.xz b5a6e1add15cbd300d1935137edd294b 21596 libdevel optional libcharls-dev_1.1.0+dfsg-2_amd64.deb 8d4cff178bd04ffd6c9bff437f7e4d76 391512 debug extra libcharls1-dbgsym_1.1.0+dfsg-2_amd64.deb c2875765463eba984554f520b0a996cf 56042 libs optional libcharls1_1.1.0+dfsg-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXQb/WAAoJEFeKBJTRxkbRaG8P/08ajM+S4QcUBJc7qp11ybwY v6gLct9pwfNyXnf4TJBEWHK2vt06Y5O9PLEQaw3VEj3IRHLNB0/9ijXUzt4Ecais mRGZc8LNpRxq22zsocNMtBJZHNOOZooRcszgmTs0L2DSqYZGCPk7B1EM+4s/s+GR bvtspxGMK8xYkaNai5RcjZ1/XtihRjdRzxAeGEzL4+d4G1Pu651Ahlpa20+G0sEl 37GQ5sTxlsnzaF86tVY4sqK+wrR8Md3Zfnpf9hw3jMOUVLb8TF88WM0bIJGK7vyM oxd+DoSZrR/7OC73z4MESjrX88r5X3jnz6eTWnzBGnOKaPswIWzopeSp3EN8nP/C XK+XiCkuJimOAdNBVaFnH6pzhkGHu3eXtjGf9HvaB1XMS1I5IQDjOZB3m1bAs21c /RZ+4PaUl+wSLz5DWKiUbsnekATkqVTUin2wy5VDByyeRBfOVCk1ouRiadRQCRXF Xyd8YENNNOun9B+IsEozv1Q9XOKkdJNMrSUv158yczJwfFQ+elsuB8qjsCJwAjph gDieE2E1PM2vP7GQp4P2BrfCJ6u6v0xRi88mbjy5OX1InfCEozXvzD27lxu7Tg4K 0PCCn4mEOwh+wNrM+vymYlOl2F2DkixuG9zpnFBa9ETwj8z+1iGiKd/aHRODpXUy r/WhpYPk7kZjY4X5/FDT =SN8y -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sun May 22 18:00:20 2016 From: ftpmaster at ftp-master.debian.org (Thorsten Alteholz) Date: Sun, 22 May 2016 18:00:20 +0000 Subject: [Debian-med-packaging] beast2-mcmc_2.4.1+dfsg-1_amd64.changes REJECTED Message-ID: Hi Andreas, please mention all licenses from the source tarball in your debian/copyright. Thanks! Thorsten === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From tille at debian.org Sun May 22 19:43:01 2016 From: tille at debian.org (Andreas Tille) Date: Sun, 22 May 2016 21:43:01 +0200 Subject: [Debian-med-packaging] Problems to find classes that should be in itext1.jar In-Reply-To: <983252db-edfc-1d8f-0e29-8a11b7d55258@apache.org> References: <20160521113423.GM5019@an3as.eu> <983252db-edfc-1d8f-0e29-8a11b7d55258@apache.org> Message-ID: <20160522194301.GJ9131@an3as.eu> On Sat, May 21, 2016 at 10:28:50PM +0200, Emmanuel Bourg wrote: > Le 21/05/2016 ? 13:34, Andreas Tille a ?crit : > > > I'm > > stumbling upon classes which should be found in itext1.jar but the build > > process can't finde these. > > What are the missing classes? ... CLASSPATH=/usr/share/java/commons-httpclient.jar:/usr/share/java/commons-lang.jar:/usr/share/java/itext1-1.4.jar jh_build --javacopts='-target 1.7' --javacopts='-source 1.7' mesquite.jar Source LibrarySource find Source LibrarySource -name *.java -and -type f -print0 | xargs -s 512000 -0 /usr/lib/jvm/default-java/bin/javac -g -cp /usr/share/java/commons-httpclient.jar:/usr/share/java/commons-lang.jar:/usr/share/java/itext1-1.4.jar:debian/_jh_build.mesquite -d debian/_jh_build.mesquite -target 1.7 -source 1.7 warning: [options] bootstrap class path not set in conjunction with -source 1.7 LibrarySource/com/lowagie/text/Rectangle.java:53: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfWriter.java:53: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:52: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:54: error: package headless.awt.geom does not exist import headless.awt.geom.AffineTransform; ^ LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:55: error: package headless.awt.print does not exist import headless.awt.print.PrinterJob; ^ LibrarySource/com/lowagie/text/Image.java:60: error: package headless.awt.color does not exist import headless.awt.color.ICC_Profile; ^ LibrarySource/com/lowagie/text/Rectangle.java:118: error: cannot find symbol protected Color color = null; ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:121: error: cannot find symbol protected Color borderColorLeft = null; ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:124: error: cannot find symbol protected Color borderColorRight = null; ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:127: error: cannot find symbol protected Color borderColorTop = null; ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:130: error: cannot find symbol protected Color borderColorBottom = null; ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:149: error: cannot find symbol protected Color background = null; ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:412: error: cannot find symbol public void setBorderColor(Color value) { ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:420: error: cannot find symbol public void setBorderColorRight(Color value) ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:429: error: cannot find symbol public void setBorderColorLeft(Color value) ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:438: error: cannot find symbol public void setBorderColorTop(Color value) ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:447: error: cannot find symbol public void setBorderColorBottom(Color value) ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:459: error: cannot find symbol public void setBackgroundColor(Color value) { ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:633: error: cannot find symbol public Color borderColor() { ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:643: error: cannot find symbol public Color backgroundColor() { ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:706: error: cannot find symbol public Color getBorderColorLeft() ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:715: error: cannot find symbol public Color getBorderColorRight() ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:724: error: cannot find symbol public Color getBorderColorTop() ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/Rectangle.java:733: error: cannot find symbol public Color getBorderColorBottom() ^ symbol: class Color location: class Rectangle LibrarySource/com/lowagie/text/pdf/PdfDocument.java:53: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfICCBased.java:48: error: package headless.awt.color does not exist import headless.awt.color.ICC_Profile; ^ LibrarySource/com/lowagie/text/Table.java:56: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/Table.java:57: error: package headless.awt does not exist import headless.awt.Dimension; ^ LibrarySource/com/lowagie/text/Table.java:58: error: package headless.awt does not exist import headless.awt.Point; ^ LibrarySource/com/lowagie/text/pdf/PdfOutline.java:58: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfSpotColor.java:53: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfWriter.java:1526: error: cannot find symbol ColorDetails addSimplePatternColorspace(Color color) { ^ symbol: class Color location: class PdfWriter LibrarySource/com/lowagie/text/pdf/PdfShading.java:49: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfPatternPainter.java:50: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfAnnotation.java:55: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:1680: error: cannot find symbol public PdfPatternPainter createPattern(float width, float height, float xstep, float ystep, Color color) { ^ symbol: class Color location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:1702: error: cannot find symbol public PdfPatternPainter createPattern(float width, float height, Color color) { ^ symbol: class Color location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:1905: error: cannot find symbol public void setColorStroke(Color color) { ^ symbol: class Color location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:1942: error: cannot find symbol public void setColorFill(Color color) { ^ symbol: class Color location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2023: error: cannot find symbol void outputColorNumbers(Color color, float tint) { ^ symbol: class Color location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2055: error: cannot find symbol public void setPatternFill(PdfPatternPainter p, Color color) { ^ symbol: class Color location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2067: error: cannot find symbol public void setPatternFill(PdfPatternPainter p, Color color, float tint) { ^ symbol: class Color location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2085: error: cannot find symbol public void setPatternStroke(PdfPatternPainter p, Color color) { ^ symbol: class Color location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2097: error: cannot find symbol public void setPatternStroke(PdfPatternPainter p, Color color, float tint) { ^ symbol: class Color location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2514: error: cannot find symbol public java.awt.Graphics2D createPrinterGraphicsShapes(float width, float height, PrinterJob printerJob) { ^ symbol: class PrinterJob location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2535: error: cannot find symbol public java.awt.Graphics2D createPrinterGraphics(float width, float height, PrinterJob printerJob) { ^ symbol: class PrinterJob location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2560: error: cannot find symbol public java.awt.Graphics2D createPrinterGraphics(float width, float height, boolean convertImagesToJPEG, float quality, PrinterJob printerJob) { ^ symbol: class PrinterJob location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2585: error: cannot find symbol public java.awt.Graphics2D createPrinterGraphicsShapes(float width, float height, boolean convertImagesToJPEG, float quality, PrinterJob printerJob) { ^ symbol: class PrinterJob location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/FontMapper.java:50: error: package headless.awt does not exist import headless.awt.Font; ^ LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2608: error: cannot find symbol public java.awt.Graphics2D createPrinterGraphics(float width, float height, FontMapper fontMapper, PrinterJob printerJob) { ^ symbol: class PrinterJob location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2635: error: cannot find symbol public java.awt.Graphics2D createPrinterGraphics(float width, float height, FontMapper fontMapper, boolean convertImagesToJPEG, float quality, PrinterJob printerJob) { ^ symbol: class PrinterJob location: class PdfContentByte LibrarySource/com/lowagie/text/pdf/PdfContentByte.java:2707: error: cannot find symbol public void transform(AffineTransform af) { ^ symbol: class AffineTransform location: class PdfContentByte LibrarySource/com/lowagie/text/Image.java:239: error: cannot find symbol protected ICC_Profile profile = null; ^ symbol: class ICC_Profile location: class Image LibrarySource/com/lowagie/text/Image.java:1620: error: cannot find symbol public void tagICC(ICC_Profile profile) { ^ symbol: class ICC_Profile location: class Image LibrarySource/com/lowagie/text/Image.java:1638: error: cannot find symbol public ICC_Profile getICCProfile() { ^ symbol: class ICC_Profile location: class Image LibrarySource/com/lowagie/text/pdf/PdfICCBased.java:62: error: cannot find symbol PdfICCBased(ICC_Profile profile) { ^ symbol: class ICC_Profile location: class PdfICCBased LibrarySource/com/lowagie/text/Table.java:172: error: cannot find symbol private Point curPosition = new Point(0, 0); ^ symbol: class Point location: class Table LibrarySource/com/lowagie/text/Cell.java:53: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/Table.java:566: error: cannot find symbol public void addCell(Cell aCell, Point aLocation) throws BadElementException { ^ symbol: class Point location: class Table LibrarySource/com/lowagie/text/Table.java:622: error: cannot find symbol public void addCell(Phrase content, Point location) throws BadElementException { ^ symbol: class Point location: class Table LibrarySource/com/lowagie/text/Table.java:661: error: cannot find symbol public void addCell(String content, Point location) throws BadElementException { ^ symbol: class Point location: class Table LibrarySource/com/lowagie/text/Table.java:698: error: cannot find symbol public void insertTable(Table aTable, Point aLocation) { ^ symbol: class Point location: class Table LibrarySource/com/lowagie/text/Table.java:780: error: cannot find symbol public void setDefaultCellBorderColor(Color color) { ^ symbol: class Color location: class Table LibrarySource/com/lowagie/text/Table.java:791: error: cannot find symbol public void setDefaultCellBackgroundColor(Color color) { ^ symbol: class Color location: class Table LibrarySource/com/lowagie/text/Table.java:1263: error: cannot find symbol public Dimension getDimension() { ^ symbol: class Dimension location: class Table LibrarySource/com/lowagie/text/Table.java:1523: error: cannot find symbol private boolean isValidLocation(Cell aCell, Point aLocation) { ^ symbol: class Point location: class Table LibrarySource/com/lowagie/text/Table.java:1559: error: cannot find symbol private void placeCell(ArrayList someRows, Cell aCell, Point aPosition) { ^ symbol: class Point location: class Table LibrarySource/com/lowagie/text/Table.java:1663: error: cannot find symbol private void setCurrentLocationToNextValidPosition(Point aLocation) { ^ symbol: class Point location: class Table LibrarySource/com/lowagie/text/pdf/PdfPRow.java:58: error: package headless.awt does not exist import headless.awt.Color; ^ LibrarySource/com/lowagie/text/pdf/PdfOutline.java:104: error: cannot find symbol private Color color; ^ symbol: class Color location: class PdfOutline LibrarySource/com/lowagie/text/pdf/PdfOutline.java:514: error: cannot find symbol public Color getColor() { ^ symbol: class Color location: class PdfOutline LibrarySource/com/lowagie/text/pdf/PdfOutline.java:522: error: cannot find symbol public void setColor(Color color) { ^ symbol: class Color location: class PdfOutline LibrarySource/com/lowagie/text/pdf/PdfSpotColor.java:70: error: cannot find symbol public Color altcs; ^ symbol: class Color location: class PdfSpotColor LibrarySource/com/lowagie/text/pdf/PdfSpotColor.java:81: error: cannot find symbol public PdfSpotColor(String name, float tint, Color altcs) { ^ symbol: class Color location: class PdfSpotColor LibrarySource/com/lowagie/text/pdf/PdfSpotColor.java:99: error: cannot find symbol public Color getAlternativeCS() { ^ symbol: class Color location: class PdfSpotColor LibrarySource/com/lowagie/text/pdf/PdfShading.java:69: error: cannot find symbol private Color cspace; ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:82: error: cannot find symbol protected void setColorSpace(Color color) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:112: error: cannot find symbol Color getColorSpace() { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:120: error: cannot find symbol public static void checkCompatibleColors(Color c1, Color c2) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:120: error: cannot find symbol public static void checkCompatibleColors(Color c1, Color c2) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:131: error: cannot find symbol public static float[] getColorArray(Color color) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:152: error: cannot find symbol public static PdfShading type1(PdfWriter writer, Color colorSpace, float domain[], float tMatrix[], PdfFunction function) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:166: error: cannot find symbol public static PdfShading type2(PdfWriter writer, Color colorSpace, float coords[], float domain[], PdfFunction function, boolean extend[]) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:184: error: cannot find symbol public static PdfShading type3(PdfWriter writer, Color colorSpace, float coords[], float domain[], PdfFunction function, boolean extend[]) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:191: error: cannot find symbol public static PdfShading simpleAxial(PdfWriter writer, float x0, float y0, float x1, float y1, Color startColor, Color endColor, boolean extendStart, boolean extendEnd) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:191: error: cannot find symbol public static PdfShading simpleAxial(PdfWriter writer, float x0, float y0, float x1, float y1, Color startColor, Color endColor, boolean extendStart, boolean extendEnd) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:198: error: cannot find symbol public static PdfShading simpleAxial(PdfWriter writer, float x0, float y0, float x1, float y1, Color startColor, Color endColor) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:198: error: cannot find symbol public static PdfShading simpleAxial(PdfWriter writer, float x0, float y0, float x1, float y1, Color startColor, Color endColor) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:202: error: cannot find symbol public static PdfShading simpleRadial(PdfWriter writer, float x0, float y0, float r0, float x1, float y1, float r1, Color startColor, Color endColor, boolean extendStart, boolean extendEnd) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:202: error: cannot find symbol public static PdfShading simpleRadial(PdfWriter writer, float x0, float y0, float r0, float x1, float y1, float r1, Color startColor, Color endColor, boolean extendStart, boolean extendEnd) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:209: error: cannot find symbol public static PdfShading simpleRadial(PdfWriter writer, float x0, float y0, float r0, float x1, float y1, float r1, Color startColor, Color endColor) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfShading.java:209: error: cannot find symbol public static PdfShading simpleRadial(PdfWriter writer, float x0, float y0, float r0, float x1, float y1, float r1, Color startColor, Color endColor) { ^ symbol: class Color location: class PdfShading LibrarySource/com/lowagie/text/pdf/PdfPatternPainter.java:60: error: cannot find symbol protected Color defaultColor; ^ symbol: class Color location: class PdfPatternPainter LibrarySource/com/lowagie/text/pdf/PdfPatternPainter.java:82: error: cannot find symbol PdfPatternPainter(PdfWriter wr, Color defaultColor) { ^ symbol: class Color location: class PdfPatternPainter LibrarySource/com/lowagie/text/pdf/PdfPatternPainter.java:182: error: cannot find symbol public Color getDefaultColor() { ^ symbol: class Color location: class PdfPatternPainter LibrarySource/com/lowagie/text/pdf/PdfPatternPainter.java:326: error: cannot find symbol public void setColorStroke(Color color) { ^ symbol: class Color location: class PdfPatternPainter LibrarySource/com/lowagie/text/pdf/PdfPatternPainter.java:334: error: cannot find symbol public void setColorFill(Color color) { ^ symbol: class Color location: class PdfPatternPainter LibrarySource/com/lowagie/text/pdf/PdfPatternPainter.java:366: error: cannot find symbol public void setPatternFill(PdfPatternPainter p, Color color, float tint) { ^ symbol: class Color location: class PdfPatternPainter LibrarySource/com/lowagie/text/pdf/PdfPatternPainter.java:374: error: cannot find symbol public void setPatternStroke(PdfPatternPainter p, Color color, float tint) { ^ symbol: class Color location: class PdfPatternPainter LibrarySource/com/lowagie/text/pdf/PdfAnnotation.java:544: error: cannot find symbol public void setColor(Color color) { ^ symbol: class Color location: class PdfAnnotation Source/org/apache/hivemind/util/PropertyAdaptor.java:166: warning: non-varargs call of varargs method with inexact argument type for last parameter; return _readMethod.invoke(target, null); ^ cast to Object for a varargs call cast to Object[] for a non-varargs call and to suppress this warning Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 errors 2 warnings debian/rules:21: recipe for target 'override_dh_auto_build' failed make[1]: *** [override_dh_auto_build] Error 123 make[1]: Leaving directory '/home/andreas/debian-maintain/alioth/debian-med_git/build-area/mesquite-3.04+dfsg' debian/rules:12: die Regel f?r Ziel ?build? scheiterte make: *** [build] Fehler 2 dpkg-buildpackage: Fehler: Fehler-Exitstatus von debian/rules build war 2 -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sun May 22 20:18:11 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 20:18:11 +0000 Subject: [Debian-med-packaging] Processing of maffilter_1.1.0-1+dfsg-2_source.changes Message-ID: maffilter_1.1.0-1+dfsg-2_source.changes uploaded successfully to localhost along with the files: maffilter_1.1.0-1+dfsg-2.dsc maffilter_1.1.0-1+dfsg-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ebourg at apache.org Sun May 22 20:18:58 2016 From: ebourg at apache.org (Emmanuel Bourg) Date: Sun, 22 May 2016 22:18:58 +0200 Subject: [Debian-med-packaging] Problems to find classes that should be in itext1.jar In-Reply-To: <20160522194301.GJ9131@an3as.eu> References: <20160521113423.GM5019@an3as.eu> <983252db-edfc-1d8f-0e29-8a11b7d55258@apache.org> <20160522194301.GJ9131@an3as.eu> Message-ID: <10ffcc97-11f3-9a89-25d7-ae8c334657fd@apache.org> Le 22/05/2016 ? 21:43, Andreas Tille a ?crit : > CLASSPATH=/usr/share/java/commons-httpclient.jar:/usr/share/java/commons-lang.jar:/usr/share/java/itext1-1.4.jar jh_build --javacopts='-target 1.7' --javacopts='-source 1.7' mesquite.jar Source LibrarySource > find Source LibrarySource -name *.java -and -type f -print0 | xargs -s 512000 -0 /usr/lib/jvm/default-java/bin/javac -g -cp /usr/share/java/commons-httpclient.jar:/usr/share/java/commons-lang.jar:/usr/share/java/itext1-1.4.jar:debian/_jh_build.mesquite -d debian/_jh_build.mesquite -target 1.7 -source 1.7 > warning: [options] bootstrap class path not set in conjunction with -source 1.7 > LibrarySource/com/lowagie/text/Rectangle.java:53: error: package headless.awt does not exist > import headless.awt.Color; > ^ > LibrarySource/com/lowagie/text/pdf/PdfWriter.java:53: error: package headless.awt does not exist > import headless.awt.Color; > ^ iText doesn't contain any headless.awt.* class. It looks like the iText code was copied and modified the turn the 'import java.awt.*' statements into 'import headless.awt.*'. I guess as some point they copied and relocated the java.awt classes to disable the exceptions on systems without a display. Since Java 1.4 this can be avoided by setting the java.awt.headless property to true. I think you have two options: 1. remove the iText source files from the LibrarySource directory and use the libitext1-java package instead 2. if it doesn't work because the itext code was further modified, patch it and replace 'headless.awt' with 'java.awt' Emmanuel Bourg From ftpmaster at ftp-master.debian.org Sun May 22 22:24:49 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 22 May 2016 22:24:49 +0000 Subject: [Debian-med-packaging] maffilter_1.1.0-1+dfsg-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 22 May 2016 21:58:51 +0200 Source: maffilter Binary: maffilter maffilter-examples Architecture: source Version: 1.1.0-1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: maffilter - process genome alignment in the Multiple Alignment Format maffilter-examples - process genome alignment in the Multiple Alignment Format (exampl Changes: maffilter (1.1.0-1+dfsg-2) unstable; urgency=medium . * Fix permissions * Properly install executable and info file Checksums-Sha1: f79bf0fcb823dc8f8a7a09ca818808ebd2532994 2215 maffilter_1.1.0-1+dfsg-2.dsc f73999abd714da4ab3b251c8bb1269665c42c912 2996 maffilter_1.1.0-1+dfsg-2.debian.tar.xz Checksums-Sha256: a8957c2db8adf0a1ca1aa931a7914ab074385f7f7f08249ca11b362a55e9813d 2215 maffilter_1.1.0-1+dfsg-2.dsc 7d4aa315114ca4ae5cbc269fbab7ddd0d48f2f790f413ae33fa858efad374767 2996 maffilter_1.1.0-1+dfsg-2.debian.tar.xz Files: 8c431ac80466ab611c5685fe567f8d56 2215 science optional maffilter_1.1.0-1+dfsg-2.dsc b0e5163493bdc6ff441273128ccc444a 2996 science optional maffilter_1.1.0-1+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXQhPGAAoJEFeKBJTRxkbRTrwQAJb53DctMQPNKPLCPc3Ptz5K oKwHuK/bcVdRmL6Mnyv5aEH7DA0CDzKf4KVJcw9FRxK/Y24UfqMhYcJDayji7cvU 24P6Wc2Y9MFOIjjkwcBnHBlWKa8f3NV2ay6TXgKB5Sr4DGks5HJ9NGOjUgaxsn4F 4V8dpoyx8T/zsJxuWxnUw9ZAMrKZ+PVb8bBnSZzG8QG541Sr3ZW+JLbC1VhGe8bg YKMcDTv3Wyx1N/hpf5LeZeSvXF3iCoHQkB8LnjjQTniQrUwcd6udDT2biuoxnj/m pRM2P5G/lb4aNWV0Oq6fxZxc+fhXdJB52mjptE9loIr8i1CwSthquKFJW3/yji72 vALjBE1xhZi4YwjN/10rTunrhGdZaezQHPYZvc3baore251UN00Es8HkW5rmaFk9 9T93huLmyvxuIL6c+TS27/2vKptEYpfrVn1L57IyHEjEDNiCaxpBrDDtIkgy2AMD wX3ZKaRKyOpRmJa0HGwTh+0opVntU5Y6kQ1uGmYrW/VOyX2aJV1udQuzHjIaoXl/ F9A81UX3nVIh8tyTYEpLc9990ekaHSczXiQumcnwwoO1dU7YD92vnm1IgT+Drx30 1fHGuSAbdZ3S6ewXBQfgwwqSkH5YTElgKA0h/srxgp2ZTa4HOb/AgXdofab9I61N ps26+FT0oswWCJTaHV4y =HdND -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From leonardossr at gmail.com Sun May 22 23:19:23 2016 From: leonardossr at gmail.com (Leonardo Rocha) Date: Sun, 22 May 2016 20:19:23 -0300 Subject: [Debian-med-packaging] Bug#825046: biomaj: [INTL:pt_BR] Brazilian Portuguese debconf templates translation In-Reply-To: <57423DA5.6010005@gmail.com> References: <57423DA5.6010005@gmail.com> Message-ID: <57423E7B.6070406@gmail.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Package: biomaj Tags: l10n patch Severity: wishlist Hello, Please, Could you update the Brazilian Portuguese Translation? Attached you will find the file pt_BR.po. It is UTF-8 encoded and it is tested with msgfmt and podebconf-display-po. Kind regards. On 11-03-2016 16:52, Herbert Fortes (hpfn) wrote: > >>>> Leonardo, eu tinha mandado o arquivo errado. Agora sim segue >>>> o patch. >>> >>> Patch aplicado. Envio novamente para revis?o. >>> >>> Obrigado revisores. >>> >>> >>> > >> Encaminho para ?ltimos coment?rios. > >> No aguardo. > > Ok. > > > abra?o, > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iQIcBAEBCAAGBQJXQj57AAoJECRiL6p+fR/iq6QP/A8Wpi+DW/NasLTTOuIKkzM2 ch1b7ViiXEYwe+IDqmmvh58EmjC4XSpRc/hlcJdlmUetmFjcYySELBMfwX//u80h hDv5dLAW0Hao3N77YOqTtcFuAw1FFuHFfNW5y5ONs1+MWMeqwvpfxX/oZsKulfh1 coSK02DMdIat9LD2qqYpYiI6q3jfDgONsgjS6cInu5BL4YRjHshYpuLfRR9ldnIH ePBqZ+u4BNJ3WAZ3pozX62tbJP1g4yRG3fCrs4uLrfmHkFmJOlCDhDbLq228mkrV Zw27wJjzedqvP7J5aLzEwBRHl6WVs7AwDNpjtw8vLHB0oFPEmRQhjuVqdiDm3Z4x ZFJM1KgI6CikhRCHP3BtNLtqUyrx+bArnad/sFFAlhnIHkg36Ta9JcBk8KPr/1lM n2/OUQSyqcFJrxcyqpsSfqtpYOLygYIGlzonDE8Nq7iIPM9PFGE+k2XKQXfVfHen bs3CNi7ueAG3WMOHQ4ewRKk1sVK3cRRRkxLuFUd2mIIHTjMgqXLHZYYqqoBkSo+B 2+qgG/3zDccjRL7jh9n2R0A7aqf8eo7YOubNaSrTw7lJhoEhGxLMmpieBGeEWPIX 3pOkc2xhwt2wNBHv/BRm+2mhBi/KBIeV/aVKceiPs6YxL7DniArojERRfyAxiJaJ hzcha2F5OB+RcL8olaLB =kgNV -----END PGP SIGNATURE----- -------------- next part -------------- A non-text attachment was scrubbed... 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Name: pt_BR.po.gz.sig.sig Type: application/pgp-signature Size: 543 bytes Desc: not available URL: From noreply at release.debian.org Mon May 23 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Mon, 23 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] sra-sdk is marked for autoremoval from testing Message-ID: sra-sdk 2.3.5-2+dfsg-1 is marked for autoremoval from testing on 2016-06-13 It is affected by these RC bugs: 824402: sra-toolkit: does not load data from fastq files to directory (and probably more problems) From satta at tetrinetsucht.de Mon May 23 08:55:18 2016 From: satta at tetrinetsucht.de (Sascha Steinbiss) Date: Mon, 23 May 2016 09:55:18 +0100 Subject: [Debian-med-packaging] Bug#824997: Bug#824997: rna-star: FTBFS on non-64bit archs In-Reply-To: <20160522140445.GE9131@an3as.eu> References: <146390971757.16212.7054713307531536455.reportbug@vagrant-debian.vagrantup.com> <20160522112027.GA9131@an3as.eu> <64B8AA08-1D59-4EFD-AB42-C01602516FC3@tetrinetsucht.de> <20160522140445.GE9131@an3as.eu> Message-ID: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Hi Andreas, thanks for the input. I was aware of the procedure, but wanted to avoid having to potentially file removals twice. I think I will add a build time test to confirm the binaries are functional, and then ask ftpmaster to remove only ones that don't build+test successfully after that. If the non-Intel amd64 archs turn out to work anyway, even better :) Cheers Sascha >>> Fine. Feel free to ask ftpmaster for removal of these >>> architectures. >> >> Ok, will do later. I?m quite inclined to just put in *amd64 as >> upstream does not say anything about supporting arm64, ppc64el, >> mips64el and the like. > > Only very few upstreams are explicitly specifying these > architectures. The default procedure is to upload for all > architectures a package builds without problems (porters are even > providing patches for *building* - without knowing whether a > package really runs as expected). Since we do not have reasons to > assume that a package does not run on an "not so common" > architecture before somebody files a bug report we assume that > everything works as expected. > >> An alternative would be to add a quick build time test for those >> arch, but if these fail I would need to request their removal >> anyway as they are currently built untested. Any preferences? > > I confirm that providing build time tests is a good idea for any > of our packages - so also for this. > > Kind regards > > Andreas. -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iQEcBAEBCAAGBQJXQsVxAAoJEKjaUsSK1PiGkgQH/jnIo4Z3x7wgCuClgVT4c+nB qcu7pkgaLGKgNpDl3SojeczyuD/qo7Xd0ZM5Caqca4U319/9iPhfABGKgt3PQTAO 5g0gaKR/mnFwsy5PZsIBcH9VHaxmZe0H1jQS6CVnIviqploJm4yst9Ftljv3lS6z FVUpB2D8EYtUI8SCU1O7iDLalq25XsskYlEvViw0iwamTH5AJjyI5k0cQHD72+Bf gchwyuwEALS0Z8wPF3daCcX0hzrv/4XU2APxnj7gET1fMrptnxbZ1WMZ/ScglN85 a9vAGdL1id5RB2i2cDMQ5b+knY0zR28k1C5Hxsp44jjIZxFOId5fw6TN48NbxkU= =GEAX -----END PGP SIGNATURE----- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From andreas at fam-tille.de Mon May 23 10:08:08 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Mon, 23 May 2016 12:08:08 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> <20160521155346.GR5019@an3as.eu> <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> Message-ID: <20160523100808.GA8507@an3as.eu> Hi Gianfranco, your very helpful hints helped me to get some steps forward. However, its not finally done. On Sun, May 22, 2016 at 06:48:36AM +0000, Gianfranco Costamagna wrote: > >Another question is how I could link against the Debian packaged f2c > >rather than building the one that comes with clapack upstream. > > I would say: remove the add_subdirectory (line 21) > and then: > 1) create a "FindF2C.cmake" file and use it as helper > (that would be the best and upstreamable choice > you can find some examples in "ettercap/cmake/Modules/Find*" > > > 2) just include_directories for helping it to find the .h file (if not in standard directory) > and target_link_libraries of the .so file. I think the .h files are not a problem. With my recent changes in Git[1] there is a problem with the linker when running the clapack test suite: ... std.dir/dtrt03.c.o CMakeFiles/xlintstd.dir/dtrt05.c.o CMakeFiles/xlintstd.dir/dtrt06.c.o CMakeFiles/xlintstd.dir/dtzt01.c.o CMakeFiles/xlintstd.dir/dtzt02.c.o CMakeFiles/xlintstd.dir/dgennd.c.o CMakeFiles/xlintstd.dir/ddrvge.c.o CMakeFiles/xlintstd.dir/ddrvgb.c.o CMakeFiles/xlintstd.dir/derrge.c.o CMakeFiles/xlintstd.dir/ddrvpo.c.o CMakeFiles/xlintstd.dir/derrpo.c.o CMakeFiles/xlintstd.dir/dlaord.c.o CMakeFiles/xlintstd.dir/__/__/INSTALL/dsecnd.c.o -o xlintstd -rdynamic ../MATGEN/libtmglib.a ../../SRC/libclapack.so.3.2.1 ../../BLAS/SRC/libcblas.so.3.2.1 -lm -lf2c -Wl,-rpath,/build/clapack-3.2.1/obj-x86_64-linux-gnu/SRC:/build/clapack-3.2.1/obj-x86_64-linux-gnu/BLAS/SRC CMakeFiles/xlintstd.dir/alaerh.c.o: In function `alaerh_': /build/clapack-3.2.1/TESTING/LIN/alaerh.c:444: undefined reference to `i_len_trim' /build/clapack-3.2.1/TESTING/LIN/alaerh.c:591: undefined reference to `i_len_trim' /build/clapack-3.2.1/TESTING/LIN/alaerh.c:604: undefined reference to `i_len_trim' /build/clapack-3.2.1/TESTING/LIN/alaerh.c:843: undefined reference to `i_len_trim' /build/clapack-3.2.1/TESTING/LIN/alaerh.c:473: undefined reference to `i_len_trim' CMakeFiles/xlintstd.dir/alaerh.c.o:/build/clapack-3.2.1/TESTING/LIN/alaerh.c:737: more undefined references to `i_len_trim' follow CMakeFiles/xlintstd.dir/dchkps.c.o: In function `dchkps_': /build/clapack-3.2.1/TESTING/LIN/dchkps.c:252: undefined reference to `i_dceiling' collect2: error: ld returned 1 exit status Any further hint? Kind regards Andreas. [1] https://anonscm.debian.org/git/debian-science/packages/clapack.git -- http://fam-tille.de From costamagnagianfranco at yahoo.it Mon May 23 10:17:15 2016 From: costamagnagianfranco at yahoo.it (Gianfranco Costamagna) Date: Mon, 23 May 2016 10:17:15 +0000 (UTC) Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <20160523100808.GA8507@an3as.eu> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> <20160521155346.GR5019@an3as.eu> <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> <20160523100808.GA8507@an3as.eu> Message-ID: <1885176891.1578048.1463998635667.JavaMail.yahoo@mail.yahoo.com> http://ftp.kevag-telekom.de/mirrors/gentoo.org/rsync/sci-libs/clapack/files/clapack-3.2.1-noblasf2c.patch seems that the i_len_trim.c file might be somewhere else, look at gentoo packaging, they seem to have not stripped it from the tarball I guess. Does this helps? G. Il Luned? 23 Maggio 2016 12:08, Andreas Tille ha scritto: Hi Gianfranco, your very helpful hints helped me to get some steps forward. However, its not finally done. On Sun, May 22, 2016 at 06:48:36AM +0000, Gianfranco Costamagna wrote: > >Another question is how I could link against the Debian packaged f2c > >rather than building the one that comes with clapack upstream. > > I would say: remove the add_subdirectory (line 21) > and then: > 1) create a "FindF2C.cmake" file and use it as helper > (that would be the best and upstreamable choice > you can find some examples in "ettercap/cmake/Modules/Find*" > > > 2) just include_directories for helping it to find the .h file (if not in standard directory) > and target_link_libraries of the .so file. I think the .h files are not a problem. With my recent changes in Git[1] there is a problem with the linker when running the clapack test suite: ... std.dir/dtrt03.c.o CMakeFiles/xlintstd.dir/dtrt05.c.o CMakeFiles/xlintstd.dir/dtrt06.c.o CMakeFiles/xlintstd.dir/dtzt01.c.o CMakeFiles/xlintstd.dir/dtzt02.c.o CMakeFiles/xlintstd.dir/dgennd.c.o CMakeFiles/xlintstd.dir/ddrvge.c.o CMakeFiles/xlintstd.dir/ddrvgb.c.o CMakeFiles/xlintstd.dir/derrge.c.o CMakeFiles/xlintstd.dir/ddrvpo.c.o CMakeFiles/xlintstd.dir/derrpo.c.o CMakeFiles/xlintstd.dir/dlaord.c.o CMakeFiles/xlintstd.dir/__/__/INSTALL/dsecnd.c.o -o xlintstd -rdynamic ../MATGEN/libtmglib.a ../../SRC/libclapack.so.3.2.1 ../../BLAS/SRC/libcblas.so.3.2.1 -lm -lf2c -Wl,-rpath,/build/clapack-3.2.1/obj-x86_64-linux-gnu/SRC:/build/clapack-3.2.1/obj-x86_64-linux-gnu/BLAS/SRC CMakeFiles/xlintstd.dir/alaerh.c.o: In function `alaerh_': /build/clapack-3.2.1/TESTING/LIN/alaerh.c:444: undefined reference to `i_len_trim' /build/clapack-3.2.1/TESTING/LIN/alaerh.c:591: undefined reference to `i_len_trim' /build/clapack-3.2.1/TESTING/LIN/alaerh.c:604: undefined reference to `i_len_trim' /build/clapack-3.2.1/TESTING/LIN/alaerh.c:843: undefined reference to `i_len_trim' /build/clapack-3.2.1/TESTING/LIN/alaerh.c:473: undefined reference to `i_len_trim' CMakeFiles/xlintstd.dir/alaerh.c.o:/build/clapack-3.2.1/TESTING/LIN/alaerh.c:737: more undefined references to `i_len_trim' follow CMakeFiles/xlintstd.dir/dchkps.c.o: In function `dchkps_': /build/clapack-3.2.1/TESTING/LIN/dchkps.c:252: undefined reference to `i_dceiling' collect2: error: ld returned 1 exit status Any further hint? Kind regards Andreas. [1] https://anonscm.debian.org/git/debian-science/packages/clapack.git -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Mon May 23 10:24:32 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 10:24:32 +0000 Subject: [Debian-med-packaging] Processing of smalt_0.7.6-6_amd64.changes Message-ID: smalt_0.7.6-6_amd64.changes uploaded successfully to localhost along with the files: smalt_0.7.6-6.dsc smalt_0.7.6-6.debian.tar.xz smalt-dbgsym_0.7.6-6_amd64.deb smalt-examples_0.7.6-6_all.deb smalt_0.7.6-6_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at fam-tille.de Mon May 23 11:02:36 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Mon, 23 May 2016 13:02:36 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <20160523100808.GA8507@an3as.eu> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> <20160521155346.GR5019@an3as.eu> <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> <20160523100808.GA8507@an3as.eu> Message-ID: <20160523110236.GB8507@an3as.eu> Sorry for replying to my own mail. I just noticed that the Debian packaged libf2c really has no symbol i_len_trim. Will check what version is packaged and how this can be fixed. On Mon, May 23, 2016 at 12:08:08PM +0200, Andreas Tille wrote: > Hi Gianfranco, > > your very helpful hints helped me to get some steps forward. However, > its not finally done. > > On Sun, May 22, 2016 at 06:48:36AM +0000, Gianfranco Costamagna wrote: > > >Another question is how I could link against the Debian packaged f2c > > >rather than building the one that comes with clapack upstream. > > > > I would say: remove the add_subdirectory (line 21) > > and then: > > 1) create a "FindF2C.cmake" file and use it as helper > > (that would be the best and upstreamable choice > > you can find some examples in "ettercap/cmake/Modules/Find*" > > > > > > 2) just include_directories for helping it to find the .h file (if not in standard directory) > > and target_link_libraries of the .so file. > > I think the .h files are not a problem. With my recent changes in Git[1] > there is a problem with the linker when running the clapack test suite: > > ... > std.dir/dtrt03.c.o CMakeFiles/xlintstd.dir/dtrt05.c.o CMakeFiles/xlintstd.dir/dtrt06.c.o CMakeFiles/xlintstd.dir/dtzt01.c.o CMakeFiles/xlintstd.dir/dtzt02.c.o CMakeFiles/xlintstd.dir/dgennd.c.o CMakeFiles/xlintstd.dir/ddrvge.c.o CMakeFiles/xlintstd.dir/ddrvgb.c.o CMakeFiles/xlintstd.dir/derrge.c.o CMakeFiles/xlintstd.dir/ddrvpo.c.o CMakeFiles/xlintstd.dir/derrpo.c.o CMakeFiles/xlintstd.dir/dlaord.c.o CMakeFiles/xlintstd.dir/__/__/INSTALL/dsecnd.c.o -o xlintstd -rdynamic ../MATGEN/libtmglib.a ../../SRC/libclapack.so.3.2.1 ../../BLAS/SRC/libcblas.so.3.2.1 -lm -lf2c -Wl,-rpath,/build/clapack-3.2.1/obj-x86_64-linux-gnu/SRC:/build/clapack-3.2.1/obj-x86_64-linux-gnu/BLAS/SRC > CMakeFiles/xlintstd.dir/alaerh.c.o: In function `alaerh_': > /build/clapack-3.2.1/TESTING/LIN/alaerh.c:444: undefined reference to `i_len_trim' > /build/clapack-3.2.1/TESTING/LIN/alaerh.c:591: undefined reference to `i_len_trim' > /build/clapack-3.2.1/TESTING/LIN/alaerh.c:604: undefined reference to `i_len_trim' > /build/clapack-3.2.1/TESTING/LIN/alaerh.c:843: undefined reference to `i_len_trim' > /build/clapack-3.2.1/TESTING/LIN/alaerh.c:473: undefined reference to `i_len_trim' > CMakeFiles/xlintstd.dir/alaerh.c.o:/build/clapack-3.2.1/TESTING/LIN/alaerh.c:737: more undefined references to `i_len_trim' follow > CMakeFiles/xlintstd.dir/dchkps.c.o: In function `dchkps_': > /build/clapack-3.2.1/TESTING/LIN/dchkps.c:252: undefined reference to `i_dceiling' > collect2: error: ld returned 1 exit status > > > Any further hint? > > Kind regards > > Andreas. > > > [1] https://anonscm.debian.org/git/debian-science/packages/clapack.git > > -- > http://fam-tille.de -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Mon May 23 11:21:16 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 11:21:16 +0000 Subject: [Debian-med-packaging] smalt_0.7.6-6_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 23 May 2016 09:58:22 +0000 Source: smalt Binary: smalt smalt-examples Architecture: source amd64 all Version: 0.7.6-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: smalt - Sequence Mapping and Alignment Tool smalt-examples - Sequence Mapping and Alignment Tool (examples) Changes: smalt (0.7.6-6) unstable; urgency=medium . * Team upload. * Remove Makefile from installed test data. This differs in cross-arch builds, breaking i386 reproducibility (and serves no purpose anyway). 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From ftpmaster at ftp-master.debian.org Mon May 23 13:15:15 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 13:15:15 +0000 Subject: [Debian-med-packaging] Processing of vtk-dicom_0.7.7-2_source.changes Message-ID: vtk-dicom_0.7.7-2_source.changes uploaded successfully to localhost along with the files: vtk-dicom_0.7.7-2.dsc vtk-dicom_0.7.7-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 23 13:19:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 13:19:35 +0000 Subject: [Debian-med-packaging] vtk-dicom_0.7.7-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 23 May 2016 12:08:25 +0000 Source: vtk-dicom Binary: libvtk-dicom-dev libvtkdicom0.7 vtk-dicom-tools python-vtk-dicom Architecture: source Version: 0.7.7-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: libvtk-dicom-dev - DICOM for VTK - dev libvtkdicom0.7 - DICOM for VTK - lib python-vtk-dicom - DICOM for VTK - Python vtk-dicom-tools - DICOM for VTK - tools Changes: vtk-dicom (0.7.7-2) unstable; urgency=medium . * d/p/repro...patch: Change date used to use non-locale month Checksums-Sha1: 888b4e55ebb0ce68fb4d7f24c4e1a75ef13a44a9 1958 vtk-dicom_0.7.7-2.dsc 4b1bd152a4c2c7c509ecfab51434b46b8bd64738 5388 vtk-dicom_0.7.7-2.debian.tar.xz Checksums-Sha256: 3881e83372e8acff40e745108de54133605508d1fada660fa39b1ab62e2b5b86 1958 vtk-dicom_0.7.7-2.dsc 6e758d6ca350fa7e1fda78ec9f913da7f7e748a61bc866e463fce52421ea2118 5388 vtk-dicom_0.7.7-2.debian.tar.xz Files: 79a6e87cd49f345ac635fa6e32d7db88 1958 graphics optional vtk-dicom_0.7.7-2.dsc 68e7052629a5fe2efbe267bea6b99dcb 5388 graphics optional vtk-dicom_0.7.7-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXQvMoAAoJEPgeNoubJquYX6UH/0xD+4/XwHaxh6p8hoUKWC0O igrLrooHS9rm9P1GIO4Oq2g184WcQO/+/q6NF352KPpRdmstKFj6tOLx2f5e4JB0 s9rzlM5PtrvMSYIyuKDQNql0SjXYEd+KEOPNyDnvfHxty418MCh1jxYp/Dgqz+Ca mv+Scef+juAKcRvBU+Efiny3VSbfRuXUVg3iFlftqqZptTZK5Dj0n5Tuc25GsRYN jvJiuy8MyVEEqziGCUvqb7N+eh1j08/Edhr6mtBrgi4VGlTPjl3fqFy3aUw+DYq5 xTwBbwUmtVX2fOsYwLJGgJ1d5eHJaeoYypW5q8wYBS/ioNfUAtUXFB3UR4Xyjgg= =qev3 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From tille at debian.org Mon May 23 13:53:52 2016 From: tille at debian.org (Andreas Tille) Date: Mon, 23 May 2016 15:53:52 +0200 Subject: [Debian-med-packaging] Problems to find classes that should be in itext1.jar In-Reply-To: <10ffcc97-11f3-9a89-25d7-ae8c334657fd@apache.org> References: <20160521113423.GM5019@an3as.eu> <983252db-edfc-1d8f-0e29-8a11b7d55258@apache.org> <20160522194301.GJ9131@an3as.eu> <10ffcc97-11f3-9a89-25d7-ae8c334657fd@apache.org> Message-ID: <20160523135352.GC8507@an3as.eu> Hi Emmanuel, On Sun, May 22, 2016 at 10:18:58PM +0200, Emmanuel Bourg wrote: > > iText doesn't contain any headless.awt.* class. It looks like the iText > code was copied and modified the turn the 'import java.awt.*' statements > into 'import headless.awt.*'. I guess as some point they copied and > relocated the java.awt classes to disable the exceptions on systems > without a display. Since Java 1.4 this can be avoided by setting the > java.awt.headless property to true. > > I think you have two options: > 1. remove the iText source files from the LibrarySource directory and > use the libitext1-java package instead > 2. if it doesn't work because the itext code was further modified, patch > it and replace 'headless.awt' with 'java.awt' Seems this worked from the itext part. I was running into other problems that are basically cause by several Mac specific things I'd tried to get rid of[1]. I admit I do not have a very good feeling by fiddling so much with the code and I have some remaining errors like: ... CLASSPATH=/usr/share/java/commons-httpclient.jar:/usr/share/java/commons-lang.jar:/usr/share/java/dom4j.jar:/usr/share/java/itext1-1.4.jar:/usr/share/java/pal-cvs.jar jh_build --javacopts='-target 1.7' --javacopts='-source 1.7' mesquite.jar Source LibrarySource find Source LibrarySource -name *.java -and -type f -print0 | xargs -s 512000 -0 /usr/lib/jvm/default-java/bin/javac -g -cp /usr/share/java/commons-httpclient.jar:/usr/share/java/commons-lang.jar:/usr/share/java/dom4j.jar:/usr/share/java/itext1-1.4.jar:/usr/share/java/pal-cvs.jar:debian/_jh_build.mesquite -d debian/_jh_build.mesquite -target 1.7 -source 1.7 warning: [options] bootstrap class path not set in conjunction with -source 1.7 Source/mesquite/genesis/lib/RateMatrixGTRModel.java:29: error: cannot find symbol TransitionProbability transProbs = null; ^ symbol: class TransitionProbability location: class RateMatrixGTRModel Source/org/apache/hivemind/util/PropertyAdaptor.java:166: warning: non-varargs call of varargs method with inexact argument type for last parameter; return _readMethod.invoke(target, null); ^ cast to Object for a varargs call cast to Object[] for a non-varargs call and to suppress this warning Source/mesquite/lib/MesquiteFile.java:1068: error: cannot find symbol MRJOSType type = MRJFileUtils.getFileCreator(writingFile); ^ symbol: class MRJOSType location: class MesquiteFile Source/mesquite/lib/MesquiteFile.java:1068: error: cannot find symbol MRJOSType type = MRJFileUtils.getFileCreator(writingFile); ^ symbol: variable MRJFileUtils location: class MesquiteFile Source/mesquite/lib/MesquiteFile.java:1103: error: cannot find symbol try {MRJFileUtils.setFileTypeAndCreator(writingFile, new MRJOSType("TEXT"), new MRJOSType(setFileType));} ^ symbol: class MRJOSType location: class MesquiteFile Source/mesquite/lib/MesquiteFile.java:1103: error: cannot find symbol try {MRJFileUtils.setFileTypeAndCreator(writingFile, new MRJOSType("TEXT"), new MRJOSType(setFileType));} ^ symbol: class MRJOSType location: class MesquiteFile Source/mesquite/lib/MesquiteFile.java:1103: error: cannot find symbol try {MRJFileUtils.setFileTypeAndCreator(writingFile, new MRJOSType("TEXT"), new MRJOSType(setFileType));} ^ symbol: variable MRJFileUtils location: class MesquiteFile Any further hints are welcome Andreas. [1] https://anonscm.debian.org/cgit/debian-med/mesquite.git/tree/debian/patches/do_not_import_apple_jar.patch -- http://fam-tille.de From ebourg at apache.org Mon May 23 14:16:32 2016 From: ebourg at apache.org (Emmanuel Bourg) Date: Mon, 23 May 2016 16:16:32 +0200 Subject: [Debian-med-packaging] Problems to find classes that should be in itext1.jar In-Reply-To: <20160523135352.GC8507@an3as.eu> References: <20160521113423.GM5019@an3as.eu> <983252db-edfc-1d8f-0e29-8a11b7d55258@apache.org> <20160522194301.GJ9131@an3as.eu> <10ffcc97-11f3-9a89-25d7-ae8c334657fd@apache.org> <20160523135352.GC8507@an3as.eu> Message-ID: Le 23/05/2016 ? 15:53, Andreas Tille a ?crit : > Source/mesquite/genesis/lib/RateMatrixGTRModel.java:29: error: cannot find symbol > TransitionProbability transProbs = null; > ^ > symbol: class TransitionProbability > location: class RateMatrixGTRModel TransitionProbability.java is in the LibrarySource/pal/substmodel directory, did you remove it from the upstream tarball? > symbol: class MRJOSType > location: class MesquiteFile > Source/mesquite/lib/MesquiteFile.java:1068: error: cannot find symbol > MRJOSType type = MRJFileUtils.getFileCreator(writingFile); If the MRJ stuff is specific to OS X I guess you can remove it. Emmanuel Bourg From andreas at an3as.eu Mon May 23 14:46:09 2016 From: andreas at an3as.eu (Andreas Tille) Date: Mon, 23 May 2016 16:46:09 +0200 Subject: [Debian-med-packaging] Problems to find classes that should be in itext1.jar In-Reply-To: References: <20160521113423.GM5019@an3as.eu> <983252db-edfc-1d8f-0e29-8a11b7d55258@apache.org> <20160522194301.GJ9131@an3as.eu> <10ffcc97-11f3-9a89-25d7-ae8c334657fd@apache.org> <20160523135352.GC8507@an3as.eu> Message-ID: <20160523144609.GD8507@an3as.eu> On Mon, May 23, 2016 at 04:16:32PM +0200, Emmanuel Bourg wrote: > Le 23/05/2016 ? 15:53, Andreas Tille a ?crit : > > > Source/mesquite/genesis/lib/RateMatrixGTRModel.java:29: error: cannot find symbol > > TransitionProbability transProbs = null; > > ^ > > symbol: class TransitionProbability > > location: class RateMatrixGTRModel > > TransitionProbability.java is in the LibrarySource/pal/substmodel > directory, did you remove it from the upstream tarball? Yes, since we have packaged this as libpal-java I removed the whole dir LibrarySource/pal. I need to check this detail. > > symbol: class MRJOSType > > location: class MesquiteFile > > Source/mesquite/lib/MesquiteFile.java:1068: error: cannot find symbol > > MRJOSType type = MRJFileUtils.getFileCreator(writingFile); > > If the MRJ stuff is specific to OS X I guess you can remove it. But deleting what? Just these very lines featuring MRJ* ? Kind regards Andreas. -- http://fam-tille.de From ebourg at apache.org Mon May 23 14:55:25 2016 From: ebourg at apache.org (Emmanuel Bourg) Date: Mon, 23 May 2016 16:55:25 +0200 Subject: [Debian-med-packaging] Problems to find classes that should be in itext1.jar In-Reply-To: <20160523144609.GD8507@an3as.eu> References: <20160521113423.GM5019@an3as.eu> <983252db-edfc-1d8f-0e29-8a11b7d55258@apache.org> <20160522194301.GJ9131@an3as.eu> <10ffcc97-11f3-9a89-25d7-ae8c334657fd@apache.org> <20160523135352.GC8507@an3as.eu> <20160523144609.GD8507@an3as.eu> Message-ID: <42ad27e4-d4fd-753d-581b-550dd23b996c@apache.org> Le 23/05/2016 ? 16:46, Andreas Tille a ?crit : > But deleting what? Just these very lines featuring MRJ* ? Delete the try catch blocks where the MRJ classes appear. Emmanuel Bourg From noreply at release.debian.org Mon May 23 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 23 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] concavity REMOVED from testing Message-ID: FYI: The status of the concavity source package in Debian's testing distribution has changed. Previous version: 0.1+dfsg-1 Current version: (not in testing) Hint: Bug #822382: concavity: non-free files (NC) The script that generates this mail tries to extract removal reasons from comments in the britney hint files. Those comments were not originally meant to be machine readable, so if the reason for removing your package seems to be nonsense, it is probably the reporting script that got confused. Please check the actual hints file before you complain about meaningless removals. -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 23 16:39:07 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 23 May 2016 16:39:07 +0000 Subject: [Debian-med-packaging] fis-gtm 6.3-000-2 MIGRATED to testing Message-ID: FYI: The status of the fis-gtm source package in Debian's testing distribution has changed. Previous version: 6.3-000-1 Current version: 6.3-000-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 23 16:39:14 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 23 May 2016 16:39:14 +0000 Subject: [Debian-med-packaging] spdlog 1.8-1 MIGRATED to testing Message-ID: FYI: The status of the spdlog source package in Debian's testing distribution has changed. Previous version: 1.6-2 Current version: 1.8-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 23 16:39:14 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 23 May 2016 16:39:14 +0000 Subject: [Debian-med-packaging] r-bioc-xvector 0.12.0-2 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-xvector source package in Debian's testing distribution has changed. Previous version: 0.12.0-1 Current version: 0.12.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Mon May 23 18:01:21 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 18:01:21 +0000 Subject: [Debian-med-packaging] pbh5tools_0.8.0+dfsg-5_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 20 Mar 2016 00:50:26 -0700 Source: pbh5tools Binary: pbh5tools python-pbh5tools python-pbh5tools-doc Architecture: source all amd64 Version: 0.8.0+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Afif Elghraoui Description: pbh5tools - tools for manipulating Pacific Biosciences HDF5 files python-pbh5tools - tools for manipulating Pacific Biosciences HDF5 files -- Python 2 python-pbh5tools-doc - tools for manipulating HDF5 files produced by Pacific Biosciences Changes: pbh5tools (0.8.0+dfsg-5) unstable; urgency=medium . * Rename source package to match primary binary package * Update email address and bump copyright year * Update VCS URLs * Bump Standards-Version * Fix path reference for multiarch-renamed compiled extension Checksums-Sha1: eeb90461fe5076f538b2bb8a32b91a3c53f57f3f 2229 pbh5tools_0.8.0+dfsg-5.dsc 31a40ef6c68ee08a2ddb6ab05d37926d07f0d613 8550283 pbh5tools_0.8.0+dfsg.orig.tar.gz d77bca2d0731ec11dd89f70cb72215d4d04eef08 6568 pbh5tools_0.8.0+dfsg-5.debian.tar.xz 4a99279f1d5b1f3659d5b493e4379f7b1ff68524 8282 pbh5tools_0.8.0+dfsg-5_all.deb 23e390fe3b7a450146c7e638594c77018458b9a8 5086 python-pbh5tools-dbgsym_0.8.0+dfsg-5_amd64.deb 3be0e5ef4b8201e1d6ba151d04c26e04f53cb832 35726 python-pbh5tools-doc_0.8.0+dfsg-5_all.deb 755838cf020113954f28b0acd93d427ddf5744e6 28990 python-pbh5tools_0.8.0+dfsg-5_amd64.deb Checksums-Sha256: 5f29c361599f87f76499373aa7228603e305c16c3ada249a83b192bd025bde2d 2229 pbh5tools_0.8.0+dfsg-5.dsc d07d38ed87d07a517bf943dea4a37f388d4c13df710576006da327e833869667 8550283 pbh5tools_0.8.0+dfsg.orig.tar.gz 3b7fc07f09cc98816db5b5b15630f916ece76383a5452855fd986964e74b2c4a 6568 pbh5tools_0.8.0+dfsg-5.debian.tar.xz 1c8c5648f9d4aa547505608bd0a4b108b62f4a519d439b2226ac674a3876dae8 8282 pbh5tools_0.8.0+dfsg-5_all.deb 431fccfa31b6eabbcc322f362524b12be88ec88a3c07d03e503fa88470907347 5086 python-pbh5tools-dbgsym_0.8.0+dfsg-5_amd64.deb f5629a9132790b701645fea83d5b512175f6532388e4aed97dce8ecc810c2990 35726 python-pbh5tools-doc_0.8.0+dfsg-5_all.deb d0514862314e49ccb33ece8a4fc7e64cb9e04cb61e0556e59abf9cbacdaeb8a0 28990 python-pbh5tools_0.8.0+dfsg-5_amd64.deb Files: 4287d0a291932b67b71a938108a589a7 2229 science optional pbh5tools_0.8.0+dfsg-5.dsc 2a34de14084b7784f9d2b21b55f9c3d5 8550283 science optional pbh5tools_0.8.0+dfsg.orig.tar.gz d16c40ff59b697bd2906d4c30ab57a2f 6568 science optional pbh5tools_0.8.0+dfsg-5.debian.tar.xz 6f4adb78da7f0f05d9282ace43a76466 8282 science optional pbh5tools_0.8.0+dfsg-5_all.deb bde2b82e98f97b803d3650b0d4249e19 5086 debug extra python-pbh5tools-dbgsym_0.8.0+dfsg-5_amd64.deb badeb5362d56f6b91567cdf3710ecda2 35726 doc optional python-pbh5tools-doc_0.8.0+dfsg-5_all.deb 7ae5346266af542dcbf3ad18b384cb29 28990 python optional python-pbh5tools_0.8.0+dfsg-5_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXGGw1AAoJEM6uatOv6Cb74tIQAKCp8F9JMzZ2gFZkLULtt3pw 4FXh+g06hPDEtLiV1OkURzSdvJbQ+zFM3vrTD+y3EGnycBZqi/d5MVmLiCxf4vMB UBD7qiB23ecpA8jagesC+v0R8UzzibVXpGM/84gtaGKi+ZZtaB0Gd0mC51hUhTT4 UTh7Ss57BYgGB9P/uWa3DYnZZB/1nBeyuRwGf7266l+DqvjDb7G/5gOB7PEGU/qp 3aBcODclDFdrBFtNgs2wtkaA51N4u1Ok+s5f2HezsodeKMRvJDeCVhZokUPWQ09k 4krvtGuUV1mvv35Zc0/w3LcZ3cxk1QzvleXXtGUFYXXNq4Vtixmi3tHdfNI5GwvU +pHOF2Osph3dWLmk8PYic7C8zeeY6jIK4LkSIqh0djrk7LJLWlU1UWUlKAn/LuRh qDRBa5O0rPE2OqqDlqLYvSXzIxDLjsjtxc2X8jdWpDgZilaGMqXXdmAsePXHZhUv d5jClU4TLTuqg6wcshOUWu3i+vO2Vroq0Z48a9kXRVyxl8P6E4y1gqbSBE27j9dh jglYKKPsfMzQ10IuGY/gZXN31Iajseaa7GHwkQvR6JM8nYiWKvhPzAIW7dDOztf9 vw48YHYuvw+7sTOE/q0SQ5QDUhfLD6MQP0SGo9bp0GDB0+U2c3fcBkkS2vws0AUb SO8+fXfM1QGDF6Gi6n1o =YVJv -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 23 18:01:29 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 18:01:29 +0000 Subject: [Debian-med-packaging] r-bioc-go.db_3.3.0-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 00:14:08 +0200 Source: r-bioc-go.db Binary: r-bioc-go.db Architecture: source all Version: 3.3.0-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-go.db - annotation maps describing the entire Gene Ontology Closes: 824805 Changes: r-bioc-go.db (3.3.0-1) unstable; urgency=low . * Initial release (closes: #824805) Checksums-Sha1: fa91e1519ee912c2ec628c07b42d870da5571828 2073 r-bioc-go.db_3.3.0-1.dsc 466fd5c967aafdca803f2cb14e61d3dd260fc3ed 32027913 r-bioc-go.db_3.3.0.orig.tar.gz 074b0fe808d256ee58bffd5f38e8b4c941b4b96f 3608 r-bioc-go.db_3.3.0-1.debian.tar.xz f1abe4f3f74dfb011627984a4aa0d6e0773919b9 16009048 r-bioc-go.db_3.3.0-1_all.deb Checksums-Sha256: 32e373aba121bcb841505bb36ae1ade9d861bcd3c55e4999d37615b0afd71382 2073 r-bioc-go.db_3.3.0-1.dsc c0f707fba1fb7bb78babc339ac8a5e7fec7d102ac0362806571cb5f4e09a5074 32027913 r-bioc-go.db_3.3.0.orig.tar.gz a233b3c77bb39145eebf58b13e110c2a7d094cf3520be2a3450b967bc029cc2f 3608 r-bioc-go.db_3.3.0-1.debian.tar.xz 824d5ea82992733370c8a074d561ef278a66a2b8515a4436178ec65da9cbdc80 16009048 r-bioc-go.db_3.3.0-1_all.deb Files: c2bb4cbf01532b9f7012b6f6583fc782 2073 gnu-r optional r-bioc-go.db_3.3.0-1.dsc 4214f5dfadcb2964173011b0e46d332b 32027913 gnu-r optional r-bioc-go.db_3.3.0.orig.tar.gz f807cdd470c81da17896f46cfbfe1508 3608 gnu-r optional r-bioc-go.db_3.3.0-1.debian.tar.xz 4358b88dc298a56bc3eba81a494785b7 16009048 gnu-r optional r-bioc-go.db_3.3.0-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXPjw9AAoJEFeKBJTRxkbRAcUP/0zphLgatziURM+U5Gk1aZCm rJZiLxL1/OZfkDY48tzNqZ992KbKjTrTSzagr8YHqSLOXVZN1dvRLFL8iak44mCi l1yhV9E3iTH+jcLQl53/XZuoF8YojqWuz1OfdznDDsHYgp1EEaTTAEYs5ismd3Lz oCCiiHYemJdtNmFMtaVvP9mNlL9vr2zOdQFVIwKE5Hj9GeCGPxaFPoVduIdObOZo 1fHSabaf5XIDqlFboEVLPfcOpXybGV7PaPHzXvOzKTdV/q7h5eCOoz2ldTY4vKKN GU5jtpEmdViY+aQgNU+bC5oA67BQENUiX/9dFbQWnFkScyCmMBJgm1+NsGIGhl6m l9/SjDvqvIH8+robg5W7IzNIKAxkd36T8BWRTBaljPhf7ImA46fsAp7ffDx41PZc 4k/wpDhfLsXtrGIQMPIIxvp1O1zrrpJZ4uPITXPAqC1pFz1siEyb5p+P8ZPKCFZq 8xYOLODiA2DXg3ePJST91RN/2Ei2zcqcHCIWheqgbOpRvXbZKSItVQPJf46tY9cR l/8I6tC38FHBkPsygIg9sCyERgzydRAwv9RECJR59ABX3E1QBJtLlzl5tMgtQ0Vu bBfklpjSDikYyt9LbWlFAu2lp8hDCCfNIrMGrN2V6EL5rF1x0Cb9p0BisVguc4qC No0405FfsHF9/3tugsKV =9xDs -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 23 18:01:31 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 18:01:31 +0000 Subject: [Debian-med-packaging] r-bioc-interactivedisplaybase_1.10.2-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 16 May 2016 08:47:01 +0200 Source: r-bioc-interactivedisplaybase Binary: r-bioc-interactivedisplaybase Architecture: source all Version: 1.10.2-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-interactivedisplaybase - base package for enabling powerful shiny web displays of Biocondu Closes: 824448 Changes: r-bioc-interactivedisplaybase (1.10.2-1) unstable; urgency=low . * Initial release (closes: #824448) Checksums-Sha1: 0dbf067c795ebcd23d6ac8c96dbefc5422066f6c 2277 r-bioc-interactivedisplaybase_1.10.2-1.dsc edb391a0638776faf84e8c5b8fab1e9557b9a53d 13810 r-bioc-interactivedisplaybase_1.10.2.orig.tar.gz 22287f221fa97b58d5d2718e67e1d52af43335b8 2992 r-bioc-interactivedisplaybase_1.10.2-1.debian.tar.xz 6aedcbbfc53e3354d9325ebd6d509806c1cf5652 33156 r-bioc-interactivedisplaybase_1.10.2-1_all.deb Checksums-Sha256: 99eff46f2dc708e6bce0ef581ce328984c2164cc642f996eca40fbf10f9bb94b 2277 r-bioc-interactivedisplaybase_1.10.2-1.dsc c2785406e1085d5afe90f525d80177d97119f0f863ec68e253e696834c7dc0c9 13810 r-bioc-interactivedisplaybase_1.10.2.orig.tar.gz 14357a5f392f934faf19c37ec8351bbc1c273beac15f35a1dc375ed0451ed493 2992 r-bioc-interactivedisplaybase_1.10.2-1.debian.tar.xz 96b12ccb4ce31343ff379d1d1dd5e66b0cf81bffae87662678f6b833571679f6 33156 r-bioc-interactivedisplaybase_1.10.2-1_all.deb Files: 880ffd06663662057d152f5f3efe45cd 2277 gnu-r optional r-bioc-interactivedisplaybase_1.10.2-1.dsc 2e382f1ed8674454d23d2b8ff845634b 13810 gnu-r optional r-bioc-interactivedisplaybase_1.10.2.orig.tar.gz 7a2ebd817ef5e39a1f8d1aa3a3b79e34 2992 gnu-r optional r-bioc-interactivedisplaybase_1.10.2-1.debian.tar.xz aada0e714191702223fe75780dfb19a0 33156 gnu-r optional r-bioc-interactivedisplaybase_1.10.2-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXOW1mAAoJEFeKBJTRxkbRcQAP/156H2OVpAZaBeZhpy+0HvJ9 nG+/kDAV3eiTABMUjyBsorpG4gQBDqnS8hKIXXTDYsOe1Apr4Sdl7EGHFt+y94PN lHtVXcg2kbo8isbm6OTX+UyAbPUHZa8+iwA9zUsv4M6HQCKYPb1/hF6nMY3e5rvL nsEc3z4d4EOAeykM8ETy3YHT256zGE+GnBbAXiRkE/pZwYifS2O1DbYdR98D+y0O nNYpFeqpnIcEY0sS+Kk+bwzejB1ty7LvHckjwzl45ScXPAVgvzVkAs9CgKkFteS6 GFN7l9QPeGnuvF/f401MixD3Murk9ASHAQo1Kz6wy4h29aAciWdSr5Wcyl3fxuGu iSgUgScHNMsx16nVUOEvczV7GVp0pxAEr131JOKdHki8d8Cx7fbx+0Xal5Ge3F/F HJUnjERFI0qv0Fx9HMCIK7R0tiIOFI8oC095d9Fw/294d6gM+zdEiQBOhoKkpuqp lNHcuyc9xpzQ3jszrFDg6UfxEf1xIv0Jq8R/G5AeH9gU9AwxAKYoXQCjjqWq4Ooh XgJYv+9jjzZKRRWevlriZwr9wY83mtSKiCD0cjMR7WM6NIe6/VexFbsDp7JpN3if rLSZchnefMr2NxCIitIfkMmlmCkZ9W3DAQzXQpoLxI+WI50ntmGmL1ZjMWhNQ9np ya3K+lQOGvOJKV0h3ibk =sku0 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 23 18:03:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 18:03:04 +0000 Subject: [Debian-med-packaging] maffilter_1.1.0-1+dfsg-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 20 May 2016 23:34:02 +0200 Source: maffilter Binary: maffilter maffilter-examples Architecture: source amd64 all Version: 1.1.0-1+dfsg-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: maffilter - process genome alignment in the Multiple Alignment Format maffilter-examples - process genome alignment in the Multiple Alignment Format (exampl Changes: maffilter (1.1.0-1+dfsg-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Mon May 23 18:03:05 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 18:03:05 +0000 Subject: [Debian-med-packaging] r-cran-rnexml_2.0.6-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 12 May 2016 18:44:02 +0200 Source: r-cran-rnexml Binary: r-cran-rnexml Architecture: source all Version: 2.0.6-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-rnexml - GNU R package for semantically rich I/O for the 'NeXML' format Changes: r-cran-rnexml (2.0.6-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. * (Build-)Depends: r-cran-stringr (>= 1.0) Checksums-Sha1: c4d337027c951695eca2eb3be716e4c0f5c386b8 2247 r-cran-rnexml_2.0.6-1~bpo8+1.dsc d77c850b75a823784c5bb6248593a079cdf7c1ea 4632 r-cran-rnexml_2.0.6-1~bpo8+1.debian.tar.xz 85a563168e15886719f0a512f52a69eb88c89196 339110 r-cran-rnexml_2.0.6-1~bpo8+1_all.deb Checksums-Sha256: 162bdac5c87a9a6b3528334d099909bf35b587a2710b32c975f309a3ff178029 2247 r-cran-rnexml_2.0.6-1~bpo8+1.dsc f71c79d43227c6f93b06be087e02fc00dd5e2eee11502ca96a99bfbdbc151801 4632 r-cran-rnexml_2.0.6-1~bpo8+1.debian.tar.xz d1148991bd1b8d2173aab391ce74afcd48c7348287f27db2d8e3f7b457921224 339110 r-cran-rnexml_2.0.6-1~bpo8+1_all.deb Files: d68ccd53e633002dc1a4b1b53c95a997 2247 gnu-r optional r-cran-rnexml_2.0.6-1~bpo8+1.dsc 8e8dda92bec7a07100111feb566153a0 4632 gnu-r optional r-cran-rnexml_2.0.6-1~bpo8+1.debian.tar.xz 9b0b185008ad59908c22c59f56b78c2e 339110 gnu-r optional r-cran-rnexml_2.0.6-1~bpo8+1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXP4dYAAoJEFeKBJTRxkbRQeUP/1Q5JTGinLGUmd9c47ECi3cw 4T1SoxG3aP4RVwi2H9KnaD9sG+4yIhP+SIgaFCmP9RaGY3sLW1hfKNVi/nNU+cug leNDCnzQqIzSvCN5cEh98bt/HrZ6+5Vv3x6dk+76eYKo7eOINaa8+TG9QWoSNcH5 AtAY0iNlUOaHFS0+OhJAziJtbKRLENsCVyNzPbPARHQwVjHS4PNWKr+LAEVv1fUa 5fmaYYBj+933yAmVAmLQ9QKZ5WPl5zolDmcf8AZACiPLapfpigcVVfD+ihqbt+Cs R25r0z3Jv9VQ2OBr6/cyVDeClqrHUAQ6GSe54NciF7TEyfZSJ/0yOqAZPpQ8wmoi EiGMG/FdFHuHJ+w+jTTX0BJ5dxZ5totAsbKwohxP+j6S7cP8Z1OcYrfexQ5BvzKp H2UdOT8Fqi6Rzxbi4xHik/ZMwMOZntN7CIwtL2WuDbYZ1WkI+1EVecq+Pa7JcVEB vPX75qY1xWx/xJq1/Ukil3zgnFtFDXAWHiEJbyX3qAz9X5wKQUUs/uGMejkG+PE+ o1xdsxOXemTScC/vgexRJcwuHJ7GRunQMK8rl2Viv36Zv5YI+OA/Veq6/phh3id+ czqU91XuKOZFZDeUNxOnuliK9XN85sUVb0rzEytbizITOOyhtw90J10+8DN2u3TS Az34YOOdNZDtlOXA8ayJ =2wll -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 23 19:01:52 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 19:01:52 +0000 Subject: [Debian-med-packaging] Processing of trinityrnaseq_2.2.0+dfsg-1_source.changes Message-ID: trinityrnaseq_2.2.0+dfsg-1_source.changes uploaded successfully to localhost along with the files: trinityrnaseq_2.2.0+dfsg-1.dsc trinityrnaseq_2.2.0+dfsg.orig.tar.xz trinityrnaseq_2.2.0+dfsg-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From tille at debian.org Mon May 23 19:02:41 2016 From: tille at debian.org (Andreas Tille) Date: Mon, 23 May 2016 21:02:41 +0200 Subject: [Debian-med-packaging] Bug#825114: ITP: r-bioc-annotationhub -- GNU R client to access AnnotationHub resources Message-ID: <20160523190241.24130.12930.reportbug@mail.an3as.eu> Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name : r-bioc-annotationhub Version : 2.4.2 Upstream Author : Martin Morgan, Marc Carlson, Dan Tenenbaum, Sonali Arora * URL : http://bioconductor.org/packages/release/bioc/html/AnnotationHub.html * License : Artistic-2.0 Programming Lang: GNU R Description : GNU R client to access AnnotationHub resources This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access. Remark: This package belongs to a set of new dependencies to update BioConductor packages in Debian. It will be maintained by the Debian Med team at svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-annotationhub/trunk/ From ftpmaster at ftp-master.debian.org Mon May 23 19:21:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 19:21:07 +0000 Subject: [Debian-med-packaging] trinityrnaseq_2.2.0+dfsg-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 23 May 2016 11:46:45 -0700 Source: trinityrnaseq Binary: trinityrnaseq trinityrnaseq-examples Architecture: source Version: 2.2.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: trinityrnaseq - RNA-Seq De novo Assembly trinityrnaseq-examples - RNA-Seq De novo Assembly common example and testing files Changes: trinityrnaseq (2.2.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Team upload * d/watch: Use xz compression for upstream source . [ Michael R. Crusoe ] * new upstream version * prune d/copyright excludes * refresh patches, drop a few included upstream * Standards-Version: '3.9.7' -> '3.9.8' Checksums-Sha1: 76c6f6fffcffbc000de3ceebea4514b4ac36e411 2274 trinityrnaseq_2.2.0+dfsg-1.dsc 9a24bf26034cc17b416a5c22cde04230f78c224a 155240328 trinityrnaseq_2.2.0+dfsg.orig.tar.xz 1421c2215653f31df5d224f8798acea12bc18fbb 16824 trinityrnaseq_2.2.0+dfsg-1.debian.tar.xz Checksums-Sha256: 8bb94f70b37719c619b36dda0ed41b24989e66bcefca63a799800ad6f653a723 2274 trinityrnaseq_2.2.0+dfsg-1.dsc 6e1702ac9868506b1dafa72be5df87a562029e26ba04c3665e9126b95fcc2332 155240328 trinityrnaseq_2.2.0+dfsg.orig.tar.xz 268f7a6f406b35608cefa840c79b19135882c5047de98b8129696c4a4dfa9241 16824 trinityrnaseq_2.2.0+dfsg-1.debian.tar.xz Files: 5a8b66680520a7154bf50be6afaa8950 2274 science optional trinityrnaseq_2.2.0+dfsg-1.dsc dcb7e8588ce25a2f868f64f8d041dbc1 155240328 science optional trinityrnaseq_2.2.0+dfsg.orig.tar.xz 2076159ab107d592b3e07ff20bf766b8 16824 science optional trinityrnaseq_2.2.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXQ1KlAAoJEDwmdj9sZ+bik/8P/A4AVkL6nrTsXvzpptdVvuDf EII5iN9WOrmkZCalgTqVHsMHTLjehOB762mlQiDyaHflbfaoV9UgYOsuV+o7pJnT B8fvloh3pw83/CKWGJdPaP8E/FdgTfu0BcjT5iCK7W2uYu3BN2sZUzBLMJ5UCbm7 dzTEUrI1ZmuIySoGphOn3n9mrDd8sSeOxftFUA2RYn6f7gNdNVRGcM3NT3pf5ok0 MhbTF7XGD1Wicnsep8+uLmABurnbi2g6RU0zzu+4pD9Kc4CeFixbIZt6HNREnfdL c7NkOGrX9IpRPnlMQoRFLP1QEg4h1+K8OErGaFbKdVflXvHTRcRlN8m0FYso0ixi xCzHS/lDdLN2xIBI4ZEgksecp9Qm95yKwL5jYVcfT0K/UwVKSq++oxXSDpGqgulX 9UT8rSFSQRjaIcm4TX043ZT58gv+QzBqH26geTFOUfZeL9rELFbwogy0U42yuGsR 3cVJBXZ5vK8qKzfbjqbf5oM6qCYh5m3RR1NbdCJyQtO5DWISLpNaLnTRLpbmZNMc bgABP9uvh7sB7EfsVP7sIB6iEHRsDur2ZlmpMhfroWZFo6h8Pf73NGn7LguhMQQO o/pH89jecQ1E/QFc2mcSHL5o9OZkLclsq9I/4ju9AW0D9ix/G6n5Ip9cio7zkmdP QndJ3ldHY0Kx24YG8BDS =BTnV -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 23 19:27:02 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 19:27:02 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-annotationhub_2.4.2-1_amd64.changes Message-ID: r-bioc-annotationhub_2.4.2-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-annotationhub_2.4.2-1.dsc r-bioc-annotationhub_2.4.2.orig.tar.gz r-bioc-annotationhub_2.4.2-1.debian.tar.xz r-bioc-annotationhub_2.4.2-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 23 19:35:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 19:35:04 +0000 Subject: [Debian-med-packaging] r-bioc-annotationhub_2.4.2-1_amd64.changes is NEW Message-ID: binary:r-bioc-annotationhub is NEW. source:r-bioc-annotationhub is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From anbe at debian.org Mon May 23 19:34:03 2016 From: anbe at debian.org (Andreas Beckmann) Date: Mon, 23 May 2016 21:34:03 +0200 Subject: [Debian-med-packaging] Bug#825119: jmodeltest: creates world writable /var/log/jmodeltest Message-ID: <20160523193403.14942.19704.reportbug@zam581.zam.kfa-juelich.de> Package: jmodeltest Version: 2.1.10+dfsg-1 Severity: serious User: debian-qa at lists.debian.org Usertags: piuparts Hi, during a test with piuparts I noticed your package creates/ships a world writable directory. >From the attached log (scroll to the bottom...): 2m4.4s DEBUG: Starting command: ['chroot', '/tmp/piupartss/tmpuBqGli', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m4.5s DUMP: ERROR: BAD PERMISSIONS drwxrwxrwx 2 root root 40 May 12 16:07 /var/log/jmodeltest 2m4.5s ERROR: Command failed (status=1): ['chroot', '/tmp/piupartss/tmpuBqGli', 'tmp/scripts/pre_remove_50_find_bad_permissions'] cheers, Andreas From ftpmaster at ftp-master.debian.org Mon May 23 19:47:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 19:47:04 +0000 Subject: [Debian-med-packaging] Processing of transdecoder_3.0.0+dfsg-2_source.changes Message-ID: transdecoder_3.0.0+dfsg-2_source.changes uploaded successfully to localhost along with the files: transdecoder_3.0.0+dfsg-2.dsc transdecoder_3.0.0+dfsg-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 23 19:48:50 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 19:48:50 +0000 Subject: [Debian-med-packaging] transdecoder_3.0.0+dfsg-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 23 May 2016 12:46:27 -0700 Source: transdecoder Binary: transdecoder transdecoder-doc Architecture: source Version: 3.0.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: transdecoder - find coding regions within RNA transcript sequences transdecoder-doc - find coding regions within transcripts Changes: transdecoder (3.0.0+dfsg-2) unstable; urgency=medium . [ Andreas Tille ] * Use xz compression for repackaged tarball * Simplify overrides * Delete unneeded empty directory * Fix permission of some file that should not be executable . [ Michael R. Crusoe ] * clean up after tests to improve reproducibility and reduce package size Checksums-Sha1: 2dd2ea1a23ce7fac5bc8f671b1a8ec684d142a25 2127 transdecoder_3.0.0+dfsg-2.dsc ffa4ff4d0e0febd9f0738bda6621e697699710e7 4784 transdecoder_3.0.0+dfsg-2.debian.tar.xz Checksums-Sha256: f3a30c529eb3e672b83dbf3cacfe0416e3ece9e2309ab0dfa18abfa18f68d2e6 2127 transdecoder_3.0.0+dfsg-2.dsc 426df98eccc13ccca4b93fb4e1b719cccfdbbb9d6e41a3031b812b834604bdca 4784 transdecoder_3.0.0+dfsg-2.debian.tar.xz Files: 405c8709ea77d3d0bd7a049e6c0b2a6a 2127 science optional transdecoder_3.0.0+dfsg-2.dsc 58508b9f86d28b0a9debb6443f73b32d 4784 science optional transdecoder_3.0.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXQ14kAAoJEDwmdj9sZ+bi3UgP+gMYoLHE3yFLbWRk8b7Lh7eK nN6q0Lnx1f5Wd0siq/9BnJyGeYNcoEFTSVjTL/H7JXSTfkMHbDgq1tST/TNRxNoA cDe9Fi0GPPS3QfVONn3Mt7FTwMRr9J+d0l7daOVFI6JJvmEiFXE94NBxS1kmYfkt B7JdzI2KhnyyHBVEwa0clVqtVtXmlacDxzj9MacLqtiTK6SMGUEM4DJ0huUiyBEH 9eDHAjFt6ngRosJfdIH1JlsRHORKN3ICYm9F8CX2L5HV3+Qqfzy50HMM2hELczzq EsHfKGiootsnmV9xA8jmzlQAMmCHBabnLpKFWKfAvdhEP0iQWnpP4ywZ8s65i1r4 c5ukEW3PUCZoSIdNy7/xBKEWeaRiiHNPbpcXmsLkiyrpi7HG4FGOXYe6fLIiPQVs kvHiycYi/aaF+enDOVEuV3azcsbb/2QEAPLJfPKnLLs87gCKIkFfSkKIokXN1FC7 DcGTl0N6JHpDAZppiVbVrDfCSWNxBrlzut3KYUkMCsy3qdtjgCKBznToxOH+MpZO ZPTJZSUBs5hHmgVXJG4KW8vyyVtD9PHFzVRfuNco77MMZGUHuMo+3BXJDLEfxh/9 TBUrCojzBGoziwvIRnY6wRtprEj1VRb+fEGc2Sw/s5ZO5SnTepiVlOKBcIbkqycC 2sS/PDDnGqSRKc5GgbdL =YbDn -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 23 20:07:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 20:07:07 +0000 Subject: [Debian-med-packaging] Processing of khmer_2.0+dfsg-7_source.changes Message-ID: khmer_2.0+dfsg-7_source.changes uploaded successfully to localhost along with the files: khmer_2.0+dfsg-7.dsc khmer_2.0+dfsg-7.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 23 20:07:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 20:07:07 +0000 Subject: [Debian-med-packaging] Processing of jaligner_1.0+dfsg-3_source.changes Message-ID: jaligner_1.0+dfsg-3_source.changes uploaded successfully to localhost along with the files: jaligner_1.0+dfsg-3.dsc jaligner_1.0+dfsg-3.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at an3as.eu Mon May 23 20:10:32 2016 From: andreas at an3as.eu (Andreas Tille) Date: Mon, 23 May 2016 22:10:32 +0200 Subject: [Debian-med-packaging] beast2-mcmc_2.4.1+dfsg-1_amd64.changes REJECTED In-Reply-To: References: Message-ID: <20160523201032.GB25265@an3as.eu> Hi Thorsten, Added copyrights of two external projects which were added after my first attempts to build the package and uploaded. Hope that's all. Thanks for the review Andreas. On Sun, May 22, 2016 at 06:00:20PM +0000, Thorsten Alteholz wrote: > > Hi Andreas, > > please mention all licenses from the source tarball in your debian/copyright. > > Thanks! > Thorsten > > === > > Please feel free to respond to this email if you don't understand why > your files were rejected, or if you upload new files which address our > concerns. > > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Mon May 23 20:12:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 20:12:07 +0000 Subject: [Debian-med-packaging] Processing of beast2-mcmc_2.4.1+dfsg-1_amd64.changes Message-ID: beast2-mcmc_2.4.1+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: beast2-mcmc_2.4.1+dfsg-1.dsc beast2-mcmc_2.4.1+dfsg.orig.tar.xz beast2-mcmc_2.4.1+dfsg-1.debian.tar.xz beast2-mcmc-doc_2.4.1+dfsg-1_all.deb beast2-mcmc-examples_2.4.1+dfsg-1_all.deb beast2-mcmc_2.4.1+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 23 20:47:15 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 20:47:15 +0000 Subject: [Debian-med-packaging] Processing of libpal-java_1.5.1+dfsg-2_amd64.changes Message-ID: libpal-java_1.5.1+dfsg-2_amd64.changes uploaded successfully to localhost along with the files: libpal-java_1.5.1+dfsg-2.dsc libpal-java_1.5.1+dfsg-2.debian.tar.xz libpal-java-doc_1.5.1+dfsg-2_all.deb libpal-java_1.5.1+dfsg-2_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 23 22:20:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 22:20:04 +0000 Subject: [Debian-med-packaging] beast2-mcmc_2.4.1+dfsg-1_amd64.changes is NEW Message-ID: binary:beast2-mcmc is NEW. binary:beast2-mcmc-doc is NEW. binary:beast2-mcmc-examples is NEW. source:beast2-mcmc is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Mon May 23 22:20:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 22:20:55 +0000 Subject: [Debian-med-packaging] jaligner_1.0+dfsg-3_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 23 May 2016 12:59:30 -0700 Source: jaligner Binary: jaligner Architecture: source Version: 1.0+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: jaligner - Smith-Waterman algorithm with Gotoh's improvement Changes: jaligner (1.0+dfsg-3) unstable; urgency=medium . * flip the reproducible switch for asciidoctor Checksums-Sha1: a81140d53845e7089fc5e824afa2fdad9f077fa7 2047 jaligner_1.0+dfsg-3.dsc e0f3817898c7e290923df2272099cc08d7ebc187 7152 jaligner_1.0+dfsg-3.debian.tar.xz Checksums-Sha256: e173b0bac93528574daa3b947066542e0052856f136de19b9658d8b9b97ad0fc 2047 jaligner_1.0+dfsg-3.dsc 89f0a9a131fd749b448db1f64b0236c11666d2d4356c955b83f39574404484be 7152 jaligner_1.0+dfsg-3.debian.tar.xz Files: ebbcf9fa318e92ce0d218081a2646739 2047 science optional jaligner_1.0+dfsg-3.dsc 6e9dec426917aef550a59e8da0b4363e 7152 science optional jaligner_1.0+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXQ2FeAAoJEDwmdj9sZ+biIGAQALfxqZ9VcIcarLkoe1tfqmpF KXxVXJRlPrJlOn+34nARt+8LCtiEMf65seq+f71lXh5YbtE8Nh8+2NYtsld1K2/T I/LmiO/ftQAv2LrMA8/+NEhkmLncjdw2FNpVX5AD5rROVnDNizeYEhSBS0hOVUSS rAXdKhTpwXfOZDHf0f+/avkuySuZ6ENXgI7RkFeia1BbQvdPMghISyNy8NSn9b+h PZGUng5CoQ6+HgHOqus1WB8dZolozFXXQ+r3zaZgbhxJpv/hPYtifNLoNxfTnhY7 vvXUJ6o3mlZlU0vrW2R+jdKvBMclt7CtXCUV/2W8T6IWq2my0KoQSiDiR7sIcxWD XUlEjZ7m8dcJFMejA5eHlkSwlJ+oyQtftN4IUcpmU/Z5X/ClCAugfYpoYNErmgtY I2I0SXgbwcinjOQ1w/HsCVGUTv1iW7S71bOFc8KvwpLSfIZQZJCuAYcfvVnBJ7h8 PrMuwsqN2/utLh2Q+3mDLF2qioDq7CGMc9ehdtd/LxLHKmIKTwjbLh59fOM6xlf8 UIukvEH0MRv/A8LFQjIXlwhU62U8O8ebGISzeK/HbRaHRGDvF0I7FjLcu15cNrOl tWVvuHzs3MqM0fWZm8HLvKdTg8Tr5E2+cHfJV26PliLA2qxRa5iTbomJPm5O684g e8f8oBHNI75cIjihP6mv =DJ80 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 23 22:21:14 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 22:21:14 +0000 Subject: [Debian-med-packaging] khmer_2.0+dfsg-7_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 23 May 2016 12:55:46 -0700 Source: khmer Binary: khmer-common khmer liboxli1 liboxli-dev Architecture: source Version: 2.0+dfsg-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: khmer - in-memory DNA sequence kmer counting, filtering & graph traversal khmer-common - common files for the khmer project tools liboxli-dev - in-memory DNA sequence analysis dev library liboxli1 - in-memory DNA sequence analysis library from the khmer project Changes: khmer (2.0+dfsg-7) unstable; urgency=medium . * make build reproducible Checksums-Sha1: b53fc9ec163e72cfbd252a6701654200968a03b9 2630 khmer_2.0+dfsg-7.dsc 19a9ffefed98f6087fc5d8e5b81579e4118bfe1c 10964 khmer_2.0+dfsg-7.debian.tar.xz Checksums-Sha256: ddfec2703949de1b703fbed06c4c15155576d549e0e0d3191834bdded95d0cfe 2630 khmer_2.0+dfsg-7.dsc 4de087026496c81fd6b48b0cf7cba0f6fc4715bba4cc79af3b8731709649e467 10964 khmer_2.0+dfsg-7.debian.tar.xz Files: 7abb73611d199b5d88fb769289f38253 2630 science optional khmer_2.0+dfsg-7.dsc 39e044573d624444343e6855c8a38e4f 10964 science optional khmer_2.0+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXQ2BhAAoJEDwmdj9sZ+biYkoP/A8aXkv1rPCP2unBQCNriWez mo/fc8pwMrMzMVsN8ilq2LrcSvI05nqs5XLp1Z/UCkADMSVakpGFYNnIZZrkPsLu YeJAXY+Dq8MA1qCpBX1s/gCkQIzg9cCG/oNVjGpMkr9lIQjLHrFppptE9DOw3gND YJF9+sN1XawA76I2wDiz9LOfuhWeFwOTX5CdRVHkFUmiZEHJ2L77SUtqZwMlZApt 243HXDD+Ha4PwM/5T8SuHNfP2NMICBwDsVEchNlBWVu6W2SpMvWYJYNcwf3YARGg z81mLHj0m5Nx09ssTvmWckBVcQHkq+nImI3YZrgz7/iOsNbVfcx4y8JpGpFJO3Xa TGIcSd3QMwebInb9pILMuygykT2zVLPQN7kds2v8TebQdP5P8jSRuy1QmCU8Gk/a TVoIs7JVjcH4+m40TUn/aD82l+mbH11C0vgVgMUBo5lQH2SBC8fMxwIl4fcS2gR+ L1y2lQNX8rCviRU+P0X8LNhCV2AztoH0kgA4XIoyN6x0aRf/ehBXsKyCmrVd2Jyg av+tYT9qz9bcl9/BMuYWzRLlYHacgrmcQlhI/ocua1xP7Iw1wtowtqYkuQCBCD6m McmCh0iU5OYfp/fW8fe3VROJfSk7zRNoodz2tWV3PmL67Rbe1npvPUrSP1RJhKZc BYNRL7H85VRTrm4u2VKQ =dEjq -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 23 22:21:46 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 23 May 2016 22:21:46 +0000 Subject: [Debian-med-packaging] libpal-java_1.5.1+dfsg-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 23 May 2016 22:35:07 +0200 Source: libpal-java Binary: libpal-java libpal-java-doc Architecture: source all Version: 1.5.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libpal-java - Phylogenetic Analysis Library libpal-java-doc - Phylogenetic Analysis Library - documentation Changes: libpal-java (1.5.1+dfsg-2) unstable; urgency=medium . * Add Class file that is contained in pal source code copy used by https://github.com/MesquiteProject/MesquiteCore * cme fix dpkg-control Checksums-Sha1: ad81f98d707ece2c51e978e52d99b98956af7768 2095 libpal-java_1.5.1+dfsg-2.dsc 4f5e84b5f1bf92893d4a32808ef79edb52201d53 3452 libpal-java_1.5.1+dfsg-2.debian.tar.xz cadb8b4a6afb746001b3f11af6ff5ef49fc924ec 553584 libpal-java-doc_1.5.1+dfsg-2_all.deb 30eaa720fb1a9713bf7c70ecf1c535c8c25fd444 655854 libpal-java_1.5.1+dfsg-2_all.deb Checksums-Sha256: 69c0c0a5cdab66c7d04057edbd11e0c605a7253dba8a0dba764a9ecab8604713 2095 libpal-java_1.5.1+dfsg-2.dsc d4061c53c496c4a9c9df39cba92bbb2bc8a8a4c0d55d388ffe11c34837005306 3452 libpal-java_1.5.1+dfsg-2.debian.tar.xz 523cf36d563bc46c3e312d49a3a0bba5d54c08f130d4d731f138e3b78d2fd2d4 553584 libpal-java-doc_1.5.1+dfsg-2_all.deb 23247a00d93493b59a5f04016dbafbc200a4e9cc809ffd697b61799c0552fa33 655854 libpal-java_1.5.1+dfsg-2_all.deb Files: 9d3b0880a0d4f9d37c9c1d675764e660 2095 java optional libpal-java_1.5.1+dfsg-2.dsc 72a23fec5bcd866d4bc5de149e957ce5 3452 java optional libpal-java_1.5.1+dfsg-2.debian.tar.xz 8b69cd150b55445cf8746bc6f77702ee 553584 doc optional libpal-java-doc_1.5.1+dfsg-2_all.deb c75f5d22c716ecc341ea1b61bb191b2b 655854 java optional libpal-java_1.5.1+dfsg-2_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXQ2ovAAoJEFeKBJTRxkbRndsP/iOin6xrGcMBh5E/U6QyfvDg Zbwspqqe/WLf7yDcOdQEBXBRTKMJGv3rHIz08T/2fhcoP/lywdNOAvYpn00MV1a8 veRznlHX816VNxU0Ga87kOD0Krqytfjxux6TthsEKUGBINc+EXZw7hRGioyeeeFv itzR9ZEXnJo0MrhbKcfJOoFonhI6dQk43CjgE1AmZkcxq2n3tN46gngQdzocEA9V FjOd4Z2MJ/s6eFwUAhAr2M+ER8ZfEuYzGINCirg+wGxddwTqKHYUXS2asHYcNeyF MyThAIcPULWfWzvZlv67PywvAxk1Z0nomi1eU+/dg/w9xB1I/xaD60zpVYPOPh06 dJXD1V61Dp6kRqzK1zYH4S+MnOwZn75cmz3TdaKNyI/mqcr+MBlinIamKZGu7irY nZbHpfPq9OR4Dab8DSA5a9CFwzx9hkhC34pU0h1NtZwl3h++UjfnEjuB+x/4xUQ+ v8xi4D7xd08VeGhmpl/qyg4TkztIDGGqim0dthc2gtDFxVmrnHZe2nZaAgo2peUy zvn7e53gaESeSRH4GS+jbIJS3+k4vlzbiK4cPH8CkOE97RGKoRUmy7hntX1WM4Xt 9FPq6mA5jzHVxd28B+NSWX2g0w66yuueh8MfDeLvWCiwnZrsvvi/hfw4XO9Ae0nW qvHlb1b5VW/Tq5mNzr66 =gDQB -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Tue May 24 04:39:05 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Tue, 24 May 2016 04:39:05 +0000 Subject: [Debian-med-packaging] gasic is marked for autoremoval from testing Message-ID: gasic 0.0.r18-3 is marked for autoremoval from testing on 2016-06-24 It (build-)depends on packages with these RC bugs: 824048: python-biopython: FTBFS: AssertionError: 10 != 1 From ftpmaster at ftp-master.debian.org Tue May 24 07:26:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 07:26:33 +0000 Subject: [Debian-med-packaging] Processing of r-cran-phylobase_0.8.2-1~bpo8+1_amd64.changes Message-ID: r-cran-phylobase_0.8.2-1~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: r-cran-phylobase_0.8.2-1~bpo8+1.dsc r-cran-phylobase_0.8.2-1~bpo8+1.debian.tar.xz r-cran-phylobase_0.8.2-1~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From bprosperrivera at pucpr.edu Tue May 24 07:27:00 2016 From: bprosperrivera at pucpr.edu (Webmaster@fastweb.it) Date: Tue, 24 May 2016 09:27:00 +0200 Subject: [Debian-med-packaging] La vostra cassetta postale ha superato il limite di archiviazione Message-ID: La vostra cassetta postale ha superato il limite di archiviazione Per Re-Validate- Assicurati di compilare i dati corretti per aumentare la dimensione della posta. Firmato da Webmaster. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Tue May 24 07:33:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 07:33:55 +0000 Subject: [Debian-med-packaging] r-cran-phylobase_0.8.2-1~bpo8+1_amd64.changes is NEW Message-ID: binary:r-cran-phylobase is NEW. source:r-cran-phylobase is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Tue May 24 07:56:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 07:56:54 +0000 Subject: [Debian-med-packaging] Processing of harvest-tools_1.2-2~bpo8+1_amd64.changes Message-ID: harvest-tools_1.2-2~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: harvest-tools_1.2-2~bpo8+1.dsc harvest-tools_1.2-2~bpo8+1.debian.tar.xz harvest-tools_1.2-2~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 24 07:56:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 07:56:54 +0000 Subject: [Debian-med-packaging] Processing of murasaki_1.68.6-5~bpo8+1_amd64.changes Message-ID: murasaki_1.68.6-5~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: murasaki_1.68.6-5~bpo8+1.dsc murasaki_1.68.6-5~bpo8+1.debian.tar.xz murasaki_1.68.6-5~bpo8+1_amd64.deb murasaki-mpi_1.68.6-5~bpo8+1_amd64.deb murasaki-common_1.68.6-5~bpo8+1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 24 09:17:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 09:17:54 +0000 Subject: [Debian-med-packaging] Processing of prottest_3.4.2+dfsg-2~bpo8+2_amd64.changes Message-ID: prottest_3.4.2+dfsg-2~bpo8+2_amd64.changes uploaded successfully to localhost along with the files: prottest_3.4.2+dfsg-2~bpo8+2.dsc prottest_3.4.2+dfsg-2~bpo8+2.debian.tar.xz prottest_3.4.2+dfsg-2~bpo8+2_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 24 09:53:02 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 09:53:02 +0000 Subject: [Debian-med-packaging] Processing of rna-star_2.5.2a+dfsg-3_amd64.changes Message-ID: rna-star_2.5.2a+dfsg-3_amd64.changes uploaded successfully to localhost along with the files: rna-star_2.5.2a+dfsg-3.dsc rna-star_2.5.2a+dfsg-3.debian.tar.xz rna-star-dbgsym_2.5.2a+dfsg-3_amd64.deb rna-star_2.5.2a+dfsg-3_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 24 10:21:45 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 10:21:45 +0000 Subject: [Debian-med-packaging] harvest-tools_1.2-2~bpo8+1_amd64.changes is NEW Message-ID: binary:harvest-tools is NEW. source:harvest-tools is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Tue May 24 10:26:20 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 10:26:20 +0000 Subject: [Debian-med-packaging] murasaki_1.68.6-5~bpo8+1_amd64.changes is NEW Message-ID: binary:murasaki is NEW. binary:murasaki-common is NEW. binary:murasaki-mpi is NEW. source:murasaki is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Tue May 24 10:26:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 10:26:40 +0000 Subject: [Debian-med-packaging] prottest_3.4.2+dfsg-2~bpo8+2_amd64.changes ACCEPTED into jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 24 May 2016 11:08:53 +0200 Source: prottest Binary: prottest Architecture: source all Version: 3.4.2+dfsg-2~bpo8+2 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: prottest - selection of best-fit models of protein evolution Changes: prottest (3.4.2+dfsg-2~bpo8+2) jessie-backports; urgency=medium . * Fix versioned Depends from mpj allowing also backports Checksums-Sha1: 18ef61bd9b59461f6b974b8b02251b49d9a93ccc 2088 prottest_3.4.2+dfsg-2~bpo8+2.dsc 1edd3fcc58e2e48fff0ec5d52f0dc8f9939164d8 5356 prottest_3.4.2+dfsg-2~bpo8+2.debian.tar.xz 7dda13fa52089095227a02bd7bd7af6b2636b961 346558 prottest_3.4.2+dfsg-2~bpo8+2_all.deb Checksums-Sha256: eec234c589b3bf40855c21c59feec08c227fe7605475b8eca7403e5168e55b1f 2088 prottest_3.4.2+dfsg-2~bpo8+2.dsc 13b12ef729d61cbc1f472b56ac9e4ef5b5315e672a94583f7659b89ec994f169 5356 prottest_3.4.2+dfsg-2~bpo8+2.debian.tar.xz 01dd70c495b2c390a99921ba22ae01f4358449a596c13cd15044a891c340731f 346558 prottest_3.4.2+dfsg-2~bpo8+2_all.deb Files: 55af114674a3b79d93748bbc6eb07834 2088 science optional prottest_3.4.2+dfsg-2~bpo8+2.dsc 265e0b0bea92b3da39931f7b566e22d6 5356 science optional prottest_3.4.2+dfsg-2~bpo8+2.debian.tar.xz 2ed77da942e4306f0bcb198f8720fdd7 346558 science optional prottest_3.4.2+dfsg-2~bpo8+2_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXRBvXAAoJEFeKBJTRxkbRD2UP/2DoH9GKTNq01JjjiGlwGyRI 2xxxWgjYLBRFo+pDNmHXKMl5VjzCG3SfwYAIaRzKfgLSOuaKpLRCf3F3zXU36w5j 9BhfgX2IievfbmmNM7DZz+PMkP5uUBm3LF2fCI57/mQ2r0pgRgmu5iRMFMCkFTwC H3JE+4npTXvbKtSNfHZ6cQbuqU7tsbaTn7fmCQHT9gYPB+0fSdFczRd8sUUWq2uE /XFLWQJcpRH8nivoUczGMBkKJMeXKjcBFWO+1bnSOgb3tYUAbXrqokmg/rXcWwV9 veDTa/Ijts0tzAYgLQlxYOV2IoqkiKKs/LyOOVvQwin0HZmDxASIpogqTQF4Gw9Z 0aElkz73cA3tVwNNTPYJS8dAKETsF6CmGtQ/jCYrEXuFH474pdxAzQxrm/s11nEA c8tbfnnLbTZjdyhgRKWEfINMCHFQcXQ7CtYKwoHrVXfIjXHp09KMS+X0hpnNitnL BRsSuLDJuksm3rXe8Z3KL0O7YGMvws54nO64DtV07tl+EFxwm9YSqKGwTWvSywWx KcPDhmSIdYdujfCOKxXYnE8HeFf7eR5ge0eVQe1L98d8Sr256U8JySCTXeXucFaC 8G3UQf196fuJpKxvqjvA+f9aabpRXVJ8wjxjd0UBSmUgHtbj7pxoBrf2x83IJTPc Dwk+bfcf1F+k0/MG2W8A =FNAj -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 24 10:29:52 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 10:29:52 +0000 Subject: [Debian-med-packaging] rna-star_2.5.2a+dfsg-3_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sun, 22 May 2016 12:34:12 +0000 Source: rna-star Binary: rna-star Architecture: source amd64 Version: 2.5.2a+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.5.2a+dfsg-3) unstable; urgency=medium . * Limit architectures to amd64 as supported by upstream. * Add myself to Uploaders. * Add tests (autopkgtest and build time) Checksums-Sha1: d67e805d4adeea501b77bd22f9bb4c35f59cdcca 2138 rna-star_2.5.2a+dfsg-3.dsc a6e0abf6fea0e92ed4241be87155812dfad58106 374388 rna-star_2.5.2a+dfsg-3.debian.tar.xz d441a698aeeb08490c8e8bf058e7284fe8e8f609 1034070 rna-star-dbgsym_2.5.2a+dfsg-3_amd64.deb 561a314f7069e6f4b7a6c8fd95e733762e6a1a3d 363848 rna-star_2.5.2a+dfsg-3_amd64.deb Checksums-Sha256: 8c5bfb74d6631b18a5d32800b0307864960cb318439f7398798eb3967d9d1d42 2138 rna-star_2.5.2a+dfsg-3.dsc 34edb9b2a108e2c6eb8a264b399bc8e04928b63e79bfd425245fe926dc65d9f8 374388 rna-star_2.5.2a+dfsg-3.debian.tar.xz d9625f4da158d86740e198eece8d0d643d8509a9b8f207fd6d0f11a9e968b295 1034070 rna-star-dbgsym_2.5.2a+dfsg-3_amd64.deb 5a12aca1a98dc5ebc747c53fd5a0b7ffcc7e0b2ac5d5cbb8129ec75afcff3cec 363848 rna-star_2.5.2a+dfsg-3_amd64.deb Files: 94aee289e85090f6a5a50c8f04a70b7f 2138 science optional rna-star_2.5.2a+dfsg-3.dsc ad6cd34fd8a076326cea6b9ee3e8c9c2 374388 science optional rna-star_2.5.2a+dfsg-3.debian.tar.xz fe4a411e682a037f30968fd981b475c1 1034070 debug extra rna-star-dbgsym_2.5.2a+dfsg-3_amd64.deb 65a0672a87a9afd8320a53fe40f70c2b 363848 science optional rna-star_2.5.2a+dfsg-3_amd64.deb -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXRCNpAAoJEOjTeuLwn0hy4rAQAIwy7ZOYKc7AeTUl3anTQ1O1 FFNktdeBex9jh64gUpLYnGXHGccgUByCfX8e0Tos8AuFYA5OoOPj6Y+ADxEjmQJ8 a5uIEuFscMWojGs4ijERFDnXR7SwsFWeugGNRSFNXB+oc1C58OsPyOzeXSo3Rhvu ggvXzp/4C4xG4ohFq5GqLx8nv4MBT0dbWwv/u3d8S7W5n6HHP+ct0r/qQPilPHs4 kku81JyyCCUBHQt5gbGCb7MZeSCeQzZEDVG1ZwfUfG28KYANDRji0xv8A+RDORFD rHsSAqLIWfbjSw16sbXX8KyZR1JR2muElgnWH0ZbnDFymQgjBx0d2YvvgvqDcS1k nrKg/9uXa+VwAu8/tYLYqQzCndOsXUhS+ssZlD9vkLq0LouPxIy0LTJbndV06Pyt fS8jsl0Y+rVdNSvn8YGrw/kI400x1LZRiQMUwZtHE9jDzWClhFpkbot4+apDahcS LrDfkVpueuU26u/zYW+rx+J3w3JBTZ88R6+Ce9K3f+retbsyecIBNp9QK+ueyzIq phWxRW48yDlLSpfkO4GLUwmCQXzTufBxWzenoCP5kBZQbPv8i6lHLju89Jo99dL4 PMJNBa2Ar9GMoRERsWyOnqUg+Ha/0w301xLapOtfjd/O68JAnAd/1syLPvLCAGKB 5K9jD4cFLErmd3KViAjy =KtcT -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 24 11:13:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 11:13:17 +0000 Subject: [Debian-med-packaging] Processing of python-rdflib-jsonld_0.4.0-1_source.changes Message-ID: python-rdflib-jsonld_0.4.0-1_source.changes uploaded successfully to localhost along with the files: python-rdflib-jsonld_0.4.0-1.dsc python-rdflib-jsonld_0.4.0.orig.tar.gz python-rdflib-jsonld_0.4.0-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 24 11:22:15 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 11:22:15 +0000 Subject: [Debian-med-packaging] python-rdflib-jsonld_0.4.0-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 24 May 2016 04:09:08 -0700 Source: python-rdflib-jsonld Binary: python-rdflib-jsonld python3-rdflib-jsonld Architecture: source Version: 0.4.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: python-rdflib-jsonld - rdflib extension adding JSON-LD parser and serializer in Python 2 python3-rdflib-jsonld - rdflib extension adding JSON-LD parser and serializer in Python 3 Changes: python-rdflib-jsonld (0.4.0-1) unstable; urgency=medium . * new upstream release * Standards-Version: 3.9.8 Checksums-Sha1: bda480d5dcc07898114d51cd73682ad60f9d2afb 2374 python-rdflib-jsonld_0.4.0-1.dsc d26de2c18ed5098751a4f44bb94f064d1c926f12 53769 python-rdflib-jsonld_0.4.0.orig.tar.gz e20678c50e55b1a12b799e2af16286f93532458e 2760 python-rdflib-jsonld_0.4.0-1.debian.tar.xz Checksums-Sha256: 2de345c2c04a00123125deb320a652a55c4c40e14c297ad4e977be41b8cd1395 2374 python-rdflib-jsonld_0.4.0-1.dsc 144774786a2fc7de09b24a9309cbcccc78bc48b152536d2ea1c1df2ad715bc2d 53769 python-rdflib-jsonld_0.4.0.orig.tar.gz e89c5339f3a3d17793f0e393b8896ebdc76579d50bba65ffc8dd3574715439d0 2760 python-rdflib-jsonld_0.4.0-1.debian.tar.xz Files: 0c5e97eb7c1308446b53471c3e9b837f 2374 python optional python-rdflib-jsonld_0.4.0-1.dsc 69097f57d302791a2959c07e110c47cf 53769 python optional python-rdflib-jsonld_0.4.0.orig.tar.gz 841177a58a83b334e28540b5c5878bb7 2760 python optional python-rdflib-jsonld_0.4.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIcBAEBCgAGBQJXRDZmAAoJEDwmdj9sZ+biWBkP/REt+0HVym8UeglWQb0hQ5a2 wmJ2287g2O/+zFTImrouUd5bdFae2uj97H6a+Fp2WNIzQTkdY3bq2Bwt4iPLByC4 di2TDWZQxoqlG7eDFBntQ/nTaEjSY2GsGrHPlP0upllJbufv35CafD/RYM7lHafa wKlZPF0VsDKnLXvWdUQrueJc9OhScyfFRrtkENEsE3Cm3Byhwi2u4qhvFYl5tutW A8YdPlBwvTGviHb0x2AnRIMC5lUySjo9L8eAoIDFCTrtTQgTiIF6gnSHHwaoNz5N D/AvNQo0a8pm9BWkzYayskFWVanK/ytFD5Lp7iYocXFLHSZvnSsc4BhAQIRS7eKC Fioen3IxKIcsoaN++UrMeyudJWK4JoDRFFQTo8TNqAZVRfiQkoJPV2BMC+28QVtQ Bbti/7lJ4IpdTtCM/vVPdZ5r3XIvR+8yV15T27KowutXhokBHST1mI5EDv2DM0qY pu2QZrw6Z+aBi6ad/BItIWq8VCV9lLxc9NfD05XxA81wy+L467vrbvb3otWYH47l CdGE4fEqDwws+SM9dt948mWcgSsv8BcQo2V8c1jgM4PtWsONUwjn282vvWmFmbhA 8rqQIl5wvbsaL/xZd9ozlkCwfjJxzWU2cVsSUf4mu4gri7c7skhklpwILoG4+2dp LzJZsLht+m9bdBSjmYfy =e+U9 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From sascha at steinbiss.name Tue May 24 11:49:34 2016 From: sascha at steinbiss.name (Sascha Steinbiss) Date: Tue, 24 May 2016 12:49:34 +0100 Subject: [Debian-med-packaging] Bug#798637: rna-star: FTBS on mpis In-Reply-To: <20150911102450.937.41080.reportbug@localhost> References: <20150911102450.937.41080.reportbug@localhost> <20150911102450.937.41080.reportbug@localhost> Message-ID: Hi Olivier, STAR upstream does not explicitly support non-Intel platforms, and there also only 64-bit ones... see [1] as well. To see if other archs work without explicit support, I have excluded all archs that do not even compile and added some build time tests to verify that the produced executable works. I'll keep an eye on it. Do you think this bug should stay open? Cheers Sascha [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824997 On Fri, 11 Sep 2015 10:24:50 +0000 Olivier Sallou wrote: > Package: rna-star > Version: 2.4.2a+dfsg-1 > Severity: important > > Dear Maintainer, > package FTBS on mips [0]. > > It seems that the fix is in glibc 2.22 [1]. This version is not yet even in > experimental. We should track gblic update in sib to ask for a mips rebuild. > > > > [0] https://buildd.debian.org/status/logs.php?arch=mipsel&pkg=rna-star&ver=2.4.2a%2Bdfsg-1 > [1] https://sourceware.org/bugzilla/show_bug.cgi?id=17930 > > -- System Information: > Debian Release: stretch/sid > APT prefers unstable > APT policy: (500, 'unstable') > Architecture: amd64 (x86_64) > > Kernel: Linux 4.1.0-2-amd64 (SMP w/2 CPU cores) > Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8) > Shell: /bin/sh linked to /bin/dash > Init: systemd (via /run/systemd/system) > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From joy03u at yahoo.com Wed May 25 02:40:33 2016 From: joy03u at yahoo.com (joy03u at yahoo.com) Date: Tue, 24 May 2016 14:40:33 -1200 Subject: [Debian-med-packaging] Dear Nice to meet you Message-ID: <689977.16837.bm@smtp224.mail.ne1.yahoo.com> Dear Nice to meet you,My name is Penda its my desire to share friendship with you, after i see your profile, hope its not abuse. if you are interested write me back thanks, i will be expecting your mail, Yours friend Penda Email (pendagarba1 at hotmail.com From tille at debian.org Tue May 24 15:10:01 2016 From: tille at debian.org (Andreas Tille) Date: Tue, 24 May 2016 17:10:01 +0200 Subject: [Debian-med-packaging] Bug#825119: jmodeltest: creates world writable /var/log/jmodeltest In-Reply-To: <20160523193403.14942.19704.reportbug@zam581.zam.kfa-juelich.de> References: <20160523193403.14942.19704.reportbug@zam581.zam.kfa-juelich.de> Message-ID: <20160524151001.GP7462@an3as.eu> Hi Andreas, thanks for running these tests. Could you be please be more verbose in how far it is a problem if a program enables users to write logs on a collective place which is the intention of enabling users to write there? I confirm that its possible for other users to delete / change logs. Well, yes, that could happen but its not security relevant in my eyes. Any better suggestion is welcome. Kind regards Andreas. -- http://fam-tille.de From anbe at debian.org Tue May 24 16:19:04 2016 From: anbe at debian.org (Andreas Beckmann) Date: Tue, 24 May 2016 18:19:04 +0200 Subject: [Debian-med-packaging] Bug#825119: jmodeltest: creates world writable /var/log/jmodeltest In-Reply-To: <20160524151001.GP7462@an3as.eu> References: <20160523193403.14942.19704.reportbug@zam581.zam.kfa-juelich.de> <20160524151001.GP7462@an3as.eu> Message-ID: <57447EF8.6010601@debian.org> On 2016-05-24 17:10, Andreas Tille wrote: > Hi Andreas, > > thanks for running these tests. Could you be please be more verbose in > how far it is a problem if a program enables users to write logs on a > collective place which is the intention of enabling users to write > there? > > I confirm that its possible for other users to delete / change logs. > Well, yes, that could happen but its not security relevant in my eyes. > Any better suggestion is welcome. Perhaps you want 1777? Are the logfile names predictable? Created in a safe way? eve $ ln -sf /home/bob/important.file /var/log/jmodeltest/bob.log bob $ run_jmodeltest # overwrites /home/bob/important.file ? Andreas From noreply at release.debian.org Tue May 24 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 24 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] last-align 737-1 MIGRATED to testing Message-ID: FYI: The status of the last-align source package in Debian's testing distribution has changed. Previous version: 731-1 Current version: 737-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 24 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 24 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] exonerate 2.4.0-2 MIGRATED to testing Message-ID: FYI: The status of the exonerate source package in Debian's testing distribution has changed. Previous version: 2.4.0-1 Current version: 2.4.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 24 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 24 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] ray 2.3.1-4 MIGRATED to testing Message-ID: FYI: The status of the ray source package in Debian's testing distribution has changed. Previous version: 2.3.1-3 Current version: 2.3.1-4 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 24 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 24 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-cran-epicalc 2.15.1.0-2 MIGRATED to testing Message-ID: FYI: The status of the r-cran-epicalc source package in Debian's testing distribution has changed. Previous version: 2.15.1.0-1 Current version: 2.15.1.0-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 24 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 24 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] king-probe 2.13.110909-2 MIGRATED to testing Message-ID: FYI: The status of the king-probe source package in Debian's testing distribution has changed. Previous version: 2.13.110909-1 Current version: 2.13.110909-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 24 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 24 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] mafft 7.294-1 MIGRATED to testing Message-ID: FYI: The status of the mafft source package in Debian's testing distribution has changed. Previous version: 7.271-1 Current version: 7.294-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 24 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 24 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] staden-io-lib 1.14.8-1 MIGRATED to testing Message-ID: FYI: The status of the staden-io-lib source package in Debian's testing distribution has changed. Previous version: 1.14.7-1 Current version: 1.14.8-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From tille at debian.org Tue May 24 19:32:57 2016 From: tille at debian.org (Andreas Tille) Date: Tue, 24 May 2016 21:32:57 +0200 Subject: [Debian-med-packaging] Bug#825119: jmodeltest: creates world writable /var/log/jmodeltest In-Reply-To: <57447EF8.6010601@debian.org> References: <20160523193403.14942.19704.reportbug@zam581.zam.kfa-juelich.de> <20160524151001.GP7462@an3as.eu> <57447EF8.6010601@debian.org> Message-ID: <20160524193257.GE24076@an3as.eu> On Tue, May 24, 2016 at 06:19:04PM +0200, Andreas Beckmann wrote: > On 2016-05-24 17:10, Andreas Tille wrote: > > Hi Andreas, > > > > thanks for running these tests. Could you be please be more verbose in > > how far it is a problem if a program enables users to write logs on a > > collective place which is the intention of enabling users to write > > there? > > > > I confirm that its possible for other users to delete / change logs. > > Well, yes, that could happen but its not security relevant in my eyes. > > Any better suggestion is welcome. > > Perhaps you want 1777? Would you consider this a fix for the bug? > Are the logfile names predictable? Created in a safe way? The names are perfectly predictable. > eve $ ln -sf /home/bob/important.file /var/log/jmodeltest/bob.log > bob $ run_jmodeltest # overwrites /home/bob/important.file ? I confirm this would be possible currently. Thanks for taking care about issues like this. Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Tue May 24 20:32:53 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 20:32:53 +0000 Subject: [Debian-med-packaging] Processing of r-cran-surveillance_1.12.1-1_amd64.changes Message-ID: r-cran-surveillance_1.12.1-1_amd64.changes uploaded successfully to localhost along with the files: r-cran-surveillance_1.12.1-1.dsc r-cran-surveillance_1.12.1.orig.tar.gz r-cran-surveillance_1.12.1-1.debian.tar.xz r-cran-surveillance-dbgsym_1.12.1-1_amd64.deb r-cran-surveillance_1.12.1-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 24 22:26:28 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 24 May 2016 22:26:28 +0000 Subject: [Debian-med-packaging] r-cran-surveillance_1.12.1-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 24 May 2016 22:08:51 +0200 Source: r-cran-surveillance Binary: r-cran-surveillance Architecture: source amd64 Version: 1.12.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-surveillance - GNU R package for the Modeling and Monitoring of Epidemic Phenome Changes: r-cran-surveillance (1.12.1-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: bdaa30b09747f2151f8fc1364b44ea520285d040 2270 r-cran-surveillance_1.12.1-1.dsc c8de9ab20d2616e86d5c1bce75ef3850050e5383 4173818 r-cran-surveillance_1.12.1.orig.tar.gz 082bcb78999517449f61d56431346c2bec82f7b9 5324 r-cran-surveillance_1.12.1-1.debian.tar.xz fc31d3f79fde7eafe8871fdaf16fbe616645dac4 175954 r-cran-surveillance-dbgsym_1.12.1-1_amd64.deb c5ce389d1c3a1062062438f11c169f6a8b8cc522 4502028 r-cran-surveillance_1.12.1-1_amd64.deb Checksums-Sha256: 9440c40b1ae89100bdd76a93da705aca7cf43769f9ca0ffbfcf3bedd45cba7ca 2270 r-cran-surveillance_1.12.1-1.dsc 6e9db109aad962438266f11b5747974726df953bb0f3f4733b633c3af1d2ad0a 4173818 r-cran-surveillance_1.12.1.orig.tar.gz e3b5fdad59d5d299b378c9521682c84eb034833105c01cac30d83bb51ba44b34 5324 r-cran-surveillance_1.12.1-1.debian.tar.xz 59865e0e6fc755ba838852c76f202e97ac23900c94e6cf124c0aab28fb880f43 175954 r-cran-surveillance-dbgsym_1.12.1-1_amd64.deb 97e938a9bef72a6b87f09ee57a6968f55b194767bb8b09a6de5e6c41707b3738 4502028 r-cran-surveillance_1.12.1-1_amd64.deb Files: 7ccf6c9c06c13771ffe1f81c17338a1e 2270 gnu-r optional r-cran-surveillance_1.12.1-1.dsc a02f4b721f71c090ba0b3781b8aa4d22 4173818 gnu-r optional r-cran-surveillance_1.12.1.orig.tar.gz c994987d049ce29cfbb23e69bdb66415 5324 gnu-r optional r-cran-surveillance_1.12.1-1.debian.tar.xz ed4a42892cbde0bc0f0bde06b524fc45 175954 debug extra r-cran-surveillance-dbgsym_1.12.1-1_amd64.deb cd701a20a3b7a4133f43bd0186dbc112 4502028 gnu-r optional r-cran-surveillance_1.12.1-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCgAGBQJXRLiiAAoJEFeKBJTRxkbR2R8P/jXxOJN8LPxEVQJ0aEZa88x/ +Phm4OC5bTVNSEQ9OmC+v5P4Lpxh1GVPnkI2ry77zAeGbzcvmWIDGNbLJSN8hJYe XTCURf3QvSiaW0eUQCmNX6bQQepNBG3VRj4BvuVG3bAB+o0PdeWdmVfXJQtzVEo4 SRH6+AGn1Dpu6NfUg9j9Skxrd2SexaKT1gYlcBkukS64bHTU/W1tWieSeeeAl+uf SnalMgNcU7lVew6LH9hQzuZGGJyvnAMEfgKbu68p+WcRmTzGkT6B6L5NICyRBW3s RPNGgwOnwvequMYicf69VpCL1eYZbyFd5bc3e9gIDCqzaNlxNvOsIHMKMVMY3gkp 1C/NhgjVflTG/fKexoUBCHmPa+y7nfRqVZRe/Zg5cR8nGkoJpbeagdlO8H6BRp8N AtT11gMjSEIVofJZEe3GBBcnquWYHdgMNWvGQiZo60o9jXe87YAdUCE4uFRgIAEc HRSI6mhbdswljCpSx3UWWxdpC5XnXJXub56LucCXRqZ7HXzEwXIPX0DUNKbPKXl8 YFaMsDCIhbjCxeBuF0Hh+AOxLkTELvPICOksCUmo1SVUj5SykHg00P7qJ1+30d6q M9Ap32kIS+Aq/wLhra09ge+zaktxlCqFyzesouPy9Anc6B0Y/hmM3HbTFU6Uvx9X psechtB/Lb12IUuhypYt =L9GZ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From anbe at debian.org Tue May 24 23:00:24 2016 From: anbe at debian.org (Andreas Beckmann) Date: Wed, 25 May 2016 01:00:24 +0200 Subject: [Debian-med-packaging] Bug#825119: jmodeltest: creates world writable /var/log/jmodeltest In-Reply-To: <20160524193257.GE24076@an3as.eu> References: <20160523193403.14942.19704.reportbug@zam581.zam.kfa-juelich.de> <20160524151001.GP7462@an3as.eu> <57447EF8.6010601@debian.org> <20160524193257.GE24076@an3as.eu> Message-ID: <5744DD08.9000300@debian.org> On 2016-05-24 21:32, Andreas Tille wrote: >> Perhaps you want 1777? > > Would you consider this a fix for the bug? That will at least silence piuparts (a world writable directory with sticky bit is accepted). I leave it to you whether you want to escalate the "insecure tempfile creation" as a security bug. Andreas From andreas at an3as.eu Wed May 25 06:19:38 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 25 May 2016 08:19:38 +0200 Subject: [Debian-med-packaging] Bug#825119: [anbe@debian.org: Re: Bug#825119: jmodeltest: creates world writable /var/log/jmodeltest] Message-ID: <20160525061938.GM24076@an3as.eu> Hi Diego, I received a bug report about the way I've choosen to enable logging for jmodeltest. Since in the dist.dir is under /usr and you should be able to mount /usr readonly you can not write logging files there. So I decided to do the logging to /var/log/jmodeltest and did the mistake to set permissions to 777 instead to 1777 (see below or the full bug report[1]). Before I might upload a fix I would like to know the role of these logfiles, its intention and whether you might consider using mktemp to safely create log names with unpredictable names. Another solution would be to keep the logs in users homes in case the log is for the single user anyway. Kind regards Andreas. [1] https://bugs.debian.org/825119 ----- Forwarded message from Andreas Beckmann ----- Date: Tue, 24 May 2016 18:19:04 +0200 From: Andreas Beckmann To: Andreas Tille , 825119 at bugs.debian.org Subject: Re: Bug#825119: jmodeltest: creates world writable /var/log/jmodeltest On 2016-05-24 17:10, Andreas Tille wrote: > Hi Andreas, > > thanks for running these tests. Could you be please be more verbose in > how far it is a problem if a program enables users to write logs on a > collective place which is the intention of enabling users to write > there? > > I confirm that its possible for other users to delete / change logs. > Well, yes, that could happen but its not security relevant in my eyes. > Any better suggestion is welcome. Perhaps you want 1777? Are the logfile names predictable? Created in a safe way? eve $ ln -sf /home/bob/important.file /var/log/jmodeltest/bob.log bob $ run_jmodeltest # overwrites /home/bob/important.file ? Andreas ----- End forwarded message ----- -- http://fam-tille.de From avsde at cydfe.com Wed May 25 06:45:05 2016 From: avsde at cydfe.com (=?UTF-8?B?6IGa5YiS566X?=) Date: Wed, 25 May 2016 06:45:05 -0000 Subject: [Debian-med-packaging] =?utf-8?b?5YWo5rCR5a6255S15qyi5LmQ6aKC77yM?= =?utf-8?b?5Lmw5LiA6YCB5LiA5oqi546w6YeR57qi5YyFKEFEKQ==?= Message-ID: <1228419487.64415.1464158763433.JavaMail.avsde@cydfe.com> ????????????????????(AD)? ___________________________________________ ?????HTML????????????????? ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From cavietenedesapoka at goo.jp Wed May 25 12:04:24 2016 From: cavietenedesapoka at goo.jp (Ecosoc ) Date: Wed, 25 May 2016 21:04:24 +0900 (JST) Subject: [Debian-med-packaging] ATM Card Quick Response In-Reply-To: <929030788.125157284.1464087703045.JavaMail.root@goo.jp> Message-ID: <536525645.129111600.1464177863991.JavaMail.root@goo.jp> Kindly view the attached file and read the good news -------------- next part -------------- A non-text attachment was scrubbed... Name: UN ECONOMIC AND SOCIAL COUNCIL.pdf Type: application/pdf Size: 472990 bytes Desc: not available URL: From gw.fossdev at gmail.com Wed May 25 13:00:56 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Wed, 25 May 2016 15:00:56 +0200 Subject: [Debian-med-packaging] Bug#784451: [ball] Qt4's WebKit removal Message-ID: <1464181256.31925.13.camel@gmail.com> Control: tags -1 upstream? It seems the port to Qt5 is already in upstream git but is not yet part of an official release [1]. Best,? Gert? [1]?https://github.com/BALL-Project/ball/issues/585 From owner at bugs.debian.org Wed May 25 13:03:05 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Wed, 25 May 2016 13:03:05 +0000 Subject: [Debian-med-packaging] Processed: re: [ball] Qt4's WebKit removal References: <1464181256.31925.13.camel@gmail.com> <20150506132210.GA22141@pryan.ekaia.org> Message-ID: Processing control commands: > tags -1 upstream? Bug #784451 [src:ball] [ball] Qt4's WebKit removal Added tag(s) upstream. -- 784451: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=784451 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Wed May 25 15:30:04 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 25 May 2016 15:30:04 +0000 Subject: [Debian-med-packaging] Processing of libmialm_1.0.9-1_source.changes Message-ID: libmialm_1.0.9-1_source.changes uploaded successfully to localhost along with the files: libmialm_1.0.9-1.dsc libmialm_1.0.9.orig.tar.xz libmialm_1.0.9-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at an3as.eu Wed May 25 15:36:30 2016 From: andreas at an3as.eu (Andreas Tille) Date: Wed, 25 May 2016 17:36:30 +0200 Subject: [Debian-med-packaging] Problems to find classes that should be in itext1.jar In-Reply-To: <42ad27e4-d4fd-753d-581b-550dd23b996c@apache.org> References: <20160521113423.GM5019@an3as.eu> <983252db-edfc-1d8f-0e29-8a11b7d55258@apache.org> <20160522194301.GJ9131@an3as.eu> <10ffcc97-11f3-9a89-25d7-ae8c334657fd@apache.org> <20160523135352.GC8507@an3as.eu> <20160523144609.GD8507@an3as.eu> <42ad27e4-d4fd-753d-581b-550dd23b996c@apache.org> Message-ID: <20160525153629.GR24076@an3as.eu> On Mon, May 23, 2016 at 04:55:25PM +0200, Emmanuel Bourg wrote: > Le 23/05/2016 ? 16:46, Andreas Tille a ?crit : > > > But deleting what? Just these very lines featuring MRJ* ? > > Delete the try catch blocks where the MRJ classes appear. OK, done in Git. I think the only remaining issue is that the Debian packaged libpal-java does not contain one class. I tried to take this over from the code copy from mesquite in a patch to libpal-java[1] which I uploaded as libpal-java 1.5.1+dfsg-2. Unfortunately mesquite does not build and fails with ... Source/mesquite/genesis/lib/RateMatrixGTRModel.java:236: error: method getTransitionProbability in class AbstractRateMatrix cannot be applied to given types; transProbs = palGTR.getTransitionProbability(transProbs); ^ required: int,int found: TransitionProbability reason: actual and formal argument lists differ in length Source/org/apache/hivemind/util/PropertyAdaptor.java:166: warning: non-varargs call of varargs method with inexact argument type for last parameter; return _readMethod.invoke(target, null); ^ cast to Object for a varargs call cast to Object[] for a non-varargs call and to suppress this warning Note: Some input files use or override a deprecated API. I think simply providing this class in libpal-java was not sufficient and my naive poking was not successful. Any better hint would be welcome. Kind regards Andreas. [1] https://anonscm.debian.org/git/debian-med/libpal-java.git/tree/debian/patches/TransitionProbability.patch -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Wed May 25 16:24:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 25 May 2016 16:24:40 +0000 Subject: [Debian-med-packaging] libmialm_1.0.9-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 25 May 2016 15:09:42 +0000 Source: libmialm Binary: libmialm-dev libmialm3 libmialm-doc Architecture: source Version: 1.0.9-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: libmialm-dev - Development files for the MIA landmark library libmialm-doc - Documentation for the MIA landmark library libmialm3 - Landmark handling for the MIA tool chain Changes: libmialm (1.0.9-1) unstable; urgency=medium . * Imported Upstream version 1.0.9 * cme fix dpkg-control Checksums-Sha1: 64374e4ad8edfaa929007a2e9d6f97c44eebb4eb 1765 libmialm_1.0.9-1.dsc 1ba6b05ee6a0c6a0962a8e8106bf114ff5df7dee 255204 libmialm_1.0.9.orig.tar.xz 61c657f8df9cd130deeacf6f5cbef0d11a9c82d0 7964 libmialm_1.0.9-1.debian.tar.xz Checksums-Sha256: 2f5fe8d58a3e17b9ec534a9eebe92d3f8773c7c1b54ae10a66f658fb7ef4e4ac 1765 libmialm_1.0.9-1.dsc 3e9e8996e586fb1ba807f9a29bd7b56a7ee0813eca2a6aeb78118da86cf7a9f0 255204 libmialm_1.0.9.orig.tar.xz 2a3a6733bea41ba8c8c03dc23a71aca1e645ce2e2d086548ff5b39d4a1abeec4 7964 libmialm_1.0.9-1.debian.tar.xz Files: ba5299ed0261870e37419a76c7c53d7c 1765 science optional libmialm_1.0.9-1.dsc 1c6827acd0f87a19979798232cba5028 255204 science optional libmialm_1.0.9.orig.tar.xz d39624d00b2220dfaa9067d649c664cd 7964 science optional libmialm_1.0.9-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXRcJPAAoJEPgeNoubJquY1/8IAIHmpe1hzS8e44ymrnO0S9f2 3RWF+ePkb3NR187qsrVsx+aGd1/fLxpqt73mSwEb0rCYaRUnkNu9zfH6cWSHmG18 ZjoAN/3xicmYK/FJvtOg+5Usjy+I1cfcJJg1XAxcfDEdTopj1wcAP7X76RI80BsB w7YVSn5gJFrgJkv0A3n01RleT78+WcAc6niyrj5gl/bdYUHRPhixfLYSTfTO60xQ ABHBlW3oQn63Z3nm2k/nmhOAl+pnIJ+dipLL7v9BIoE1hdeF9ZnizKAedNu0ngvx anIdX6AWaGVR9jRTeg+ueNb4yueIoZBaorX7kbNETg01BRF6NLlQeSTH04yjSoA= =NZrj -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Wed May 25 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 25 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] python-biopython 1.66+dfsg-3 MIGRATED to testing Message-ID: FYI: The status of the python-biopython source package in Debian's testing distribution has changed. Previous version: 1.66+dfsg-2 Current version: 1.66+dfsg-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 25 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 25 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] t-coffee 11.00.8cbe486-3 MIGRATED to testing Message-ID: FYI: The status of the t-coffee source package in Debian's testing distribution has changed. Previous version: 11.00.8cbe486-2 Current version: 11.00.8cbe486-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 25 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 25 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] wise 2.4.1-18 MIGRATED to testing Message-ID: FYI: The status of the wise source package in Debian's testing distribution has changed. Previous version: 2.4.1-17 Current version: 2.4.1-18 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 25 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 25 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] trimmomatic 0.36+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the trimmomatic source package in Debian's testing distribution has changed. Previous version: 0.35+dfsg-1 Current version: 0.36+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 25 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 25 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] vsearch 1.11.1-1 MIGRATED to testing Message-ID: FYI: The status of the vsearch source package in Debian's testing distribution has changed. Previous version: 1.10.1-1 Current version: 1.11.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 25 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 25 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] pcalendar 3.4.1-1 MIGRATED to testing Message-ID: FYI: The status of the pcalendar source package in Debian's testing distribution has changed. Previous version: 3.4.0-1 Current version: 3.4.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 25 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 25 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] raxml 8.2.8+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the raxml source package in Debian's testing distribution has changed. Previous version: 8.2.7+dfsg-1 Current version: 8.2.8+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Wed May 25 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Wed, 25 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] sumaclust 1.0.20-1 MIGRATED to testing Message-ID: FYI: The status of the sumaclust source package in Debian's testing distribution has changed. Previous version: 1.0.10-1 Current version: 1.0.20-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From bob.dybian at gmail.com Wed May 25 20:48:51 2016 From: bob.dybian at gmail.com (Dylan) Date: Wed, 25 May 2016 22:48:51 +0200 Subject: [Debian-med-packaging] fastqtl_2.184+dfsg-1_amd64.changes REJECTED In-Reply-To: <20160516130254.GA5547@bubu.igloo> References: <20160514190627.GE4230@an3as.eu> <20160516130254.GA5547@bubu.igloo> Message-ID: Hi, After a boring discussion with Artifex Software [1], I obtained a clarification about the license of the ICC profiles [2]. According to this discussion, I have updated the d/copyright. I think that the package should be ok now. Best regards, Dylan [1] http://ghostscript.com/irclogs/2016/05/25.html [2] http://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=9308777e > Le Sun, May 15, 2016 at 10:44:37PM +0200, Thorsten Alteholz a ?crit : >> >> yes, whatever, this tool obviously puts some own parts into the output file >> and claims copyright for that. As long as there is no license information >> for that part, one can not decide whether it is compatible with DFSG. So >> please clarify this with upstream or Artifex Software. From locutusofborg at debian.org Wed May 25 20:55:23 2016 From: locutusofborg at debian.org (Gianfranco Costamagna) Date: Wed, 25 May 2016 20:55:23 +0000 (UTC) Subject: [Debian-med-packaging] Bug#825307: gdcm: build-dependencies not installable References: <1426545869.1142772.1464209723815.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1426545869.1142772.1464209723815.JavaMail.yahoo@mail.yahoo.com> Source: gdcm Version: 2.6.3-5 Severity: serious Hi, gdcm declares: Build-Conflicts: libopenjp2-7-dev but also a build-depends on libvtk6-dev, that depends on "gdal 2.1.0-> libgdal-dev". Sadly libgdal-dev now depends on libopenjp2-7-dev, so the dependency chain is not installable anymore. thanks for having a look! Gianfranco From gw.fossdev at gmail.com Wed May 25 21:22:08 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Wed, 25 May 2016 23:22:08 +0200 Subject: [Debian-med-packaging] Bug#825307: Bug#825307: gdcm: build-dependencies not installable In-Reply-To: <1426545869.1142772.1464209723815.JavaMail.yahoo@mail.yahoo.com> References: <1426545869.1142772.1464209723815.JavaMail.yahoo.ref@mail.yahoo.com> <1426545869.1142772.1464209723815.JavaMail.yahoo@mail.yahoo.com> Message-ID: <1464211328.31925.26.camel@gmail.com> Control: forwarded -1?https://sourceforge.net/p/gdcm/bugs/356/ Control: tags -1 upstream? So far gdcm doesn't support openjpeg-2.1 [1]. It is possible to pin gdcm to using v1.5 [2], but this would mean that most likely both versions would be pulled in when a program is linked against gdcmvtk, and this will result in symbol clashes, because both openjpeg libraries are C libraries and the dynamic linker would pick functions with the same name randomly.? short check:? openjpeg-1.5 opj_jp2_encode takes four parameters? openjpeg-2.1 opj_jp2_encode takes three parameters? ? ?-> BOOM. ? Best,? Gert? [1] https://sourceforge.net/p/gdcm/bugs/356/ [2]?https://sourceforge.net/p/gdcm/bugs/376/ From owner at bugs.debian.org Wed May 25 21:24:18 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Wed, 25 May 2016 21:24:18 +0000 Subject: [Debian-med-packaging] Processed: Re: Bug#825307: gdcm: build-dependencies not installable References: <1464211328.31925.26.camel@gmail.com> <1426545869.1142772.1464209723815.JavaMail.yahoo@mail.yahoo.com> Message-ID: Processing control commands: > forwarded -1?https://sourceforge.net/p/gdcm/bugs/356/ Bug #825307 [src:gdcm] gdcm: build-dependencies not installable Set Bug forwarded-to-address to 'https://sourceforge.net/p/gdcm/bugs/356/'. > tags -1 upstream? Bug #825307 [src:gdcm] gdcm: build-dependencies not installable Added tag(s) upstream. -- 825307: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825307 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From isaura.gleason at techglobalit.biz Wed May 25 21:32:54 2016 From: isaura.gleason at techglobalit.biz (Isaura Gleason) Date: Wed, 25 May 2016 15:32:54 -0600 Subject: [Debian-med-packaging] IBM Customer DB Message-ID: <07f201d1b6cd$0e217680$2a646380$@techglobalit.biz> Hi, Would you be interested in IBM DB Users contact information in excel sheet for unlimited marketing usage? We provide Top Decision Makers information like Name, Email, Title, Phone and company details of companies using IBM DB. MySQL Sybase SQL Server Teradata Hadoop Informatica Netezza And many more... Please let me know your thoughts so that I can send you cost of the list. Appreciate your time and look forward to hear from you. Regards, Isaura Marketing Consultant If you are not the right person, feel free to forward this email to the right person in your organization. | List acquisition | Technology Lists | Email/Data Appending | Search Engine Optimization | If you don't want to include yourself in our mailing list, please reply back "Leave Out" in a subject line -------------- next part -------------- An HTML attachment was scrubbed... URL: From owner at bugs.debian.org Wed May 25 21:48:35 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Wed, 25 May 2016 21:48:35 +0000 Subject: [Debian-med-packaging] Processed: your mail References: <1640706146.1210471.1464211838096.JavaMail.yahoo@mail.yahoo.com> Message-ID: Processing commands for control at bugs.debian.org: > severity 825307 serious Bug #825307 [src:gdcm] gdcm: build-dependencies not installable Severity set to 'serious' from 'normal' > thanks Stopping processing here. Please contact me if you need assistance. -- 825307: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825307 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Thu May 26 06:13:32 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 26 May 2016 06:13:32 +0000 Subject: [Debian-med-packaging] Processing of toppred_1.10-3_source.changes Message-ID: toppred_1.10-3_source.changes uploaded successfully to localhost along with the files: toppred_1.10-3.dsc toppred_1.10-3.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 26 06:18:45 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 26 May 2016 06:18:45 +0000 Subject: [Debian-med-packaging] toppred_1.10-3_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 25 May 2016 21:15:14 +0000 Source: toppred Binary: toppred Architecture: source Version: 1.10-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: toppred - transmembrane topology prediction Changes: toppred (1.10-3) unstable; urgency=medium . * Team upload. * Make build reproducible. - Fix $SHELL/CONFIG_SHELL to /bin/sh. 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From ftpmaster at ftp-master.debian.org Thu May 26 07:13:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 26 May 2016 07:13:40 +0000 Subject: [Debian-med-packaging] Processing of fastqtl_2.184+dfsg-1_amd64.changes Message-ID: fastqtl_2.184+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: fastqtl_2.184+dfsg-1.dsc fastqtl_2.184+dfsg.orig.tar.xz fastqtl_2.184+dfsg-1.debian.tar.xz fastqtl-dbgsym_2.184+dfsg-1_amd64.deb fastqtl-doc_2.184+dfsg-1_all.deb fastqtl_2.184+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Thu May 26 07:18:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 26 May 2016 07:18:35 +0000 Subject: [Debian-med-packaging] fastqtl_2.184+dfsg-1_amd64.changes is NEW Message-ID: binary:fastqtl is NEW. binary:fastqtl-doc is NEW. source:fastqtl is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From andreas at an3as.eu Thu May 26 07:26:37 2016 From: andreas at an3as.eu (Andreas Tille) Date: Thu, 26 May 2016 09:26:37 +0200 Subject: [Debian-med-packaging] fastqtl_2.184+dfsg-1_amd64.changes REJECTED In-Reply-To: References: <20160514190627.GE4230@an3as.eu> <20160516130254.GA5547@bubu.igloo> Message-ID: <20160526072637.GH13619@an3as.eu> Hi Dylan, On Wed, May 25, 2016 at 10:48:51PM +0200, Dylan wrote: > Hi, > After a boring discussion with Artifex Software [1], I obtained a > clarification about the license of the ICC profiles [2]. Thanks for also doing the boring parts of Debian package maintenance. :-) Re-uploaded to new Andreas. > According to this discussion, I have updated the d/copyright. > I think that the package should be ok now. > > Best regards, > Dylan > > [1] http://ghostscript.com/irclogs/2016/05/25.html > [2] http://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=9308777e > > > > Le Sun, May 15, 2016 at 10:44:37PM +0200, Thorsten Alteholz a ?crit : > >> > >> yes, whatever, this tool obviously puts some own parts into the output file > >> and claims copyright for that. As long as there is no license information > >> for that part, one can not decide whether it is compatible with DFSG. So > >> please clarify this with upstream or Artifex Software. > -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Thu May 26 09:00:09 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 26 May 2016 09:00:09 +0000 Subject: [Debian-med-packaging] Processing of bowtie_1.1.2-4_source.changes Message-ID: bowtie_1.1.2-4_source.changes uploaded successfully to localhost along with the files: bowtie_1.1.2-4.dsc bowtie_1.1.2-4.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From owner at bugs.debian.org Thu May 26 09:33:13 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Thu, 26 May 2016 09:33:13 +0000 Subject: [Debian-med-packaging] Processed: your mail References: Message-ID: Processing commands for control at bugs.debian.org: > forwarded 825339 https://github.com/uclouvain/openjpeg/issues/3 Bug #825339 [libopenjp2-7-dev] Need public function to tell kernel type used (5x3 vs 9x7) Set Bug forwarded-to-address to 'https://github.com/uclouvain/openjpeg/issues/3'. > tags 825307 upstream Bug #825307 [src:gdcm] gdcm: build-dependencies not installable Ignoring request to alter tags of bug #825307 to the same tags previously set > block 825307 by 825339 Bug #825307 [src:gdcm] gdcm: build-dependencies not installable 825307 was not blocked by any bugs. 825307 was not blocking any bugs. Added blocking bug(s) of 825307: 825339 > End of message, stopping processing here. Please contact me if you need assistance. -- 825307: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825307 825339: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825339 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From ftpmaster at ftp-master.debian.org Thu May 26 10:19:22 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 26 May 2016 10:19:22 +0000 Subject: [Debian-med-packaging] bowtie_1.1.2-4_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 25 May 2016 22:25:27 +0000 Source: bowtie Binary: bowtie bowtie-examples Architecture: source Version: 1.1.2-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: bowtie - Ultrafast memory-efficient short read aligner bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short read al Changes: bowtie (1.1.2-4) unstable; urgency=medium . * Team upload. * Make build reproducible. - Use fixed build hostname and compiler version. * Fix autopkgtest by adjusting directory. * Enable full hardening. * Bump Standards-Version. * Use secure Vcs-Browser. 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From andreas at an3as.eu Thu May 26 11:17:02 2016 From: andreas at an3as.eu (Andreas Tille) Date: Thu, 26 May 2016 13:17:02 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> <20160521155346.GR5019@an3as.eu> <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> Message-ID: <20160526111701.GB19887@an3as.eu> Hi Gianfranco, On Sun, May 22, 2016 at 06:48:36AM +0000, Gianfranco Costamagna wrote: > ... > I would say: remove the add_subdirectory (line 21) > and then: > 1) create a "FindF2C.cmake" file and use it as helper > (that would be the best and upstreamable choice > you can find some examples in "ettercap/cmake/Modules/Find*" thanks to these hints I managed to build against Debian packaged libf2c. This involved adding two files missing in libf2c source which I took over as a patch. I can confirm that I builded several times on my local disk successfully including the build time tests. At first this did not worked until I made sure that Debian's default CFLAGS are also used for libf2c. Once I have uploaded libf2c2 version 20130926-1 the build somehow stopped working again. I can not even reproduce things with a local rebuild. I always get something like: ... Start 76: xeigtstd_lse_in 76/76 Test #76: xeigtstd_lse_in ..................***Failed 0.01 sec Running: /home/tillea/debian-maintain/alioth/debian-science/git/packages/build-area/clapack-3.2.1/obj-x86_64-linux-gnu/TESTING/EIG//xeigtstd ARGS= OUTPUT_FILE;/home/tillea/debian-maintain/alioth/debian-science/git/packages/build-area/clapack-3.2.1/obj-x86_64-linux-gnu/TESTING/dlse.out;ERROR_FILE;/home/tillea/debian-maintain/alioth/debian-science/git/packages/build-area/clapack-3.2.1/obj-x86_64-linux-gnu/TESTING/dlse.out.err;INPUT_FILE;/home/tillea/debian-maintain/alioth/debian-science/git/packages/build-area/clapack-3.2.1/TESTING/lse.in CMake Error at /home/tillea/debian-maintain/alioth/debian-science/git/packages/build-area/clapack-3.2.1/TESTING/runtest.cmake:29 (message): Test /home/tillea/debian-maintain/alioth/debian-science/git/packages/build-area/clapack-3.2.1/obj-x86_64-linux-gnu/TESTING/EIG//xeigtstd returned Segmentation fault (for all the 76 tests not just the last one). Please note that I'm skipping those tests mentioned by Danny Edel[1] inside the patch skip_tests_triggering_stack_overflow.patch (see updated Git[2]). So what I'd like to know: What's the difference between building the code copy of libf2c comming with clapack (which can be proved by deactivating use_debian_packaged_f2c.patch) and using libf2c2. (Bonus question is what I have done differently when it worked here with local builds of libf2c2 when it worked as well - but it might need more than super power brain reading abilities. :-() Any help would be welcome Andreas. [1] https://lists.debian.org/debian-mentors/2016/05/msg00406.html [2] https://anonscm.debian.org/git/debian-science/packages/clapack.git -- http://fam-tille.de From locutusofborg at debian.org Thu May 26 11:34:12 2016 From: locutusofborg at debian.org (Gianfranco Costamagna) Date: Thu, 26 May 2016 11:34:12 +0000 (UTC) Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <20160526111701.GB19887@an3as.eu> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> <20160521155346.GR5019@an3as.eu> <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> <20160526111701.GB19887@an3as.eu> Message-ID: <279235523.1694459.1464262452097.JavaMail.yahoo@mail.yahoo.com> Hi Andreas, >o what I'd like to know: What's the difference between building the >code copy of libf2c comming with clapack (which can be proved by >deactivating use_debian_packaged_f2c.patch) and using libf2c2. (Bonus I would look at both build logs and gcc versions. maybe some new gcc compiler trigers some issues, or something different is happening there (e.g. some part of the library built on 2013, with old gcc and the new one patches wit the new libstdc++) or maybe something different, e.g. you are using two different library versions I would try to copy the debian libf2c2 over the embedded one, and see with git diff if they are different. if they are, try to copy and replace it over the embedded one, and see if with a debian dpkg-buildpackage build you reproduce the issue. (or try to debug the segfault) cheers, G. From mjiservz at popularv.com Thu May 26 04:42:04 2016 From: mjiservz at popularv.com (Betsy Barney Realty LLC) Date: Wed, 25 May 2016 23:42:04 -0500 Subject: [Debian-med-packaging] Good Tiding Opportunity. Message-ID: <20160526043611.6D2B14EBB9B@mail.qiet.ac.ir> I have very important information / opportunity that will be highly favorable to us. Please reply to my personal email address at ( leechinx22 at gmail.com ) for details. From tille at debian.org Thu May 26 13:07:25 2016 From: tille at debian.org (Andreas Tille) Date: Thu, 26 May 2016 15:07:25 +0200 Subject: [Debian-med-packaging] Trying to update htsjdk but some tests are failing In-Reply-To: <5740D5BB.1090501@free.fr> References: <20160520095105.GZ5019@an3as.eu> <573F62F1.80103@free.fr> <20160520215035.GI5019@an3as.eu> <5740D5BB.1090501@free.fr> Message-ID: <20160526130725.GF19887@an3as.eu> Hi Vincent, On Sat, May 21, 2016 at 11:40:11PM +0200, Vincent Danjean wrote: > Le 20/05/2016 23:50, Andreas Tille a ?crit : > > On Fri, May 20, 2016 at 09:18:09PM +0200, Vincent Danjean wrote: > >> I'm not sure if the right fix is in the test suite (as I propose) > >> or in the DeflaterFactory class. So, I did not commit anything for > >> now. > > > > Please be so kind to commit. Thanks. > > Done The current state in Git does not build for me: [testng] PASSED: testReadAndSkipWithMultipleBlocks([null of CHAR, null of CHAR, null of CHAR]) [testng] FAILED: testLazyInstance [testng] java.lang.AssertionError: expected [1.46426744E12] but found [1.46426757E12] [testng] at org.testng.Assert.fail(Assert.java:94) [testng] at org.testng.Assert.failNotEquals(Assert.java:513) [testng] at org.testng.Assert.assertEquals(Assert.java:260) [testng] at org.testng.Assert.assertEquals(Assert.java:273) [testng] at htsjdk.samtools.util.RelativeIso8601DateTest.testLazyInstance(RelativeIso8601DateTest.java:19) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [testng] at java.lang.reflect.Method.invoke(Method.java:498) [testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:86) [testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:643) [testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:820) [testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1128) [testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) [testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) [testng] at org.testng.TestRunner.privateRun(TestRunner.java:782) [testng] at org.testng.TestRunner.run(TestRunner.java:632) [testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) [testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) [testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) [testng] at org.testng.SuiteRunner.run(SuiteRunner.java:268) [testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) [testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) [testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1244) [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1169) [testng] at org.testng.TestNG.run(TestNG.java:1064) [testng] at org.testng.TestNG.privateMain(TestNG.java:1385) [testng] at org.testng.TestNG.main(TestNG.java:1354) [testng] [testng] [testng] =============================================== [testng] Ant test [testng] Tests run: 22478, Failures: 1, Skips: 0 [testng] =============================================== [testng] [testng] [testng] =============================================== [testng] htsjdk-tests [testng] Total tests run: 22478, Failures: 1, Skips: 0 [testng] =============================================== [testng] [testng] [TestNG] Time taken by org.testng.reporters.SuiteHTMLReporter at 3d82c5f3: 429 ms [testng] [TestNG] Time taken by [FailedReporter passed=0 failed=0 skipped=0]: 27 ms [testng] [TestNG] Time taken by org.testng.reporters.EmailableReporter2 at 73a8dfcc: 541 ms [testng] [TestNG] Time taken by org.testng.reporters.XMLReporter at 4cdf35a9: 960 ms [testng] [TestNG] Time taken by org.testng.reporters.JUnitReportReporter at 3f8f9dd6: 302 ms [testng] [TestNG] Time taken by org.testng.reporters.jq.Main at 66cd51c3: 1994 ms [testng] The tests failed. [junitreport] the file /build/htsjdk-2.3.0+dfsg.1/dist/test/TESTS-TestSuites.xml is not a valid testsuite XML document [junitreport] Error while accessing file /build/htsjdk-2.3.0+dfsg.1/dist/test/testng-failed.xml: testng.org [junitreport] the file /build/htsjdk-2.3.0+dfsg.1/dist/test/testng-results.xml is not a valid testsuite XML document [junitreport] Processing /build/htsjdk-2.3.0+dfsg.1/dist/test/TESTS-TestSuites.xml to /build/htsjdk-2.3.0+dfsg.1/dist/test/junit-noframes.html [junitreport] Loading stylesheet /build/htsjdk-2.3.0+dfsg.1/etc/test/junit-noframes.xsl [junitreport] Transform time: 45ms [copy] Copying 1 file to /build/htsjdk-2.3.0+dfsg.1/dist/test BUILD FAILED /build/htsjdk-2.3.0+dfsg.1/build.xml:180: The following error occurred while executing this line: /build/htsjdk-2.3.0+dfsg.1/build.xml:174: There were failed unit tests Total time: 1 minute 26 seconds dh_auto_build: ant -Dant.build.javac.source=1.8 -Dant.build.javac.target=1.8 -Ddebug=true test returned exit code 1 debian/rules:26: recipe for target 'override_dh_auto_test' failed Could you confirm that it builds for you in a clean pbuilder chroot? Kind regards Andreas. -- http://fam-tille.de From e.canassa55 at terra.com.br Thu May 26 14:01:00 2016 From: e.canassa55 at terra.com.br (e.canassa55 at terra.com.br) Date: Thu, 26 May 16 14:01:00 +0000 Subject: [Debian-med-packaging] =?utf-8?q?Intimacao_Extra_Judicial_MPF?= Message-ID: An HTML attachment was scrubbed... URL: From gw.fossdev at gmail.com Thu May 26 14:27:25 2016 From: gw.fossdev at gmail.com (Gert Wollny) Date: Thu, 26 May 2016 16:27:25 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <20160526111701.GB19887@an3as.eu> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> <20160521155346.GR5019@an3as.eu> <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> <20160526111701.GB19887@an3as.eu> Message-ID: <1464272845.5768.45.camel@gmail.com> Hello Andres,? > Once I have uploaded libf2c2 version 20130926-1 the build somehow? > stopped working again.??I can not even reproduce things with a local? > rebuild.I always get something like: > > ... > ??????Start 76: xeigtstd_lse_in > 76/76 Test #76: xeigtstd_lse_in ..................***Failed????0.01 > sec Assuming you are on amd64:? In ./INCLUDE there is a f2c.h file that is not patched (unlike the version of the system libf2c). The result is, that certain data types in libf2c are assumed to be of type int (size=4), and with the unpatched f2c.h file that is actually included when compiling clapack, the same data type is long (8 byte).? Hence some data structures assume different sizes within the library and on the callers side resulting in the segfault. Removing the file INCLUDE/f2c.h solves the problem, because then the system f2c.h will be used. (It may also be necessary to remove F2CLIBS/f2c.h, I already deleted the whole directory before testing). Best,? Gert? ? From perezmeyer at gmail.com Thu May 26 14:38:56 2016 From: perezmeyer at gmail.com (Lisandro =?UTF-8?Q?Dami=C3=A1n?= Nicanor =?UTF-8?Q?P=C3=A9rez?= Meyer) Date: Thu, 26 May 2016 11:38:56 -0300 Subject: [Debian-med-packaging] Bug#784451: [ball] Qt4's WebKit removal In-Reply-To: <1464181256.31925.13.camel@gmail.com> References: <1464181256.31925.13.camel@gmail.com> Message-ID: I have read the bug and I would like to note that so far no one has stepped up for packaging QtWebEngine. -- Lisandro Dami?n Nicanor P?rez Meyer http://perezmeyer.com.ar/ http://perezmeyer.blogspot.com/ From bts-link-upstream at lists.alioth.debian.org Thu May 26 19:50:00 2016 From: bts-link-upstream at lists.alioth.debian.org (bts-link-upstream at lists.alioth.debian.org) Date: Thu, 26 May 2016 19:50:00 -0000 Subject: [Debian-med-packaging] [bts-link] source package src:gdcm Message-ID: <20160526193832.18331.8481.btslink@sonntag.debian.org> # # bts-link upstream status pull for source package src:gdcm # see http://lists.debian.org/debian-devel-announce/2006/05/msg00001.html # user bts-link-upstream at lists.alioth.debian.org # remote status report for #825307 (http://bugs.debian.org/825307) # Bug title: gdcm: build-dependencies not installable # * https://sourceforge.net/p/gdcm/bugs/356/ # * remote status changed: (?) -> open usertags 825307 + status-open thanks From ntyni at debian.org Thu May 26 20:35:55 2016 From: ntyni at debian.org (Niko Tyni) Date: Thu, 26 May 2016 23:35:55 +0300 Subject: [Debian-med-packaging] Bug#825429: bioperl: FTBFS with Perl 5.24: Can't redeclare "my" in "my" at Bio/Tools/Alignment/Consed.pm Message-ID: <20160526203555.GA20104@estella.local.invalid> Package: bioperl Version: 1.6.924-3 Severity: important User: debian-perl at lists.debian.org Usertags: perl-5.24-transition This package fails to build with Perl 5.24 (currently in experimental): # Failed test 'use Bio::Tools::Alignment::Consed;' # at t/Tools/Alignment/Consed.t line 19. # Tried to use 'Bio::Tools::Alignment::Consed'. # Error: Can't redeclare "my" in "my" at Bio/Tools/Alignment/Consed.pm line 1712, at end of line # Compilation failed in require at t/Tools/Alignment/Consed.t line 19. # BEGIN failed--compilation aborted at t/Tools/Alignment/Consed.t line 19. # Looks like you failed 1 test of 15. The corresponding line is my ($r_source,my $r_destination) = @_; and it looks like Perl has become stricter about this particular error, as documented in http://search.cpan.org/~rjbs/perl-5.24.0/pod/perldiag.pod#Can%27t_redeclare_%22%s%22_in_%22%s%22 -- Niko Tyni ntyni at debian.org From dom at earth.li Thu May 26 20:59:19 2016 From: dom at earth.li (Dominic Hargreaves) Date: Thu, 26 May 2016 21:59:19 +0100 Subject: [Debian-med-packaging] Bug#825432: libbio-graphics-perl: please Build-Depend on rename Message-ID: <20160526205919.GU3769@urchin.earth.li> Source: libbio-graphics-perl Version: 2.39-4 Severity: normal User: debian-perl at lists.debian.org Usertags: perl-5.24-transition rename-deprecation Dear maintainer, This package was found to contain uses of the 'rename' and/or 'prename' (which is an alias) command. This was previously implemented by a script added to the perl package by Debian, but there is now a maintained alternative in the 'rename' package. Please add a Build-Depends on 'rename', to avoid breakage in your package when we remove the rename script from the perl package (expected after the release of stretch). Additionally, if you are currently using 'prename', please use 'rename' (which is handled by the alternatives mechanism) or file-rename, which is the new implementation. You can see more background about this change at . Thanks, Dominic Details of the use of (p)rename in your package follow: debian/rules 11: rename 's/\.pl//' debian/libbio-graphics-perl/usr/bin/*.pl 15: rename 's/\.pl//' debian/libbio-graphics-perl/usr/share/man/man1/*.pl.* From sanvila at unex.es Fri May 27 00:29:28 2016 From: sanvila at unex.es (Santiago Vila) Date: Fri, 27 May 2016 02:29:28 +0200 Subject: [Debian-med-packaging] Bug#825461: staden: FTBFS in testing Message-ID: <20160527002928.GA14930@nuc> Package: src:staden Version: 2.0.0+b10-5 Severity: serious X-Debbugs-Cc: sanvila at debian.org Dear maintainer: This package fails to build from source in stretch. ------------------------------------------------------------------ capture.o: In function `tcl_capture': /<>/staden-2.0.0+b10/tk_utils/capture.c:31: warning: the use of `tmpnam' is dangerous, better use `mkstemp' /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/Scrt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: error: ld returned 1 exit status /<>/staden-2.0.0+b10/./tk_utils/Makefile:83: recipe for target '/<>/staden-2.0.0+b10/lib/libtk_utils.so' failed make[2]: *** [/<>/staden-2.0.0+b10/lib/libtk_utils.so] Error 1 make[2]: Leaving directory '/<>/staden-2.0.0+b10/tk_utils' ------------------------------------------------------------------ I first discovered about this while checking for "dpkg-buildpackage -A", but you can also get a full build log from the reproducible builds page: https://reproducible.debian.net/rb-pkg/unstable/amd64/staden.html Thanks. From ftpmaster at ftp-master.debian.org Fri May 27 06:16:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 06:16:33 +0000 Subject: [Debian-med-packaging] Processing of libbio-graphics-perl_2.39-5_amd64.changes Message-ID: libbio-graphics-perl_2.39-5_amd64.changes uploaded successfully to localhost along with the files: libbio-graphics-perl_2.39-5.dsc libbio-graphics-perl_2.39-5.debian.tar.xz libbio-graphics-perl_2.39-5_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 27 06:18:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 06:18:33 +0000 Subject: [Debian-med-packaging] libbio-graphics-perl_2.39-5_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 27 May 2016 08:07:25 +0200 Source: libbio-graphics-perl Binary: libbio-graphics-perl Architecture: source all Version: 2.39-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbio-graphics-perl - Generate GD images of Bio::Seq objects Closes: 825432 Changes: libbio-graphics-perl (2.39-5) unstable; urgency=medium . * Build-Depends: rename Closes: #825432 * cme fix dpkg-control Checksums-Sha1: 4b4b595c550cb68ef53b22c2f564ca8d59f2702b 2238 libbio-graphics-perl_2.39-5.dsc e9485b7f94be02f36faefdc2b69039bdff914c8a 7924 libbio-graphics-perl_2.39-5.debian.tar.xz 56478a5445921025f740004cd8221ad811571a27 604528 libbio-graphics-perl_2.39-5_all.deb Checksums-Sha256: 9fbf169297a83651a0ba4ab7880bfbf8d2922d3e0e6987259dbd626f81e3973d 2238 libbio-graphics-perl_2.39-5.dsc 5886972b87177aab7e881690b86b789ba6acd38e83d1efdfc4971b2a389ff3f9 7924 libbio-graphics-perl_2.39-5.debian.tar.xz fbdd4ab7373568bd16dcd59512a07e75bb85d41d1705d45889243d6835c87d9a 604528 libbio-graphics-perl_2.39-5_all.deb Files: e0cea61865e6ec0c2f3a485f95a778ec 2238 perl optional libbio-graphics-perl_2.39-5.dsc 0323c10e7c323c6de6aaa34bab3a22f2 7924 perl optional libbio-graphics-perl_2.39-5.debian.tar.xz 99cef6c975b5d49a51731e664f2d187e 604528 perl optional libbio-graphics-perl_2.39-5_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXR+T8AAoJEFeKBJTRxkbRM0oP/1E8Jxzg5jE7Qm+ftEyp/qEJ dR4AT6qqj91tRpxBGdWl8w9IfZAeh3uusz9qqqRclbQJvif9qy0SA2ksfja3avN3 WRkWF2RnImviKgIrwnu36bkV8M0GiCzP+VnVmLLhIq1EX+gFKxrOEVkQYUTxXrA4 Y+kVqY9w2vFO8YfwVNaWQXAIzCF7whMyWXH/R+qJ5n8gIlm92Swp0PBDbaLUNvCG KVuCofKOAoDuIWqlgvbM1sHObzb3nk7eVe7EDME3/MCgkWYP99lYzSmFlWvK2oxe sqrZImd2QesplIB8IFH+k/PbJN5QgJshgK58143epeUmK3LCylBdzBBB6SB8nAVl RqeoXBwycACzYGayX9y/mZBedRUgp98+xH+c1xbmn1BaqGctz9QpnZhjprxwtY5w tRBI0jkirljXyxDVeqeHPe9Y1Y2DOh6IkQsEf9D9/3aL7N4FpcuGTTiMeFJq31bv g/416axWRFrkx2j1VQpP4hjfAfmTs3AR2j2V6OLLIo2/MbSKLXvInipP1EDi21M/ msiGtU+3p7/avqTj/cBnkooBi5ibrP8yAdq3Y+jXeCYuSXuGzu8OCdfotvq2kUzf 5ygrNBnqggc3tc8wKXsJQo4ZeKOdscyVbuQpTxrRHE+qszIfEyr5EZBKSrFgWRLi sTUNN4b3r8OrT5hy9/9e =50ls -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Fri May 27 06:21:05 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 27 May 2016 06:21:05 +0000 Subject: [Debian-med-packaging] Bug#825432: marked as done (libbio-graphics-perl: please Build-Depend on rename) References: <20160526205919.GU3769@urchin.earth.li> Message-ID: Your message dated Fri, 27 May 2016 06:18:33 +0000 with message-id and subject line Bug#825432: fixed in libbio-graphics-perl 2.39-5 has caused the Debian Bug report #825432, regarding libbio-graphics-perl: please Build-Depend on rename to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 825432: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825432 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Dominic Hargreaves Subject: libbio-graphics-perl: please Build-Depend on rename Date: Thu, 26 May 2016 21:59:19 +0100 Size: 2608 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#825432: fixed in libbio-graphics-perl 2.39-5 Date: Fri, 27 May 2016 06:18:33 +0000 Size: 5295 URL: From malat at debian.org Fri May 27 07:18:13 2016 From: malat at debian.org (Mathieu Malaterre) Date: Fri, 27 May 2016 09:18:13 +0200 Subject: [Debian-med-packaging] Bug#825307: gdcm: build-dependencies not installable Message-ID: Control: tags -1 fixed-upstream While not 100% perfect, one can pull two patches from upstream: 4f793f6005c794de633d01e42e00d37f80340fac & 0511b1d6d356a1c5d1f4e22cd5bb862ef233a332 to have this issue fixed. The behavior is not fantastic, but at least GDCM do compile against OPJ 2.1.0, and the change should be unnoticeable by most users. From owner at bugs.debian.org Fri May 27 07:21:06 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 27 May 2016 07:21:06 +0000 Subject: [Debian-med-packaging] Processed: gdcm: build-dependencies not installable References: <1426545869.1142772.1464209723815.JavaMail.yahoo@mail.yahoo.com> Message-ID: Processing control commands: > tags -1 fixed-upstream Bug #825307 [src:gdcm] gdcm: build-dependencies not installable Added tag(s) fixed-upstream. -- 825307: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825307 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From prudentialinsurancerog at gmail.com Fri May 27 07:36:02 2016 From: prudentialinsurancerog at gmail.com (Marion Johnson) Date: Fri, 27 May 2016 08:36:02 +0100 Subject: [Debian-med-packaging] Investment Partnership Message-ID: Dear Friend , How are you doing ? I contacted you because of your last Name due to my search, Please Read The Following Information Carefully, I am an officer in the Bank in Foreign Remittance Department, where I manage private client?s accounts as a Director for Credit & Marketing. I handle most of our Investor's Direct Capital Funds and secretly extract 1.2% Excess Maximum Return Capital Profit (EMRCP) per Annum on each of the Investor's Capital Funds. As an expert, I have made US$21.6 million over time from Investor's EMRCP and hereby looking for someone to trust who would be willing to stand as an Investor to receive the funds as Tenure Investment Proceeds in his or her account. Brief history of funds: I have more than 98 Corporate Investors attached to my portfolio whose Capital Investment Funds are being managed and administered by me. This Capital Investment Funds is been used for trading in Stock Market, Sales and Purchases of Bonds with Profit Returns. Every end of year,each corporate investor is expected to receive interest from his total Investment Capital Funds. However, I make an excess of 1.2% from the Investor's Investment Capital Funds annually which have exceeded our targeted 20% of Total Investment Capital Funds. This extra of 1.2% from the 21.2% is been retained by me as my personal profits for managing the Capital Investment. However, I cannot claim these funds without presenting someone to stand as an Investor to claim these funds otherwise our establishment will convert the funds into the bank's treasury at the end of second quarter and this is where you come in. This is a fair deal without any risk attached either on your part or on my part. Since I have exclusive access to every file and with my proximity, I can put you in as an Investor to my Bank and attached the profit fund to your portfolio in order to speedily facilitate the remittance of the funds out of my Bank. I already have a master plan to see this project through without hitches.Meanwhile, at the successful completion of this project, I am willing to give you 40% of the total funds for your assistance and you will keep the 60% for me safely in your account until my arrival at your place. However, I would want to know if it will be possible for you to first come to London and have a meeting with me so that we can know ourselves very well and to also clear any doubts that you might be having at the moment? This will help us to know each other and to discuss and deliberate further on how to make the whole money available to you without hitches. Please if you are interested to partner with me in this project, I demand you to get back to me so I can provide you with further details and the best way to complete the project. On the other hand, if this proposal is of no appeal to you, kindly delete this message and forget I ever contacted you. You owe me no obligation for refusing my proposal as this is of mutual benefit. I look forward to hearing from you. Sincerely, Mr.Marion Johnson -------------- next part -------------- An HTML attachment was scrubbed... URL: From andreas at an3as.eu Fri May 27 07:27:00 2016 From: andreas at an3as.eu (Andreas Tille) Date: Fri, 27 May 2016 09:27:00 +0200 Subject: [Debian-med-packaging] Bug#825461: [Help] Re: Bug#825461: staden: FTBFS in testing In-Reply-To: <20160527002928.GA14930@nuc> References: <20160527002928.GA14930@nuc> Message-ID: <20160527072700.GC14586@an3as.eu> Hi, On Fri, May 27, 2016 at 02:29:28AM +0200, Santiago Vila wrote: > ------------------------------------------------------------------ > capture.o: In function `tcl_capture': > /<>/staden-2.0.0+b10/tk_utils/capture.c:31: warning: the use of `tmpnam' is dangerous, better use `mkstemp' I've fixed this in Git, but this does not help. :-( > /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/Scrt1.o: In function `_start': > (.text+0x20): undefined reference to `main' > collect2: error: ld returned 1 exit status Any help would be welcome Andreas. -- http://fam-tille.de From locutusofborg at debian.org Fri May 27 07:53:45 2016 From: locutusofborg at debian.org (Gianfranco Costamagna) Date: Fri, 27 May 2016 07:53:45 +0000 (UTC) Subject: [Debian-med-packaging] Bug#825461: [Help] Re: Bug#825461: staden: FTBFS in testing In-Reply-To: <20160527072700.GC14586@an3as.eu> References: <20160527002928.GA14930@nuc> <20160527072700.GC14586@an3as.eu> Message-ID: <1880447731.221112.1464335625065.JavaMail.yahoo@mail.yahoo.com> Hi, some quick googling found some possible solutions https://www.google.it/search?client=ubuntu&channel=fs&q=%22Scrt1.o%3A+In+function+`_start%27%3A%22&ie=utf-8&oe=utf-8&gfe_rd=cr&ei=5ftHV7_JI8fA8geO-LmABQ I remember having that issue on ettercap some years ago, this is how I fixed it [1], but probably it was a little different issue. [1] https://github.com/Ettercap/ettercap/commit/cf90ed99361b266e4d0d8a24f61fe5ffa82fc323 however, it seems to be related to some build flags missing or added (in a library used or in that tool itself) HTH Gianfranco Il Venerd? 27 Maggio 2016 9:27, Andreas Tille ha scritto: Hi, On Fri, May 27, 2016 at 02:29:28AM +0200, Santiago Vila wrote: > ------------------------------------------------------------------ > capture.o: In function `tcl_capture': > /<>/staden-2.0.0+b10/tk_utils/capture.c:31: warning: the use of `tmpnam' is dangerous, better use `mkstemp' I've fixed this in Git, but this does not help. :-( > /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/Scrt1.o: In function `_start': > (.text+0x20): undefined reference to `main' > collect2: error: ld returned 1 exit status Any help would be welcome Andreas. -- http://fam-tille.de From jwilk at debian.org Fri May 27 08:05:03 2016 From: jwilk at debian.org (Jakub Wilk) Date: Fri, 27 May 2016 10:05:03 +0200 Subject: [Debian-med-packaging] Bug#825461: [Help] Re: Bug#825461: staden: FTBFS in testing In-Reply-To: <20160527072700.GC14586@an3as.eu> References: <20160527002928.GA14930@nuc> <20160527072700.GC14586@an3as.eu> Message-ID: <20160527080434.GA5969@jwilk.net> * Andreas Tille , 2016-05-27, 09:27: >>/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/Scrt1.o: In function `_start': >>(.text+0x20): undefined reference to `main' >>collect2: error: ld returned 1 exit status The command line that causes this is: gcc -shared -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b10/./tk_utils -I/build/staden-2.0.0+b10/./Misc -I/build/staden-2.0.0+b10/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b10/./seq_utils -I/build/staden-2.0.0+b10 -DSVN_VERSION="" -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b10/./tk_utils -I/build/staden-2.0.0+b10/./Misc -I/build/staden-2.0.0+b10/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b10/./seq_utils -I/build/staden-2.0.0+b10 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b10/lib -Wl,-z,relro -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b10/lib/libtk_utils.so cli_arg.o tclXkeylist.o tclXutil.o tcl_utils.o tcl_debug.o misc.o init.o text_output.o tkRaster.o tkRasterBuiltIn.o sheet.o tkSheet.o tkSheet_common.o trace_print.o postscript.o split.o tkTrace.o tkTraceComp.o tkTraceIO.o tkTraceDisp.o capture.o canvas_box.o ruler_tick.o restriction_enzyme_map.o element_canvas.o container.o container_ruler.o tcl_io_lib.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -fPIE -pie -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lieee -lm -lmisc -lpng -lz This is trying to build a shared library with -pie, which is not going to fly. -pie (and -fPIE) is only for executables. Now, I don't see any mention of pie in debian/rules, or in the old build log, so I guess this flag must have come from a (broken) library. -- Jakub Wilk From andreas at an3as.eu Fri May 27 08:18:56 2016 From: andreas at an3as.eu (Andreas Tille) Date: Fri, 27 May 2016 10:18:56 +0200 Subject: [Debian-med-packaging] Bug#825461: [Help] Re: Bug#825461: staden: FTBFS in testing In-Reply-To: <1880447731.221112.1464335625065.JavaMail.yahoo@mail.yahoo.com> References: <20160527002928.GA14930@nuc> <20160527072700.GC14586@an3as.eu> <1880447731.221112.1464335625065.JavaMail.yahoo@mail.yahoo.com> Message-ID: <20160527081856.GH14586@an3as.eu> Hi Gianfranco, On Fri, May 27, 2016 at 07:53:45AM +0000, Gianfranco Costamagna wrote: > Hi, some quick googling found some possible solutions > https://www.google.it/search?client=ubuntu&channel=fs&q=%22Scrt1.o%3A+In+function+`_start%27%3A%22&ie=utf-8&oe=utf-8&gfe_rd=cr&ei=5ftHV7_JI8fA8geO-LmABQ > > I remember having that issue on ettercap some years ago, this is how I fixed it [1], but probably it was a little different issue. > > > [1] https://github.com/Ettercap/ettercap/commit/cf90ed99361b266e4d0d8a24f61fe5ffa82fc323 Hmmm, both is not really enlightening my poor brain - but thanks for the pointers any way. > however, it seems to be related to some build flags missing or added (in a library used or in that tool itself) Its probably some other Build-Depends that changed since staden packaging itself is rather static. Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Fri May 27 08:22:21 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 08:22:21 +0000 Subject: [Debian-med-packaging] Processing of odil_0.6.0-2_amd64.changes Message-ID: odil_0.6.0-2_amd64.changes uploaded successfully to localhost along with the files: odil_0.6.0-2.dsc odil_0.6.0-2.debian.tar.xz libodil0-dbgsym_0.6.0-2_amd64.deb libodil0-dev_0.6.0-2_amd64.deb libodil0-doc_0.6.0-2_all.deb libodil0_0.6.0-2_amd64.deb odil_0.6.0-2_all.deb python-odil-dbgsym_0.6.0-2_amd64.deb python-odil_0.6.0-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From jwilk at debian.org Fri May 27 08:24:38 2016 From: jwilk at debian.org (Jakub Wilk) Date: Fri, 27 May 2016 10:24:38 +0200 Subject: [Debian-med-packaging] Bug#825461: [Help] Re: Bug#825461: staden: FTBFS in testing In-Reply-To: <20160527080434.GA5969@jwilk.net> References: <20160527002928.GA14930@nuc> <20160527072700.GC14586@an3as.eu> <20160527080434.GA5969@jwilk.net> Message-ID: <20160527082438.GA5865@jwilk.net> * Jakub Wilk , 2016-05-27, 10:05: >gcc -shared -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b10/./tk_utils -I/build/staden-2.0.0+b10/./Misc -I/build/staden-2.0.0+b10/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b10/./seq_utils -I/build/staden-2.0.0+b10 -DSVN_VERSION="" -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b10/./tk_utils -I/build/staden-2.0.0+b10/./Misc -I/build/staden-2.0.0+b10/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b10/./seq_utils -I/build/staden-2.0.0+b10 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b10/lib -Wl,-z,relro -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b10/lib/libtk_utils.so cli_arg.o tclXkeylist.o tclXutil.o tcl_utils.o tcl_debug.o misc.o init.o text_output.o tkRaster.o tkRasterBuiltIn.o sheet.o tkSheet.o tkSheet_common.o trace_print.o postscript.o split.o tkTrace.o tkTraceComp.o tkTraceIO.o tkTraceDisp.o capture.o canvas_box.o ruler_tick.o restriction_enzyme_map.o element_canvas.o container.o container_ruler.o tcl_io_lib.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -fPIE -pie -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lieee -lm -lmisc -lpng -lz > >This is trying to build a shared library with -pie, which is not going >to fly. -pie (and -fPIE) is only for executables. > >Now, I don't see any mention of pie in debian/rules, or in the old >build log, so I guess this flag must have come from a (broken) >library. If you grep for -pie in config.log you get this: IO_LIB_LDFLAGS='-L/usr/lib/i386-linux-gnu -lstaden-read -fPIE -pie -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz' which was apparently generated by: $ io_lib-config --libs -L/usr/lib/i386-linux-gnu -lstaden-read -fPIE -pie -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz This will have to be fixed in libstaden-read-dev. -- Jakub Wilk From ftpmaster at ftp-master.debian.org Fri May 27 08:27:21 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 08:27:21 +0000 Subject: [Debian-med-packaging] Processing of dicom3tools_1.00~20160516104835-2_source.changes Message-ID: dicom3tools_1.00~20160516104835-2_source.changes uploaded successfully to localhost along with the files: dicom3tools_1.00~20160516104835-2.dsc dicom3tools_1.00~20160516104835-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From tille at debian.org Fri May 27 08:27:44 2016 From: tille at debian.org (Andreas Tille) Date: Fri, 27 May 2016 10:27:44 +0200 Subject: [Debian-med-packaging] Bug#825461: [Help] Re: Bug#825461: staden: FTBFS in testing In-Reply-To: <20160527080434.GA5969@jwilk.net> References: <20160527002928.GA14930@nuc> <20160527072700.GC14586@an3as.eu> <20160527080434.GA5969@jwilk.net> Message-ID: <20160527082744.GJ14586@an3as.eu> On Fri, May 27, 2016 at 10:05:03AM +0200, Jakub Wilk wrote: > * Andreas Tille , 2016-05-27, 09:27: > >>/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/Scrt1.o: In function `_start': > >>(.text+0x20): undefined reference to `main' > >>collect2: error: ld returned 1 exit status > > The command line that causes this is: > > gcc -shared -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b10/./tk_utils -I/build/staden-2.0.0+b10/./Misc -I/build/staden-2.0.0+b10/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b10/./seq_utils -I/build/staden-2.0.0+b10 -DSVN_VERSION="" -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b10/./tk_utils -I/build/staden-2.0.0+b10/./Misc -I/build/staden-2.0.0+b10/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-2.0.0+b10/./seq_utils -I/build/staden-2.0.0+b10 -DSVN_VERSION="" -fPIC -L/build/staden-2.0.0+b10/lib -Wl,-z,relro -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-2.0.0+b10/lib/libtk_utils.so cli_arg.o tclXkeylist.o tclXutil.o tcl_utils.o tcl_debug.o misc.o init.o text_output.o tkRaster.o tkRasterBuiltIn.o sheet.o tkSheet.o tkSheet_common.o trace_print.o postscript.o split.o tkTrace.o tkTraceComp.o tkTraceIO.o tkTraceDisp.o capture.o canvas_box.o ruler_tick.o restriction_enzyme_map.o element_canvas.o container.o container_ruler.o tcl_io_lib.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -fPIE -pie -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lieee -lm -lmisc -lpng -lz > > This is trying to build a shared library with -pie, which is not going to > fly. -pie (and -fPIE) is only for executables. > > Now, I don't see any mention of pie in debian/rules, or in the old build > log, so I guess this flag must have come from a (broken) library. Most probably this is due to libstaden-read-dev where I added export DEB_BUILD_MAINT_OPTIONS = hardening=+all I'll revert this change and see what might happen ... Thanks for the pointer Andreas. -- http://fam-tille.de From andreas at an3as.eu Fri May 27 08:52:39 2016 From: andreas at an3as.eu (Andreas Tille) Date: Fri, 27 May 2016 10:52:39 +0200 Subject: [Debian-med-packaging] Bug#825461: [Help] Re: Bug#825461: staden: FTBFS in testing In-Reply-To: <20160527082438.GA5865@jwilk.net> References: <20160527002928.GA14930@nuc> <20160527072700.GC14586@an3as.eu> <20160527080434.GA5969@jwilk.net> <20160527082438.GA5865@jwilk.net> Message-ID: <20160527085239.GK14586@an3as.eu> On Fri, May 27, 2016 at 10:24:38AM +0200, Jakub Wilk wrote: > > If you grep for -pie in config.log you get this: > > IO_LIB_LDFLAGS='-L/usr/lib/i386-linux-gnu -lstaden-read -fPIE -pie -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz' > > which was apparently generated by: > > $ io_lib-config --libs > -L/usr/lib/i386-linux-gnu -lstaden-read -fPIE -pie -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz > > This will have to be fixed in libstaden-read-dev. This was actually my suspicion. Question: Do you think I just need to fix the output of io_lib-config --libs or should be prevented -fPIE -pie also to build staden-io-lib package? Kind regards Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Fri May 27 10:19:53 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 10:19:53 +0000 Subject: [Debian-med-packaging] dicom3tools_1.00~20160516104835-2_source.changes REJECTED Message-ID: dicom3tools_1.00~20160516104835-2.dsc: Invalid size hash for dicom3tools_1.00~20160516104835.orig.tar.bz2: According to the control file the size hash should be 967532, but dicom3tools_1.00~20160516104835.orig.tar.bz2 has 958071. If you did not include dicom3tools_1.00~20160516104835.orig.tar.bz2 in your upload, a different version might already be known to the archive software. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From ftpmaster at ftp-master.debian.org Fri May 27 10:26:20 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 10:26:20 +0000 Subject: [Debian-med-packaging] odil_0.6.0-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 26 May 2016 08:32:47 +0200 Source: odil Binary: libodil0 libodil0-dev libodil0-doc python-odil odil Architecture: source amd64 all Version: 0.6.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Julien Lamy Description: libodil0 - C++11 library for the DICOM standard libodil0-dev - C++11 library for the DICOM standard (development files) libodil0-doc - C++11 library for the DICOM standard (documentation) odil - C++11 library for the DICOM standard (application) python-odil - C++11 library for the DICOM standard (Python wrappers) Changes: odil (0.6.0-2) unstable; urgency=medium . * Make build reproducible Checksums-Sha1: 50860100b8df20388682099cf7c4c0eebdad1efb 2392 odil_0.6.0-2.dsc 871f6b367eb181ac7baa9cf80f88f4eba97ef099 14668 odil_0.6.0-2.debian.tar.xz 22e5f299ef69f6a0775bbba9b5453cca055152ca 9739840 libodil0-dbgsym_0.6.0-2_amd64.deb b3e6eff0716f086a1e81267e51693e566cace4bc 71226 libodil0-dev_0.6.0-2_amd64.deb 21e02cf5570fab0dc73bc778e158479a98aeaa43 230002 libodil0-doc_0.6.0-2_all.deb 971de4f0eb8576edf0777251f8aebddb9ce36eff 1070736 libodil0_0.6.0-2_amd64.deb 782004d1e0f59f5e8df3c99fd3d796838efb97ee 13908 odil_0.6.0-2_all.deb 84582f9203a5da3dc8868ce5340f7d45ac1ed768 9503674 python-odil-dbgsym_0.6.0-2_amd64.deb 68923468eaca547638fb16cc22ead3701b5f949e 680396 python-odil_0.6.0-2_amd64.deb Checksums-Sha256: 4c1fb4086360fd26d08d19c8c6fdbc00f414b66f68feddf3d1670c7339e26be5 2392 odil_0.6.0-2.dsc cb91ef4313f0c6d02e5828d6dc26c5338e77c6813c86037e606f6651ff3c7729 14668 odil_0.6.0-2.debian.tar.xz fedc2810abb49bdd4c199d449344c0b631e2b60cb11577f227fe78a06da44203 9739840 libodil0-dbgsym_0.6.0-2_amd64.deb e241dac9df70e7995e9fe140f9041271e5d667245142879fdb8d9c546ba5d01e 71226 libodil0-dev_0.6.0-2_amd64.deb 41e8a9568612732bdfc9b93656198bcd8390d14bb09be4ae72221434d325dcbd 230002 libodil0-doc_0.6.0-2_all.deb 9c53d538be5721745abae14c358b13a3e5c9cd5e5b90bab43648e9ef1a57ee1b 1070736 libodil0_0.6.0-2_amd64.deb 9d5e9954354851770309ef6416a5796484a7248776f6b9ffee713344b64d12f5 13908 odil_0.6.0-2_all.deb 03501ce54989804ec1756f7d33a6d4f0bea4a00560c5ce59944432f3d5d3a076 9503674 python-odil-dbgsym_0.6.0-2_amd64.deb 03e61e75a1ac12d85887fb4baa6043ea17d084b02f5faf4d72557fc45b22d705 680396 python-odil_0.6.0-2_amd64.deb Files: e46bdf8d4d7d6d921a41f27fd2d2fc6c 2392 science optional odil_0.6.0-2.dsc 1101eed8289e17db4893c38bd764d1ee 14668 science optional odil_0.6.0-2.debian.tar.xz bc80b5eee6f0d7a41a9a92661e76315e 9739840 debug extra libodil0-dbgsym_0.6.0-2_amd64.deb d0f38baf0126c3e4e3d70813b3907e34 71226 libdevel optional libodil0-dev_0.6.0-2_amd64.deb 5d2067249f24ba1c64af68f3e7d6fb7e 230002 doc optional libodil0-doc_0.6.0-2_all.deb f6f2f3b65410972cebff4fef5d976f7e 1070736 libs optional libodil0_0.6.0-2_amd64.deb f6f9fbb1381ab83d55f49822051f25a4 13908 science optional odil_0.6.0-2_all.deb 16e9801e7a4cc341666496e1caef08e1 9503674 debug extra python-odil-dbgsym_0.6.0-2_amd64.deb 03e8cf50b8e876873c88e2a04503e91c 680396 python optional python-odil_0.6.0-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXSAM7AAoJEFeKBJTRxkbRSkIP/0wyjvHg3Yty+1rVawp6UZgA 8NmtgB6HDyfa0BRO9oANrcOgZQql39LT+q0iMgpPpzLObaf/9EBHDoP5z3VsAk8C 0iYd3/vAdZwn3OiiBxJDLpr7FJY3k1iLKS4RG88RiXPIFwH2toogfss2dhLsJFwu UOfhGZA+QUb/sDyA/UghxhCMTV5IP7g6aRq5zhMKwa5nNsOecsMCst9Mw7V68R3d iFOW5u1Hwg+vRO3c98ty68UhC97sQAY2akhKmXxWX6HeD/qwX73VRG4ePh/fISpS DTKOyMI3LeVohjtkc7VCNqlegrgEmxsVtvB8g64jvn2T6KD2YFRR8UgGPZ1fskci rHLw86eL4beXauqSqlZUWdNbfv0xXcGAYGHyEfOo5EahRyLILsXLr3Rm/xQ9IMh+ tapnNKYHjp3NKXpJR9UQWPmjvvSdvXBo9ju2J5fwRmWBgqCN39OsbdIwtYRbPQ+e Xna/5FShEkqx7g16azOkYUiIJ9VxGTOBBdc81x0YzH2LMBJO7rvRr/t3V/6+4vEV Pce7mGFmP+NfNtDxqV1eO0Cu1xsb5aqIManCZ8aJfx23Xok2PiS4qnn9QSa08EM1 g/dUG1cNO9h4gZQNpypPKIsgrpbDc7nKcaZdoaKruXjLeAoQmxy2h0OKrdMYjUur xJ3UirATiOqomM9vf5+g =AsQD -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 27 10:38:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 10:38:06 +0000 Subject: [Debian-med-packaging] Processing of dicom3tools_1.00~20160516104835-2_source.changes Message-ID: dicom3tools_1.00~20160516104835-2_source.changes uploaded successfully to localhost along with the files: dicom3tools_1.00~20160516104835-2.dsc dicom3tools_1.00~20160516104835-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 27 10:52:10 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 10:52:10 +0000 Subject: [Debian-med-packaging] dicom3tools_1.00~20160516104835-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 27 May 2016 07:23:02 +0000 Source: dicom3tools Binary: dicom3tools Architecture: source Version: 1.00~20160516104835-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: dicom3tools - DICOM medical image files manipulation and conversion tools Changes: dicom3tools (1.00~20160516104835-2) unstable; urgency=medium . * d/control: Add dependency on gawk to fix FTBFS on non-english locale Checksums-Sha1: f54c12b69475258e91cb199ca9729500e666c11b 1825 dicom3tools_1.00~20160516104835-2.dsc 1435e96ca4442f03f026070e3039fc372993b8c7 10720 dicom3tools_1.00~20160516104835-2.debian.tar.xz Checksums-Sha256: 7a82d180bc1f04a0197ecb2d59c9018b46999286e489c184562e3c0ae26e2486 1825 dicom3tools_1.00~20160516104835-2.dsc d92170b52c62a542b9c4e97f0ce48fd5850203895142322cb6df569238106e45 10720 dicom3tools_1.00~20160516104835-2.debian.tar.xz Files: 51bc9ecc9bebe02ec8cdb356e1c35d97 1825 graphics optional dicom3tools_1.00~20160516104835-2.dsc b5d31c4d368b02ab796f3f9caed32684 10720 graphics optional dicom3tools_1.00~20160516104835-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXSCJ+AAoJEPgeNoubJquYYqwH/ApE2wfemIojDoK5ETj7nDsl t11jrJFeq+ciA4h4oIsHgHQjKHXWVhmkBLOqOhTxp/PK65mhB/ANMjiHxZyg/43v hLl30b9w/f/3n9qzkkHsjhnmonNBXoKb//n/042Fu/iWdLV6nHyQx6CQouwWPqkF D7EM7GLGF+EVkbkKEycLqYNKnNV7B0TQSIA5NrLv/Dg++AHFpX8xsV3dj1ve88hc Jl9uF3vKE8IpDxS89NVQr/HxCXV9w0/5lGk+kVT+l3HGP+/0hPOav9BDjmoF4vQQ 9mt44+gNd8itWLVxiUBcs6UnlC8MXZqsy0sDqN0deKAHtcTsL8VNuFX7aHBqiR4= =NC3e -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 27 12:05:14 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 12:05:14 +0000 Subject: [Debian-med-packaging] Bug#825412: Removed package(s) from unstable Message-ID: We believe that the bug you reported is now fixed; the following package(s) have been removed from unstable: fis-gtm-6.2-002 | 6.2-002A-3 | amd64, i386 ------------------- Reason ------------------- RoQA; NBS; manual decrufting needed ---------------------------------------------- Note that the package(s) have simply been removed from the tag database and may (or may not) still be in the pool; this is not a bug. The package(s) will be physically removed automatically when no suite references them (and in the case of source, when no binary references it). Please also remember that the changes have been done on the master archive and will not propagate to any mirrors until the next dinstall run at the earliest. Packages are usually not removed from testing by hand. Testing tracks unstable and will automatically remove packages which were removed from unstable when removing them from testing causes no dependency problems. The release team can force a removal from testing if it is really needed, please contact them if this should be the case. Bugs which have been reported against this package are not automatically removed from the Bug Tracking System. Please check all open bugs and close them or re-assign them to another package if the removed package was superseded by another one. The version of this package that was in Debian prior to this removal can still be found using http://snapshot.debian.org/. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 825412 at bugs.debian.org. The full log for this bug can be viewed at https://bugs.debian.org/825412 This message was generated automatically; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster at ftp-master.debian.org. Debian distribution maintenance software pp. Scott Kitterman (the ftpmaster behind the curtain) From sascha at steinbiss.name Fri May 27 12:22:20 2016 From: sascha at steinbiss.name (Sascha Steinbiss) Date: Fri, 27 May 2016 13:22:20 +0100 Subject: [Debian-med-packaging] Bug#798637: Bug#798637: rna-star: FTBS on mpis In-Reply-To: References: <20150911102450.937.41080.reportbug@localhost> <20150911102450.937.41080.reportbug@localhost> Message-ID: <175b274c-0982-ea6e-3b29-fe236c0693a9@steinbiss.name> Hi, just a gentle reminder that I will be filing a removal request for the non-building or non-functional architectures soon. According to my build time tests, rna-star builds _and_ works on amd64, arm64, ppc64el and mips64el [1]. I will disable all others -- please let me know if you have objections. Cheers Sascha [1] https://buildd.debian.org/status/package.php?p=rna-star On 24/05/2016 12:49, Sascha Steinbiss wrote: > Hi Olivier, > > STAR upstream does not explicitly support non-Intel platforms, and there > also only 64-bit ones... see [1] as well. > To see if other archs work without explicit support, I have excluded all > archs that do not even compile and added some build time tests to verify > that the produced executable works. I'll keep an eye on it. > Do you think this bug should stay open? > > Cheers > Sascha > > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824997 > > > On Fri, 11 Sep 2015 10:24:50 +0000 Olivier Sallou > wrote: >> Package: rna-star >> Version: 2.4.2a+dfsg-1 >> Severity: important >> >> Dear Maintainer, >> package FTBS on mips [0]. >> >> It seems that the fix is in glibc 2.22 [1]. This version is not yet even in >> experimental. We should track gblic update in sib to ask for a mips rebuild. >> >> >> >> [0] https://buildd.debian.org/status/logs.php?arch=mipsel&pkg=rna-star&ver=2.4.2a%2Bdfsg-1 >> [1] https://sourceware.org/bugzilla/show_bug.cgi?id=17930 >> >> -- System Information: >> Debian Release: stretch/sid >> APT prefers unstable >> APT policy: (500, 'unstable') >> Architecture: amd64 (x86_64) >> >> Kernel: Linux 4.1.0-2-amd64 (SMP w/2 CPU cores) >> Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8) >> Shell: /bin/sh linked to /bin/dash >> Init: systemd (via /run/systemd/system) >> >> > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From ftpmaster at ftp-master.debian.org Fri May 27 13:05:35 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 13:05:35 +0000 Subject: [Debian-med-packaging] Processing of gnumed-server_21.6-1_amd64.changes Message-ID: gnumed-server_21.6-1_amd64.changes uploaded successfully to localhost along with the files: gnumed-server_21.6-1.dsc gnumed-server_21.6.orig.tar.gz gnumed-server_21.6-1.debian.tar.xz gnumed-server_21.6-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 27 13:23:26 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 13:23:26 +0000 Subject: [Debian-med-packaging] gnumed-server_21.6-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 27 May 2016 15:01:32 +0200 Source: gnumed-server Binary: gnumed-server Architecture: source all Version: 21.6-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gnumed-server - medical practice management - server Changes: gnumed-server (21.6-1) unstable; urgency=medium . * New upstream version * cme fix dpkg-control Checksums-Sha1: c54d2ebd055ec4fabce590c3d94d43fbf3f2af1b 2034 gnumed-server_21.6-1.dsc 30fedfd7478ee3eb17e447a74bae4e97531578ea 14189016 gnumed-server_21.6.orig.tar.gz 4b539fb9b36239bdf8e2158677e13d0e49cdff37 10692 gnumed-server_21.6-1.debian.tar.xz c103b7c0fac88bf7f13f41fb8cd6c5749218267e 13227478 gnumed-server_21.6-1_all.deb Checksums-Sha256: 715bcaba25c675166253c6369803e51b417aefcbdb0ba5dc612190ec07a952ac 2034 gnumed-server_21.6-1.dsc a22377fd40077fc185043f60cce4a4eb9b1d969b4c318ba431f06dbe3b9026b9 14189016 gnumed-server_21.6.orig.tar.gz 3d8c264425a0f2277e53a0b47a6f5ae528369c66d623cfc5e43ca8c24febcbfa 10692 gnumed-server_21.6-1.debian.tar.xz 249965c9497978cf8f140a41337141a53fb585efda36719bde3909440e01c086 13227478 gnumed-server_21.6-1_all.deb Files: 334512e98f89835b952d955937d8b0dd 2034 misc optional gnumed-server_21.6-1.dsc 07b0af9adcc4f4e6f2fdcb172e5eae22 14189016 misc optional gnumed-server_21.6.orig.tar.gz e927918ba00d6f771af73415b39ee2fc 10692 misc optional gnumed-server_21.6-1.debian.tar.xz 90d113d35c5ab3c278962260e7e9a1a9 13227478 misc optional gnumed-server_21.6-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXSEWZAAoJEFeKBJTRxkbRV7AP/0CowG8jF98zHpS7ypVVYVb9 KgrYBe0Gs+ErK4NkkzIohCHZJzDmlcBDPul+eIUdR2RXZiX+Ss52hVleBO7zYh45 sD6W6ikFhq54KkH0QQX2kUa8/TQoXGzHss4lJQKjivdbVuD/HBUhBtLm8bwgoO0/ chTGLqflkGDm+1bRuwhxGv/znmPDTuF7rKW2tE0VLybdhMNDO2HhyJsSYu6mF1hv kzj9F8X/rqMFpP/nouEV7Lmi+eq3bK5KKPWOxnlYoTBS4rxxy+knFJRAzWHl5Zng m/75x1k42uEwSbJsj4n6cN5lhLT7/rYy7lHXE5BKpm9VqQx37FooNEal43nUnT5X NvjkGHGyeESxDFLx3/QBRXd06Jq3YI4T4BwoWcmphjXK5MpEKrg8iTAIaEJWFG/o qAUdolpm3FmcICMs+XU3lOhKv1RwK/T+ptlWaHFDOOSoPjfVr+k3YFWn9Y2nK27N IKnk4ScRUrJs7FmccvLj07xpx7AfdojVNYgDdEizNYe3A9T4Tx1MaUcVtw1Bt4HR IUw2ZibfUqTpInti02YbNnMbBRaMkxVHgAnjJRhT4lWvwYaNn3GLhptXL5sMyvbg z5kAFLCuk0f1VEYbZ9kNGF4j5s2+AxbVDn+U+PhCH3EJ06pTNdJ1AGdoQOmjCucM jugYDZ/znFEs2v2gLFOB =Te0N -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Fri May 27 13:36:01 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 13:36:01 +0000 Subject: [Debian-med-packaging] Processing of gnumed-client_1.6.6+dfsg-1_amd64.changes Message-ID: gnumed-client_1.6.6+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: gnumed-client_1.6.6+dfsg-1.dsc gnumed-client_1.6.6+dfsg.orig.tar.xz gnumed-client_1.6.6+dfsg-1.debian.tar.xz gnumed-client-de_1.6.6+dfsg-1_all.deb gnumed-client_1.6.6+dfsg-1_all.deb gnumed-common_1.6.6+dfsg-1_all.deb gnumed-doc_1.6.6+dfsg-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Fri May 27 13:49:07 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 13:49:07 +0000 Subject: [Debian-med-packaging] gnumed-client_1.6.6+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 27 May 2016 15:23:23 +0200 Source: gnumed-client Binary: gnumed-client gnumed-client-de gnumed-common gnumed-doc Architecture: source all Version: 1.6.6+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gnumed-client - medical practice management - Client gnumed-client-de - medical practice management - Client for German users gnumed-common - medical practice management - common files gnumed-doc - medical practice management - Documentation Changes: gnumed-client (1.6.6+dfsg-1) unstable; urgency=medium . * New upstream version * Set PYTHONPATH for gm-import_incoming Checksums-Sha1: aa5e5fdf077cdda3361c619d24828fb82cfcaf7c 2301 gnumed-client_1.6.6+dfsg-1.dsc 6367f2f0f35274b634efd281860b9e5788368024 7058588 gnumed-client_1.6.6+dfsg.orig.tar.xz 71df199b69aa71b0fc5ce743cfd32e7f3069d75a 71664 gnumed-client_1.6.6+dfsg-1.debian.tar.xz bf3022fd8f222f5fcf2a981f7880d3c3e1c8e282 17412 gnumed-client-de_1.6.6+dfsg-1_all.deb e5018ec115ca427edf95380dac2f588bb42964de 1382152 gnumed-client_1.6.6+dfsg-1_all.deb a23a51f2653c4234c3e7619e4561d11edffeb84f 121344 gnumed-common_1.6.6+dfsg-1_all.deb 50d3845a722084d85b6d41b8b8deb9dc0b546bb8 1116054 gnumed-doc_1.6.6+dfsg-1_all.deb Checksums-Sha256: b812c14890fcaec5eb2b8d44d71a6541f94e09bc09940c2d7c2f2728997a09d7 2301 gnumed-client_1.6.6+dfsg-1.dsc 0776bc3243539cbc9094e3fc8ff1b62995c275566709c6a1f4af0119cda69374 7058588 gnumed-client_1.6.6+dfsg.orig.tar.xz 601fc059a30a6e70c0e3bcfd57dda07fae3b6cc3ae9467e314a126cbe09c3a73 71664 gnumed-client_1.6.6+dfsg-1.debian.tar.xz e444f6f6da786392086aa68588a703385bd3db0d1147e9bff391044bff8c281e 17412 gnumed-client-de_1.6.6+dfsg-1_all.deb fd0227c1d07a5228d5f3405e02a02bff240b950e84d097610ac830db80b56855 1382152 gnumed-client_1.6.6+dfsg-1_all.deb f3a68a0a9b136507e3463ee64c75ff12393868d2422a7b5598d668effb7986ee 121344 gnumed-common_1.6.6+dfsg-1_all.deb 470535254512369fdbfb9499911d5c119a4e69722ab76e5aad1dc7754f0d7c9f 1116054 gnumed-doc_1.6.6+dfsg-1_all.deb Files: bf8cc5a2bd4397f9d6803c79c59c0afb 2301 misc optional gnumed-client_1.6.6+dfsg-1.dsc d127694377c448f4a440ad11f8778784 7058588 misc optional gnumed-client_1.6.6+dfsg.orig.tar.xz 949088c1292c003b6d8e4014ea069994 71664 misc optional gnumed-client_1.6.6+dfsg-1.debian.tar.xz fc53db617a34676b758a62439448571a 17412 misc optional gnumed-client-de_1.6.6+dfsg-1_all.deb 812cf90f75e1488aa7f167d318bf4335 1382152 misc optional gnumed-client_1.6.6+dfsg-1_all.deb 839ebd2a03ef37f22639d98e729a170b 121344 misc optional gnumed-common_1.6.6+dfsg-1_all.deb f9aff2b6e99837c972a70a14a13aba8d 1116054 doc optional gnumed-doc_1.6.6+dfsg-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXSEx6AAoJEFeKBJTRxkbRbvYP/31meTX5tOwxexhzxh7cMWJK ELdiWa24GpAw4kb+qzFGq1RabRZBznmmwD/7PWPa0qKryV8e+jEuEYMsKsInyvJj okDvp+423oNli3cw8Gm3VmeqJtd3NBU7xDf5PvueY2rlCLaNs3IdnD2DiM/gtI6n /ub0blaYx/8ypIpiaKKOm4xhAnazQYj6JtlHIahbCMTUGmoh23PuAwyNpn8GWDi2 EvLgEbx5kGSejdkaH0rO4JdRMkqv560VywHc1/LAY/TSFEsNP76+fanvqrpMIa+U W4eqbi2TfcLE+VLbF7P5IdYjW+l3C8DXXnHQR+lDEWVfPWpAfVHh6xlCfJiOs6Lw 5EtGPkSRqsbTigLX02C6hCCX2tvocnlh5ExOsF5j2AJAtp9QWeLDb3VleYd9lB0y R/b/nsuHo+1scE0fm0PH5JaW4WcYD+5F/Aoa3ufyNEfb3oWtEQoJ182HWhnOAtZf de/4TuwNbgArZU//iiwTnoltrpBbug6LntPGf/jPeq1Vccj9rjwjCHAa/8cnqc2Q aFh9LExoyWzgvxa0c3h8JXPL+JmHo6V3kF8BxRB/e5HbCHGptaBPbb55TLFSyhdN d6cON5QoiJ4XBfyypfUBQ7n8NEd/yjOhxzDh6uSYj7xMfR6HHIU93p5qA4mPujWq PW2QRJ3lFm0VMWECoPDZ =MqoQ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From tille at debian.org Fri May 27 13:49:07 2016 From: tille at debian.org (Andreas Tille) Date: Fri, 27 May 2016 13:49:07 +0000 Subject: [Debian-med-packaging] Accepted gnumed-client 1.6.6+dfsg-1 (source all) into unstable Message-ID: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 27 May 2016 15:23:23 +0200 Source: gnumed-client Binary: gnumed-client gnumed-client-de gnumed-common gnumed-doc Architecture: source all Version: 1.6.6+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gnumed-client - medical practice management - Client gnumed-client-de - medical practice management - Client for German users gnumed-common - medical practice management - common files gnumed-doc - medical practice management - Documentation Changes: gnumed-client (1.6.6+dfsg-1) unstable; urgency=medium . * New upstream version * Set PYTHONPATH for gm-import_incoming Checksums-Sha1: 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PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXSEx6AAoJEFeKBJTRxkbRbvYP/31meTX5tOwxexhzxh7cMWJK ELdiWa24GpAw4kb+qzFGq1RabRZBznmmwD/7PWPa0qKryV8e+jEuEYMsKsInyvJj okDvp+423oNli3cw8Gm3VmeqJtd3NBU7xDf5PvueY2rlCLaNs3IdnD2DiM/gtI6n /ub0blaYx/8ypIpiaKKOm4xhAnazQYj6JtlHIahbCMTUGmoh23PuAwyNpn8GWDi2 EvLgEbx5kGSejdkaH0rO4JdRMkqv560VywHc1/LAY/TSFEsNP76+fanvqrpMIa+U W4eqbi2TfcLE+VLbF7P5IdYjW+l3C8DXXnHQR+lDEWVfPWpAfVHh6xlCfJiOs6Lw 5EtGPkSRqsbTigLX02C6hCCX2tvocnlh5ExOsF5j2AJAtp9QWeLDb3VleYd9lB0y R/b/nsuHo+1scE0fm0PH5JaW4WcYD+5F/Aoa3ufyNEfb3oWtEQoJ182HWhnOAtZf de/4TuwNbgArZU//iiwTnoltrpBbug6LntPGf/jPeq1Vccj9rjwjCHAa/8cnqc2Q aFh9LExoyWzgvxa0c3h8JXPL+JmHo6V3kF8BxRB/e5HbCHGptaBPbb55TLFSyhdN d6cON5QoiJ4XBfyypfUBQ7n8NEd/yjOhxzDh6uSYj7xMfR6HHIU93p5qA4mPujWq PW2QRJ3lFm0VMWECoPDZ =MqoQ -----END PGP SIGNATURE----- From ftpmaster at ftp-master.debian.org Fri May 27 14:21:36 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 14:21:36 +0000 Subject: [Debian-med-packaging] Processing of staden-io-lib_1.14.8-2_amd64.changes Message-ID: staden-io-lib_1.14.8-2_amd64.changes uploaded successfully to localhost along with the files: staden-io-lib_1.14.8-2.dsc staden-io-lib_1.14.8-2.debian.tar.xz libstaden-read-dev_1.14.8-2_amd64.deb libstaden-read11-dbgsym_1.14.8-2_amd64.deb libstaden-read11_1.14.8-2_amd64.deb staden-io-lib-examples_1.14.8-2_all.deb staden-io-lib-utils-dbgsym_1.14.8-2_amd64.deb staden-io-lib-utils_1.14.8-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at fam-tille.de Fri May 27 14:48:39 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Fri, 27 May 2016 16:48:39 +0200 Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <1464272845.5768.45.camel@gmail.com> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> <20160521155346.GR5019@an3as.eu> <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> <20160526111701.GB19887@an3as.eu> <1464272845.5768.45.camel@gmail.com> Message-ID: <20160527144839.GS14586@an3as.eu> Hi Gert, On Thu, May 26, 2016 at 04:27:25PM +0200, Gert Wollny wrote: > ... > Removing the file INCLUDE/f2c.h solves the problem, because then the > ... This tip saved my evening yesterday - thanks a lot. The only remaining issue is now E: libclapack3: binary-or-shlib-defines-rpath usr/lib/x86_64-linux-gnu/libclapack.so.3.2.1 /build/clapack-3.2.1+dfsg/obj-x86_64-linux-gnu/BLAS/SRC Is there any trick how I could tweak cmake files to prevent the inclusion of rpath or is the only chance to solve this to use chrpath --delete ? Kind regards Andreas. -- http://fam-tille.de From locutusofborg at debian.org Fri May 27 15:21:29 2016 From: locutusofborg at debian.org (Gianfranco Costamagna) Date: Fri, 27 May 2016 15:21:29 +0000 (UTC) Subject: [Debian-med-packaging] Trying to disable error=format-security for clapack In-Reply-To: <20160527144839.GS14586@an3as.eu> References: <20160516090743.GA31593@an3as.eu> <13220075.4521102.1463390070094.JavaMail.yahoo@mail.yahoo.com> <1463392922.18357.21.camel@gmail.com> <2114308793.4727773.1463393789155.JavaMail.yahoo@mail.yahoo.com> <1463394066.18357.24.camel@gmail.com> <20160521155346.GR5019@an3as.eu> <436368640.620871.1463899716145.JavaMail.yahoo@mail.yahoo.com> <20160526111701.GB19887@an3as.eu> <1464272845.5768.45.camel@gmail.com> <20160527144839.GS14586@an3as.eu> Message-ID: <473986796.682193.1464362489608.JavaMail.yahoo@mail.yahoo.com> Hi, > E: libclapack3: binary-or-shlib-defines-rpath usr/lib/x86_64-linux-gnu/libclapack.so.3.2.1 /build/clapack-3.2.1+dfsg/obj-x86_64-linux-gnu/BLAS/SRC >Is there any trick how I could tweak cmake files to prevent the >inclusion of rpath or is the only chance to solve this to use > > chrpath --delete It shoulnd't be needed. set(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE) might help, but by default somewhen in dh_install rpath should be removed (debhelper?cmake?) e.g. in ettercap I don't set it, and the cmake make install works beautifully. Since we have an ettercap-text-only that we build and install in a custom way, we have to strip rpath on that file https://buildd.debian.org/status/fetch.php?pkg=ettercap&arch=amd64&ver=1%3A0.8.2-2%2Bb1&stamp=1446812919 just search for something like: INSTALL_RPATH ${INSTALL_LIBDIR}) this should be how in cmake they set the RPATH. G. From noreply at release.debian.org Fri May 27 16:39:14 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 27 May 2016 16:39:14 +0000 Subject: [Debian-med-packaging] mobyle 1.5.5+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the mobyle source package in Debian's testing distribution has changed. Previous version: 1.5.3+dfsg-3 Current version: 1.5.5+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 27 16:39:14 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 27 May 2016 16:39:14 +0000 Subject: [Debian-med-packaging] mrs REMOVED from testing Message-ID: FYI: The status of the mrs source package in Debian's testing distribution has changed. Previous version: 6.0.5+dfsg-1 Current version: (not in testing) Hint: # 822466,816569 The script that generates this mail tries to extract removal reasons from comments in the britney hint files. Those comments were not originally meant to be machine readable, so if the reason for removing your package seems to be nonsense, it is probably the reporting script that got confused. Please check the actual hints file before you complain about meaningless removals. -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 27 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 27 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] dicom3tools 1.00~20160516104835-1 MIGRATED to testing Message-ID: FYI: The status of the dicom3tools source package in Debian's testing distribution has changed. Previous version: 1.00~20160402132920-1 Current version: 1.00~20160516104835-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 27 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 27 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] andi 0.10-2 MIGRATED to testing Message-ID: FYI: The status of the andi source package in Debian's testing distribution has changed. Previous version: 0.9.6.1-1 Current version: 0.10-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 27 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 27 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] datatables.js 1.10.12+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the datatables.js source package in Debian's testing distribution has changed. Previous version: 1.10.11+dfsg-3 Current version: 1.10.12+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Fri May 27 16:39:11 2016 From: noreply at release.debian.org (Debian testing watch) Date: Fri, 27 May 2016 16:39:11 +0000 Subject: [Debian-med-packaging] circos 0.69.2+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the circos source package in Debian's testing distribution has changed. Previous version: 0.69-1 Current version: 0.69.2+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Fri May 27 16:52:23 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 27 May 2016 16:52:23 +0000 Subject: [Debian-med-packaging] staden-io-lib_1.14.8-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 27 May 2016 16:07:11 +0200 Source: staden-io-lib Binary: staden-io-lib-utils libstaden-read-dev libstaden-read11 staden-io-lib-examples Architecture: source amd64 all Version: 1.14.8-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libstaden-read-dev - development files for libstaden-read libstaden-read11 - Staden library for reading and writing DNA sequencing results staden-io-lib-examples - programs for maniuplating DNA sequencing files (usage examples) staden-io-lib-utils - programs for maniuplating DNA sequencing files Changes: staden-io-lib (1.14.8-2) unstable; urgency=medium . * make sure io_lib-config --libs will not return -pie (see #825461) Checksums-Sha1: e73fe61933f4c5e45fddacfc5f6828df25e4c2ca 2408 staden-io-lib_1.14.8-2.dsc e77bbb14065820ef20878d31f070368a7eb35a03 9196 staden-io-lib_1.14.8-2.debian.tar.xz 277686268ed71a6212c3e2469725b1a4d9ce1f82 390462 libstaden-read-dev_1.14.8-2_amd64.deb 632cd13618997d162e58fccc12366d147d0a6a78 472054 libstaden-read11-dbgsym_1.14.8-2_amd64.deb 0d6fbab4e722310643a48b0eff9012fcd33cd42a 311414 libstaden-read11_1.14.8-2_amd64.deb 6c1a061c51578319a91e842a8af50bf44b1590bc 1308780 staden-io-lib-examples_1.14.8-2_all.deb 256629247c55c765a0db64d87258143312bc9f14 329180 staden-io-lib-utils-dbgsym_1.14.8-2_amd64.deb a2caad463747d8fe0c4c10d3b1ffc5fb900e0f59 250430 staden-io-lib-utils_1.14.8-2_amd64.deb Checksums-Sha256: adebe97ede55ba510e635ed81087644c65ebbdaf99651d1e823fe492d1f6140b 2408 staden-io-lib_1.14.8-2.dsc f666d73a544d0d9aad5d342f787ce37c27a1c52b869ba4f133e2863ae631b326 9196 staden-io-lib_1.14.8-2.debian.tar.xz eb16cb4e70e13bd7854077233322313561abfd5ba5e5706fcb767743361eee30 390462 libstaden-read-dev_1.14.8-2_amd64.deb 6c6d4a8cdfc9ed63a68c1bc42ccee1d7ce74d1fbdc3e4e4ee6c9598689b81b0e 472054 libstaden-read11-dbgsym_1.14.8-2_amd64.deb 48011b9086722560b3cbb0cd3b068df2beb21573d65711e1ccb4aa46df8bd97e 311414 libstaden-read11_1.14.8-2_amd64.deb 9c8a48a9b5769a65c4e75040a1976f987c6ab78a0db684ff927bf5cf5b86b613 1308780 staden-io-lib-examples_1.14.8-2_all.deb 8e51a70c98b5aea3e7fba9353959f6146baff9de9511963debb789c36084d789 329180 staden-io-lib-utils-dbgsym_1.14.8-2_amd64.deb a2edebb72ac23fb03a295c8d76488b0fc9b3ae4e9d4df6181a369bfd74f2f5cb 250430 staden-io-lib-utils_1.14.8-2_amd64.deb Files: 0ecbc864f61229715f4b0b8a2c722041 2408 science optional staden-io-lib_1.14.8-2.dsc 97faf939e5aec29ea758e15682aa078a 9196 science optional staden-io-lib_1.14.8-2.debian.tar.xz d7b02b095d39b785c79a2e0080b05f56 390462 libdevel optional libstaden-read-dev_1.14.8-2_amd64.deb 497ff8d0265b82ec6c25af4c5ad91267 472054 debug extra libstaden-read11-dbgsym_1.14.8-2_amd64.deb c59a96a5cf147a366ea68c370c39a1b1 311414 libs optional libstaden-read11_1.14.8-2_amd64.deb e6f78e209692ccdbddb0db50260f48e4 1308780 science optional staden-io-lib-examples_1.14.8-2_all.deb 653dc50ebbe01ff987282789e4ff6b24 329180 debug extra staden-io-lib-utils-dbgsym_1.14.8-2_amd64.deb c1cdcdfdae51ac3c439b3d6a111aba0b 250430 science optional staden-io-lib-utils_1.14.8-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXSFbSAAoJEFeKBJTRxkbRcaAP/2U3pmGQRvRy+Jzjc3R2f3+J H06NXjrPveazBh0pjZOvQZKT53Y41v+MqyCFyq5JzhGtrBIVtfSKZ7Q8QRYreiUz xOdvYsen0q9hceAJBUM7cZxpbPmUxJbW9NCujU7h0xmB8p8CWXPRNiF+AokxKwJM Y2Ca6sb7NR3l9nkRGO9f+YUP1accvbURMLt1yAuRgWVGqz13s+Gcf5IQs+1wV6MI fGaGbcxrx7WJZmioC5XPzt3vspJaOKM5jyH95v5SFgsiDcpXzYm5RAKA6PaBzhAA 5Esc6WcbFnPFYxqUiUVhlw2l2B2kLAJJkJGTAm/CowigbIuu+1TPEFOxfo3b2NKi xJqcAgf4/nTnVeCkYkkMj5JclukYZfRBp2T4N3GcpTLb6aRFSZxgJSNX53FbSHnX swfKGaChqH10qTp4nYn9TgKiXeJGvGNuq7JzYG7PRS5JZuzhdIeMQJ/oFd71LQ+G qkdglabaYFuTxtkFdRprB/AsmRfQO3IiuXTW8QGRcK6QnoqY4XTI7xBw37oRsipr bjy7PSuXhEfRsZnA1XmliTiteGA+YexY3RVRzupmNYzBHVh0jP7j73DoiE9FXWqI Romc5v6yCss4AOO03i/qAW1WFia2ZBobpVlx/okZPJmMREDXp2nYoWQZ5+1y2RY9 6L3/dh8bDEIRMYyGtjUA =I/Ri -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From anbe at debian.org Fri May 27 23:22:55 2016 From: anbe at debian.org (Andreas Beckmann) Date: Sat, 28 May 2016 01:22:55 +0200 Subject: [Debian-med-packaging] Bug#825582: cd-hit: ships broken symlinks: /usr/bin/psi-cd-hit* Message-ID: <20160527232255.1580.80124.reportbug@zam581.zam.kfa-juelich.de> Package: cd-hit Version: 4.6.5-1 Severity: important User: debian-qa at lists.debian.org Usertags: piuparts Hi, during a test with piuparts I noticed your package ships several broken symlinks in /usr/bin: /usr/bin/psi-cd-hit -> ../lib/cd-hit/psi-cd-hit.pl /usr/bin/psi-cd-hit-local -> ../lib/cd-hit/psi-cd-hit-local.pl /usr/bin/psi-cd-hit-2d -> ../lib/cd-hit/psi-cd-hit-2d.pl /usr/bin/psi-cd-hit-2d-g1 -> ../lib/cd-hit/psi-cd-hit-2d-g1.pl Andreas From noreply at release.debian.org Sat May 28 04:39:05 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:05 +0000 Subject: [Debian-med-packaging] vtk-dicom is marked for autoremoval from testing Message-ID: vtk-dicom 0.7.7-1 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] mia is marked for autoremoval from testing Message-ID: mia 2.2.7-5 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] plastimatch is marked for autoremoval from testing Message-ID: plastimatch 1.6.2+dfsg-3 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:05 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:05 +0000 Subject: [Debian-med-packaging] camitk is marked for autoremoval from testing Message-ID: camitk 4.0.0~beta-2 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] python-casmoothing is marked for autoremoval from testing Message-ID: python-casmoothing 0.2-1 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:05 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:05 +0000 Subject: [Debian-med-packaging] elastix is marked for autoremoval from testing Message-ID: elastix 4.8-8 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] orthanc-dicomweb is marked for autoremoval from testing Message-ID: orthanc-dicomweb 0.2+dfsg-1 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] insighttoolkit4 is marked for autoremoval from testing Message-ID: insighttoolkit4 4.9.1-1 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] orthanc-webviewer is marked for autoremoval from testing Message-ID: orthanc-webviewer 2.1-1 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] miaviewit is marked for autoremoval from testing Message-ID: miaviewit 1.0.2-1 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] gdcm is marked for autoremoval from testing Message-ID: gdcm 2.6.3-5 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:03 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:03 +0000 Subject: [Debian-med-packaging] pymia is marked for autoremoval from testing Message-ID: pymia 0.1.7-2 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From noreply at release.debian.org Sat May 28 04:39:04 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Sat, 28 May 2016 04:39:04 +0000 Subject: [Debian-med-packaging] ginkgocadx is marked for autoremoval from testing Message-ID: ginkgocadx 3.8.2-1 is marked for autoremoval from testing on 2016-06-26 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From ftpmaster at ftp-master.debian.org Sat May 28 06:31:31 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 06:31:31 +0000 Subject: [Debian-med-packaging] Processing of cain_1.10+dfsg-2_amd64.changes Message-ID: cain_1.10+dfsg-2_amd64.changes uploaded successfully to localhost along with the files: cain_1.10+dfsg-2.dsc cain_1.10+dfsg-2.debian.tar.xz cain-examples_1.10+dfsg-2_all.deb cain-solvers-dbgsym_1.10+dfsg-2_amd64.deb cain-solvers_1.10+dfsg-2_amd64.deb cain_1.10+dfsg-2_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 28 06:33:54 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 06:33:54 +0000 Subject: [Debian-med-packaging] cain_1.10+dfsg-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 27 May 2016 10:15:44 +0000 Source: cain Binary: cain cain-solvers cain-examples Architecture: source all amd64 Version: 1.10+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: cain - simulations of chemical reactions cain-examples - examples for cain cain-solvers - solvers for cain Changes: cain (1.10+dfsg-2) unstable; urgency=medium . * Team upload. * Fix build by making sure directory exists. * Make build reproducible. - Use stable order for files in help HTB. - Use consistent timezone. - Use consistent file permissions. * d/README.Debian: drop duplicate word * Use secure Vcs-Git. * Remove menu file to comply with new standards. * Enable full hardening. Checksums-Sha1: 07e7d3ca27c4ce7212b5eacb4042dccc6e8eb2e1 2097 cain_1.10+dfsg-2.dsc cf2623752221f92ad7b7278bbed0fc1b22ba861f 7692 cain_1.10+dfsg-2.debian.tar.xz 8019ef0a7f45b7632f171c402e792fc3af280c45 169506 cain-examples_1.10+dfsg-2_all.deb 8667cba354557da2de7c4b595b4c727422370d23 18536184 cain-solvers-dbgsym_1.10+dfsg-2_amd64.deb 66d1e5fccef42aabd2fb03e593de0eada419496c 1085706 cain-solvers_1.10+dfsg-2_amd64.deb 65b5e6b3669cc005d83e18366c53474ee40f35e1 10756446 cain_1.10+dfsg-2_all.deb Checksums-Sha256: 702a4c50562bc882cd0388b4821888069e97b462f8062717e7bd5ee71024a606 2097 cain_1.10+dfsg-2.dsc 350ec9a28299b14ff52956e9d59ce9e4e24dd211104f0ec449e00fefdcac1da5 7692 cain_1.10+dfsg-2.debian.tar.xz df84054129c8e16b7c50d1212f54ef56dbd12e9a7c677b783b799b5e536cc282 169506 cain-examples_1.10+dfsg-2_all.deb 1142e57969542a92113ac36fd26c7c3960e093ecb807b83e34a8ea0e20ffbbe8 18536184 cain-solvers-dbgsym_1.10+dfsg-2_amd64.deb 0467f29a88d85d8569de513952f4eaafb07cda8518f00cdea03f4e75d1bdcc91 1085706 cain-solvers_1.10+dfsg-2_amd64.deb 9a3edea5d81260518b646acc2c55d874d88a6203ec7464cc499418e6a1b5ece6 10756446 cain_1.10+dfsg-2_all.deb Files: 07da9f466347d6dd45ec2c8721c467db 2097 science optional cain_1.10+dfsg-2.dsc 6dc50e23aeceff141ac16db59d88508b 7692 science optional cain_1.10+dfsg-2.debian.tar.xz 7aafed02424fe98abbd72d55a00d690c 169506 science optional cain-examples_1.10+dfsg-2_all.deb c6c91425d428bc97c12ab1d80c46c251 18536184 debug extra cain-solvers-dbgsym_1.10+dfsg-2_amd64.deb 03eb69f0bc56c95aad388c52b22221c8 1085706 science optional cain-solvers_1.10+dfsg-2_amd64.deb 041abdaf4e18b67f392c5529e6ca9748 10756446 science optional cain_1.10+dfsg-2_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXSTeOAAoJEFeKBJTRxkbRYWwP/3g/9Zexn9g8y1JrEJAr6jFX Tah4SK80Y2Mk47o0690nY8GBpkiVMm+LIcR1KwhVwpyCFINZGyFSSEJHESpL+1MJ SUbaxnJQUOaDHi+NxYJ4cRiCBy7Veg2Wqj3dKzhe1vjtApH4AopRR0feiZ1SJ8R9 w5N422fmVuoB5OFn2pYbNrA1waIeVnLzletH6rA1E3gIo6B4khjpqLkcRfLRL8uI CPt7x2dErZ6/GgVmhNfJZzHThRQfIO2OH17BrRhBAUuP6PFuEJDPKEnoxVsvZGmD 8NoGXRGin5sfcRA6b2BtwaQcQr36ZFgwbooQL2jxXGyiEKJMIM67wHTucB5Zpr4c kC7bJFmsQ6KvJgZ62ZCMcJxgB09hDgWeay5PbOn/cR5T4viJZBrS71vmvbtwzhDU 4EB3r5GaywVJbIVY9gtzerKjwUJw4gsi+rxhOmyQ2RgMdWEwIjgr2W/KxE+9fVz9 UX1HNt200lhw9iWKiYpcJ4+7YDMEgUspOFZPun1eXRg7NyIrdcoGpNYQLV/8/WUa JOdzRMdY7uKIw2PDHyn+R3Dx8Xy3KI2dMe1029WNmTbobJJofyXl7LXete9lHoT2 1zrIEaDUWaa3tFHLOtfLKe2Ud28kTjP6r3M6ulcVp2355SYLzhxQ/ntOeMQjAQv+ VVqtbhjPT8QTrDSRnTmN =8M4B -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From andreas at fam-tille.de Sat May 28 07:03:09 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Sat, 28 May 2016 09:03:09 +0200 Subject: [Debian-med-packaging] Bug#825461: staden: FTBFS in testing In-Reply-To: <20160527002928.GA14930@nuc> References: <20160527002928.GA14930@nuc> Message-ID: <20160528070309.GC880@an3as.eu> Hi, after dealing with the actual issue reported in bug #825461[1] I noticed that more strict gcc fails at other parts. I fixed an implicit declaration issue[2] and I'm now stumbling upon ... gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-2.0.0+b10/./gap5 -I/build/staden-2.0.0+b10/./Misc -I"/usr sam_index.c:321:14: error: conflicting types for 'append_int' static char *append_int(char *cp, int i) { ^ In file included from /usr/include/io_lib/scram.h:52:0, from sam_pileup.h:4, from sam_index.c:17: /usr/include/io_lib/bam.h:758:16: note: previous declaration of 'append_int' was here unsigned char *append_int(unsigned char *cp, int32_t i); ^ sam_index.c: In function 'parse_sam_or_bam': sam_index.c:2268:6: warning: implicit declaration of function 'contig_visible_start' [-Wimplicit-function-declaration] contig_visible_start(io, bio->c->rec, CITER_CSTART); ^ sam_index.c:2269:6: warning: implicit declaration of function 'contig_visible_end' [-Wimplicit-function-declaration] contig_visible_end (io, bio->c->rec, CITER_CEND); ^ /build/staden-2.0.0+b10/./gap5/../global.mk:388: recipe for target 'sam_index.o' failed which is caused by staden-io-lib version 1.14.8. The function append_int is defined in staden-io-lib io_lib/bam.c differently from staden gap5/sam_index.c. It would be great if you could sort this out. Kind regards Andreas. [1] https://bugs.debian.org/825461 [2] https://anonscm.debian.org/git/debian-med/staden.git/tree/debian/patches/fix_implicit_declaration.patch -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Sat May 28 07:46:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 07:46:55 +0000 Subject: [Debian-med-packaging] Processing of soapdenovo2_240+dfsg-3_amd64.changes Message-ID: soapdenovo2_240+dfsg-3_amd64.changes uploaded successfully to localhost along with the files: soapdenovo2_240+dfsg-3.dsc soapdenovo2_240+dfsg-3.debian.tar.xz soapdenovo2-dbgsym_240+dfsg-3_amd64.deb soapdenovo2_240+dfsg-3_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 28 07:49:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 07:49:06 +0000 Subject: [Debian-med-packaging] soapdenovo2_240+dfsg-3_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 27 May 2016 20:24:56 +0000 Source: soapdenovo2 Binary: soapdenovo2 Architecture: source amd64 Version: 240+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: soapdenovo2 - short-read assembly method to build de novo draft assembly Changes: soapdenovo2 (240+dfsg-3) unstable; urgency=medium . [ Sascha Steinbiss ] * Team upload. * Migrate package to Git. * Make build reproducible. - Use fixed build time and date. * Remove duplicated license in d/copyright. * Bump Standards-Version. . 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From ftpmaster at ftp-master.debian.org Sat May 28 07:51:58 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 07:51:58 +0000 Subject: [Debian-med-packaging] Processing of cd-hit_4.6.5-2_amd64.changes Message-ID: cd-hit_4.6.5-2_amd64.changes uploaded successfully to localhost along with the files: cd-hit_4.6.5-2.dsc cd-hit_4.6.5-2.debian.tar.xz cd-hit-dbgsym_4.6.5-2_amd64.deb cd-hit_4.6.5-2_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 28 10:19:38 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 10:19:38 +0000 Subject: [Debian-med-packaging] cd-hit_4.6.5-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sat, 28 May 2016 09:24:04 +0200 Source: cd-hit Binary: cd-hit Architecture: source amd64 Version: 4.6.5-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: cd-hit - suite of programs designed to quickly group sequences Closes: 825582 Changes: cd-hit (4.6.5-2) unstable; urgency=medium . * Remove links to scripts that were removed in this version Closes: #825582 * cme fix dpkg-control * Better hardening Checksums-Sha1: 915e4cc14dc2a71c4b3d747989191beae4932bef 1966 cd-hit_4.6.5-2.dsc 836b746150511501ab0a272e5cc40028e505cfd6 4828 cd-hit_4.6.5-2.debian.tar.xz 3cb2b9eca5c8bf37b26d573800ad09eee5f64e5a 1696984 cd-hit-dbgsym_4.6.5-2_amd64.deb d5bbc57b9a08027f41acb0c808673dae9d93ce11 852944 cd-hit_4.6.5-2_amd64.deb Checksums-Sha256: 7e799596d6589cfb5c9d6400504cfb03eb999dbb636137609a2545cd7d470054 1966 cd-hit_4.6.5-2.dsc aae05e3e4fceb97879ff2457b6c8ce500ffb8a85b3826d58c76943ada735dd83 4828 cd-hit_4.6.5-2.debian.tar.xz 5e57155c6e1caf05c19fd49b6878a360f8ce88353f006ea55eded01f94543616 1696984 cd-hit-dbgsym_4.6.5-2_amd64.deb f2585152712c55b25ad9d76b184358a38d701c8f70c0d88678d21e677bd60951 852944 cd-hit_4.6.5-2_amd64.deb Files: 5d74cfbbb9e87213fcb033c5bf75c97e 1966 science optional cd-hit_4.6.5-2.dsc 94d99087830a84db5bc2592476c427fa 4828 science optional cd-hit_4.6.5-2.debian.tar.xz d624df2a5ad3aae1704392826126d569 1696984 debug extra cd-hit-dbgsym_4.6.5-2_amd64.deb 4673f572ed14f6c3799e674ec0f3b74a 852944 science optional cd-hit_4.6.5-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXSUx/AAoJEFeKBJTRxkbRqSoQAIePve3Cc21sb2jpRtTXOY2+ mf+0Sj+hnFvxjkDmOc6mFZqLnMRkhzjd44eiq3uzBFSOBEu4n97DZFYgT/U4izaI Vt4QMWf7lBjTAf0we/56CMhgg0OcGQ2XvjtJz4Dy2KyUCguZztPA4voYE/lp4Glp gn7gPtWQ5f08LG623lBNTucQpXlcKYI9lYlq2VuL0OKtLr0vW1Ryq9SHU9gUeNQ0 0h7G2nyZ+f3L8qlkbUIsAPEkW803Q4tLxO5OJ3jXFRFO56EZ7P77m2cY1a+lxn5s j00wK4E3+Jao0J9jxCuqRBxY9plfkL8NXbnLQGhAzfBjQWhx9V588l+XKJcry7Ge 0uLe7VUJKnPWCnx2VhSEexW2k122N6iQQaNumg/d2E28Ovf44kiHY/JXJmTjwl6Y GmWWCVEs2EGvIq1bldU4aZT3RUyxIcXL5FxZaYznhk1H20QNClMNQngX3sCG3g1h RSOKXUEPnXL/sDh+nQQ3K+QMup26uWW/cIBlggL4+ljQRunuGYmEwJibmsATI2vJ oqEklXM9V7thw10oWOoC/yv+o8IlyCHL9BH7rPqHPTH65NV9GDzHtIEK0SwX198R g9DHz8b70+i4bivv6WdCYY6EjN7dC/sG+aE8LG7pr8vETZQBYbKhb+6rFKVcfVzp nY6TCy2Qnhvon22qcXF2 =t2Lh -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Sat May 28 10:21:07 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sat, 28 May 2016 10:21:07 +0000 Subject: [Debian-med-packaging] Bug#825582: marked as done (cd-hit: ships broken symlinks: /usr/bin/psi-cd-hit*) References: <20160527232255.1580.80124.reportbug@zam581.zam.kfa-juelich.de> Message-ID: Your message dated Sat, 28 May 2016 10:19:38 +0000 with message-id and subject line Bug#825582: fixed in cd-hit 4.6.5-2 has caused the Debian Bug report #825582, regarding cd-hit: ships broken symlinks: /usr/bin/psi-cd-hit* to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 825582: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825582 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Andreas Beckmann Subject: cd-hit: ships broken symlinks: /usr/bin/psi-cd-hit* Date: Sat, 28 May 2016 01:22:55 +0200 Size: 2124 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#825582: fixed in cd-hit 4.6.5-2 Date: Sat, 28 May 2016 10:19:38 +0000 Size: 5412 URL: From dom at earth.li Sat May 28 10:56:26 2016 From: dom at earth.li (Dominic Hargreaves) Date: Sat, 28 May 2016 11:56:26 +0100 Subject: [Debian-med-packaging] Bug#825632: libgo-perl: please Build-Depend on rename Message-ID: <20160528105625.GI3769@urchin.earth.li> Source: libgo-perl Version: 0.15-1 Severity: normal User: debian-perl at lists.debian.org Usertags: perl-5.24-transition rename-deprecation Dear maintainer, This package was found to contain uses of the 'rename' and/or 'prename' (which is an alias) command. This was previously implemented by a script added to the perl package by Debian, but there is now a maintained alternative in the 'rename' package. Please add a Build-Depends on 'rename', to avoid breakage in your package when we remove the rename script from the perl package (expected after the release of stretch). Additionally, if you are currently using 'prename', please use 'rename' (which is handled by the alternatives mechanism) or file-rename, which is the new implementation. You can see more background about this change at . Thanks, Dominic Details of the use of (p)rename in your package follow: debian/rules 8: prename 's/\.pl//' $(CURDIR)/debian/libgo-perl/usr/bin/* 9: prename 's/\.pl//' $(CURDIR)/debian/libgo-perl/usr/share/man/man1/*.pl* From ftpmaster at ftp-master.debian.org Sat May 28 14:27:44 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 14:27:44 +0000 Subject: [Debian-med-packaging] Processing of libgo-perl_0.15-2_amd64.changes Message-ID: libgo-perl_0.15-2_amd64.changes uploaded successfully to localhost along with the files: libgo-perl_0.15-2.dsc libgo-perl_0.15-2.debian.tar.xz libgo-perl_0.15-2_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sat May 28 14:32:47 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 14:32:47 +0000 Subject: [Debian-med-packaging] Processing of jmodeltest_2.1.10+dfsg-2_amd64.changes Message-ID: jmodeltest_2.1.10+dfsg-2_amd64.changes uploaded successfully to localhost along with the files: jmodeltest_2.1.10+dfsg-2.dsc jmodeltest_2.1.10+dfsg-2.debian.tar.xz jmodeltest_2.1.10+dfsg-2_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From andreas at fam-tille.de Sat May 28 14:49:32 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Sat, 28 May 2016 16:49:32 +0200 Subject: [Debian-med-packaging] Bug#825119: [anbe@debian.org: Re: Bug#825119: jmodeltest: creates world writable /var/log/jmodeltest] In-Reply-To: <5748783F.4090207@gmail.com> References: <20160525061938.GM24076@an3as.eu> <5748783F.4090207@gmail.com> Message-ID: <20160528144932.GJ880@an3as.eu> Hi Diego, thans for the hint. I've just uploaded a package where /var/log/jmodeltest is set to 1777. Kind regards Andreas. On Fri, May 27, 2016 at 06:39:27PM +0200, Diego Darriba wrote: > Hi Andreas, > > Log files can be used as checkpoint files for restarting a failed execution, and also for checking > PhyML output in case of an external error. The name of the log files is the name of the input > alignment followed by the timestamp. There is no reason for using this naming convention, apart from > being more user-friendly, so they could be randomly generated as well. > > I'd suggest to use /var/log/jmodeltest rather than home directory by default, because probably > nobody expects a tool to automatically generate files there. The user can change the log directory > or disable logging in jmodeltest.conf file. > > Best Regards, > Diego. > > On 25.05.2016 08:19, Andreas Tille wrote: > > Hi Diego, > > > > I received a bug report about the way I've choosen to enable logging for > > jmodeltest. Since in the dist.dir is under /usr and you should be able > > to mount /usr readonly you can not write logging files there. So I > > decided to do the logging to /var/log/jmodeltest and did the mistake > > to set permissions to 777 instead to 1777 (see below or the full bug > > report[1]). > > > > Before I might upload a fix I would like to know the role of these > > logfiles, its intention and whether you might consider using mktemp to > > safely create log names with unpredictable names. > > > > Another solution would be to keep the logs in users homes in case the > > log is for the single user anyway. > > > > Kind regards > > > > Andreas. > > > > [1] https://bugs.debian.org/825119 > > > > ----- Forwarded message from Andreas Beckmann ----- > > > > Date: Tue, 24 May 2016 18:19:04 +0200 > > From: Andreas Beckmann > > To: Andreas Tille , 825119 at bugs.debian.org > > Subject: Re: Bug#825119: jmodeltest: creates world writable /var/log/jmodeltest > > > > On 2016-05-24 17:10, Andreas Tille wrote: > >> Hi Andreas, > >> > >> thanks for running these tests. Could you be please be more verbose in > >> how far it is a problem if a program enables users to write logs on a > >> collective place which is the intention of enabling users to write > >> there? > >> > >> I confirm that its possible for other users to delete / change logs. > >> Well, yes, that could happen but its not security relevant in my eyes. > >> Any better suggestion is welcome. > > > > Perhaps you want 1777? > > > > Are the logfile names predictable? Created in a safe way? > > > > eve $ ln -sf /home/bob/important.file /var/log/jmodeltest/bob.log > > bob $ run_jmodeltest # overwrites /home/bob/important.file ? > > > > > > Andreas > > > > > > > > ----- End forwarded message ----- > > > > -- http://fam-tille.de From yejingx at szlanyou.com Sat May 28 15:09:25 2016 From: yejingx at szlanyou.com (=?utf-8?B?SVTpg6g=?=) Date: Sat, 28 May 2016 23:09:25 +0800 Subject: [Debian-med-packaging] =?utf-8?q?debian-med-packaging=E9=82=AE?= =?utf-8?b?566x57Sn5oCl5aSE55CG6Zeu6aKY77yB77yB?= Message-ID: <804C9DC5DF75621CC7251B7D017F9A28@nwzknnbo> debian-med-packaging at lists.alioth.debian.org ?????????? ???????????????????????????????OA?????????? ?????????? ??Email:secrice????????????????????????????? ????????????????????????Secvrstr at foxmail.com ??? ??? ??? ????? ??????? ????? ????? -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at release.debian.org Sat May 28 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] charls 1.1.0+dfsg-2 MIGRATED to testing Message-ID: FYI: The status of the charls source package in Debian's testing distribution has changed. Previous version: 1.0-7 Current version: 1.1.0+dfsg-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 28 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] bowtie2 2.2.9-2 MIGRATED to testing Message-ID: FYI: The status of the bowtie2 source package in Debian's testing distribution has changed. Previous version: 2.2.9-1 Current version: 2.2.9-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 28 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-hilbertvis 1.30.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-hilbertvis source package in Debian's testing distribution has changed. Previous version: 1.28.0-2 Current version: 1.30.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 28 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-genefilter 1.54.2-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-genefilter source package in Debian's testing distribution has changed. Previous version: 1.52.1-1 Current version: 1.54.2-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 28 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-cran-vegan 2.3-5-1 MIGRATED to testing Message-ID: FYI: The status of the r-cran-vegan source package in Debian's testing distribution has changed. Previous version: 2.3-1-1 Current version: 2.3-5-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 28 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-limma 3.28.4+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-limma source package in Debian's testing distribution has changed. Previous version: 3.26.1+dfsg-1 Current version: 3.28.4+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Sat May 28 16:54:46 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 16:54:46 +0000 Subject: [Debian-med-packaging] jmodeltest_2.1.10+dfsg-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sat, 28 May 2016 16:21:50 +0200 Source: jmodeltest Binary: jmodeltest Architecture: source all Version: 2.1.10+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: jmodeltest - HPC selection of models of nucleotide substitution Closes: 825119 Changes: jmodeltest (2.1.10+dfsg-2) unstable; urgency=medium . * Added missing copyright statements * Better permissions for log dir Closes: #825119 Checksums-Sha1: 395411a731c9fbe777b4180c98e9cdea38f5d410 2232 jmodeltest_2.1.10+dfsg-2.dsc 577c6a33b941300f4aae67966490865ece35b764 4676 jmodeltest_2.1.10+dfsg-2.debian.tar.xz 771340a0ec10e1c1abbe21a44f8fc40dc7231845 978226 jmodeltest_2.1.10+dfsg-2_all.deb Checksums-Sha256: bd6107692e6cf9fda8b23ecb02b9fbe1e0e054c09e445ea7045e4f6948d88a86 2232 jmodeltest_2.1.10+dfsg-2.dsc d0d5fd35f6eef99337d26e51b0826e711a671e6850fcea72b187583e80735d55 4676 jmodeltest_2.1.10+dfsg-2.debian.tar.xz 90d548a8b1a0dea6a4180ea575b9d5f741ec51cc37a0e66f4609bb0a2992c324 978226 jmodeltest_2.1.10+dfsg-2_all.deb Files: a76468a1c088db9532be9029be5f5d11 2232 science optional jmodeltest_2.1.10+dfsg-2.dsc 86b11e21018ff0f88cb74fc92abe2060 4676 science optional jmodeltest_2.1.10+dfsg-2.debian.tar.xz 603443db8b866821c39b9ade80f12908 978226 science optional jmodeltest_2.1.10+dfsg-2_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXSaqHAAoJEFeKBJTRxkbR00oP/jQ7thiURMnAWeRTAM3FF0Xv qe2VPGbjmVIGQZOzRq/Wve3IuXEy1UNHMcnN058eJ/K59RE3OCpbbQIiQVSrvAzr iCT5osz5dOaXRLU2WDm9oi5Y5CemtRCHo9sbg2gHUsntIayqZp+N6jjAF6kmzi6m weCDwo4Aqy7EZLeC5qcZSS9KaMKUHkl/PnZMw/n0RUz804aI5LPJ+IjaVC8PZaJl GUTw5eMywcSMWVcsYtCF5wSoQinHxv3aF/274u+1N7imaA2+iWDjSu7jxKpceBwn eIOByHmGUyPL5MU+v3TdPixqGoy7vHxyLOEvKMirWkXGC97PUzAqi9iJH6Ea2DUQ Oz6U85axhM6btP5iCrfIJdcoVQgSc3ZpQRpL4KxshsTA/Vj4Fpi1pI7ifz5GomuG OgiKyvxQrCfeAFbgIEu8846gVjYEXXYTDazO4J+5NvFavv8BoRfQ0hyod8dH5S1X 1ZY3OwzWeg0Z/Ftg7nfdusR3w6E8ORqjOPYzfAn9zP4IZBDqniP9MtSpl8tRaXS9 h0mfm4WyPKgu9c+OkCv8zoj9X0fMUP0SY4VcRUTa/GKDFgLxvXuDgBlCzRbCevD+ vG7AXNtn+adcMG7rq/SS/PfJQaAtPwTYUaFaLHZPTYJonzfBnaVmhyBQbKNxX03o DGlv1Du+7ygbpIDklkHO =xGZW -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Sat May 28 16:56:31 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sat, 28 May 2016 16:56:31 +0000 Subject: [Debian-med-packaging] libgo-perl_0.15-2_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sat, 28 May 2016 16:14:28 +0200 Source: libgo-perl Binary: libgo-perl Architecture: source all Version: 0.15-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libgo-perl - perl modules for GO and other OBO ontologies Closes: 825632 Changes: libgo-perl (0.15-2) unstable; urgency=medium . * Team upload * Build-Depends: rename Closes: #825632 * cme fix dpkg-control * Update copyright Checksums-Sha1: faca7838d8d817b4b4d2b3f76bea3d5d20b30a7c 2136 libgo-perl_0.15-2.dsc a9eb3d25ca2d47918f0f01ae38c5ae55e0372f79 5808 libgo-perl_0.15-2.debian.tar.xz c5871a06e3051515f8a52d027bb6b9d107504a42 268174 libgo-perl_0.15-2_all.deb Checksums-Sha256: e7416c4c01c51cadc024f31b3ed38b6389c23da53513507e2886b80f2742682f 2136 libgo-perl_0.15-2.dsc 46c77881620c43ac919071d7023aa1edb6c8279b4dc9105548d40fc3a92d2ea5 5808 libgo-perl_0.15-2.debian.tar.xz 1a21f457582cbf5a3e90abca6c112dc1ddc1f71c642144780634e50eb2aa53c7 268174 libgo-perl_0.15-2_all.deb Files: 5a1b2c70bfa3869742f1c4ddfa4dd904 2136 perl optional libgo-perl_0.15-2.dsc 8f20434ccd9b39a97d2a4d4a54e26b7b 5808 perl optional libgo-perl_0.15-2.debian.tar.xz f49a775a0144562aac969e640c8aeac4 268174 perl optional libgo-perl_0.15-2_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXSamWAAoJEFeKBJTRxkbREEkP/igYXlYfkIrjfBe/Zr0lYeDL 5cWuUHMPpwlhxv4JC6Sq8+qG2zMr88sxpIIvCbgYcucfwU6xaow+kU9Gncb6B7PP b503DVAjb0Uwxsnk4tVZDRPkY1AoZ4lyGZN/7B082YOApOAYwznCy4lK/ic5KN/U bphD1T1d+oovkB9XC0YkhxU9Xj4YaZEVA9Dopu+6IiLDYaqrpTOCTGxEdqggn059 ipI7OJjyyrBQoqSjoKBxNFnOZkLgIFhIvtdf9iDTqUxvd4pAJwCZDCp15TDs/XyC 0Y5l6D7w6KM8ZQ8Hr33DX3moxzEKwFkCGlYlxtSRIPkKqkAUjlJ/EKGhKCLyFKzO Yoj26NIg6V2MRgkqq5FVKNeG+4SfU8wlflT+g3mivlBOzMMfrS5rsh81HarlTxay Eekiutog+9ZAwPLlH7FfiXqFz2wQI+G+z46n8qZwEjZLZXnyFBz+GKdKbEZPmztp 6NfU91dPwYjTlW0Cvp3bbtsVWHkbZnVr5Niej4SpiMXLKVX5o8bk0ny/3hIfv51T s/Ka4c7P43HC2D1qhEiecor23EGxDFvFZOBRrE4MS5wtw/v1t7kQUAAu/jqc07cZ aBQUvdFjQqbWoit02putSIOTBEe11Y83CBSGREbmW55j+jt/Q4CkQ8/8nvPdEuFo b9YRvo2ubfoaA0uKjCld =CwW1 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From owner at bugs.debian.org Sat May 28 16:57:11 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sat, 28 May 2016 16:57:11 +0000 Subject: [Debian-med-packaging] Bug#825119: marked as done (jmodeltest: creates world writable /var/log/jmodeltest) References: <20160523193403.14942.19704.reportbug@zam581.zam.kfa-juelich.de> Message-ID: Your message dated Sat, 28 May 2016 16:54:46 +0000 with message-id and subject line Bug#825119: fixed in jmodeltest 2.1.10+dfsg-2 has caused the Debian Bug report #825119, regarding jmodeltest: creates world writable /var/log/jmodeltest to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 825119: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825119 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Andreas Beckmann Subject: jmodeltest: creates world writable /var/log/jmodeltest Date: Mon, 23 May 2016 21:34:03 +0200 Size: 2337 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#825119: fixed in jmodeltest 2.1.10+dfsg-2 Date: Sat, 28 May 2016 16:54:46 +0000 Size: 5244 URL: From owner at bugs.debian.org Sat May 28 16:57:17 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sat, 28 May 2016 16:57:17 +0000 Subject: [Debian-med-packaging] Bug#825632: marked as done (libgo-perl: please Build-Depend on rename) References: <20160528105625.GI3769@urchin.earth.li> Message-ID: Your message dated Sat, 28 May 2016 16:56:31 +0000 with message-id and subject line Bug#825632: fixed in libgo-perl 0.15-2 has caused the Debian Bug report #825632, regarding libgo-perl: please Build-Depend on rename to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 825632: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825632 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Dominic Hargreaves Subject: libgo-perl: please Build-Depend on rename Date: Sat, 28 May 2016 11:56:26 +0100 Size: 2586 URL: -------------- next part -------------- An embedded message was scrubbed... From: Andreas Tille Subject: Bug#825632: fixed in libgo-perl 0.15-2 Date: Sat, 28 May 2016 16:56:31 +0000 Size: 5148 URL: From noreply at release.debian.org Sat May 28 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-aroma.light 3.2.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-aroma.light source package in Debian's testing distribution has changed. Previous version: 3.0.0-2 Current version: 3.2.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 28 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-cran-matrixstats 0.50.2-1 MIGRATED to testing Message-ID: FYI: The status of the r-cran-matrixstats source package in Debian's testing distribution has changed. Previous version: 0.14.2-1 Current version: 0.50.2-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 28 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-ebseq 1.12.0-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-ebseq source package in Debian's testing distribution has changed. Previous version: 1.10.0-1 Current version: 1.12.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sat May 28 16:39:13 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sat, 28 May 2016 16:39:13 +0000 Subject: [Debian-med-packaging] r-bioc-edger 3.14.0+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the r-bioc-edger source package in Debian's testing distribution has changed. Previous version: 3.12.0+dfsg-1 Current version: 3.14.0+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From mknoetze at nssfasteners.co.za Fri May 27 03:00:21 2016 From: mknoetze at nssfasteners.co.za (Marilize Knoetze.) Date: 27 May 2016 06:00:21 +0300 Subject: [Debian-med-packaging] Purchase order No and revision : D008-PRT-PO 0119 Message-ID: <20160527060021.578C2306694BB028@nssfasteners.co.za> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PRT- #PO 01019.zip Type: application/zip Size: 138800 bytes Desc: not available URL: From bibl at orelsau.ru Sat May 28 20:53:23 2016 From: bibl at orelsau.ru (bibl at orelsau.ru) Date: Sat, 28 May 2016 19:53:23 -0100 Subject: [Debian-med-packaging] Its me Ruth Message-ID: Its me Ruth, bekommen Sie per E-Mail? schreiben Sie mir bitte sofort zur?ck, um mich wissen zu lassen, K?sse. Ruth, Warten. Its me Ruth, are you getting my email? please write me back immediately to let me know, kisses. Ruth, Waiting. From ftpmaster at ftp-master.debian.org Sun May 29 00:02:55 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 29 May 2016 00:02:55 +0000 Subject: [Debian-med-packaging] Processing of plast_2.3.1+dfsg-4_amd64.changes Message-ID: plast_2.3.1+dfsg-4_amd64.changes uploaded successfully to localhost along with the files: plast_2.3.1+dfsg-4.dsc plast_2.3.1+dfsg-4.debian.tar.xz plast-dbgsym_2.3.1+dfsg-4_amd64.deb plast-example_2.3.1+dfsg-4_all.deb plast_2.3.1+dfsg-4_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Sun May 29 00:35:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 29 May 2016 00:35:34 +0000 Subject: [Debian-med-packaging] plast_2.3.1+dfsg-4_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sat, 28 May 2016 11:31:47 +0000 Source: plast Binary: plast plast-example Architecture: source amd64 all Version: 2.3.1+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: plast - Parallel Local Sequence Alignment Search Tool plast-example - Parallel Local Sequence Alignment Search Tool (example data) Changes: plast (2.3.1+dfsg-4) unstable; urgency=medium . * Team upload. * Make build reproducible. - Use predictable strings for build date and OS. * Bump Standards-Version. * Enable full hardening. * Fix Vcs-Git. 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From ftpmaster at ftp-master.debian.org Sun May 29 07:03:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 29 May 2016 07:03:12 +0000 Subject: [Debian-med-packaging] harvest-tools_1.2-2~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 24 May 2016 09:48:12 +0200 Source: harvest-tools Binary: harvest-tools Architecture: source amd64 Version: 1.2-2~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: harvest-tools - archiving and postprocessing for reference-compressed genomic mul Changes: harvest-tools (1.2-2~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Sun May 29 07:03:38 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 29 May 2016 07:03:38 +0000 Subject: [Debian-med-packaging] r-cran-phylobase_0.8.2-1~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 24 May 2016 09:15:55 +0200 Source: r-cran-phylobase Binary: r-cran-phylobase Architecture: source amd64 Version: 0.8.2-1~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-cran-phylobase - GNU R base package for phylogenetic structures and comparative da Changes: r-cran-phylobase (0.8.2-1~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From ftpmaster at ftp-master.debian.org Sun May 29 07:03:29 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 29 May 2016 07:03:29 +0000 Subject: [Debian-med-packaging] murasaki_1.68.6-5~bpo8+1_amd64.changes ACCEPTED into jessie-backports, jessie-backports Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 16 Mar 2016 08:20:16 +0100 Source: murasaki Binary: murasaki murasaki-mpi murasaki-common Architecture: source amd64 all Version: 1.68.6-5~bpo8+1 Distribution: jessie-backports Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: murasaki - homology detection tool across multiple large genomes murasaki-common - homology detection tool across multiple large genomes (common fil murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio Changes: murasaki (1.68.6-5~bpo8+1) jessie-backports; urgency=medium . * Rebuild for jessie-backports. 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From christian at iwakd.de Sun May 29 11:42:44 2016 From: christian at iwakd.de (Christian Seiler) Date: Sun, 29 May 2016 13:42:44 +0200 Subject: [Debian-med-packaging] Bug#819617: bcftools: FTBFS: test suite fails on several architectures In-Reply-To: <145343335662.27443.1119837475829094147.reportbug@ghostwheel.internal.ucko.debian.net> References: <145343335662.27443.1119837475829094147.reportbug@ghostwheel.internal.ucko.debian.net> <145343335662.27443.1119837475829094147.reportbug@ghostwheel.internal.ucko.debian.net> Message-ID: <574AD5B4.3060607@iwakd.de> On Thu, 21 Jan 2016 22:29:16 -0500 "Aaron M. Ucko" wrote: > * On i386 and kfreebsd-i386, 57 other test cases failed with output > differences (perhaps related to floating-point unit idiosyncracies -- > it normally works with double-extended precision internally, rather > than rounding at every step). I don't have anything to do with the package, but saw the bug referenced on debian-release, and know a bit about the x86 FPU. You can actually set the x86 FPU to use double precision internally (80bit long double calculations will not work as expected then, though, because the coprocessor will always truncate them to 64bit), by using: static void set_fpu_mode() { #ifdef __i386__ unsigned short cw; asm volatile ("fnstcw %0" : "=m" (cw)); cw = (cw & ~0x100) | 0x200; asm volatile ("fldcw %0" :: "m" (cw)); #endif } (double extended precision is 0x300, double is 0x200 and single is 0x0, in case you want to change it back. There are other settings in the control word, so I would recommend touching only the bits 0x100 and 0x200.) Other platforms (including x86_64) shouldn't have this trouble, because even if they support other floating point types, operations with the double data type are always done in double precision. (Alternatively, you could use -msse2 as a compiler flag on new enough x86_32 processors, the compiler would then use the SIMD instructions instead of the older FPU, but that has the problem that the code then won't run on older processors, which are still supported in Debian at the moment.) Hope that helps. Regards, Christian -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: OpenPGP digital signature URL: From tille at debian.org Sun May 29 12:31:25 2016 From: tille at debian.org (Andreas Tille) Date: Sun, 29 May 2016 14:31:25 +0200 Subject: [Debian-med-packaging] Bug#819617: bcftools: FTBFS: test suite fails on several architectures In-Reply-To: <574AD5B4.3060607@iwakd.de> References: <145343335662.27443.1119837475829094147.reportbug@ghostwheel.internal.ucko.debian.net> <145343335662.27443.1119837475829094147.reportbug@ghostwheel.internal.ucko.debian.net> <574AD5B4.3060607@iwakd.de> Message-ID: <20160529123125.GB26611@an3as.eu> Hi Christian, thanks for the hints. On Sun, May 29, 2016 at 01:42:44PM +0200, Christian Seiler wrote: > On Thu, 21 Jan 2016 22:29:16 -0500 "Aaron M. Ucko" wrote: > > * On i386 and kfreebsd-i386, 57 other test cases failed with output > > differences (perhaps related to floating-point unit idiosyncracies -- > > it normally works with double-extended precision internally, rather > > than rounding at every step). > > I don't have anything to do with the package, but saw the bug > referenced on debian-release, and know a bit about the x86 FPU. > You can actually set the x86 FPU to use double precision internally > (80bit long double calculations will not work as expected then, > though, because the coprocessor will always truncate them to 64bit), > by using: > > static void set_fpu_mode() > { > #ifdef __i386__ > unsigned short cw; > asm volatile ("fnstcw %0" : "=m" (cw)); > cw = (cw & ~0x100) | 0x200; > asm volatile ("fldcw %0" :: "m" (cw)); > #endif > } > > (double extended precision is 0x300, double is 0x200 and single > is 0x0, in case you want to change it back. There are other > settings in the control word, so I would recommend touching only > the bits 0x100 and 0x200.) > > Other platforms (including x86_64) shouldn't have this trouble, > because even if they support other floating point types, operations > with the double data type are always done in double precision. > > (Alternatively, you could use -msse2 as a compiler flag on new > enough x86_32 processors, the compiler would then use the SIMD > instructions instead of the older FPU, but that has the problem > that the code then won't run on older processors, which are still > supported in Debian at the moment.) If you ask me the best solution would be to use -msse2 and just add some code to throw an error if the machine has a to old FPU. Typically nobody will use those tools on old hardware anyway - so that's no practical constraint. > Hope that helps. Yes, thanks for the hint Andreas. > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging at lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de From christian at iwakd.de Sun May 29 13:07:26 2016 From: christian at iwakd.de (Christian Seiler) Date: Sun, 29 May 2016 15:07:26 +0200 Subject: [Debian-med-packaging] Bug#819617: bcftools: FTBFS: test suite fails on several architectures In-Reply-To: <20160529123125.GB26611@an3as.eu> References: <145343335662.27443.1119837475829094147.reportbug@ghostwheel.internal.ucko.debian.net> <145343335662.27443.1119837475829094147.reportbug@ghostwheel.internal.ucko.debian.net> <574AD5B4.3060607@iwakd.de> <20160529123125.GB26611@an3as.eu> Message-ID: <574AE98E.9020900@iwakd.de> On 05/29/2016 02:31 PM, Andreas Tille wrote: > If you ask me the best solution would be to use -msse2 and just add some > code to throw an error if the machine has a to old FPU. Typically > nobody will use those tools on old hardware anyway - so that's no > practical constraint. Note that Adam Borowski plans to package something that you'll be able to depend on that will show a nice error on package installation if the processor doesn't support SSE2. So in the future you could just have Depends: sse2-support [i386] in your package, and it wouldn't be an issue. See Bug.#823672 for details. Unfortunately, that's not packaged yet. If you want to figure out if the CPU supports SSE2, you can use the following piece of code: int cpu_supports_sse2_or_is_not_x86() { #ifdef __i386__ int mode = 1; int flags = 0; #ifdef __PIC__ /* Can't automatically clobber %ebx in PIC mode, so save value in %edi and clobber that. */ asm volatile ("movl %%ebx, %%edi\n\t" "cpuid\n\t" "movl %%edi, %%ebx" : "=d" (flags) : "a" (mode) : "edi", "ecx"); #else asm volatile ("cpuid" : "=d" (flags) : "a" (mode) : "ebx", "ecx"); #endif return (flags & (0x1U << 26)) != 0; #else /* either x86_64, which all support sse2, or non-x86, where this * isn't relevant */ return 1; #endif } Regards, Christian -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: OpenPGP digital signature URL: From ftpmaster at ftp-master.debian.org Sun May 29 14:12:59 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 29 May 2016 14:12:59 +0000 Subject: [Debian-med-packaging] Processing of gdcm_2.6.3-6_source.changes Message-ID: gdcm_2.6.3-6_source.changes uploaded successfully to localhost along with the files: gdcm_2.6.3-6.dsc gdcm_2.6.3-6.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From owner at bugs.debian.org Sun May 29 14:27:07 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sun, 29 May 2016 14:27:07 +0000 Subject: [Debian-med-packaging] Processed: block 823667 with 825307 References: <1464531851-2516-bts-pino@debian.org> Message-ID: Processing commands for control at bugs.debian.org: > block 823667 with 825307 Bug #823667 [release.debian.org] transition: poppler 0.44 823667 was not blocked by any bugs. 823667 was not blocking any bugs. Added blocking bug(s) of 823667: 825307 > thanks Stopping processing here. Please contact me if you need assistance. -- 823667: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=823667 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From jb_koffi08 at daum.net Sun May 29 15:32:34 2016 From: jb_koffi08 at daum.net (Johnbosco Koffi) Date: Mon, 30 May 2016 00:32:34 +0900 (KST) Subject: [Debian-med-packaging] =?utf-8?q?=EF=BB=BFFrom_Johnbosco_Koffi=2E?= Message-ID: <20160530003234.HM.0000000000008kI@jb_koffi08.wwl1543.hanmail.net> An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Sun May 29 16:38:22 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Sun, 29 May 2016 16:38:22 +0000 Subject: [Debian-med-packaging] gdcm_2.6.3-6_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 29 May 2016 13:18:50 +0000 Source: gdcm Binary: libgdcm2.6 libgdcm-tools libgdcm2-dev libgdcm2.6-dbg libgdcm-cil python-gdcm libvtkgdcm2.6 libvtkgdcm2-dev libvtkgdcm-cil python-vtkgdcm libvtkgdcm-tools gdcm-doc libgdcm-java libvtkgdcm-java Architecture: source Version: 2.6.3-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: gdcm-doc - Grassroots DICOM documentation libgdcm-cil - Grassroots DICOM CLI bindings libgdcm-java - Grassroots DICOM Java bindings libgdcm-tools - Grassroots DICOM tools and utilities libgdcm2-dev - Grassroots DICOM development libraries and headers libgdcm2.6 - Grassroots DICOM runtime libraries libgdcm2.6-dbg - Grassroots DICOM runtime libraries, debug version libvtkgdcm-cil - Grassroots DICOM VTK CLI bindings libvtkgdcm-java - Grassroots DICOM VTK Java bindings libvtkgdcm-tools - Grassroots DICOM VTK tools and utilities libvtkgdcm2-dev - Grassroots DICOM VTK development libraries and headers libvtkgdcm2.6 - Grassroots DICOM VTK runtime libraries python-gdcm - Grassroots DICOM Python bindings python-vtkgdcm - Grassroots DICOM VTK/Python bindings Closes: 825307 Changes: gdcm (2.6.3-6) unstable; urgency=medium . * d/control,d/p/10+11: compile against openjpeg-2.1 Closes: #825307 * d/control, d/p/12: update to and require lincharls-dev >= 1.1.0 Checksums-Sha1: 35447cd84f2f94d966427d85c9362388657b30cc 3269 gdcm_2.6.3-6.dsc db41c0df78b496cd8708d25bec8a8befa9940df5 27004 gdcm_2.6.3-6.debian.tar.xz Checksums-Sha256: 6111b9d1e40ab086aa1f9a3dea043343bc84c74b17b2d1f8f05f1d8a7f5f1d73 3269 gdcm_2.6.3-6.dsc 315fba2d6a92edae49597d217eb7f5904c09b8ab9438bee78bfb77e6de9b2afe 27004 gdcm_2.6.3-6.debian.tar.xz Files: f1aa5758ece4131d8c354782ce4a1c4a 3269 libs optional gdcm_2.6.3-6.dsc 7cf725f79319ede030fd7d0d38343155 27004 libs optional gdcm_2.6.3-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXSvNvAAoJEPgeNoubJquYXzsIAIQ8d/GkUPjBfz6oJPBdxJhY nZtqD7GJ+pxHIyBlkDXhzeSxfdoB8VenW8hcYueroL3CZ61bX7HNkq4SjMdKSz+e TTAsAb4OYLFYit9KyebThI7VsQVb7Wc+b82Dnp1pKqNjT+aJUNU/Gin1uvZ5U4KO Qxdc5zGde10UT3f0DmPOTu6PPR++lkCkSUly+oBWk8uDww+K7D2kaE76jKJzwdRQ pQMI3g6hCNlACHeOYGJPhjl7Jwz5fTYUVIE0sFuo32l9mfku9FAG6UUMUvKpwN7d T/tjDM/O53GpfqTywqf++yRo2BYME4PTPr1fGI4ydAFtrBY1195Tba5loZIRRdU= =te/G -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Sun May 29 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 29 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] libpal-java 1.5.1+dfsg-2 MIGRATED to testing Message-ID: FYI: The status of the libpal-java source package in Debian's testing distribution has changed. Previous version: 1.5.1+dfsg-1 Current version: 1.5.1+dfsg-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 29 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 29 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] trinityrnaseq 2.2.0+dfsg-1 MIGRATED to testing Message-ID: FYI: The status of the trinityrnaseq source package in Debian's testing distribution has changed. Previous version: 2.1.1+dfsg2-1 Current version: 2.2.0+dfsg-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 29 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 29 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] transdecoder 3.0.0+dfsg-2 MIGRATED to testing Message-ID: FYI: The status of the transdecoder source package in Debian's testing distribution has changed. Previous version: 2.0.1+dfsg-3 Current version: 3.0.0+dfsg-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 29 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 29 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] khmer 2.0+dfsg-7 MIGRATED to testing Message-ID: FYI: The status of the khmer source package in Debian's testing distribution has changed. Previous version: 2.0+dfsg-6 Current version: 2.0+dfsg-7 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 29 16:39:08 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 29 May 2016 16:39:08 +0000 Subject: [Debian-med-packaging] jaligner 1.0+dfsg-3 MIGRATED to testing Message-ID: FYI: The status of the jaligner source package in Debian's testing distribution has changed. Previous version: 1.0+dfsg-2 Current version: 1.0+dfsg-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 29 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 29 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] vtk-dicom 0.7.7-2 MIGRATED to testing Message-ID: FYI: The status of the vtk-dicom source package in Debian's testing distribution has changed. Previous version: 0.7.7-1 Current version: 0.7.7-2 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Sun May 29 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Sun, 29 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] smalt 0.7.6-6 MIGRATED to testing Message-ID: FYI: The status of the smalt source package in Debian's testing distribution has changed. Previous version: 0.7.6-4 Current version: 0.7.6-6 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From owner at bugs.debian.org Sun May 29 16:39:12 2016 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Sun, 29 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] Bug#825307: marked as done (gdcm: build-dependencies not installable) References: <1426545869.1142772.1464209723815.JavaMail.yahoo@mail.yahoo.com> Message-ID: Your message dated Sun, 29 May 2016 16:38:22 +0000 with message-id and subject line Bug#825307: fixed in gdcm 2.6.3-6 has caused the Debian Bug report #825307, regarding gdcm: build-dependencies not installable to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner at bugs.debian.org immediately.) -- 825307: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825307 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Gianfranco Costamagna Subject: gdcm: build-dependencies not installable Date: Wed, 25 May 2016 20:55:23 +0000 (UTC) Size: 3542 URL: -------------- next part -------------- An embedded message was scrubbed... From: Gert Wollny Subject: Bug#825307: fixed in gdcm 2.6.3-6 Date: Sun, 29 May 2016 16:38:22 +0000 Size: 5523 URL: From noreply at release.debian.org Mon May 30 04:39:02 2016 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Mon, 30 May 2016 04:39:02 +0000 Subject: [Debian-med-packaging] vtk-dicom is marked for autoremoval from testing Message-ID: vtk-dicom 0.7.7-2 is marked for autoremoval from testing on 2016-06-27 It (build-)depends on packages with these RC bugs: 819714: vtk6: nifti2dicom: FTBFS: No rule to make target '/usr/lib/x86_64-linux-gnu/libproj.so' From ftpmaster at ftp-master.debian.org Mon May 30 07:51:40 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 30 May 2016 07:51:40 +0000 Subject: [Debian-med-packaging] Processing of tm-align_20160521+dfsg-1_amd64.changes Message-ID: tm-align_20160521+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: tm-align_20160521+dfsg-1.dsc tm-align_20160521+dfsg.orig.tar.xz tm-align_20160521+dfsg-1.debian.tar.xz tm-align-dbgsym_20160521+dfsg-1_amd64.deb tm-align_20160521+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 30 08:27:19 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 30 May 2016 08:27:19 +0000 Subject: [Debian-med-packaging] Processing of seqtk_1.2-1_amd64.changes Message-ID: seqtk_1.2-1_amd64.changes uploaded successfully to localhost along with the files: seqtk_1.2-1.dsc seqtk_1.2.orig.tar.gz seqtk_1.2-1.debian.tar.xz seqtk-dbgsym_1.2-1_amd64.deb seqtk_1.2-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 30 08:57:39 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 30 May 2016 08:57:39 +0000 Subject: [Debian-med-packaging] Processing of fsm-lite_1.0-2~bpo8+1_amd64.changes Message-ID: fsm-lite_1.0-2~bpo8+1_amd64.changes uploaded successfully to localhost along with the files: fsm-lite_1.0-2~bpo8+1.dsc fsm-lite_1.0-2~bpo8+1.debian.tar.xz fsm-lite_1.0-2~bpo8+1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 30 10:23:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 30 May 2016 10:23:12 +0000 Subject: [Debian-med-packaging] fsm-lite_1.0-2~bpo8+1_amd64.changes is NEW Message-ID: binary:fsm-lite is NEW. source:fsm-lite is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Mon May 30 10:39:02 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 30 May 2016 10:39:02 +0000 Subject: [Debian-med-packaging] seqtk_1.2-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 30 May 2016 10:14:57 +0200 Source: seqtk Binary: seqtk Architecture: source amd64 Version: 1.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: seqtk - Fast and lightweight tool for processing sequences in the FASTA o Changes: seqtk (1.2-1) unstable; urgency=medium . * New upstream version * Fix watch file * cme fix dpkg-control * Better hardening Checksums-Sha1: 5a908c933cdf1d76cc539236d78379d30a5ff350 1903 seqtk_1.2-1.dsc 243242d1432817743243593c181824127f9c9bc2 24809 seqtk_1.2.orig.tar.gz 0e8e66f7213f52cd4fee5643e61179422488dbaf 2776 seqtk_1.2-1.debian.tar.xz 908df10d1a95ce855e2b04a5298fff9371d72293 47638 seqtk-dbgsym_1.2-1_amd64.deb e8aa002e7120115ed868f5f23e122851fd8a4ff3 28606 seqtk_1.2-1_amd64.deb Checksums-Sha256: 9e1151a3e0d246b8102d9eff765680cf72f486b81263cc8a0b4c55cb951037b9 1903 seqtk_1.2-1.dsc bd53316645ab10f0aaba59e1e72c28442ee4c9c37fddaacce5e24757eff78d7b 24809 seqtk_1.2.orig.tar.gz cded19461e71c79b5698f8b065dc851b90efd197ea3ad994b4f00d9b7f1a5757 2776 seqtk_1.2-1.debian.tar.xz 3d5644a428a0687bb89cae850100c2166e641677a72b478abba94d7f1d12bb93 47638 seqtk-dbgsym_1.2-1_amd64.deb 43128a9c28107725081b5e31910c646b42b84eafd70f650e7d4142d4435b6fca 28606 seqtk_1.2-1_amd64.deb Files: f7f0664f9aa40d8eee5d2caf638f1dbf 1903 science optional seqtk_1.2-1.dsc 255ffe05bf2f073dc57abcff97f11a37 24809 science optional seqtk_1.2.orig.tar.gz d116a4a27acc6913f3aaaaa01ebc9bf7 2776 science optional seqtk_1.2-1.debian.tar.xz 9d95dab164632ce98ee27813c904954f 47638 debug extra seqtk-dbgsym_1.2-1_amd64.deb 4522f124f5bf4fc607c2184dbade8ecd 28606 science optional seqtk_1.2-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXS/hAAAoJEFeKBJTRxkbR9vYP/1xR9ehMbNkAtislUPhor0nk AOUTODAPw1+AvAmOzpRVujpFE3ECqNHho7DLj9Zr+NMpbWKUXvDBhHY/Q0vWMyL7 7jpcQY07ovgRStDfjgRi4pgJSxQD21et+oMohvuz3Glj+xHUmqWiE6DMonOyymB1 D+TEJhsbQijMBd4BBbk3gFqSyLCTCk8Wcs73fa93r0GvK3eg4q9O1S2C8jdHp0t7 zkAFXrCFCLkb3/m3VGFd+PhTr6fBLkMxM3zO0If553S4NIJ+wOl70UnuvIJpHP0R WBY1oJEuARDVgzeAJPmZ6OcJl8RPmUJsB0QBhO3wkUcHEa9nMHhXIJ3RpyJt1deh WT5kpyRkT45M9uTfprlZctvQIrVLFCeTApkW8u2C1LwKTyhfSaUtnj6XSpgoOfK5 p6iRAWV4wq40nG9vSNaZlSyN7VjEinR/L+jUq6RBtwKPGBdo3ftdwJTRus/EYtkn NP5wbpI3WqMX9aYWAJ1ZRXhnBeTQI5KE6X3sv2oj4dA55AcK0JxqsO5Ljz+rU6tK osiWJgD1SuLR1eryFs5x3Yxr3mA/QYLYbTdTwXbfcNsf3EyiwYM4KeqvzZmuY8UY 54ZBBMqIafyUo9FXDAgyDM+IYG1/+XEVtDLi/z0gJDOwU/afk6qkWD9XcuB8DQ9i t9gAz5avvvyp6McTPI2t =Y7VF -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Mon May 30 10:39:20 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 30 May 2016 10:39:20 +0000 Subject: [Debian-med-packaging] tm-align_20160521+dfsg-1_amd64.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 30 May 2016 09:35:45 +0200 Source: tm-align Binary: tm-align Architecture: source amd64 Version: 20160521+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: tm-align - structual alignment of proteins Changes: tm-align (20160521+dfsg-1) unstable; urgency=medium . * New upstream version * Moved packaging from SVN to Git * Use xz compression in watch file * cme fix dpkg-control * Better hardening Checksums-Sha1: 224bf3f774d50f72c0a8ee7eabd6e8ead03be863 2052 tm-align_20160521+dfsg-1.dsc 0b78dc5b8a28ff6723261df2b1516917635b09a4 20316 tm-align_20160521+dfsg.orig.tar.xz 84995f8fd9dbe72c2eb2f0d902d2a07b0e276bea 7444 tm-align_20160521+dfsg-1.debian.tar.xz b488a7c9a9050b64a010f7c0020511c2a61dc3ac 5402 tm-align-dbgsym_20160521+dfsg-1_amd64.deb 5c20aadbf4ceaee9dced79c6ce972cf22c943764 57338 tm-align_20160521+dfsg-1_amd64.deb Checksums-Sha256: 0d3c922adde74e3a0286d434f674c4fea8fb763baed74762625f4f432e4cd3b3 2052 tm-align_20160521+dfsg-1.dsc cafb3d22a6fb44061b6529a6d29df441c1022b665967bbb2ef1356a6ef675e0f 20316 tm-align_20160521+dfsg.orig.tar.xz 85522efaefbda990cbb08b3c88a58af63f11a5ac0230188afe614ae628ed7e0b 7444 tm-align_20160521+dfsg-1.debian.tar.xz 78e4ead0dbd306a413ce72eb00a3967ca29687f53ca64e08926e383fedbddae2 5402 tm-align-dbgsym_20160521+dfsg-1_amd64.deb 252544c0bb92ee2023d7b5041c936484471825a21c6e2aa5ee9e720e2ef2f9d9 57338 tm-align_20160521+dfsg-1_amd64.deb Files: 3613bf22947e781509092e1a014ad110 2052 science optional tm-align_20160521+dfsg-1.dsc d668296117e8a723daa0440a22347c83 20316 science optional tm-align_20160521+dfsg.orig.tar.xz a9585dfdcc7150ce97c3ab7f19d95532 7444 science optional tm-align_20160521+dfsg-1.debian.tar.xz cc1e5f1b5b0f17d44e8982470d835d0d 5402 debug extra tm-align-dbgsym_20160521+dfsg-1_amd64.deb 9f12a46acdf85527e4c83bf153f672d1 57338 science optional tm-align_20160521+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXS+/EAAoJEFeKBJTRxkbR/AIQAJbxlTGHkWxqFahMsnvTlDmw ioeUF0rQV7TJXA2hxP4tC9Aq2PlujpfDD8CeSfM7F6+ccMfOmUN0i1H5YQtFeAAH ns8Kb058bxS3boJhQ1yPpXuK1dRY8dOV9Vcz3yrLLuEk3JE61323xmBd1xLIJgiD v6kZnfqhPG4PzdYaIL3eW/uTnNP0hthzSOE0xyQz7uNs+A/2hhedJhfAL0QJJO54 C6wbMO4Dfm7jzR6cFG9qDrcKUtSD9GTsZmmMFVVlrwFRvhiuPaBs2pUocRXvEzYh OxkyXxsC8qF7TWd8itm9SIaxDdX9rWs9iqKZ9q2vYh72ZMwjBylBByfVa5yP2VRx CW92BgDF9NseTgOanOWtb65HVwUey5tajUCdsSUlo08QzagFG8jW6QPREn2JRLYm J9pch6zrHAYrbA/H96lKupLyOXlpqAJygVMopvQrImqM8qPkCYoJDd+92DNoMeDr r4/jIx5C2wd+6HHfHtwTfvPgJtf1IGqYICNgmbxszbn7Dk74/eS0yNVsYHlb5UDJ OE2+D4X0V4cWhWzFvvQ5A7yPiYHunUBJKZmrfeqK/yfmwVIztWCXa6Z1FQBuyccQ 26lkyqNVnpC6wPZAi46e1xyNJ364lhwabwDm5naEaD2uDyEbAljceL1qb4Wlda1t 51kRJqdXXi79W8nr6jXv =3+QX -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From hpi_pusat at hapindo.co.id Mon May 30 10:30:14 2016 From: hpi_pusat at hapindo.co.id (MAERSK DRILLING QATAR) Date: Mon, 30 May 2016 17:30:14 +0700 (WIB) Subject: [Debian-med-packaging] MAERSK DRILLING QATAR RECRUITMENT Message-ID: <1642553504.125626.1464604214582.JavaMail.zimbra@hapindo.co.id> Dear Candidate, MAERSK DRILLING QATAR is recruiting the services of professional's in all fields. Kindly submit your CV/Resume is highly needed to work with MAERSK DRILLING QATAR Email:info.maerskoilqa at asia.com) for Employment.Job Location:Doha Qatar Salary Rate: $3000 USD --$50,000 USD Kindly state below information Your Present Salary: Expected Salary : Current Position : Regards Mrs Hannah Myrick Human resources Manager MAERSK DRILLING QATAR -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Mon May 30 13:29:34 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 30 May 2016 13:29:34 +0000 Subject: [Debian-med-packaging] Processing of mia_2.2.7-6_source.changes Message-ID: mia_2.2.7-6_source.changes uploaded successfully to localhost along with the files: mia_2.2.7-6.dsc mia_2.2.7-6.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Mon May 30 13:34:17 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 30 May 2016 13:34:17 +0000 Subject: [Debian-med-packaging] mia_2.2.7-6_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 30 May 2016 11:43:01 +0000 Source: mia Binary: libmia-2.2-4 libmia-2.2-dev libmia-2.2-doc mia-tools mia-tools-doc Architecture: source Version: 2.2.7-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: libmia-2.2-4 - library for 2D and 3D gray scale image processing libmia-2.2-dev - library for 2D and 3D gray scale image processing, development fi libmia-2.2-doc - library for 2D and 3D gray scale image processing, documentation mia-tools - Command line tools for gray scale image processing mia-tools-doc - Cross-referenced documentation of the MIA command line tools Changes: mia (2.2.7-6) unstable; urgency=medium . * d/p/04, d/control, d/rules: separate doc build and switch to automatic debug symbols Checksums-Sha1: b32a966909c5086842ad8102ee6763735d9b0e7a 2215 mia_2.2.7-6.dsc b8e7f9a337c749496d0fbb3d4605c2ea8bd4b27c 13732 mia_2.2.7-6.debian.tar.xz Checksums-Sha256: 80ed91071f0fd5d4c710d1c6aa2e874f4a7eee0becfe5b1092c166232a6f3b73 2215 mia_2.2.7-6.dsc 990648eec8f43928260e518d12cd74b73c2099fc5686075712d40838f9e35ea0 13732 mia_2.2.7-6.debian.tar.xz Files: 3dd4ec70326e770b9261cc3b8fa15f28 2215 science optional mia_2.2.7-6.dsc 53bbeb8c4f27f1daf6136997172b77dd 13732 science optional mia_2.2.7-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXTD7zAAoJEPgeNoubJquYyjsH/iIXHmokxp6bgiUqOY9as6Xn s3D8238yjriJhcIOmlSJupVQF9ZWpuScKWh7q1Bvb7hdCbphsiOy5yeWG/YHQF/B 9x2j2EwTKatyvu3hQj1VY8OWn3px2EMl94d9wDrKfFHnlhmmycNXoXGLvo+V5uN5 uCe5m8xne87Jg8/6oJLKxc+Q7xep4uxGMTmz4Vb9gJbU8emw77LM1MxtT448N4nb kvc9h+BA/zSAdF4jkA0acXryrHSMXD2hYk5xDGw3HTPOPuuI2NCMVxYnR4FNOlB0 fY3ngacgLYVrqQVK6Lv14z02qybf+f+YhuzrN8TKZkFs6ff2LY3fBzOBVCE+XfA= =GMy+ -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Mon May 30 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 30 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] mpj 0.44+dfsg-3 MIGRATED to testing Message-ID: FYI: The status of the mpj source package in Debian's testing distribution has changed. Previous version: 0.44+dfsg-2 Current version: 0.44+dfsg-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 30 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 30 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] python-rdflib-jsonld 0.4.0-1 MIGRATED to testing Message-ID: FYI: The status of the python-rdflib-jsonld source package in Debian's testing distribution has changed. Previous version: 0.3-1 Current version: 0.4.0-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Mon May 30 16:39:12 2016 From: noreply at release.debian.org (Debian testing watch) Date: Mon, 30 May 2016 16:39:12 +0000 Subject: [Debian-med-packaging] r-cran-surveillance 1.12.1-1 MIGRATED to testing Message-ID: FYI: The status of the r-cran-surveillance source package in Debian's testing distribution has changed. Previous version: 1.10-0-2 Current version: 1.12.1-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From ftpmaster at ftp-master.debian.org Mon May 30 17:21:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Mon, 30 May 2016 17:21:12 +0000 Subject: [Debian-med-packaging] Bug#825838: Removed package(s) from unstable Message-ID: We believe that the bug you reported is now fixed; the following package(s) have been removed from unstable: stacks | 1.38-1 | armhf, mips, powerpc, s390x ------------------- Reason ------------------- ROM; Remove architectures where stacks does not build any more ---------------------------------------------- Note that the package(s) have simply been removed from the tag database and may (or may not) still be in the pool; this is not a bug. The package(s) will be physically removed automatically when no suite references them (and in the case of source, when no binary references it). Please also remember that the changes have been done on the master archive and will not propagate to any mirrors until the next dinstall run at the earliest. Packages are usually not removed from testing by hand. Testing tracks unstable and will automatically remove packages which were removed from unstable when removing them from testing causes no dependency problems. The release team can force a removal from testing if it is really needed, please contact them if this should be the case. Bugs which have been reported against this package are not automatically removed from the Bug Tracking System. Please check all open bugs and close them or re-assign them to another package if the removed package was superseded by another one. The version of this package that was in Debian prior to this removal can still be found using http://snapshot.debian.org/. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 825838 at bugs.debian.org. The full log for this bug can be viewed at https://bugs.debian.org/825838 This message was generated automatically; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster at ftp-master.debian.org. Debian distribution maintenance software pp. Scott Kitterman (the ftpmaster behind the curtain) From e09ddi0010i at sepdf.gob.mx Mon May 30 21:36:55 2016 From: e09ddi0010i at sepdf.gob.mx (Chevrolet) Date: Mon, 30 May 2016 22:36:55 +0100 Subject: [Debian-med-packaging] =?utf-8?q?Chevrolet-d=C3=ADj?= Message-ID: J? h?r, hogy te a Chevrolet T?rsas?g Uk.Your email-bels? ?tm?r? lett kiv?lasztva A Chevrolet Auto Mobil d?jat 2016.The ?sszege $ 570,000,00USD kapta ?nnek, mint a kedvezm?nyezett. K?ldje el adatait k?vetel?s: chevroletcompnay00 at outlook.com N?v: Add: Mobil sz?m: Orsz?g: V?lasz on: chevroletcompnay00 at outlook.com A titkos PIN-k?d: (25512560) Jegy sz?ma: 15975357357344 Sorsz?m: pTYR-Y67546537 K?dsz?m: 344521 Chevrolet Company Uk. V?lasz on: chevroletcompnay00 at outlook.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From ftpmaster at ftp-master.debian.org Mon May 30 22:00:23 2016 From: ftpmaster at ftp-master.debian.org (Thorsten Alteholz) Date: Mon, 30 May 2016 22:00:23 +0000 Subject: [Debian-med-packaging] fsa_1.15.9+dfsg-1_amd64.changes REJECTED Message-ID: Hi Andreas, according to COPYING, README and FAQ.html the license is GPL-3, nevertheless some file headers say they are under GPL-2+. This seems to be a mismatch to your debian/copyright. Also, MW/src/RMComm/MW-File/chirp* display/mad/JpegImagesToMovie.java src/util/regexp.cc should be mentioned. Thanks! Thorsten === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. From bsaici at galenika.rs Tue May 31 01:53:52 2016 From: bsaici at galenika.rs (Biljana Saicic) Date: Mon, 30 May 2016 18:53:52 -0700 Subject: [Debian-med-packaging] Galenika A.D. Order Message-ID: <20160531015301.A83F2480077@mail.tmsgroup.com.my> Hello, Please find our order as attached. Best regards, _________________________________________________ Biljana Saicic Galenika a.d. | Batajnicki drum bb | 11080 Belgrade, Serbia Tel: +381 11 307 1940 | Fax: +381 11 307 1030 E-mail: bsaici at galenika.rs | Web: www.galenika.rs -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PO-GKAD6374522.jar Type: application/octet-stream Size: 141539 bytes Desc: not available URL: From ftpmaster at ftp-master.debian.org Tue May 31 06:19:13 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 06:19:13 +0000 Subject: [Debian-med-packaging] Processing of galileo_0.5.0~git160510-1_amd64.changes Message-ID: galileo_0.5.0~git160510-1_amd64.changes uploaded successfully to localhost along with the files: galileo_0.5.0~git160510-1.dsc galileo_0.5.0~git160510.orig.tar.gz galileo_0.5.0~git160510-1.debian.tar.xz galileo_0.5.0~git160510-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 31 06:33:39 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 06:33:39 +0000 Subject: [Debian-med-packaging] galileo_0.5.0~git160510-1_amd64.changes is NEW Message-ID: binary:galileo is NEW. source:galileo is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Tue May 31 07:01:00 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 07:01:00 +0000 Subject: [Debian-med-packaging] r-bioc-annotationhub_2.4.2-1_amd64.changes ACCEPTED into unstable, unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 23 May 2016 21:07:01 +0200 Source: r-bioc-annotationhub Binary: r-bioc-annotationhub Architecture: source all Version: 2.4.2-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: r-bioc-annotationhub - GNU R client to access AnnotationHub resources Closes: 825114 Changes: r-bioc-annotationhub (2.4.2-1) unstable; urgency=low . * Initial release (closes: #825114) Checksums-Sha1: 05e489f8a8d3ef3e5f019baceadc0c22d1b3407f 2241 r-bioc-annotationhub_2.4.2-1.dsc 5c02ec4826b26bf88065c7477c0378915118110c 415393 r-bioc-annotationhub_2.4.2.orig.tar.gz be07ad6260bcb667574d44a162e5c8b337027aae 3488 r-bioc-annotationhub_2.4.2-1.debian.tar.xz 7d9e59d739e3fb7307aa3b7e0a20cb105353932b 380780 r-bioc-annotationhub_2.4.2-1_all.deb Checksums-Sha256: be6d0bd87fc32851a350fe8712a722a1c71a69f0772b9f77e7199f1d35088dd0 2241 r-bioc-annotationhub_2.4.2-1.dsc c40393c0db039157eff03a4a9e3cfe5ddd863880fc30936a86d2f1c70b0e54ca 415393 r-bioc-annotationhub_2.4.2.orig.tar.gz 136d58176dba3941d544f2e380f60a324b20d62491c4206c2d9c84dd708956e7 3488 r-bioc-annotationhub_2.4.2-1.debian.tar.xz e7df72e019f436ac876daf19e5f0e5cd2996569a309ae7b14815e789d2c3b472 380780 r-bioc-annotationhub_2.4.2-1_all.deb Files: 84ab04bc3091490ae1ec276a01eadab9 2241 gnu-r optional r-bioc-annotationhub_2.4.2-1.dsc f626af5b32ca7e41c83fce471e22a05d 415393 gnu-r optional r-bioc-annotationhub_2.4.2.orig.tar.gz de58db308369fcb70c8a4bebe5ea5689 3488 gnu-r optional r-bioc-annotationhub_2.4.2-1.debian.tar.xz 49811411000a7ec89d1b7d62440d7344 380780 gnu-r optional r-bioc-annotationhub_2.4.2-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXQ1avAAoJEFeKBJTRxkbRwJ4P/ReB6x1pMfqUhyCtPXaDHOzk wk0LYT+iQ+rRST7KhjhlWJzLG+3FMv62U0slcLsaP2MfHpUw216ofkwIKEYwWBGq HBQmwuNOwSAuA9ixs+kllD5EzKuYqNi5UYm85gPJAGFyO0k/7tqYsgXhl8yjLUlB 44xR1wkWy/XcW4Y+2HtA8WcaNMHKGBZIqufKbkU3ArcZT+ZPVuMfX2LJ6slGrebe XpsTWfbwmiqBisxEIIuUBwSvcnbvDN+S1SRdEbKftBJwZtuLtsJDQ9dbzmBkR8Of PHZzm2C+oNfOJSLEzO/3Oo+LEPKXmV8Wf4d6DEURyUoJ8PF/QeglSILOI0JBpEy6 JWFp6t6TqUVjQJhChAjg0vl61fqGISU9kxzhx2du+U/4hHy9zZ906WjXh3mOoOen liw/WRg/ajIscylmwviavVYDW28EuIT/2UPWC+IDmbsKUNlEQuYmwXOWQjGfxSCv 90FQB1DB7m73JC4UFElLOH6/xocj/WyFIPSs5uw8XdmHU6SJ42KtcnTPOwbo8OFv FxF3rZvBD1azOfqwB5Af/ZyQuH0YS/CN3ixJfPFTffoDID7vOMmypGNCpDDXCK58 iCnalgqtF5VIl8vFPBgK0sYZov/1Z3qEogNJFAlJgGlzQ0vcnhQoDYDZryuC+ORK OCnZi9d/jHQI7MFeYCUQ =ulUw -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From info at freelotto.org Tue May 31 07:24:21 2016 From: info at freelotto.org (Free Lotto) Date: Tue, 31 May 2016 10:24:21 +0300 Subject: [Debian-med-packaging] (no subject) Message-ID: <20160531073030.8E258BD884FF@mail.isra.edu.pk> YOUR EMAIL ADDRESS HAS WON $2,000,000.00USD IN THE FREELOTTO UK PROMO. FOR CLAIMS, EMAIL (YOUR FULL NAME,COUNTRY & MOBILE #) FOR MORE DETAILS. From andreas at fam-tille.de Tue May 31 08:38:03 2016 From: andreas at fam-tille.de (Andreas Tille) Date: Tue, 31 May 2016 10:38:03 +0200 Subject: [Debian-med-packaging] fsa_1.15.9+dfsg-1_amd64.changes REJECTED In-Reply-To: References: Message-ID: <20160531083803.GJ6645@an3as.eu> Hi Thorsten, On Mon, May 30, 2016 at 10:00:23PM +0000, Thorsten Alteholz wrote: > according to COPYING, README and FAQ.html the license is GPL-3, nevertheless > some file headers say they are under GPL-2+. This seems to be a mismatch to > your debian/copyright. Mentioned in d/copyright > Also, > MW/src/RMComm/MW-File/chirp* Added. > display/mad/JpegImagesToMovie.java Whole display/ dir removed since its not used anyway due to other non-free components and this file has a not-for-aircraft restriction. > src/util/regexp.cc Added. Thanks for checking Andreas. -- http://fam-tille.de From ftpmaster at ftp-master.debian.org Tue May 31 08:40:03 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 08:40:03 +0000 Subject: [Debian-med-packaging] Processing of fsa_1.15.9+dfsg-1_amd64.changes Message-ID: fsa_1.15.9+dfsg-1_amd64.changes uploaded successfully to localhost along with the files: fsa_1.15.9+dfsg-1.dsc fsa_1.15.9+dfsg.orig.tar.xz fsa_1.15.9+dfsg-1.debian.tar.xz fsa-dbgsym_1.15.9+dfsg-1_amd64.deb fsa_1.15.9+dfsg-1_amd64.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From afif at debian.org Tue May 31 08:41:31 2016 From: afif at debian.org (Afif Elghraoui) Date: Tue, 31 May 2016 01:41:31 -0700 Subject: [Debian-med-packaging] Bug#819617: bcftools: FTBFS: test suite fails on several architectures In-Reply-To: <574AD5B4.3060607@iwakd.de> References: <145343335662.27443.1119837475829094147.reportbug@ghostwheel.internal.ucko.debian.net> <145343335662.27443.1119837475829094147.reportbug@ghostwheel.internal.ucko.debian.net> <574AD5B4.3060607@iwakd.de> Message-ID: <574D4E3B.5060105@debian.org> ??? ????? 29 ???? 2016 ?04:42? ??? Christian Seiler: > Hope that helps. It's very much appreciated! I don't have the chance to try it out myself for a while, but I've notified upstream about your suggestions. We'll see how it goes. Many thanks and regards Afif -- Afif Elghraoui | ???? ??????? http://afif.ghraoui.name From jkb at sanger.ac.uk Tue May 31 09:14:12 2016 From: jkb at sanger.ac.uk (James Bonfield) Date: Tue, 31 May 2016 10:14:12 +0100 Subject: [Debian-med-packaging] Bug#825461: staden: FTBFS in testing In-Reply-To: <20160528070309.GC880@an3as.eu> References: <20160527002928.GA14930@nuc> <20160528070309.GC880@an3as.eu> Message-ID: <20160531091412.GW1308@sanger.ac.uk> Hello Andreas, On Sat, May 28, 2016 at 09:03:09AM +0200, Andreas Tille wrote: > after dealing with the actual issue reported in bug #825461[1] I noticed > that more strict gcc fails at other parts. I fixed an implicit declaration > issue[2] and I'm now stumbling upon There are a lot of old and unsupported parts of the Staden Package (eg that eba tool), so it doesn't suprise me newer compiler options throw up warnings. I assume this is now an issue due to -Werror=format-security. The append_int function is entirely my fault though and recent. Sorry. I should go through the package with a modern gcc and stress test it locally. I can't support the old legacy bits, but at the very least they should be able to compile. Thanks for the bug report. James -- James Bonfield (jkb at sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From tille at debian.org Tue May 31 09:25:07 2016 From: tille at debian.org (Andreas Tille) Date: Tue, 31 May 2016 11:25:07 +0200 Subject: [Debian-med-packaging] Bug#825906: ITP: r-bioc-ensembldb -- GNU R utilities to create and use an Ensembl based annotation database Message-ID: <20160531092507.31402.89595.reportbug@mail.an3as.eu> Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name : r-bioc-ensembldb Version : 1.4.3 Upstream Author : Johannes Rainer * URL : http://bioconductor.org/packages/release/bioc/html/ensembldb.html * License : LGPL Programming Lang: GNU R Description : GNU R utilities to create and use an Ensembl based annotation database The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. Remark: This package is needed to upgrade other r-bioc-* packages and will be maintained by the Debian Med team at svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-ensembldb/trunk/ From jm18 at sanger.ac.uk Tue May 31 10:01:24 2016 From: jm18 at sanger.ac.uk (John Marshall) Date: Tue, 31 May 2016 11:01:24 +0100 Subject: [Debian-med-packaging] Bug#822701: Bug#822701: Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure; References: <1461693748.2750823.590308017.767C5093@webmail.messagingengine.com> <20160427011231.GB12206@falafel.plessy.net> <20160427043803.GA29652@falafel.plessy.net> <57282F19.1050006@debian.org> Message-ID: <188B76E2-A16C-4C31-BCD3-C0CDBCB4BD10@sanger.ac.uk> On Mon, 2 May 2016 21:54:49 -0700 Afif Elghraoui wrote: > This seems to happen with every htslib upgrade in the past few releases. > bcftools builds have also been breaking as a result and I was a little > confused. Aren't backwards-compatibility breaks supposed to be indicated > by soname bumps? Or is this because samtools, bcftools, and htslib are > all maintained by the same group, so they rely on the unstable internal > interfaces? Afif, please explain these comments if you would like upstream to listen to you in future. In fact we take htslib API/ABI compatibility very seriously. Regards, John -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From ftpmaster at ftp-master.debian.org Tue May 31 10:10:37 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 10:10:37 +0000 Subject: [Debian-med-packaging] Processing of miaviewit_1.0.2-2_source.changes Message-ID: miaviewit_1.0.2-2_source.changes uploaded successfully to localhost along with the files: miaviewit_1.0.2-2.dsc miaviewit_1.0.2-2.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 31 10:15:38 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 10:15:38 +0000 Subject: [Debian-med-packaging] Processing of r-bioc-ensembldb_1.4.3-1_amd64.changes Message-ID: r-bioc-ensembldb_1.4.3-1_amd64.changes uploaded successfully to localhost along with the files: r-bioc-ensembldb_1.4.3-1.dsc r-bioc-ensembldb_1.4.3.orig.tar.gz r-bioc-ensembldb_1.4.3-1.debian.tar.xz r-bioc-ensembldb_1.4.3-1_all.deb Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 31 10:20:38 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 10:20:38 +0000 Subject: [Debian-med-packaging] fsa_1.15.9+dfsg-1_amd64.changes is NEW Message-ID: binary:fsa is NEW. source:fsa is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Tue May 31 10:32:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 10:32:06 +0000 Subject: [Debian-med-packaging] miaviewit_1.0.2-2_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 31 May 2016 09:11:11 +0000 Source: miaviewit Binary: libmiaviewit0 libmiaviewit-dev mia-viewit Architecture: source Version: 1.0.2-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: libmiaviewit-dev - development files for the 3D visualization library libmiaviewit0 - MIA addon library for 3D visualization mia-viewit - Viewer program for 3D data sets created by using MIA Changes: miaviewit (1.0.2-2) unstable; urgency=medium . * d/rules,d/control: Switch to automatic debug packages and update standards version * d/control: cme fix dpkg-control * d/rules: add -WL,-z,now to linker flags Checksums-Sha1: e2ddad789d06478d9f26c4eae389820da7c952d6 1854 miaviewit_1.0.2-2.dsc 1cb129f8bc52c3ee93354e217dbdfe30d65f4047 3280 miaviewit_1.0.2-2.debian.tar.xz Checksums-Sha256: 81651e0c39fea0775ed218c538c918adfc6c22a1cbbb13f85d5a98a1abf0e1b5 1854 miaviewit_1.0.2-2.dsc 92eb7efbf6c10182766f78b8905aea52a002f97ffd12da7dca3a8d975a7e408c 3280 miaviewit_1.0.2-2.debian.tar.xz Files: 1e32ccf5bf5008e723e14aeb9d77141c 1854 science optional miaviewit_1.0.2-2.dsc aa54c7a2057700efbb4d3091a1bb39d4 3280 science optional miaviewit_1.0.2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXTWCvAAoJEPgeNoubJquYT0kH/jaMvmaaJebS6sc+irC9xzLx xE9qJGAV5fGoI42pMccYVPPdplTsx4LgVZHmUC6iystPnB955OoquiDeniKFExke q7Y/qPO3AH6TkM8F7r2QHmLcnrpODoD0awaqhp2aW2yMt2FyIoh2bhmnEqcJfb0y iGRh/Le3eiPIRfZb7nirJV8nk9Kgu8okOa1pyuZhLXpauYh7kUyvVC736O5Y8odv jJ7SIAkL9AhKq29u9L1JbVTH4cMLshteFkNgo1aGscV8F5wpP9mjrHwBKlAZyk1d EZmzJLKdst4olX2cROWquk51mLJEZJw7E2W7yis0jgGhcn1/1mp28mcpndi4TaY= =qYm3 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From ftpmaster at ftp-master.debian.org Tue May 31 10:34:06 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 10:34:06 +0000 Subject: [Debian-med-packaging] r-bioc-ensembldb_1.4.3-1_amd64.changes is NEW Message-ID: binary:r-bioc-ensembldb is NEW. source:r-bioc-ensembldb is NEW. Your package has been put into the NEW queue, which requires manual action from the ftpteam to process. The upload was otherwise valid (it had a good OpenPGP signature and file hashes are valid), so please be patient. Packages are routinely processed through to the archive, and do feel free to browse the NEW queue[1]. If there is an issue with the upload, you will receive an email from a member of the ftpteam. If you have any questions, you may reply to this email. [1]: https://ftp-master.debian.org/new.html From ftpmaster at ftp-master.debian.org Tue May 31 10:35:45 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 10:35:45 +0000 Subject: [Debian-med-packaging] Processing of pymia_0.1.7-3_source.changes Message-ID: pymia_0.1.7-3_source.changes uploaded successfully to localhost along with the files: pymia_0.1.7-3.dsc pymia_0.1.7-3.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From mail at ismayilli-xeberleri.info Tue May 31 10:26:58 2016 From: mail at ismayilli-xeberleri.info (INTERNATIONAL PROMOTIONS/PRIZE AWARD DEPT) Date: Tue, 31 May 2016 12:26:58 +0200 Subject: [Debian-med-packaging] SEHR GEEHRTER GEWINNER Message-ID: INTERNATIONAL PROMOTIONS/PRIZE AWARD DEPT VE NTURA 24 S.A PZA.DE.ESPANA 88,28013 MADRID. REFERENZ NUMMER:ED5M9H/965456/15/ESP DATUM.31/05/2016 OFFIZIELLEGEWINNER BRIEF Es freunen uns lhnen mitzuteilen dass die Gewinnliste INTERNACIONALE LOTTO COMMISSION am 21/04/2016 erschient ist. Der offiziellen Liste der Gewinnern erschient am 31/05/2016 lhre Email wurd mit der nummer:025.11464992.750 und mit superza(45)haben in der dritte Kategorie gewonnen.Sie sind damit Gewinner(in)von:?935,470.00 genehmigt worden(NEUN HUNDERT FUNFUNDDREIZIG TAUSEND VIER HUNDERT UND SIEBZIG EUROS)Die summeergibt sich aus einer Gewiinausschuettung von ?11,225,640.00(ELF MILLIONE ZWEI HUNDERT FUNFUNDZWANZIG TAUSEND SECHS HUNDERT VIERZIG EUROS)geteilt unter den zwolf internationalen Gewinnern in der gleiche Kategorie. HERZLICHEN GLUECKWUNSCH!!! Des Gewinnes ist bei der GLOBAL SEGURIDAD SICHERHEITSFIRMA S.L MADRID hinterlegt und auf lhrem email versichert.Um keine Komplikationen bei der Abwicklung der Zahlung zu vermeiden bitten wir Sie diese Offizielle Mitteilung diskret zu behandeln.Es ist unsere Sicherheitsprotokolls und garantiern wir lhnen einen problemloss Ablauf.Alle Gewinnern wurden per Computer aus 6,080 Emails aus ganzen Europa,Asien,Australien und Amerika als Teil unserer Internationalen Promtion Programm ausgewaehlt,welche wir drei mal in Jahr veranstalten.Bitte kontaktieren Sie unsere Auslandsachbearbeiterin. Isabel de Paula bei der GLOBAL SEGURIDAD S.L.MADRID TEL:0034-631-281-986 FAX:0034 911-881 373 oder Email addresse:global_seguridad at representative.com F?r die bearbeitung und auszahlung lhre gewinnes.Bitte denken Sie daran jeder Gewinnanspruch muss bis zum 30/06/2016 angemeldet sein.lrgend welche unangemeldet Gewinnes verfaellt und geht zurueck zum Stadtkasse.Bitte beachten sie auch dass nach erhalt des gewinnes mussen Sie 10% ihre Lotterie gewinn zu GLOBAL SEGURIDAD S.L MADRID zuruck zahlen.Diese 10% sind erst nach Erhalt des Gewinnes faellig weil es ist noch lhre email versichert.WICHTIG:Um Verzoegerungen und Komplikationen zu vermeiden bitten wir Sie lhre Referenznummer und Bearbeitungsnummer anzugeben wenn Sie lhre sachbearbeiter anrufen.Adresseaenderungen bitte so schnell wie moeglich mitteilen.Schneiden Sie bitte diese Anmeldeformular aus,und fuellen sie es aus und zuruck sendend durch FAX:0034 911-881-373 DON LUIS ALBERTO (PRESIDENT) BITTE FUELLEN SIE DIESE FORMULAR SORGSAM AUS UND FAXEN SIE ES ZURUCK AN GLOBAL SEGURIDAD S.L NAME:......................................................... 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Name: SEHR GEEHRTER GEWINNER.pdf Type: application/octet-stream Size: 465317 bytes Desc: not available URL: From ftpmaster at ftp-master.debian.org Tue May 31 11:23:33 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 11:23:33 +0000 Subject: [Debian-med-packaging] pymia_0.1.7-3_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 31 May 2016 10:24:52 +0000 Source: pymia Binary: python-mia python3-mia Architecture: source Version: 0.1.7-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: python-mia - Python-2 bindings for the MIA image processing library python3-mia - Python-3 bindings for the MIA image processing library Changes: pymia (0.1.7-3) unstable; urgency=medium . * d/control: cme fix dpkg-control * d/rules: add -Wl,-z,now linker flag * d/control: update browsing url * d/rules, d/control: switch to automatic debug packages Checksums-Sha1: b2dbb10f10a322f0bf86235c47020a7e6df0b2af 1716 pymia_0.1.7-3.dsc fe34dc914cc15493db4a5a8959adf2c6a092c2e5 7272 pymia_0.1.7-3.debian.tar.xz Checksums-Sha256: 6f1a7ba844712ab7e55c0f746c43a1a41ceeaf7be871f65353572016f88d54ef 1716 pymia_0.1.7-3.dsc 8327e9a13765a7b12888a9e23ebfc3646e524b934872e5c174bc8be1daf901ac 7272 pymia_0.1.7-3.debian.tar.xz Files: 95b90692c4a4525565bdffea3a7dd8f9 1716 science optional pymia_0.1.7-3.dsc 0c3e8e8c74d6c9c07289272f393e9b5d 7272 science optional pymia_0.1.7-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXTWesAAoJEPgeNoubJquY1gYIAKJ5vzWY78NRn6zqr4eXYeEq rTwV3sHG39MZ/3Xx60wbl/UlYEVNMIkKnq8mPFPckFsj0TkwyjkXMb7MZA1Ihoxh Maj/uUzq+b5Ad4f8HZx9PcNN51rDVxD+Mt8USMUIigNZX2x05cMXl9pNQq9H6XB1 eygPv6/bcllPj/408rxMOsABXI9WfRRsN9oJhSfNbloKpc0Pao26Nc9Ni9Pbs/bl U7KvwDj0KsZVPrJas/Gb4HHlom/2TvkQXO+Tg45bNPDL7XXhWfxvtlYCVqSw4GAK h0OtbeOWl6osc4IkUz5/MNct20HatX/+nd8Wax6J0HO3azsRdnbFTz31Ts+aM6k= =LGk4 -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From colpontealtato at sefaz.to.gov.br Tue May 31 08:23:27 2016 From: colpontealtato at sefaz.to.gov.br (Google Inc) Date: Tue, 31 May 2016 05:23:27 -0300 (BRT) Subject: [Debian-med-packaging] Powered By Google In-Reply-To: <1123735028.197275.1464682599159.JavaMail.zimbra@sefaz.to.gov.br> References: <1953040899.171318.1464670037908.JavaMail.zimbra@sefaz.to.gov.br> <399083224.193104.1464679685283.JavaMail.zimbra@sefaz.to.gov.br> <1139354984.193520.1464679942249.JavaMail.zimbra@sefaz.to.gov.br> <1101765753.194093.1464680344462.JavaMail.zimbra@sefaz.to.gov.br> <543953948.195061.1464681083789.JavaMail.zimbra@sefaz.to.gov.br> <542404857.195333.1464681313063.JavaMail.zimbra@sefaz.to.gov.br> <1259745382.196389.1464682057435.JavaMail.zimbra@sefaz.to.gov.br> <1123735028.197275.1464682599159.JavaMail.zimbra@sefaz.to.gov.br> Message-ID: <1255928857.197885.1464683007852.JavaMail.zimbra@sefaz.to.gov.br> Dear Google User, You have been selected as a winner for using Google services. 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Name: Google.jpg Type: image/jpeg Size: 762074 bytes Desc: not available URL: From ftpmaster at ftp-master.debian.org Tue May 31 14:53:45 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 14:53:45 +0000 Subject: [Debian-med-packaging] Processing of vtk-dicom_0.7.8-1_source.changes Message-ID: vtk-dicom_0.7.8-1_source.changes uploaded successfully to localhost along with the files: vtk-dicom_0.7.8-1.dsc vtk-dicom_0.7.8.orig.tar.gz vtk-dicom_0.7.8-1.debian.tar.xz Greetings, Your Debian queue daemon (running on host franck.debian.org) From ftpmaster at ftp-master.debian.org Tue May 31 16:33:12 2016 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Tue, 31 May 2016 16:33:12 +0000 Subject: [Debian-med-packaging] vtk-dicom_0.7.8-1_source.changes ACCEPTED into unstable Message-ID: Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 31 May 2016 13:44:03 +0000 Source: vtk-dicom Binary: libvtk-dicom-dev libvtkdicom0.7 vtk-dicom-tools python-vtk-dicom Architecture: source Version: 0.7.8-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Gert Wollny Description: libvtk-dicom-dev - DICOM for VTK - dev libvtkdicom0.7 - DICOM for VTK - lib python-vtk-dicom - DICOM for VTK - Python vtk-dicom-tools - DICOM for VTK - tools Changes: vtk-dicom (0.7.8-1) unstable; urgency=medium . * Imported Upstream version 0.7.8 * d/p/01 update patch * d/control: Add -Wl,-z,now * d/control: correct git URL to secure version Checksums-Sha1: 3f7a36c81a251ffa6c9dde0b999fba033d0af2ca 1953 vtk-dicom_0.7.8-1.dsc 43e6b6414da0f4df6adf006fee4730d5bbb0fae5 1008309 vtk-dicom_0.7.8.orig.tar.gz e7c27324b2b21ec177980b0694fe4ca502563663 5396 vtk-dicom_0.7.8-1.debian.tar.xz Checksums-Sha256: ce1f461c97430921b48568997480c998463d655d765d41d44cb25c2daf4adb17 1953 vtk-dicom_0.7.8-1.dsc 05dcc08d1e0b8ce229f5556fea620327ef747afbeffb28939dd982807c030e3b 1008309 vtk-dicom_0.7.8.orig.tar.gz dce89b392d1fc14dc902c88ab263928d725970a3de1baf2a59cbfbd7b88aa7f5 5396 vtk-dicom_0.7.8-1.debian.tar.xz Files: 131fb788d05e924e5cb51fd78420f3f8 1953 graphics optional vtk-dicom_0.7.8-1.dsc 74e725bbf47f6ebfa0a15b2fa62a057b 1008309 graphics optional vtk-dicom_0.7.8.orig.tar.gz eb05957a7a8ce9e89751b1f2d719e861 5396 graphics optional vtk-dicom_0.7.8-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBCAAGBQJXTZVIAAoJEPgeNoubJquY+PcH/0DYSrygaxKE7ky5e4DkNoRO tIwgNvcZclc1NtAH8JrWiaIZ4Eio0sxF9YOnUh+oDXLy8mCJQnuKqv7YIR2Uqdl4 OdBYXHgofLy3C7XMEj7Dusyq1e4z2reBQA4n5Qc+x8ltOlKqiy3dmzfrccNCY8fp VeQqyLALuhziyk67lfPyrC8pakCXHRL0IIeASp7ZDkoTapM9TAoBiX7at1VGwkjO UQm3KceXGFQlhw2ImDlqN4iyBXu86/oQTcq5AjmWa29a5C7EEK/SaY/09YUv352q OmYGwrvGWClCIoNT1HqxhvV49BDWAv+xBEYit7/RWE+CIuJe+ZZbZPd2ZtsvuFg= =NLoY -----END PGP SIGNATURE----- Thank you for your contribution to Debian. From noreply at release.debian.org Tue May 31 16:39:09 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 31 May 2016 16:39:09 +0000 Subject: [Debian-med-packaging] libmialm 1.0.9-1 MIGRATED to testing Message-ID: FYI: The status of the libmialm source package in Debian's testing distribution has changed. Previous version: 1.0.8-3 Current version: 1.0.9-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 31 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 31 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] stacks 1.40-1 MIGRATED to testing Message-ID: FYI: The status of the stacks source package in Debian's testing distribution has changed. Previous version: 1.37-1 Current version: 1.40-1 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information. From noreply at release.debian.org Tue May 31 16:39:10 2016 From: noreply at release.debian.org (Debian testing watch) Date: Tue, 31 May 2016 16:39:10 +0000 Subject: [Debian-med-packaging] toppred 1.10-3 MIGRATED to testing Message-ID: FYI: The status of the toppred source package in Debian's testing distribution has changed. Previous version: 1.10-2 Current version: 1.10-3 -- This email is automatically generated once a day. As the installation of new packages into testing happens multiple times a day you will receive later changes on the next day. See https://release.debian.org/testing-watch/ for more information.