[med-svn] [SCM] samtools branch, meta, updated. meta/0.1.18-1-4-gb8d566c
Charles Plessy
plessy at debian.org
Sat Mar 30 08:54:49 UTC 2013
The following commit has been merged in the meta branch:
commit d8ba64137ad2aa7cac5234499cc7c3d1cafb7264
Author: Charles Plessy <plessy at debian.org>
Date: Sat Mar 30 17:46:53 2013 +0900
Build logs for 0.1.18-3.
diff --git a/armel.log b/armel.log
index 76ddbc1..9e0130a 100644
--- a/armel.log
+++ b/armel.log
@@ -1,60 +1,61 @@
-From buildd at alain.debian.org Fri Jul 27 15:14:52 2012
-Return-path: <buildd at alain.debian.org>
+From buildd at antheil.debian.org Fri Jul 27 15:49:07 2012
+Return-path: <buildd at antheil.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
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+ CN=antheil.debian.org, EMAIL=hostmaster at antheil.debian.org (verified)
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-Date: Fri, 27 Jul 2012 15:14:49 +0000
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-From: buildd on alain <buildd at alain.debian.org>
-To: buildd-porters at alain.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.18-2 on armel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at antheil.debian.org>)
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+Date: Fri, 27 Jul 2012 15:49:05 +0000
+Message-Id: <E1Summn-0000j0-9W at antheil.debian.org>
+From: buildd on antheil <buildd at antheil.debian.org>
+To: buildd-porters at antheil.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.18-3 on armel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alain.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on antheil.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (armel) 27 Jul 2012 15:05 ║
+║ samtools 0.1.18-3 (armel) 27 Jul 2012 15:39 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: armel
Get:1 http://incoming.debian.org unstable InRelease [249 kB]
Get:2 http://ftp.uk.debian.org unstable InRelease [249 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6315 kB]
Ign http://incoming.debian.org InRelease
-Get:3 http://incoming.debian.org Release.gpg [836 B]
-Get:4 http://incoming.debian.org Release [1601 B]
-Get:5 http://ftp.uk.debian.org unstable/main Sources [6315 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:7 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
-Get:8 http://ftp.uk.debian.org unstable/non-free Sources [98.1 kB]
-Get:9 http://ftp.uk.debian.org unstable/main armel Packages [5978 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:12 http://incoming.debian.org unstable/main armel Packages [5978 kB]
-Get:13 http://ftp.uk.debian.org unstable/contrib armel Packages [37.6 kB]
-Get:14 http://incoming.debian.org unstable/contrib armel Packages [37.6 kB]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 25.6 MB in 1min 39s (256 kB/s)
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [98.1 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armel Packages [5978 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
+Get:11 http://incoming.debian.org unstable/main armel Packages [5978 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib armel Packages [37.6 kB]
+Get:13 http://incoming.debian.org unstable/contrib armel Packages [37.6 kB]
+Get:14 http://incoming.debian.org Release [1601 B]
+Get:15 http://incoming.debian.org Sources [14.5 kB]
+Get:16 http://incoming.debian.org Packages [117 kB]
+Fetched 25.6 MB in 1min 41s (252 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,10 +77,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (335 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (298 kB/s)
Download complete and in download only mode
Check arch
@@ -200,7 +201,7 @@ Get:24 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.9-
Get:25 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
Get:26 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.7.dfsg-13 [211 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.4 MB in 5s (1762 kB/s)
+Fetched 10.4 MB in 5s (1798 kB/s)
Selecting previously unselected package libpipeline1:armel.
(Reading database ... 10640 files and directories currently installed.)
Unpacking libpipeline1:armel (from .../libpipeline1_1.2.1-1_armel.deb) ...
@@ -303,12 +304,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -321,7 +322,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
@@ -329,25 +330,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -367,10 +368,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -383,12 +384,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -423,8 +424,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -439,10 +440,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -463,24 +464,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -502,14 +503,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -517,14 +518,14 @@ Line 2, sequence length 35 vs 8960 from CIGAR
Parse error at line 2: CIGAR and sequence length are inconsistent
make[1]: *** [ex1.bam] Aborted
make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1514
+Build finished at 20120727-1549
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-c8a6ce86-8609-468e-8b01-5d381ee6ae5e/build/buildd-samtools_0.1.18-2-armel-5narhz
+Purging /var/lib/schroot/mount/sid-armel-sbuild-6b9b83f9-bc18-46e0-945b-39cd8ecff13a/build/buildd-samtools_0.1.18-3-armel-zkuM87
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -536,15 +537,15 @@ Build-Space: 6464
Build-Time: 318
Distribution: sid
Fail-Stage: build
-Install-Time: 101
-Job: samtools_0.1.18-2
+Install-Time: 103
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 554
-Source-Version: 0.1.18-2
+Package-Time: 560
+Source-Version: 0.1.18-3
Space: 6464
Status: attempted
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1514
-Build needed 00:09:14, 6464k disc space
+Finished at 20120727-1549
+Build needed 00:09:20, 6464k disc space
diff --git a/armhf.log b/armhf.log
index 14ec90c..15a59bd 100644
--- a/armhf.log
+++ b/armhf.log
@@ -1,62 +1,60 @@
-From buildd at hildegard.debian.org Fri Jul 27 15:14:14 2012
-Return-path: <buildd at hildegard.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at henze.debian.org Fri Jul 27 15:47:24 2012
+Return-path: <buildd at henze.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at hildegard.debian.org>)
- id 1SumF3-0003Wp-VA
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:14:14 +0000
-Received: from hildegard.ynic.york.ac.uk ([144.32.168.74]
- helo=hildegard.debian.org)
+ (Exim 4.72) (envelope-from <buildd at henze.debian.org>)
+ id 1Suml9-0006EV-Nl
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:47:24 +0000
+Received: from [217.140.96.70] (helo=henze.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=hildegard.debian.org,
- EMAIL=hostmaster at hildegard.debian.org (verified)
- by merikanto.debian.org with esmtps
- (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.72)
- (envelope-from <buildd at hildegard.debian.org>) id 1SumF2-0004AS-Rf
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:14:13 +0000
-Received: from buildd by hildegard.debian.org with local (Exim 4.80)
- (envelope-from <buildd at hildegard.debian.org>)
- id 1SumEz-00005l-GY; Fri, 27 Jul 2012 15:14:09 +0000
-From: buildd on hildegard <buildd at hildegard.debian.org>
-To: logs at buildd.debian.org,buildd-porters at hildegard.debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on armhf (dist=sid)
+ CN=henze.debian.org, EMAIL=hostmaster at henze.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
+ (Exim 4.72) (envelope-from <buildd at henze.debian.org>)
+ id 1Suml8-000208-L2
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:47:22 +0000
+Received: from buildd by henze.debian.org with local (Exim 4.80)
+ (envelope-from <buildd at henze.debian.org>)
+ id 1Suml1-0002dV-07; Fri, 27 Jul 2012 15:47:15 +0000
+From: buildd on henze <buildd at henze.debian.org>
+To: logs at buildd.debian.org,buildd-porters at henze.debian.org
+Subject: Log for successful build of samtools_0.1.18-3 on armhf (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1SumEz-00005l-GY at hildegard.debian.org>
-Date: Fri, 27 Jul 2012 15:14:09 +0000
+Message-Id: <E1Suml1-0002dV-07 at henze.debian.org>
+Date: Fri, 27 Jul 2012 15:47:15 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hildegard.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on henze.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (armhf) 27 Jul 2012 15:04 ║
+║ samtools 0.1.18-3 (armhf) 27 Jul 2012 15:38 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: armhf
-Get:1 http://ftp.uk.debian.org unstable InRelease [249 kB]
-Get:2 http://incoming.debian.org unstable InRelease [249 kB]
+Get:1 http://incoming.debian.org unstable InRelease [249 kB]
+Get:2 http://ftp.uk.debian.org unstable InRelease [249 kB]
Get:3 http://ftp.uk.debian.org unstable/main Sources [6315 kB]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [98.1 kB]
-Get:8 http://ftp.uk.debian.org unstable/main armhf Packages [5950 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib armhf Packages [36.1 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:12 http://incoming.debian.org unstable/main armhf Packages [5950 kB]
-Get:13 http://incoming.debian.org unstable/contrib armhf Packages [36.1 kB]
+Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:5 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
+Get:6 http://ftp.uk.debian.org unstable/non-free Sources [98.1 kB]
+Get:7 http://ftp.uk.debian.org unstable/main armhf Packages [5950 kB]
+Get:8 http://ftp.uk.debian.org unstable/contrib armhf Packages [36.1 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
+Get:11 http://incoming.debian.org unstable/main armhf Packages [5950 kB]
+Get:12 http://incoming.debian.org unstable/contrib armhf Packages [36.1 kB]
+Get:13 http://incoming.debian.org Release.gpg [836 B]
Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 25.5 MB in 1min 29s (284 kB/s)
+Get:15 http://incoming.debian.org Sources [14.5 kB]
+Get:16 http://incoming.debian.org Packages [117 kB]
+Fetched 25.5 MB in 1min 28s (289 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,10 +76,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 2s (185 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (326 kB/s)
Download complete and in download only mode
Check arch
@@ -101,12 +99,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 43 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 43 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -115,11 +113,11 @@ Checking correctness of dependencies...
Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-33)
-gcc: already installed (4:4.6.3-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-6 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-34)
+gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.4.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 9.20120608
cdbs: missing
@@ -134,70 +132,53 @@ Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libncurses5 libpcre3 libpipeline1 libtinfo-dev libtinfo5
- libunistring0 libxml2 man-db ncurses-bin po-debconf
+ libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-The following packages will be upgraded:
- libncurses5 libtinfo5 ncurses-bin
-3 upgraded, 26 newly installed, 0 to remove and 40 not upgraded.
-Need to get 10.8 MB of archives.
+0 upgraded, 26 newly installed, 0 to remove and 23 not upgraded.
+Need to get 10.1 MB of archives.
After this operation, 25.3 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main ncurses-bin armhf 5.9-10 [329 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libtinfo5 armhf 5.9-10 [260 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libncurses5 armhf 5.9-10 [87.9 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.1-1 [33.2 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armhf 0.18.1.1-9 [26.4 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.11-2 [199 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 1:8.30-5 [240 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.8.0+dfsg1-5 [785 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.32.3-1 [1896 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.5-1 [134 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armhf 0.18.1.1-9 [122 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.3 [204 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-9 [1031 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.2-1 [1014 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.11-2 [51.5 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-9 [130 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-9 [1828 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main diffstat armhf 1.55-3 [27.5 kB]
-Get:26 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armhf 5.9-10 [83.9 kB]
-Get:27 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armhf 5.9-10 [194 kB]
-Get:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:29 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.7.dfsg-13 [209 kB]
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.1-1 [33.2 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armhf 0.18.1.1-9 [26.4 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.11-2 [199 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 1:8.30-5 [240 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.8.0+dfsg1-5 [785 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.32.3-1 [1896 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.5-1 [134 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armhf 0.18.1.1-9 [122 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.3 [204 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-9 [1031 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.2-1 [1014 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.11-2 [51.5 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-9 [130 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-9 [1828 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main diffstat armhf 1.55-3 [27.5 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armhf 5.9-10 [83.9 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armhf 5.9-10 [194 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.7.dfsg-13 [209 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.8 MB in 4s (2664 kB/s)
-(Reading database ... 10757 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.9-9 (using .../ncurses-bin_5.9-10_armhf.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-10) ...
-(Reading database ... 10757 files and directories currently installed.)
-Preparing to replace libtinfo5:armhf 5.9-9 (using .../libtinfo5_5.9-10_armhf.deb) ...
-Unpacking replacement libtinfo5:armhf ...
-Setting up libtinfo5:armhf (5.9-10) ...
-(Reading database ... 10757 files and directories currently installed.)
-Preparing to replace libncurses5:armhf 5.9-9 (using .../libncurses5_5.9-10_armhf.deb) ...
-Unpacking replacement libncurses5:armhf ...
-Setting up libncurses5:armhf (5.9-10) ...
+Fetched 10.1 MB in 4s (2033 kB/s)
Selecting previously unselected package libpipeline1:armhf.
-(Reading database ... 10757 files and directories currently installed.)
+(Reading database ... 10766 files and directories currently installed.)
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-9_armhf.deb) ...
@@ -261,8 +242,8 @@ Setting up libcroco3:armhf (0.6.5-1) ...
Setting up libunistring0:armhf (0.9.3-5+b1) ...
Setting up libgettextpo0:armhf (0.18.1.1-9) ...
Setting up bsdmainutils (9.0.3) ...
-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.
+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 groff-base (1.21-9) ...
Setting up man-db (2.6.2-1) ...
Building database of manual pages ...
@@ -283,11 +264,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 3.2.0-3-mx5 armhf (armv7l)
-Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-7 gcc-4.6_4.6.3-7 libc6-dev_2.13-33 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 linux-libc-dev_3.2.21-1
-Package versions: apt_0.9.6 base-files_6.11 base-passwd_3.5.26 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-6 cpp-4.6_4.6.3-7 dash_0.5.7-3 debconf_1.5.44 debconf-i18n_1.5.44 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-6 g++-4.6_4.6.3-7 gcc_4:4.6.3-6 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7-base_4.7.1-1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.6 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.3 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-1 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.4-3 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-33 ncurses-base_5.9-9 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.3p2-1.1 sysv-rc_2.88dsf-27 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Kernel: Linux 3.2.0-2-mx5 armhf (armv7l)
+Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
+Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-3 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-3 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -298,12 +279,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -316,7 +297,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
@@ -324,25 +305,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -362,10 +343,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -378,12 +359,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -418,8 +399,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -434,10 +415,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -458,24 +439,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -497,14 +478,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -530,7 +511,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -565,8 +546,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -592,7 +573,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -607,64 +588,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_armhf.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_armhf.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_armhf.deb'.
- dpkg-genchanges -B -marmhf Build Daemon (hildegard) <buildd_armhf-hildegard at buildd.debian.org> >../samtools_0.1.18-2_armhf.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_armhf.deb'.
+ dpkg-genchanges -B -marmhf Build Daemon (henze) <buildd_armhf-henze at buildd.debian.org> >../samtools_0.1.18-3_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1514
+Build finished at 20120727-1547
-samtools_0.1.18-2_armhf.changes:
+samtools_0.1.18-3_armhf.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: armhf
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
-Maintainer: armhf Build Daemon (hildegard) <buildd_armhf-hildegard at buildd.debian.org>
+Maintainer: armhf Build Daemon (henze) <buildd_armhf-henze at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- 874726fa4892b7f3c0bb1375900383b05f85ff9a 507940 samtools_0.1.18-2_armhf.deb
- 6a27f0b89422affff54a3216792a2dbae4fd62be 144508 libbam-dev_0.1.18-2_armhf.deb
+ 98301b0be383c90d436c8fe8c35ca44f5b598918 508386 samtools_0.1.18-3_armhf.deb
+ 1ccd5f495a33014e0be19b668338c46bd458bac4 144934 libbam-dev_0.1.18-3_armhf.deb
Checksums-Sha256:
- 8815c9c6d4112812d1afcc175aa5a71d246aacc20c3d6cbf4ddf47852eb76a20 507940 samtools_0.1.18-2_armhf.deb
- 74e4b80a0e6ff565b98fcdf6e3df735f8fbc9e0781340ed5339a3def53e45f03 144508 libbam-dev_0.1.18-2_armhf.deb
+ b6163dfe429a6fe61c3be508f7314e8cf69da69c047fc3c4ac1ebfa2fbc4dc8a 508386 samtools_0.1.18-3_armhf.deb
+ cbdcfe98ebd9891164efbfffaa156f18e9554f8939c0b7680bb568bb95fd679e 144934 libbam-dev_0.1.18-3_armhf.deb
Files:
- 99a0f91f8a750922081f03c4f41ea1e0 507940 science optional samtools_0.1.18-2_armhf.deb
- 994c236405596dcd86ddc86b16cba98b 144508 libdevel optional libbam-dev_0.1.18-2_armhf.deb
+ 047b370d947bd6141610ebebe7582b48 508386 science optional samtools_0.1.18-3_armhf.deb
+ b940a08a4f0aaaca8428bc51cacd420b 144934 libdevel optional libbam-dev_0.1.18-3_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_armhf.deb
+samtools_0.1.18-3_armhf.deb
───────────────────────────
new debian package, version 2.0.
- size 507940 bytes: control archive=1776 bytes.
+ size 508386 bytes: control archive=1778 bytes.
817 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 828
@@ -680,68 +662,68 @@ samtools_0.1.18-2_armhf.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:13 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:13 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/samtools/
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5778 2012-07-27 15:13 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 1966 2012-07-27 15:13 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2012-07-27 15:13 ./usr/share/doc/samtools/examples/ex1.bam.gz
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/lib/samtools/
+-rwxr-xr-x root/root 12900 2012-07-27 15:46 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6484 2012-07-27 15:46 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 5892 2012-07-27 15:46 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8480 2012-07-27 15:46 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 5892 2012-07-27 15:46 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/bin/
+-rwxr-xr-x root/root 17620 2012-07-27 15:46 ./usr/bin/razip
+-rwxr-xr-x root/root 248724 2012-07-27 15:46 ./usr/bin/samtools
+-rwxr-xr-x root/root 88388 2012-07-27 15:46 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2012-07-27 15:46 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 1966 2012-07-27 15:46 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/bin/
--rwxr-xr-x root/root 248724 2012-07-27 15:13 ./usr/bin/samtools
--rwxr-xr-x root/root 17620 2012-07-27 15:13 ./usr/bin/razip
--rwxr-xr-x root/root 88388 2012-07-27 15:13 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/samtools/
--rwxr-xr-x root/root 5892 2012-07-27 15:13 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8480 2012-07-27 15:13 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 12900 2012-07-27 15:13 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6484 2012-07-27 15:13 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 5892 2012-07-27 15:13 ./usr/lib/samtools/maq2sam-long
-lrwxrwxrwx root/root 0 2012-07-27 15:13 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-2_armhf.deb
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:46 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:46 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/samtools/
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 5778 2012-07-27 15:46 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+lrwxrwxrwx root/root 0 2012-07-27 15:46 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-3_armhf.deb
─────────────────────────────
new debian package, version 2.0.
- size 144508 bytes: control archive=927 bytes.
+ size 144934 bytes: control archive=925 bytes.
674 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 335
@@ -755,25 +737,25 @@ libbam-dev_0.1.18-2_armhf.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/include/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/include/samtools/
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/
--rw-r--r-- root/root 200906 2012-07-27 15:13 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/lib/
+-rw-r--r-- root/root 200906 2012-07-27 15:46 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -787,7 +769,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-bc82cb11-d080-4070-95cb-9743779d586a/build/buildd-samtools_0.1.18-2-armhf-hZG9OI
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-b65709ff-8ea2-4ff6-a981-4312e96ea285/build/buildd-samtools_0.1.18-3-armhf-XcQV5o
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -795,19 +777,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armhf
-Build-Space: 9472
-Build-Time: 333
+Build-Space: 9480
+Build-Time: 327
Distribution: sid
-Install-Time: 117
-Job: samtools_0.1.18-2
+Install-Time: 69
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 575
-Source-Version: 0.1.18-2
-Space: 9472
+Package-Time: 515
+Source-Version: 0.1.18-3
+Space: 9480
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1514
-Build needed 00:09:35, 9472k disc space
-Signature with key '0E1957C5' requested:
+Finished at 20120727-1547
+Build needed 00:08:35, 9480k disc space
+Signature with key '3CE79B5E' requested:
diff --git a/hurd-i386.log b/hurd-i386.log
index 08976e4..2944255 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,139 +1,64 @@
-From buildd at mozart.debian.net Tue Sep 06 09:41:15 2011
-Return-path: <buildd at mozart.debian.net>
-Received: from callisto.debian.net ([80.87.129.151])
+From buildd at ironforge.sceen.net Fri Jul 27 16:25:30 2012
+Return-path: <buildd at ironforge.sceen.net>
+Received: from ironforge.sceen.net ([46.105.42.111])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
- id 1R0s9a-0003VY-4e
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:41:15 +0000
-Received: from mozart.debian.net ([10.1.0.1])
- by callisto.debian.net with esmtp (Exim 4.69)
- (envelope-from <buildd at mozart.debian.net>)
- id 1R0s9R-00073Q-VQ; Tue, 06 Sep 2011 10:41:06 +0100
-Received: from buildd by mozart.debian.net with local (Exim 4.76)
- (envelope-from <buildd at mozart.debian.net>)
- id 1R0s9R-0001Ag-24; Tue, 06 Sep 2011 09:41:05 +0000
-MIME-Version: 1.0
+ (Exim 4.72) (envelope-from <buildd at ironforge.sceen.net>)
+ id 1SunM0-0003gm-Pm
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 16:25:29 +0000
+Received: from buildd by ironforge.sceen.net with local (Exim 4.77)
+ (envelope-from <buildd at ironforge.sceen.net>)
+ id 1SunLy-0000lN-2u; Fri, 27 Jul 2012 18:25:26 +0200
Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.78; A2.07; B3.08; Q3.08)
-Date: Tue, 6 Sep 2011 09:41:04 +0000
-From: Build Daemon <buildd at mozart.debian.net>
-To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
- logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on hurd-i386 (dist=sid)
-Message-Id: <E1R0s9R-0001Ag-24 at mozart.debian.net>
+MIME-Version: 1.0
+X-Mailer: MIME::Lite 3.027 (F2.82; B3.13; Q3.13)
+Date: Fri, 27 Jul 2012 18:25:26 +0200
+From: Build Daemon <buildd at ironforge.sceen.net>
+To: samuel.thibault at ens-lyon.org,mbanck at gmx.net,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.18-3 on hurd-i386 (dist=sid)
+Message-Id: <E1SunLy-0000lN-2u at ironforge.sceen.net>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on mozart.debian.net
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ironforge.sceen.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (hurd-i386) 06 sept. 2011 09:33 ║
+║ samtools 0.1.18-3 (hurd-i386) 27 Jul 2012 18:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
-Distribution: sid
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: hurd-i386
-
-I: NOTICE: Log filtering will replace 'build/samtools-jFRcSJ/samtools-0.1.18' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-jFRcSJ' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'home/buildd/build/chroot-sid' with '«CHROOT»'
-W: Stripped single quote from command for security:
- use strict;
- use warnings;
- use POSIX;
- use FileHandle;
-
- my $lockfile="/var/lock/sbuild";
- my $try = 0;
-
- repeat:
- if (!sysopen( F, $lockfile, O_WRONLY|O_CREAT|O_TRUNC|O_EXCL, 0644 )){
- if ($! == EEXIST) {
- # lock file exists, wait
- goto repeat if !open( F, "<$lockfile" );
- my $line = <F>;
- my ($job, $pid, $user);
- close( F );
- if ($line !~ /^(\S+)\s+(\S+)\s+(\S+)/) {
- print STDERR "Bad lock file contents ($lockfile) -- still trying\n";
- } else {
- ($job, $pid, $user) = ($1, $2, $3);
- if (kill( 0, $pid ) == 0 && $! == ESRCH) {
- # process doesn't exist anymore, remove stale lock
- print STDERR "Removing stale lock file $lockfile ".
- "(job $job, pid $pid, user $user)\n";
- if (!unlink($lockfile)) {
- if ($! != ENOENT) {
- print STDERR "Cannot remove chroot lock file $lockfile: $!\n";
- exit 1;
- }
- }
- }
- }
- ++$try;
- if ($try > 120) {
- print STDERR "Lockfile $lockfile still present after " .
- 120 * 5 . " seconds -- giving up\n";
- exit 1;
- }
- print STDERR "Another sbuild process (job $job, pid $pid by user $user) is currently using the build chroot; waiting...\n"
- if $try == 1;
- sleep 5;
- goto repeat;
- } else {
- print STDERR "Can't create lock file $lockfile: $!\n";
- exit 1;
- }
- }
-
- F->print("samtools_0.1.18-1 2503 buildd\n");
- F->close();
-
- exit 0;
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Update chroot │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Hit http://ftp.uk.debian.org sid InRelease
-Hit http://ftp.fr.debian.org sid InRelease
+Ign file: ./ InRelease
+Ign file: ./ Release.gpg
+Ign file: ./ Release
+Ign file: ./ Translation-en
+Get:1 http://ftp.fr.debian.org sid InRelease [249 kB]
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
-Ign http://ftp.debian-ports.org unreleased InRelease
-Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex
-Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
-Get:1 http://ftp.uk.debian.org sid/main TranslationIndex [2045 B]
-Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
-Hit http://ftp.fr.debian.org sid/main Sources/DiffIndex
-Hit http://ftp.debian-ports.org unreleased Release.gpg
-Get:2 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
+Hit http://incoming.debian.org sid/main hurd-i386 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib hurd-i386 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
+Hit http://incoming.debian.org sid/main Translation-en/DiffIndex
+Get:2 http://ftp.fr.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:3 http://incoming.debian.org Release.gpg [836 B]
Hit http://ftp.fr.debian.org sid/contrib Sources/DiffIndex
Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.debian-ports.org unreleased Release
-Get:3 http://incoming.debian.org Release [1604 B]
+Get:4 http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex [7876 B]
Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.fr.debian.org sid/non-free hurd-i386 Packages/DiffIndex
-Ign http://ftp.fr.debian.org sid/contrib TranslationIndex
-Get:4 http://ftp.fr.debian.org sid/main TranslationIndex [2045 B]
-Ign http://ftp.fr.debian.org sid/non-free TranslationIndex
-Get:5 http://incoming.debian.org Sources [33.2 kB]
-Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Ign http://ftp.fr.debian.org sid/contrib Translation-en
-Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
-Ign http://ftp.fr.debian.org sid/non-free Translation-en
-Ign http://ftp.uk.debian.org sid/contrib Translation-en
-Ign http://ftp.uk.debian.org sid/non-free Translation-en
-Get:6 http://incoming.debian.org Packages [352 kB]
-Ign http://ftp.debian-ports.org unreleased/main Translation-en
+Hit http://ftp.fr.debian.org sid/contrib Translation-en/DiffIndex
+Get:5 http://ftp.fr.debian.org sid/main Translation-en [4032 kB]
+Get:6 http://ftp.fr.debian.org sid/main 2012-07-27-1414.10.pdiff [1291 B]
+Get:7 http://incoming.debian.org Release [1601 B]
+Get:8 http://ftp.fr.debian.org sid/main 2012-07-27-1414.10.pdiff [1291 B]
+Get:9 http://ftp.fr.debian.org sid/main hurd-i386 2012-07-27-1414.10.pdiff [2019 B]
+Get:10 http://incoming.debian.org Sources [14.9 kB]
+Get:11 http://incoming.debian.org Packages [121 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 391 kB in 50s (7751 B/s)
+Get:12 http://ftp.fr.debian.org sid/main hurd-i386 2012-07-27-1414.10.pdiff [2019 B]
+Fetched 4439 kB in 28s (154 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -154,110 +79,204 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 2s (145 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (215 kB/s)
Download complete and in download only mode
Check arch
──────────
-Merged Build-Depends: build-essential, fakeroot
-Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-JKVjjF/apt_archive/sbuild-build-depends-core-dummy.deb'.
-gpg: WARNING: using insecure memory!
-gpg: please see http://www.gnupg.org/faq.html for more information
-OK
-Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (apt-based resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Installing build dependencies
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5+b1)
+fakeroot: already installed (1.18.4-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+ adduser groff-base libboost-iostreams1.46.1 libboost-iostreams1.49.0
+ libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
+ man-db
Use 'apt-get autoremove' to remove them.
-The following NEW packages will be installed:
- sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 30 not upgraded.
-Need to get 0 B/712 B of archives.
-After this operation, 0 B of additional disk space will be used.
-WARNING: The following packages cannot be authenticated!
- sbuild-build-depends-core-dummy
-Authentication warning overridden.
-Selecting previously deselected package sbuild-build-depends-core-dummy.
-(Reading database ... 13753 files and directories currently installed.)
-Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
-Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-c_dlCz/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
-gpg: WARNING: using insecure memory!
-gpg: please see http://www.gnupg.org/faq.html for more information
-OK
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+Removing negative dependencies:
Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ adduser groff-base libboost-iostreams1.46.1 libboost-iostreams1.49.0
+ libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
+ man-db
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (apt-based resolver) │
+│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Installing build dependencies
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
+Checking for already installed dependencies...
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-3)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3+b1)
+debianutils: already installed (4.3.2)
+diffutils: already installed (1:3.2-6+b1)
+dpkg: already installed (1.16.7)
+e2fsprogs: already installed (1.42.4-3)
+findutils: already installed (4.4.2-4+b1)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11+b1)
+hurd: already installed (20120605-2)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-12)
+sed: already installed (4.2.1-10)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
+tar: already installed (1.26-4+b1)
+bsdutils: already installed (1:2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc0.3-dev: already installed (2.13-34)
+gcc: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2+b1)
+dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+hurd-dev: already installed (20120605-2)
+debhelper: missing
+Using default version 9.20120608
+cdbs: missing
+quilt: missing
+libncurses5-dev: missing
+zlib1g-dev: missing
+Checking for dependency conflicts...
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+ adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
+ libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- cdbs diffstat libncurses5-dev quilt zlib1g-dev
+ diffstat file gettext gettext-base html2text intltool-debian libasprintf0c2
+ libcroco3 libexpat1 libffi5 libgettextpo0 libglib2.0-0 libmagic1
+ libtinfo-dev libunistring0 libxml2 po-debconf
Suggested packages:
- devscripts ncurses-doc procmail graphviz
+ devscripts dh-make gettext-doc ncurses-doc libmail-box-perl procmail
+ graphviz default-mta mail-transport-agent
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs diffstat libncurses5-dev quilt sbuild-build-depends-samtools-dummy
- zlib1g-dev
-0 upgraded, 6 newly installed, 0 to remove and 30 not upgraded.
-Need to get 0 B/1111 kB of archives.
-After this operation, 3113 kB of additional disk space will be used.
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libtinfo-dev libunistring0 libxml2 po-debconf
+ quilt zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 25 not upgraded.
+Need to get 0 B/8216 kB of archives.
+After this operation, 22.5 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- cdbs diffstat libncurses5-dev quilt zlib1g-dev
- sbuild-build-depends-samtools-dummy
+ libasprintf0c2 libmagic1 libxml2 libffi5 libglib2.0-0 libcroco3 libexpat1
+ libunistring0 libgettextpo0 file gettext-base cdbs html2text gettext
+ intltool-debian po-debconf debhelper diffstat libtinfo-dev libncurses5-dev
+ quilt zlib1g-dev
Authentication warning overridden.
-Selecting previously deselected package cdbs.
-(Reading database ... 13753 files and directories currently installed.)
-Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
-Selecting previously deselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_hurd-i386.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_hurd-i386.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
-Selecting previously deselected package sbuild-build-depends-samtools-dummy.
-Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+Selecting previously unselected package libasprintf0c2:hurd-i386.
+(Reading database ... 14550 files and directories currently installed.)
+Unpacking libasprintf0c2:hurd-i386 (from .../libasprintf0c2_0.18.1.1-9_hurd-i386.deb) ...
+Selecting previously unselected package libmagic1:hurd-i386.
+Unpacking libmagic1:hurd-i386 (from .../libmagic1_5.11-2_hurd-i386.deb) ...
+Selecting previously unselected package libxml2:hurd-i386.
+Unpacking libxml2:hurd-i386 (from .../libxml2_2.8.0+dfsg1-5_hurd-i386.deb) ...
+Selecting previously unselected package libffi5:hurd-i386.
+Unpacking libffi5:hurd-i386 (from .../libffi5_3.0.10-3+b1_hurd-i386.deb) ...
+Selecting previously unselected package libglib2.0-0:hurd-i386.
+Unpacking libglib2.0-0:hurd-i386 (from .../libglib2.0-0_2.32.3-1+b2_hurd-i386.deb) ...
+Selecting previously unselected package libcroco3:hurd-i386.
+Unpacking libcroco3:hurd-i386 (from .../libcroco3_0.6.5-1+b1_hurd-i386.deb) ...
+Selecting previously unselected package libexpat1:hurd-i386.
+Unpacking libexpat1:hurd-i386 (from .../libexpat1_2.1.0-1+b1_hurd-i386.deb) ...
+Selecting previously unselected package libunistring0:hurd-i386.
+Unpacking libunistring0:hurd-i386 (from .../libunistring0_0.9.3-5+b1_hurd-i386.deb) ...
+Selecting previously unselected package libgettextpo0:hurd-i386.
+Unpacking libgettextpo0:hurd-i386 (from .../libgettextpo0_0.18.1.1-9_hurd-i386.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../file_5.11-2_hurd-i386.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_hurd-i386.deb) ...
+Selecting previously unselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15+b2_hurd-i386.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_hurd-i386.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_hurd-i386.deb) ...
+Selecting previously unselected package libtinfo-dev:hurd-i386.
+Unpacking libtinfo-dev:hurd-i386 (from .../libtinfo-dev_5.9-10_hurd-i386.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_hurd-i386.deb) ...
+Selecting previously unselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Selecting previously unselected package zlib1g-dev:hurd-i386.
+Unpacking zlib1g-dev:hurd-i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_hurd-i386.deb) ...
Processing triggers for man-db ...
-Setting up cdbs (0.4.96) ...
-Setting up diffstat (1.54-1) ...
-Setting up libncurses5-dev (5.9-1) ...
-Setting up quilt (0.48-7) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build environment │
-└──────────────────────────────────────────────────────────────────────────────┘
-
+Setting up libasprintf0c2:hurd-i386 (0.18.1.1-9) ...
+Setting up libmagic1:hurd-i386 (5.11-2) ...
+Setting up libxml2:hurd-i386 (2.8.0+dfsg1-5) ...
+Setting up libffi5:hurd-i386 (3.0.10-3+b1) ...
+Setting up libglib2.0-0:hurd-i386 (2.32.3-1+b2) ...
+No schema files found: doing nothing.
+Setting up libcroco3:hurd-i386 (0.6.5-1+b1) ...
+Setting up libexpat1:hurd-i386 (2.1.0-1+b1) ...
+Setting up libunistring0:hurd-i386 (0.9.3-5+b1) ...
+Setting up libgettextpo0:hurd-i386 (0.18.1.1-9) ...
+Setting up file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up cdbs (0.4.116) ...
+Setting up html2text (1.3.2a-15+b2) ...
+Setting up gettext (0.18.1.1-9) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:hurd-i386 (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:hurd-i386 (1:1.2.7.dfsg-13) ...
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
+ libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.0.3 g++-4.5_4.5.3-8 g++-4.6_4.6.1-7+hurd.1 gcc-4.4_4.4.6-7 gcc-4.5_4.5.3-8 gcc-4.6_4.6.1-7+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 hurd-dev_20110519-3 libc0.3-dev_2.13-18 libstdc++6_4.6.1-7+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-7+hurd.1
-Package versions: adduser_3.113 apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.4_4.4.6-7 cpp-4.5_4.5.3-8 cpp-4.6_4.6.1-7+hurd.1 cron_3.0pl1-119 dash_0.5.5.1-7.4 debconf_1.5.41 debfoster_2.6-2 debhelper_8.9.4 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 deborphan_1.7.28.5 dialog_1.1-20110707-1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.15.1-1 file_5.03-5+b1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-2 g++-4.5_4.5.3-8 g++-4.6_4.6.1-7+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-2 gcc-4.4_4.4.6-7 gcc-4.4-base_4.4.6-7 gcc-4.5_4.5.3-8 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-7+hurd.1 gcc-4.6-base_4.6.1-7+hurd.1 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-2 gfortran-4.6_4.6.1-7+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-7 gpgv_1.4.11-3 grep_2.9-1 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-6 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc0.3_2.13-18 libc0.3-dev_2.13-18 libc0.3-xen_2.13-18 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-3 libept1_1.0.5 libexpat1_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgcc1_1:4.6.1-7+hurd.1 libgdbm3_1.8.3-10 libgfortran3_4.6.1-7+hurd.1 libglib2.0-0_2.28.6-1 libglib2.0-data_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-7+hurd.1 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.03-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libobjc2_4.5.3-8 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libpwl5_0.11.2-3 libquadmath0_4.6.1-7+hurd.1 libreadline6_6.2-4 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0d-3 libstdc++6_4.6.1-7+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-7+hurd.1 libsysfs2_2.1.0+repack-1 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libuuid1_2.19.1-5 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-4 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-16 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-05-06-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 quilt_0.48-7 random-egd_0.5-0+hurd.1 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-2 ttf-bitstream-vera_1.10-8 ttf-dejavu-core_2.33-1 ttf-freefont_20100919-1 type-handling_0.2.23 tzdata_2011h-3 ucf_3.0025+nmu2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.7_4.7.1-5 gcc-4.7_4.7.1-5 gnumach-dev_2:1.3.99.dfsg.git20120610-1 hurd-dev_20120605-2 libc0.3-dev_2.13-34 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5
+Package versions: adduser_3.113+nmu3 apt_0.9.7.1 apt-utils_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 bash-completion_1:2.0-1 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpio_2.11-8 cpp_4:4.7.1-1 cpp-4.7_4.7.1-5 dash_0.5.7-3+b1 debconf_1.5.45 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debian-ports-archive-keyring_2012.01.08 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6+b1 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4+b1 g++_4:4.7.1-1 g++-4.7_4.7.1-5 gawk_1:4.0.1+dfsg-2 gcc_4:4.7.1-1 gcc-4.4-base_4.4.7-1+b1 gcc-4.5-base_4.5.4-1 gcc-4.6-base_4.6.3-8 gcc-4.7_4.7.1-5 gcc-4.7-base_4.7.1-5 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnumach-dev_2:1.3.99.dfsg.git20120610-1 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11+b1 html2text_1.3.2a-15+b2 hurd_20120605-2 hurd-dev_20120605-2 initscripts_2.88dsf-22 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-inst1.5_0.9.7.1 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libboost-iostreams1.46.1_1.46.1-8+b1 libboost-iostreams1.48.0_1.48.0-3+b1 libboost-iostreams1.49.0_1.49.0-3.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc0.3_2.13-34 libc0.3-dev_2.13-34 libc0.3-i686_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1+b1 libcwidget3_0.5.16-3.4 libdb5.1_5.1.29-5+b1 libdpkg-perl_1.16.7 libexpat1_2.1.0-1+b1 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-5 libgcrypt11_1.5.0-3+b1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1+b2 libgmp10_2:5.0.5+dfsg-2 libgnutls26_2.12.20-1 libgomp1_4.7.1-5 libgpg-error0_1.10-3+b1 libldap-2.4-2_2.4.28-1.3+b2 liblocale-gettext-perl_1.05-7+b2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libncursesw5_5.9-10 libp11-kit0_0.12-3+b1 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libparted0debian1_2.3-10 libpciaccess0_0.13.1-2+b1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1+b1 libpng12-0_1.2.49-2 libpopt0_1.16-7 libprocps0_1:3.3.3-2 libquadmath0_4.7.1-5 libreadline6_6.2-8+b1 libsasl2-2_2.1.25.dfsg1-4+b2 libsigc++-2.0-0c2a_2.2.10-0.2 libsigsegv2_2.9-4+b1 libslang2_2.2.4-15 libss2_1.42.4-3 libssl1.0.0_1.0.1c-3 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-1.2 libtasn1-3_2.13-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libuuid1_2.20.1-5.1 libxapian22_1.2.8-1 libxml2_2.8.0+dfsg1-5 lsb-base_4.1+Debian7 make_3.81-8.2+b1 man-db_2.6.2-1 mawk_1.3.3-17+b1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 netbase_5.0 netcat-traditional_1.10-40 netdde_0.0.20120520-2 passwd_1:4.1.5.1-1 patch_2.6.1-3+b1 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 procps_1:3.3.3-2 psmisc_22.19-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4+b1 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -268,210 +287,198 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying fix_coverage_cap.patch
Check disc space
────────────────
-Sufficient free space for build
-
-User Environment
-────────────────
-
-FAKEROOTEGID=0
-FAKEROOTEUID=0
-FAKEROOTFGID=0
-FAKEROOTFUID=0
-FAKEROOTGID=0
-FAKEROOTSGID=0
-FAKEROOTSUID=0
-FAKEROOTUID=0
-HOME=/home/buildd
-LOGNAME=buildd
-OLDPWD=/
-PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin
-PWD=/«PKGBUILDDIR»
-SHELL=/bin/sh
-SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env'
-SUDO_GID=105
-SUDO_UID=60000
-SUDO_USER=buildd
-TERM=rxvt-unicode
-USER=buildd
-USERNAME=root
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_coverage_cap.patch
+Restoring bam2depth.c
+
+Removing patch fix_segfault_with_small_ref.patch
+Restoring bam_plcmd.c
+
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+ debian/rules build-arch
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+Applying patch fix_segfault_with_small_ref.patch
+patching file bam_plcmd.c
+
+Applying patch fix_coverage_cap.patch
+patching file bam2depth.c
+
+Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
bam_reheader.c: In function 'bam_reheader':
bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
em.c: In function 'bcf_em1':
em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/«PKGBUILDDIR»'
-make[3]: Entering directory `/«PKGBUILDDIR»'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»'
-make[3]: Entering directory `/«PKGBUILDDIR»/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[3]: Entering directory `/«PKGBUILDDIR»/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/misc'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+md5.c: In function 'MD5Final':
+md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
+md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+md5.c: In function 'MD5Final':
+md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
+md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
seqtk.c: In function 'stk_subseq':
@@ -482,42 +489,43 @@ seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but ar
seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
-gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-[sam_header_read2] 2 sequences loaded.
-make[1]: Entering directory `/«PKGBUILDDIR»/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/examples'
../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+[sam_header_read2] 2 sequences loaded.
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
[bam_rmdup_core] processing reference seq1...
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
+../samtools index ex1.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
+../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
+../samtools rmdup ex1f.bam ex1f-rmduppe.bam
+../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
+../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/«PKGBUILDDIR»/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -552,8 +560,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /«PKGBUILDDIR»/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /«PKGBUILDDIR»/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -579,7 +587,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«PKGBUILDDIR»/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -594,81 +602,69 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_hurd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_hurd-i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../samtools_0.1.18-1_hurd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org> >../samtools_0.1.18-3_hurd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110906-0940
-
-Finished
-────────
-
-I: Built successfully
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Changes │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.18-1_hurd-i386.changes:
-────────────────────────────────────
+Build finished at 20120727-1825
+samtools_0.1.18-3_hurd-i386.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.18-1
+Version: 0.1.18-3
Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org>
+Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 653042 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- [b990d9d3] New upstream release.
- [d59366b9] Updated copyright statements.
- [aa08abe5] Compress binary packages with xz.
- [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- 0c06c1042e7683c687458c5c6ebc0b7f9f5a41ba 533060 samtools_0.1.18-1_hurd-i386.deb
- 6feba00b744214746124c60e3a995b91f1b0db83 160788 libbam-dev_0.1.18-1_hurd-i386.deb
+ f71b952addac0c145b43b14b692a17402669ef2e 534442 samtools_0.1.18-3_hurd-i386.deb
+ c2a33de935822b4ffd9d70160cf7dfa7b296e132 160908 libbam-dev_0.1.18-3_hurd-i386.deb
Checksums-Sha256:
- 48da71bb7ee2f198f5df366b262eed3264f383235a9ced77346d54c5613f13c6 533060 samtools_0.1.18-1_hurd-i386.deb
- ac0b99fef941bb84e08a4d9ca99090d30c66d938d9e4b47a91b436324545318a 160788 libbam-dev_0.1.18-1_hurd-i386.deb
+ 65bfafcd6251e4985631a5a6e3cd75300333440be055329531dd9073c1521e96 534442 samtools_0.1.18-3_hurd-i386.deb
+ 118c152b18028edce4a8019446eacb806a34d0bafde868a012b523bf71238b8d 160908 libbam-dev_0.1.18-3_hurd-i386.deb
Files:
- 7cca252aad346a52f0b77fb947ada7a0 533060 science optional samtools_0.1.18-1_hurd-i386.deb
- 0494c70de6fe467a62f6a0f129e7070c 160788 libdevel optional libbam-dev_0.1.18-1_hurd-i386.deb
+ b29980c288d7398951be60d50cd83582 534442 science optional samtools_0.1.18-3_hurd-i386.deb
+ 342f588266c0e963b7c1c465e3a190d1 160908 libdevel optional libbam-dev_0.1.18-3_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_hurd-i386.deb
+samtools_0.1.18-3_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 533060 bytes: control archive= 1767 bytes.
- 792 bytes, 16 lines control
+ size 534442 bytes: control archive= 1761 bytes.
+ 798 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-3
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1120
- Depends: libc0.3 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1041
+ Depends: libc0.3 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -680,71 +676,71 @@ samtools_0.1.18-1_hurd-i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-09-06 09:38 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-09-06 09:39 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-09-06 09:38 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-09-06 09:38 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-09-06 09:39 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/bin/
--rwxr-xr-x root/root 133848 2011-09-06 09:39 ./usr/bin/bcftools
--rwxr-xr-x root/root 25860 2011-09-06 09:39 ./usr/bin/razip
--rwxr-xr-x root/root 391432 2011-09-06 09:39 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/lib/
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/lib/samtools/
--rwxr-xr-x root/root 17036 2011-09-06 09:39 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6736 2011-09-06 09:39 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6736 2011-09-06 09:39 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10452 2011-09-06 09:39 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7424 2011-09-06 09:39 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-1_hurd-i386.deb
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2011-09-06 09:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-09-06 09:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5502 2011-09-06 09:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 3225 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2010-11-17 05:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 98 2010-11-17 05:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2011-04-22 05:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2012-07-27 18:24 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 33578 2011-03-01 20:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2012-07-27 18:24 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10122 2011-09-02 18:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1826 2012-07-27 17:15 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 18:24 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 18:24 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 18:25 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2011-07-07 04:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 05:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 05:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 04:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 05:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 05:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 05:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 05:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 05:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2010-11-17 05:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 05:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 05:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2012-07-27 18:25 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/bin/
+-rwxr-xr-x root/root 137508 2012-07-27 18:24 ./usr/bin/bcftools
+-rwxr-xr-x root/root 25104 2012-07-27 18:24 ./usr/bin/razip
+-rwxr-xr-x root/root 400116 2012-07-27 18:24 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/lib/samtools/
+-rwxr-xr-x root/root 16696 2012-07-27 18:24 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7128 2012-07-27 18:24 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7128 2012-07-27 18:24 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10876 2012-07-27 18:24 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7816 2012-07-27 18:24 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-3_hurd-i386.deb
─────────────────────────────────
new debian package, version 2.0.
- size 160788 bytes: control archive= 931 bytes.
+ size 160908 bytes: control archive= 924 bytes.
678 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-3
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 456
+ Installed-Size: 432
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -755,64 +751,94 @@ libbam-dev_0.1.18-1_hurd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/lib/
--rw-r--r-- root/root 293478 2011-09-06 09:39 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/include/
-drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/include/samtools/
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 18:25 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5502 2011-09-06 09:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 33578 2011-03-01 20:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10122 2011-09-02 18:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1826 2012-07-27 17:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 18:25 ./usr/lib/
+-rw-r--r-- root/root 300240 2012-07-27 18:25 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/include/samtools/
+-rw-r--r-- root/root 24720 2011-09-02 18:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-11 00:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 20:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 05:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 05:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
+│ Finished │
└──────────────────────────────────────────────────────────────────────────────┘
+Built successfully
+────────────────────────────────────────────────────────────────────────────────
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Cleanup │
+│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /«BUILDDIR»
+Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+ adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
+ libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+ adduser groff-base libboost-iostreams1.46.1 libboost-iostreams1.49.0
+ libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
+ man-db
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* diffstat* libncurses5-dev* quilt* sbuild-build-depends-core-dummy*
- sbuild-build-depends-samtools-dummy* zlib1g-dev*
-0 upgraded, 0 newly installed, 7 to remove and 30 not upgraded.
-After this operation, 3113 kB disk space will be freed.
-(Reading database ... 13968 files and directories currently installed.)
-Removing sbuild-build-depends-samtools-dummy ...
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libasprintf0c2* libcroco3* libexpat1* libffi5*
+ libgettextpo0* libglib2.0-0* libmagic1* libncurses5-dev* libtinfo-dev*
+ libunistring0* libxml2* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 22 to remove and 25 not upgraded.
+After this operation, 22.5 MB disk space will be freed.
+(Reading database ... 15646 files and directories currently installed.)
Removing cdbs ...
+Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libasprintf0c2:hurd-i386 ...
+Removing libcroco3:hurd-i386 ...
+Purging configuration files for libcroco3:hurd-i386 ...
+Removing libexpat1:hurd-i386 ...
+Purging configuration files for libexpat1:hurd-i386 ...
+Removing libglib2.0-0:hurd-i386 ...
+Purging configuration files for libglib2.0-0:hurd-i386 ...
+Removing libffi5:hurd-i386 ...
+Purging configuration files for libffi5:hurd-i386 ...
+Removing libgettextpo0:hurd-i386 ...
+Removing libmagic1:hurd-i386 ...
+Purging configuration files for libmagic1:hurd-i386 ...
Removing libncurses5-dev ...
-Removing sbuild-build-depends-core-dummy ...
-Removing zlib1g-dev ...
+Removing libtinfo-dev:hurd-i386 ...
+Removing libunistring0:hurd-i386 ...
+Purging configuration files for libunistring0:hurd-i386 ...
+Removing libxml2:hurd-i386 ...
+Purging configuration files for libxml2:hurd-i386 ...
+Removing zlib1g-dev:hurd-i386 ...
Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -820,17 +846,17 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 10392
-Build-Time: 243
+Build-Space: 11400
+Build-Time: 85
Distribution: sid
-Install-Time: 80
-Job: samtools_0.1.18-1
+Install-Time: 15
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 419
-Source-Version: 0.1.18-1
-Space: 10392
+Package-Time: 137
+Source-Version: 0.1.18-3
+Space: 11400
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-0940
-Build needed 00:06:59, 10392k disc space
+Finished at 20120727-1825
+Build needed 00:02:17, 11400k disc space
diff --git a/i386.log b/i386.log
index ffc4773..5c5c025 100644
--- a/i386.log
+++ b/i386.log
@@ -1,61 +1,64 @@
-From buildd at biber.debian.org Fri Jul 27 15:15:41 2012
-Return-path: <buildd at biber.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at murphy.debian.org Fri Jul 27 15:40:39 2012
+Return-path: <buildd at murphy.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
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+ id 1Sumea-00029k-Kg; Fri, 27 Jul 2012 15:40:36 +0000
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MIME-Version: 1.0
Content-Transfer-Encoding: binary
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-Date: Fri, 27 Jul 2012 15:15:39 +0000
-From: buildd on biber <buildd at biber.debian.org>
-To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on i386 (dist=sid)
-Key-Id: 6EBCB100
+Date: Fri, 27 Jul 2012 15:40:36 +0000
+From: buildd on murphy <buildd at murphy.debian.org>
+To: logs at buildd.debian.org,buildd-admin at murphy.debian.org
+Subject: Log for successful build of samtools_0.1.18-3 on i386 (dist=sid)
+Key-Id: 2B54027C
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on murphy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (i386) 27 Jul 2012 15:13 ║
+║ samtools 0.1.18-3 (i386) 27 Jul 2012 15:39 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable InRelease [249 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [6315 kB]
-Get:3 http://incoming.debian.org unstable InRelease [249 kB]
-Get:4 http://ftp.gr.debian.org unstable/contrib Sources [53.9 kB]
-Get:5 http://ftp.gr.debian.org unstable/non-free Sources [98.1 kB]
-Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [6138 kB]
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [46.1 kB]
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:8 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main i386 Packages [6138 kB]
-Get:12 http://incoming.debian.org unstable/contrib i386 Packages [46.1 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 25.9 MB in 19s (1330 kB/s)
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Get:1 http://ftp.us.debian.org sid InRelease [249 kB]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/main i386 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib i386 Packages/DiffIndex
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://incoming.debian.org Release [1601 B]
+Get:4 http://ftp.us.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:5 http://incoming.debian.org Sources [14.5 kB]
+Get:6 http://incoming.debian.org Packages [117 kB]
+Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
+Get:7 http://ftp.us.debian.org sid/main i386 Packages/DiffIndex [7876 B]
+Hit http://ftp.us.debian.org sid/contrib i386 Packages/DiffIndex
+Get:8 http://ftp.us.debian.org sid/main 2012-07-27-1414.10.pdiff [1291 B]
+Get:9 http://ftp.us.debian.org sid/main 2012-07-27-1414.10.pdiff [1291 B]
+Get:10 http://ftp.us.debian.org sid/main i386 2012-07-27-1414.10.pdiff [1837 B]
+Get:11 http://ftp.us.debian.org sid/main i386 2012-07-27-1414.10.pdiff [1837 B]
+Fetched 402 kB in 8s (48.6 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -77,10 +80,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (209 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (285 kB/s)
Download complete and in download only mode
Check arch
@@ -100,12 +103,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -116,7 +119,7 @@ Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diff
Checking for already installed dependencies...
base-files: already installed (6.11)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-3)
+bash: already installed (4.2-4)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
debianutils: already installed (4.3.2)
@@ -171,39 +174,12 @@ The following NEW packages will be installed:
html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 29 not upgraded.
-Need to get 10.8 MB of archives.
-After this operation, 28.4 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.1-1 [38.6 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main libasprintf0c2 i386 0.18.1.1-9 [26.7 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.11-2 [204 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 1:8.30-5 [240 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.8.0+dfsg1-5 [893 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main libffi5 i386 3.0.10-3 [21.0 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.32.3-1 [2074 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.5-1 [151 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5 [442 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main libgettextpo0 i386 0.18.1.1-9 [140 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 9.0.3 [205 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-9 [1131 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.2-1 [1055 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.11-2 [51.5 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-9 [131 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-9 [1916 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.55-3 [29.3 kB]
-Get:23 http://ftp.gr.debian.org/debian/ unstable/main libtinfo-dev i386 5.9-10 [93.2 kB]
-Get:24 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.9-10 [212 kB]
-Get:25 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.7.dfsg-13 [212 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.8 MB in 0s (11.9 MB/s)
+0 upgraded, 26 newly installed, 0 to remove and 14 not upgraded.
+Need to get 0 B/10.8 MB of archives.
+After this operation, 28.4 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1:i386.
-(Reading database ... 10801 files and directories currently installed.)
+(Reading database ... 10967 files and directories currently installed.)
Unpacking libpipeline1:i386 (from .../libpipeline1_1.2.1-1_i386.deb) ...
Selecting previously unselected package libasprintf0c2:i386.
Unpacking libasprintf0c2:i386 (from .../libasprintf0c2_0.18.1.1-9_i386.deb) ...
@@ -289,11 +265,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.7_4.7.1-3 gcc-4.7_4.7.1-3 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.7-dev_4.7.1-3 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.7.1-1 cpp-4.7_4.7.1-3 dash_0.5.7-3 debconf_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.7.1-1 g++-4.7_4.7.1-3 gcc_4:4.7.1-1 gcc-4.7_4.7.1-3 gcc-4.7-base_4.7.1-3 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-3 libitm1_4.7.1-3 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libquadmath0_4.7.1-3 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-3 libstdc++6-4.7-dev_4.7.1-3 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
+Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.7_4.7.1-5 gcc-4.7_4.7.1-5 libc6-dev_2.13-34 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5 linux-libc-dev_3.2.21-3
+Package versions: apt_0.9.7.2 base-files_6.11 base-passwd_3.5.26 bash_4.2-4 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.7.1-1 cpp-4.7_4.7.1-5 dash_0.5.7-3 debconf_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.7.1-1 g++-4.7_4.7.1-5 gawk_1:4.0.1+dfsg-2 gcc_4:4.7.1-1 gcc-4.7_4.7.1-5 gcc-4.7-base_4.7.1-5 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.2 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-5 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-5 libitm1_4.7.1-5 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libquadmath0_4.7.1-5 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libsigsegv2_2.9-4 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012d-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -304,12 +280,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -322,7 +298,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
@@ -330,25 +306,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -368,10 +344,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -384,12 +360,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -424,8 +400,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -440,10 +416,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -464,24 +440,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
@@ -509,14 +485,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -542,7 +518,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -577,8 +553,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -604,7 +580,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -620,65 +596,66 @@ dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is no
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.18-2_i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../samtools_0.1.18-3_i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1515
+Build finished at 20120727-1540
-samtools_0.1.18-2_i386.changes:
+samtools_0.1.18-3_i386.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
+Maintainer: i386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- dd73578b3f260e1de73b8d63c9a159884d2d911f 534640 samtools_0.1.18-2_i386.deb
- 828b62ebc7704bb4ac7f751a3a96d80ae4f3f761 160934 libbam-dev_0.1.18-2_i386.deb
+ 361b092fd97df955921190b3f3dd33e09f592339 534260 samtools_0.1.18-3_i386.deb
+ 142d7e62801391d8bb946b64a86ce65abb7b9cba 160760 libbam-dev_0.1.18-3_i386.deb
Checksums-Sha256:
- e26ece5bfb41a51243941c49f505b024b5cfe9980642d51d325e558508bd9088 534640 samtools_0.1.18-2_i386.deb
- ce0841dee2ba4087dae49b6bb4a382434ce5ff533b617101f16da49e6390b135 160934 libbam-dev_0.1.18-2_i386.deb
+ 4ce81914e581e0c10fb05a7f632f34e2096b1e90995e143632983639e03509b2 534260 samtools_0.1.18-3_i386.deb
+ 39358eb7dcde66cabdf97f2c1c6bcc5d27f16abfdb587ac018c1eddbd50b9168 160760 libbam-dev_0.1.18-3_i386.deb
Files:
- d27965e80c3c3ced041c73c5ecd5707a 534640 science optional samtools_0.1.18-2_i386.deb
- 5ed8aa277faa83b9aef3d5f79311b191 160934 libdevel optional libbam-dev_0.1.18-2_i386.deb
+ 422474d529562816060920858b4bb60e 534260 science optional samtools_0.1.18-3_i386.deb
+ ed448671fefad2122b9144f6ddb55889 160760 libdevel optional libbam-dev_0.1.18-3_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_i386.deb
+samtools_0.1.18-3_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 534640 bytes: control archive= 1768 bytes.
+ size 534260 bytes: control archive= 1760 bytes.
791 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1036
@@ -694,68 +671,68 @@ samtools_0.1.18-2_i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/lib/samtools/
--rwxr-xr-x root/root 7484 2012-07-27 15:15 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6860 2012-07-27 15:15 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6860 2012-07-27 15:15 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10608 2012-07-27 15:15 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 16536 2012-07-27 15:15 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/bin/
--rwxr-xr-x root/root 134308 2012-07-27 15:15 ./usr/bin/bcftools
--rwxr-xr-x root/root 24740 2012-07-27 15:15 ./usr/bin/razip
--rwxr-xr-x root/root 400020 2012-07-27 15:15 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/bin/
+-rwxr-xr-x root/root 134308 2012-07-27 15:40 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24740 2012-07-27 15:40 ./usr/bin/razip
+-rwxr-xr-x root/root 400020 2012-07-27 15:40 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7484 2012-07-27 15:40 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6860 2012-07-27 15:40 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 16536 2012-07-27 15:40 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 10608 2012-07-27 15:40 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6860 2012-07-27 15:40 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2012-07-27 15:40 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2012-07-27 15:40 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/samtools/
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 5778 2012-07-27 15:40 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2012-07-27 15:15 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 126609 2012-07-27 15:40 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2012-07-27 15:15 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1966 2012-07-27 15:40 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2012-07-27 15:15 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2012-07-27 15:15 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2012-07-27 15:15 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-lrwxrwxrwx root/root 0 2012-07-27 15:15 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+lrwxrwxrwx root/root 0 2012-07-27 15:40 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.18-2_i386.deb
+libbam-dev_0.1.18-3_i386.deb
────────────────────────────
new debian package, version 2.0.
- size 160934 bytes: control archive= 926 bytes.
+ size 160760 bytes: control archive= 923 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 432
@@ -769,25 +746,25 @@ libbam-dev_0.1.18-2_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/lib/
--rw-r--r-- root/root 299796 2012-07-27 15:15 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/include/samtools/
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/include/samtools/
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/lib/
+-rw-r--r-- root/root 299796 2012-07-27 15:40 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -801,8 +778,62 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-ad398d8d-23c5-4b5f-91a8-8eb0ec51e338/build/buildd-samtools_0.1.18-2-i386-8lTd72
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-i386-sbuild-8ef2d0ee-2250-4951-b2c9-2f3744c63220/build/buildd-samtools_0.1.18-3-i386-D3LzxQ
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base*
+ groff-base* html2text* intltool-debian* libasprintf0c2* libcroco3* libffi5*
+ libgettextpo0* libglib2.0-0* libmagic1* libncurses5-dev* libpcre3*
+ libpipeline1* libtinfo-dev* libunistring0* libxml2* man-db* po-debconf*
+ quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 26 to remove and 14 not upgraded.
+After this operation, 28.4 MB disk space will be freed.
+(Reading database ... 12572 files and directories currently installed.)
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing debhelper ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing bsdmainutils ...
+Purging configuration files for bsdmainutils ...
+Removing cdbs ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libasprintf0c2:i386 ...
+Removing libcroco3:i386 ...
+Purging configuration files for libcroco3:i386 ...
+Removing libglib2.0-0:i386 ...
+Purging configuration files for libglib2.0-0:i386 ...
+Removing libffi5:i386 ...
+Purging configuration files for libffi5:i386 ...
+Removing libgettextpo0:i386 ...
+Removing libmagic1:i386 ...
+Purging configuration files for libmagic1:i386 ...
+Removing libncurses5-dev ...
+Removing libpcre3:i386 ...
+Purging configuration files for libpcre3:i386 ...
+Removing libpipeline1:i386 ...
+Purging configuration files for libpipeline1:i386 ...
+Removing libtinfo-dev:i386 ...
+Removing libunistring0:i386 ...
+Purging configuration files for libunistring0:i386 ...
+Removing libxml2:i386 ...
+Purging configuration files for libxml2:i386 ...
+Removing zlib1g-dev:i386 ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
@@ -810,17 +841,17 @@ Not cleaning session: cloned chroot in use
Architecture: i386
Build-Space: 11392
-Build-Time: 55
+Build-Time: 62
Distribution: sid
-Install-Time: 43
-Job: samtools_0.1.18-2
+Install-Time: 11
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 132
-Source-Version: 0.1.18-2
+Package-Time: 90
+Source-Version: 0.1.18-3
Space: 11392
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1515
-Build needed 00:02:12, 11392k disc space
-Signature with key '6EBCB100' requested:
+Finished at 20120727-1540
+Build needed 00:01:30, 11392k disc space
+Signature with key '2B54027C' requested:
diff --git a/ia64.log b/ia64.log
index ff7d9e7..b24f02b 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,4 +1,4 @@
-From buildd at alkman.debian.org Fri Jul 27 15:11:30 2012
+From buildd at alkman.debian.org Fri Jul 27 15:43:03 2012
Return-path: <buildd at alkman.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,23 +6,23 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
- id 1SumCQ-0002qa-JO
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:11:30 +0000
+ id 1Sumgw-00057W-Nn
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:43:03 +0000
Received: from alkman.debian.org ([192.25.206.63])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
- id 1SumCO-00048K-Vx
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:11:29 +0000
+ id 1Sumgu-0005hX-VG
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:43:01 +0000
Received: from buildd by alkman.debian.org with local (Exim 4.72)
(envelope-from <buildd at alkman.debian.org>)
- id 1SumCL-00037k-Ek; Fri, 27 Jul 2012 15:11:25 +0000
-Date: Fri, 27 Jul 2012 15:11:25 +0000
-Message-Id: <E1SumCL-00037k-Ek at alkman.debian.org>
+ id 1Sumgs-0004XD-PR; Fri, 27 Jul 2012 15:42:58 +0000
+Date: Fri, 27 Jul 2012 15:42:58 +0000
+Message-Id: <E1Sumgs-0004XD-PR at alkman.debian.org>
From: buildd on alkman <buildd at alkman.debian.org>
To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on ia64 (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-3 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -30,31 +30,31 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (ia64) 27 Jul 2012 15:06 ║
+║ samtools 0.1.18-3 (ia64) 27 Jul 2012 15:37 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: ia64
Get:1 http://spohr.debian.org unstable InRelease [249 kB]
Get:2 http://incoming.debian.org unstable InRelease [249 kB]
Get:3 http://spohr.debian.org unstable/main Sources [6315 kB]
-Get:4 http://spohr.debian.org unstable/contrib Sources [53.9 kB]
-Get:5 http://spohr.debian.org unstable/non-free Sources [98.1 kB]
-Get:6 http://spohr.debian.org unstable/main ia64 Packages [5831 kB]
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:8 http://spohr.debian.org unstable/contrib ia64 Packages [38.3 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main ia64 Packages [5831 kB]
+Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:5 http://spohr.debian.org unstable/contrib Sources [53.9 kB]
+Get:6 http://spohr.debian.org unstable/non-free Sources [98.1 kB]
+Get:7 http://spohr.debian.org unstable/main ia64 Packages [5831 kB]
+Get:8 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:9 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
+Get:10 http://incoming.debian.org unstable/main ia64 Packages [5831 kB]
+Get:11 http://spohr.debian.org unstable/contrib ia64 Packages [38.3 kB]
Get:12 http://incoming.debian.org unstable/contrib ia64 Packages [38.3 kB]
Get:13 http://incoming.debian.org Release.gpg [836 B]
Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 25.3 MB in 28s (873 kB/s)
+Get:15 http://incoming.debian.org Sources [14.5 kB]
+Get:16 http://incoming.debian.org Packages [117 kB]
+Fetched 25.3 MB in 28s (876 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,10 +76,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (374 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (327 kB/s)
Download complete and in download only mode
Check arch
@@ -200,7 +200,7 @@ Get:24 http://spohr.debian.org/debian/ unstable/main libncurses5-dev ia64 5.9-10
Get:25 http://spohr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
Get:26 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.7.dfsg-13 [252 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.7 MB in 5s (2496 kB/s)
+Fetched 12.7 MB in 13s (951 kB/s)
Selecting previously unselected package libpipeline1:ia64.
(Reading database ... 10682 files and directories currently installed.)
Unpacking libpipeline1:ia64 (from .../libpipeline1_1.2.1-1_ia64.deb) ...
@@ -303,12 +303,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -321,7 +321,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
@@ -329,25 +329,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -367,10 +367,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -383,12 +383,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -417,8 +417,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -433,10 +433,10 @@ gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=6
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -457,24 +457,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -488,14 +488,14 @@ gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -521,7 +521,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -556,8 +556,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -583,7 +583,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -598,27 +598,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_ia64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.18-2_ia64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.18-3_ia64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1511
+Build finished at 20120727-1542
-samtools_0.1.18-2_ia64.changes:
+samtools_0.1.18-3_ia64.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
@@ -626,36 +626,37 @@ Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- ae3896cf5f6f086ed8d8fda397ee66bb8dd94712 604618 samtools_0.1.18-2_ia64.deb
- 6b92dce40573e1c7b939593264ba0353e0ea33b1 194458 libbam-dev_0.1.18-2_ia64.deb
+ 0048f28a935a290fb4de007996d13e977fb008c6 604856 samtools_0.1.18-3_ia64.deb
+ 9aff0a6300b11d3411923da9ebd22d2ecebea523 194500 libbam-dev_0.1.18-3_ia64.deb
Checksums-Sha256:
- 9e6d5b251cc0e4f54409e9074b362472a38a6cb16092df2cae7332104614a4e9 604618 samtools_0.1.18-2_ia64.deb
- 6393a7e2ee28f7f3b9ec8328a4cadd9d68897292f7736afb82370fa34cccbfb6 194458 libbam-dev_0.1.18-2_ia64.deb
+ 457a80d639ea00ef758e946e30637361c12bcddc648eb50df1235c8a33326206 604856 samtools_0.1.18-3_ia64.deb
+ 16371abafac995a01d52c3407e9f8c5fde97e40db96d23fbff273474775f6a66 194500 libbam-dev_0.1.18-3_ia64.deb
Files:
- c842e4c8116350286a423bf5f120136e 604618 science optional samtools_0.1.18-2_ia64.deb
- 226a9878a76be7aa84c9c6b905dc5848 194458 libdevel optional libbam-dev_0.1.18-2_ia64.deb
+ 53a16dd9c18be2dedc1e9dedbf810b0d 604856 science optional samtools_0.1.18-3_ia64.deb
+ 7f775e9b785114b641b4c9635fdf0cc5 194500 libdevel optional libbam-dev_0.1.18-3_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_ia64.deb
+samtools_0.1.18-3_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 604618 bytes: control archive= 1762 bytes.
+ size 604856 bytes: control archive= 1759 bytes.
793 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1638
@@ -671,22 +672,22 @@ samtools_0.1.18-2_ia64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/lib/samtools/
--rwxr-xr-x root/root 30976 2012-07-27 15:11 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13136 2012-07-27 15:11 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13136 2012-07-27 15:11 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 21952 2012-07-27 15:11 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 14944 2012-07-27 15:11 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/bin/
--rwxr-xr-x root/root 303936 2012-07-27 15:11 ./usr/bin/bcftools
--rwxr-xr-x root/root 50640 2012-07-27 15:11 ./usr/bin/razip
--rwxr-xr-x root/root 826608 2012-07-27 15:11 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2012-07-27 15:11 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/lib/samtools/
+-rwxr-xr-x root/root 30976 2012-07-27 15:42 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13136 2012-07-27 15:42 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13136 2012-07-27 15:42 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 21952 2012-07-27 15:42 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 14944 2012-07-27 15:42 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/bin/
+-rwxr-xr-x root/root 303936 2012-07-27 15:42 ./usr/bin/bcftools
+-rwxr-xr-x root/root 50640 2012-07-27 15:42 ./usr/bin/razip
+-rwxr-xr-x root/root 826608 2012-07-27 15:42 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2012-07-27 15:42 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
@@ -699,18 +700,18 @@ drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/samtools/
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:11 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:11 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:42 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:42 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/samtools/
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-07-27 15:11 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2012-07-27 15:10 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2012-07-27 15:42 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2012-07-27 15:42 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
@@ -720,19 +721,19 @@ drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/doc/samtools/example
-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-lrwxrwxrwx root/root 0 2012-07-27 15:11 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+lrwxrwxrwx root/root 0 2012-07-27 15:42 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.18-2_ia64.deb
+libbam-dev_0.1.18-3_ia64.deb
────────────────────────────
new debian package, version 2.0.
- size 194458 bytes: control archive= 925 bytes.
+ size 194500 bytes: control archive= 923 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 672
@@ -746,22 +747,22 @@ libbam-dev_0.1.18-2_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/include/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/include/samtools/
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/lib/
--rw-r--r-- root/root 581530 2012-07-27 15:11 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/lib/
+-rw-r--r-- root/root 581530 2012-07-27 15:42 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
@@ -778,7 +779,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-bf5273e5-2a1a-43e0-98fa-fd27b951b76e/build/buildd-samtools_0.1.18-2-ia64-5ePQLX
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-d882d7c1-376a-484a-a7b5-ea9c093d4d7f/build/buildd-samtools_0.1.18-3-ia64-5Oj98m
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -789,16 +790,16 @@ Architecture: ia64
Build-Space: 17976
Build-Time: 160
Distribution: sid
-Install-Time: 77
-Job: samtools_0.1.18-2
+Install-Time: 81
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 290
-Source-Version: 0.1.18-2
+Package-Time: 295
+Source-Version: 0.1.18-3
Space: 17976
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1511
-Build needed 00:04:50, 17976k disc space
+Finished at 20120727-1542
+Build needed 00:04:55, 17976k disc space
Signature with key '94AE7BC0' requested:
diff --git a/info b/info
index f1f1af5..ff7bd35 100644
--- a/info
+++ b/info
@@ -1,12 +1,14 @@
-s390~1343401612~sid~successful
-powerpc~1343401854~sid~successful
-ia64~1343401891~sid~successful
-s390x~1343401918~sid~failed
-kfreebsd-i386~1343402036~sid~successful
-armhf~1343402054~sid~successful
-armel~1343402092~sid~failed
-i386~1343402142~sid~successful
-sparc~1343402299~sid~failed
-kfreebsd-amd64~1343402896~sid~successful
-mipsel~1343403117~sid~successful
-mips~1343403208~sid~successful
+i386~1343403644~sid~successful
+ia64~1343403784~sid~successful
+powerpc~1343403802~sid~successful
+kfreebsd-amd64~1343403831~sid~successful
+kfreebsd-i386~1343403844~sid~successful
+sparc~1343403938~sid~failed
+mipsel~1343403951~sid~successful
+s390x~1343403961~sid~failed
+s390~1343403978~sid~successful
+armhf~1343404044~sid~successful
+armel~1343404148~sid~failed
+mips~1343405070~sid~successful
+hurd-i386~1343406337~sid~successful
+s390x~1346209716~sid~failed
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 32e912a..28554fa 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,4 +1,4 @@
-From buildd at fano.debian.org Fri Jul 27 15:28:16 2012
+From buildd at fano.debian.org Fri Jul 27 15:43:51 2012
Return-path: <buildd at fano.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,25 +6,25 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1SumSe-00009c-Aa
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:28:16 +0000
+ id 1Sumhj-0005L9-6D
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:43:51 +0000
Received: from fano.debian.org ([206.12.19.110])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1SumSd-0004sC-2Q; Fri, 27 Jul 2012 15:28:15 +0000
+ id 1Sumhh-0005iT-OW; Fri, 27 Jul 2012 15:43:50 +0000
Received: from buildd by fano.debian.org with local (Exim 4.72)
(envelope-from <buildd at fano.debian.org>)
- id 1SumSa-00006z-VG; Fri, 27 Jul 2012 15:28:12 +0000
-Message-Id: <E1SumSa-00006z-VG at fano.debian.org>
+ id 1Sumhf-00064E-FF; Fri, 27 Jul 2012 15:43:47 +0000
+Message-Id: <E1Sumhf-00064E-FF at fano.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:28:12 +0000
+Date: Fri, 27 Jul 2012 15:43:47 +0000
From: buildd on fano <buildd at fano.debian.org>
To: logs at buildd.debian.org,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on kfreebsd-amd64
+Subject: Log for successful build of samtools_0.1.18-3 on kfreebsd-amd64
(dist=sid)
Key-Id: 4584BE29
Delivered-To: logs at buildd.debian.org
@@ -32,21 +32,21 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (kfreebsd-amd64) 27 Jul 2012 15:23 ║
+║ samtools 0.1.18-3 (kfreebsd-amd64) 27 Jul 2012 15:39 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: kfreebsd-amd64
Get:1 http://incoming.debian.org unstable InRelease [249 kB]
Get:2 http://mirror-ubc.debian.org unstable InRelease [249 kB]
Get:3 http://mirror-ubc.debian.org unstable/main Sources [6315 kB]
+Get:4 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
+Get:5 http://mirror-ubc.debian.org unstable/non-free Sources [98.1 kB]
+Get:6 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [5657 kB]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
-Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [98.1 kB]
-Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [5657 kB]
+Get:7 http://incoming.debian.org unstable/main Sources [6315 kB]
Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [37.4 kB]
Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
@@ -54,9 +54,9 @@ Get:11 http://incoming.debian.org unstable/main kfreebsd-amd64 Packages [5657 kB
Get:12 http://incoming.debian.org unstable/contrib kfreebsd-amd64 Packages [37.4 kB]
Get:13 http://incoming.debian.org Release.gpg [836 B]
Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [114 kB]
-Fetched 25.0 MB in 23s (1052 kB/s)
+Get:15 http://incoming.debian.org Sources [14.5 kB]
+Get:16 http://incoming.debian.org Packages [117 kB]
+Fetched 25.0 MB in 16s (1471 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,9 +78,9 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
Fetched 390 kB in 1s (364 kB/s)
Download complete and in download only mode
@@ -198,7 +198,7 @@ Get:22 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreeb
Get:23 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
Get:24 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.4 MB in 0s (15.3 MB/s)
+Fetched 10.4 MB in 0s (16.3 MB/s)
Selecting previously unselected package libpipeline1:kfreebsd-amd64.
(Reading database ... 11559 files and directories currently installed.)
Unpacking libpipeline1:kfreebsd-amd64 (from .../libpipeline1_1.2.1-1_kfreebsd-amd64.deb) ...
@@ -293,12 +293,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -311,7 +311,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
@@ -319,25 +319,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -357,10 +357,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -373,12 +373,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -407,8 +407,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -423,10 +423,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -447,24 +447,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
@@ -484,14 +484,14 @@ gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-s
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -517,7 +517,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -552,8 +552,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -579,7 +579,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -594,27 +594,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_kfreebsd-amd64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.18-2_kfreebsd-amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.18-3_kfreebsd-amd64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1528
+Build finished at 20120727-1543
-samtools_0.1.18-2_kfreebsd-amd64.changes:
+samtools_0.1.18-3_kfreebsd-amd64.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
@@ -622,36 +622,37 @@ Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- 166e5a6448196b1de06d7c8d595b1342f706e8c7 532224 samtools_0.1.18-2_kfreebsd-amd64.deb
- 3b4a76a4b48da0352866a57453199d0a936e7a3c 156374 libbam-dev_0.1.18-2_kfreebsd-amd64.deb
+ d7dcbda7c1b14e7936a007915c21285e451e756a 532312 samtools_0.1.18-3_kfreebsd-amd64.deb
+ 14198a76d6077e1c30accb7f547de10886a77a51 156480 libbam-dev_0.1.18-3_kfreebsd-amd64.deb
Checksums-Sha256:
- 926a6f84e198b3368e1f35c621f7ffdd040babbcafdf9f79a23fcdbfcc21f611 532224 samtools_0.1.18-2_kfreebsd-amd64.deb
- ee0a28ab625a8a48039c30937a457e783832a3a611e1e0ed4d23f22bad95b16e 156374 libbam-dev_0.1.18-2_kfreebsd-amd64.deb
+ 31a120bd7599bbda862e18d910e80fc9338a08d17e310443d6099cd0a5a03dc0 532312 samtools_0.1.18-3_kfreebsd-amd64.deb
+ 82e2abd996ea077becb0afcda2823e4d762633d220ccf4b6f07f72d9ff2b2dc7 156480 libbam-dev_0.1.18-3_kfreebsd-amd64.deb
Files:
- 44b2ad6bbf66c531a379864281b0073d 532224 science optional samtools_0.1.18-2_kfreebsd-amd64.deb
- 0c90e18b15ac65490405229b86ad2afc 156374 libdevel optional libbam-dev_0.1.18-2_kfreebsd-amd64.deb
+ 504f6102707976bbacc29245dd416f61 532312 science optional samtools_0.1.18-3_kfreebsd-amd64.deb
+ 474366270710ae0b25ec14ddaa1b2edb 156480 libdevel optional libbam-dev_0.1.18-3_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_kfreebsd-amd64.deb
+samtools_0.1.18-3_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 532224 bytes: control archive= 1767 bytes.
+ size 532312 bytes: control archive= 1767 bytes.
802 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 968
@@ -667,31 +668,31 @@ samtools_0.1.18-2_kfreebsd-amd64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/doc/samtools/examples/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2012-07-27 15:27 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2012-07-27 15:43 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-07-27 15:27 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-07-27 15:43 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:27 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:27 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/samtools/
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:43 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:43 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/samtools/
-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
@@ -704,31 +705,31 @@ drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-07-27 15:28 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/bin/
--rwxr-xr-x root/root 130696 2012-07-27 15:28 ./usr/bin/bcftools
--rwxr-xr-x root/root 24912 2012-07-27 15:28 ./usr/bin/razip
--rwxr-xr-x root/root 372576 2012-07-27 15:28 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/lib/samtools/
--rwxr-xr-x root/root 18208 2012-07-27 15:28 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8440 2012-07-27 15:28 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8360 2012-07-27 15:28 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 12104 2012-07-27 15:28 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8896 2012-07-27 15:28 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-2_kfreebsd-amd64.deb
+-rwxr-xr-x root/root 5778 2012-07-27 15:43 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/bin/
+-rwxr-xr-x root/root 130696 2012-07-27 15:43 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24912 2012-07-27 15:43 ./usr/bin/razip
+-rwxr-xr-x root/root 372576 2012-07-27 15:43 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18208 2012-07-27 15:43 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8440 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8360 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 12104 2012-07-27 15:43 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8896 2012-07-27 15:43 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-3_kfreebsd-amd64.deb
──────────────────────────────────────
new debian package, version 2.0.
- size 156374 bytes: control archive= 934 bytes.
+ size 156480 bytes: control archive= 928 bytes.
683 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 432
@@ -742,20 +743,20 @@ libbam-dev_0.1.18-2_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/lib/
--rw-r--r-- root/root 332474 2012-07-27 15:28 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/include/samtools/
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
+-rw-r--r-- root/root 332474 2012-07-27 15:43 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/samtools/
-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
@@ -774,7 +775,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1343402622-97734/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1343403586-20770/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -783,17 +784,17 @@ Not cleaning session: cloned chroot in use
Architecture: kfreebsd-amd64
Build-Space: 13452
-Build-Time: 66
+Build-Time: 61
Distribution: sid
-Install-Time: 58
-Job: samtools_0.1.18-2
+Install-Time: 39
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 268
-Source-Version: 0.1.18-2
+Package-Time: 237
+Source-Version: 0.1.18-3
Space: 13452
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1528
-Build needed 00:04:28, 13452k disc space
+Finished at 20120727-1543
+Build needed 00:03:57, 13452k disc space
Signature with key '4584BE29' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index f790c47..aa86631 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,62 +1,62 @@
-From buildd at fils.debian.org Fri Jul 27 15:13:56 2012
-Return-path: <buildd at fils.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at finzi.debian.org Fri Jul 27 15:44:04 2012
+Return-path: <buildd at finzi.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fils.debian.org>)
- id 1SumEm-0003SU-1o
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:13:56 +0000
-Received: from fils.debian.org ([82.195.75.89])
+ (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
+ id 1Sumhw-0005Qe-4O
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:44:04 +0000
+Received: from finzi.debian.org ([206.12.19.111])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=fils.debian.org, EMAIL=hostmaster at fils.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fils.debian.org>)
- id 1SumEl-0004AH-2a; Fri, 27 Jul 2012 15:13:55 +0000
-Received: from buildd by fils.debian.org with local (Exim 4.72)
- (envelope-from <buildd at fils.debian.org>)
- id 1SumEj-000KwE-Vx; Fri, 27 Jul 2012 15:13:53 +0000
-Message-Id: <E1SumEj-000KwE-Vx at fils.debian.org>
+ CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
+ id 1Sumhu-0001rE-RA; Fri, 27 Jul 2012 15:44:03 +0000
+Received: from buildd by finzi.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at finzi.debian.org>)
+ id 1Sumhs-000Lq2-Oh; Fri, 27 Jul 2012 15:44:00 +0000
+Message-Id: <E1Sumhs-000Lq2-Oh at finzi.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:13:53 +0000
-From: buildd on fils <buildd at fils.debian.org>
+Date: Fri, 27 Jul 2012 15:44:00 +0000
+From: buildd on finzi <buildd at finzi.debian.org>
To: logs at buildd.debian.org,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on kfreebsd-i386
+Subject: Log for successful build of samtools_0.1.18-3 on kfreebsd-i386
(dist=sid)
-Key-Id: 52E1CE73
+Key-Id: B3DA9773
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fils.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (kfreebsd-i386) 27 Jul 2012 15:12 ║
+║ samtools 0.1.18-3 (kfreebsd-i386) 27 Jul 2012 15:40 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: kfreebsd-i386
-Get:1 http://debian.netcologne.de unstable InRelease [249 kB]
-Get:2 http://debian.netcologne.de unstable/main Sources [6317 kB]
-Get:3 http://incoming.debian.org unstable InRelease [249 kB]
-Get:4 http://debian.netcologne.de unstable/contrib Sources [53.9 kB]
-Get:5 http://debian.netcologne.de unstable/non-free Sources [98.1 kB]
-Get:6 http://debian.netcologne.de unstable/main kfreebsd-i386 Packages [5652 kB]
-Get:7 http://debian.netcologne.de unstable/contrib kfreebsd-i386 Packages [37.0 kB]
+Get:1 http://incoming.debian.org unstable InRelease [249 kB]
+Get:2 http://mirror-ubc.debian.org unstable InRelease [249 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [6315 kB]
+Get:4 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
+Get:5 http://mirror-ubc.debian.org unstable/non-free Sources [98.1 kB]
+Get:6 http://mirror-ubc.debian.org unstable/main kfreebsd-i386 Packages [5652 kB]
Ign http://incoming.debian.org InRelease
-Get:8 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main kfreebsd-i386 Packages [5652 kB]
-Get:12 http://incoming.debian.org unstable/contrib kfreebsd-i386 Packages [37.0 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 24.9 MB in 15s (1594 kB/s)
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org Release [1601 B]
+Get:9 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:10 http://mirror-ubc.debian.org unstable/contrib kfreebsd-i386 Packages [37.0 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
+Get:13 http://incoming.debian.org unstable/main kfreebsd-i386 Packages [5652 kB]
+Get:14 http://incoming.debian.org unstable/contrib kfreebsd-i386 Packages [37.0 kB]
+Get:15 http://incoming.debian.org Sources [14.5 kB]
+Get:16 http://incoming.debian.org Packages [117 kB]
+Fetched 24.9 MB in 18s (1380 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,10 +78,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (287 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (359 kB/s)
Download complete and in download only mode
Check arch
@@ -175,34 +175,34 @@ The following NEW packages will be installed:
0 upgraded, 26 newly installed, 0 to remove and 13 not upgraded.
Need to get 10.7 MB of archives.
After this operation, 26.4 MB of additional disk space will be used.
-Get:1 http://debian.netcologne.de/debian/ unstable/main libpipeline1 kfreebsd-i386 1.2.1-1 [38.4 kB]
-Get:2 http://debian.netcologne.de/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.18.1.1-9 [26.7 kB]
-Get:3 http://debian.netcologne.de/debian/ unstable/main libmagic1 kfreebsd-i386 5.11-2 [204 kB]
-Get:4 http://debian.netcologne.de/debian/ unstable/main libpcre3 kfreebsd-i386 1:8.30-5 [241 kB]
-Get:5 http://debian.netcologne.de/debian/ unstable/main libxml2 kfreebsd-i386 2.8.0+dfsg1-5 [904 kB]
-Get:6 http://debian.netcologne.de/debian/ unstable/main libffi5 kfreebsd-i386 3.0.10-3 [20.3 kB]
-Get:7 http://debian.netcologne.de/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.32.3-1 [2060 kB]
-Get:8 http://debian.netcologne.de/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.5-1 [151 kB]
-Get:9 http://debian.netcologne.de/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5 [440 kB]
-Get:10 http://debian.netcologne.de/debian/ unstable/main libgettextpo0 kfreebsd-i386 0.18.1.1-9 [140 kB]
-Get:11 http://debian.netcologne.de/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.3 [204 kB]
-Get:12 http://debian.netcologne.de/debian/ unstable/main groff-base kfreebsd-i386 1.21-9 [1095 kB]
-Get:13 http://debian.netcologne.de/debian/ unstable/main man-db kfreebsd-i386 2.6.2-1 [1038 kB]
-Get:14 http://debian.netcologne.de/debian/ unstable/main file kfreebsd-i386 5.11-2 [51.5 kB]
-Get:15 http://debian.netcologne.de/debian/ unstable/main gettext-base kfreebsd-i386 0.18.1.1-9 [131 kB]
-Get:16 http://debian.netcologne.de/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://debian.netcologne.de/debian/ unstable/main html2text kfreebsd-i386 1.3.2a-15 [101 kB]
-Get:18 http://debian.netcologne.de/debian/ unstable/main gettext kfreebsd-i386 0.18.1.1-9 [1894 kB]
-Get:19 http://debian.netcologne.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://debian.netcologne.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://debian.netcologne.de/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://debian.netcologne.de/debian/ unstable/main diffstat kfreebsd-i386 1.55-3 [29.0 kB]
-Get:23 http://debian.netcologne.de/debian/ unstable/main libtinfo-dev kfreebsd-i386 5.9-10 [93.1 kB]
-Get:24 http://debian.netcologne.de/debian/ unstable/main libncurses5-dev kfreebsd-i386 5.9-10 [210 kB]
-Get:25 http://debian.netcologne.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://debian.netcologne.de/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.7.dfsg-13 [213 kB]
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.2.1-1 [38.4 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.18.1.1-9 [26.7 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 5.11-2 [204 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 kfreebsd-i386 1:8.30-5 [241 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.8.0+dfsg1-5 [904 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-i386 3.0.10-3 [20.3 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.32.3-1 [2060 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.5-1 [151 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5 [440 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-i386 0.18.1.1-9 [140 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.3 [204 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.21-9 [1095 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.6.2-1 [1038 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-i386 5.11-2 [51.5 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.18.1.1-9 [131 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-i386 1.3.2a-15 [101 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-i386 0.18.1.1-9 [1894 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-i386 1.55-3 [29.0 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-i386 5.9-10 [93.1 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-i386 5.9-10 [210 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.7 MB in 1s (6041 kB/s)
+Fetched 10.7 MB in 1s (10.6 MB/s)
Selecting previously unselected package libpipeline1:kfreebsd-i386.
(Reading database ... 11227 files and directories currently installed.)
Unpacking libpipeline1:kfreebsd-i386 (from .../libpipeline1_1.2.1-1_kfreebsd-i386.deb) ...
@@ -305,12 +305,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -323,7 +323,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
@@ -331,25 +331,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -369,10 +369,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -385,12 +385,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -425,8 +425,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -441,10 +441,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -465,24 +465,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
@@ -510,14 +510,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -543,7 +543,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -578,8 +578,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -605,7 +605,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -620,64 +620,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_kfreebsd-i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org> >../samtools_0.1.18-2_kfreebsd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.18-3_kfreebsd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1513
+Build finished at 20120727-1543
-samtools_0.1.18-2_kfreebsd-i386.changes:
+samtools_0.1.18-3_kfreebsd-i386.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org>
+Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- e6caa849974d817e29efb83bf5e3d56e832f4769 533754 samtools_0.1.18-2_kfreebsd-i386.deb
- e4239efcd784e9fbbadabbd3ed88d38c3997f64a 160586 libbam-dev_0.1.18-2_kfreebsd-i386.deb
+ 62d5dd1176b665472c645ed79219ba0916b9043b 533734 samtools_0.1.18-3_kfreebsd-i386.deb
+ 301e198be416c2fbc53c0fb898c221d98e7a8383 160710 libbam-dev_0.1.18-3_kfreebsd-i386.deb
Checksums-Sha256:
- 66fe54b4d029aeb954eaf9da191f15b0b425fdf69ea1db2fed3f622b51aa950d 533754 samtools_0.1.18-2_kfreebsd-i386.deb
- d1ec8eb701ab60344ba07ab5c7d3ebb26d49bb38793f4c387bde978fb7fe69e8 160586 libbam-dev_0.1.18-2_kfreebsd-i386.deb
+ 4b7593ea23b756d10e6c1abfe96c8c5721f78e44853216228d142ad1012d0263 533734 samtools_0.1.18-3_kfreebsd-i386.deb
+ 2269e3ee3c2e9486b9715e754aa0e1212e09f3880c835a9380c9d60d883d3883 160710 libbam-dev_0.1.18-3_kfreebsd-i386.deb
Files:
- 9592907ebb2fff8a8f42e17bd07f1aa5 533754 science optional samtools_0.1.18-2_kfreebsd-i386.deb
- 7cf87258eb269a602a7ee4deefe1f6d9 160586 libdevel optional libbam-dev_0.1.18-2_kfreebsd-i386.deb
+ 176fe81a452f916674dbf0d376eb4d7e 533734 science optional samtools_0.1.18-3_kfreebsd-i386.deb
+ f10f8b19b1ff958d5aaaee2b3449ff8e 160710 libdevel optional libbam-dev_0.1.18-3_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_kfreebsd-i386.deb
+samtools_0.1.18-3_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 533754 bytes: control archive= 1769 bytes.
+ size 533734 bytes: control archive= 1766 bytes.
801 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 990
@@ -693,31 +694,31 @@ samtools_0.1.18-2_kfreebsd-i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/samtools/examples/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2012-07-27 15:13 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2012-07-27 15:43 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-07-27 15:13 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-07-27 15:43 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:13 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:13 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/samtools/
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:43 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:43 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/samtools/
-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
@@ -730,31 +731,31 @@ drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-07-27 15:13 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/bin/
--rwxr-xr-x root/root 134212 2012-07-27 15:13 ./usr/bin/bcftools
--rwxr-xr-x root/root 24676 2012-07-27 15:13 ./usr/bin/razip
--rwxr-xr-x root/root 399924 2012-07-27 15:13 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/samtools/
--rwxr-xr-x root/root 16472 2012-07-27 15:13 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6844 2012-07-27 15:13 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6844 2012-07-27 15:13 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10576 2012-07-27 15:13 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7452 2012-07-27 15:13 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-2_kfreebsd-i386.deb
+-rwxr-xr-x root/root 5778 2012-07-27 15:43 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/bin/
+-rwxr-xr-x root/root 134212 2012-07-27 15:43 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24676 2012-07-27 15:43 ./usr/bin/razip
+-rwxr-xr-x root/root 399924 2012-07-27 15:43 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/samtools/
+-rwxr-xr-x root/root 16472 2012-07-27 15:43 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6844 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6844 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10576 2012-07-27 15:43 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7452 2012-07-27 15:43 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-3_kfreebsd-i386.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 160586 bytes: control archive= 929 bytes.
+ size 160710 bytes: control archive= 929 bytes.
682 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 400
@@ -768,20 +769,20 @@ libbam-dev_0.1.18-2_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/
--rw-r--r-- root/root 299796 2012-07-27 15:13 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/include/samtools/
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
+-rw-r--r-- root/root 299796 2012-07-27 15:43 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/samtools/
-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
@@ -800,7 +801,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1343401937-78235/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1343403637-81390/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -809,17 +810,17 @@ Not cleaning session: cloned chroot in use
Architecture: kfreebsd-i386
Build-Space: 11026
-Build-Time: 49
+Build-Time: 71
Distribution: sid
-Install-Time: 8
-Job: samtools_0.1.18-2
+Install-Time: 23
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 94
-Source-Version: 0.1.18-2
+Package-Time: 199
+Source-Version: 0.1.18-3
Space: 11026
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1513
-Build needed 00:01:34, 11026k disc space
-Signature with key '52E1CE73' requested:
+Finished at 20120727-1543
+Build needed 00:03:19, 11026k disc space
+Signature with key 'B3DA9773' requested:
diff --git a/mips.log b/mips.log
index d192cd8..410e135 100644
--- a/mips.log
+++ b/mips.log
@@ -1,41 +1,42 @@
-From buildd2 at corelli.debian.org Fri Jul 27 15:33:27 2012
-Return-path: <buildd2 at corelli.debian.org>
+From buildd at lucatelli.debian.org Fri Jul 27 16:04:29 2012
+Return-path: <buildd at lucatelli.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd2 at corelli.debian.org>)
- id 1SumXf-0002B0-FW
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:33:27 +0000
-Received: from corelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4489])
+ (Exim 4.72) (envelope-from <buildd at lucatelli.debian.org>)
+ id 1Sun1h-0000IO-EZ
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 16:04:29 +0000
+Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=corelli.debian.org, EMAIL=hostmaster at corelli.debian.org (verified)
+ CN=lucatelli.debian.org,
+ EMAIL=hostmaster at lucatelli.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd2 at corelli.debian.org>)
- id 1SumXd-00055o-QE
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:33:26 +0000
-Received: from buildd2 by corelli.debian.org with local (Exim 4.72)
- (envelope-from <buildd2 at corelli.debian.org>) id 1SumXa-0005ZD-OG
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:33:22 +0000
-Date: Fri, 27 Jul 2012 15:33:22 +0000
-Message-Id: <E1SumXa-0005ZD-OG at corelli.debian.org>
-From: buildd on corelli <buildd2 at corelli.debian.org>
+ (Exim 4.72) (envelope-from <buildd at lucatelli.debian.org>)
+ id 1Sun1f-0006Qs-DS
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 16:04:28 +0000
+Received: from buildd by lucatelli.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at lucatelli.debian.org>) id 1Sun1c-0006ab-Lp
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 16:04:24 +0000
+Date: Fri, 27 Jul 2012 16:04:24 +0000
+Message-Id: <E1Sun1c-0006ab-Lp at lucatelli.debian.org>
+From: buildd on lucatelli <buildd at lucatelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on mips (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-3 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on corelli.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (mips) 27 Jul 2012 15:07 ║
+║ samtools 0.1.18-3 (mips) 27 Jul 2012 15:38 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: mips
Get:1 http://mirror-ubc.debian.org unstable InRelease [249 kB]
Get:2 http://incoming.debian.org unstable InRelease [249 kB]
@@ -52,9 +53,9 @@ Get:11 http://incoming.debian.org unstable/main mips Packages [5964 kB]
Get:12 http://mirror-ubc.debian.org unstable/contrib mips Packages [38.3 kB]
Get:13 http://incoming.debian.org unstable/contrib mips Packages [38.3 kB]
Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 25.6 MB in 1min 36s (264 kB/s)
+Get:15 http://incoming.debian.org Sources [14.5 kB]
+Get:16 http://incoming.debian.org Packages [117 kB]
+Fetched 25.6 MB in 1min 39s (256 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,10 +77,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (361 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (347 kB/s)
Download complete and in download only mode
Check arch
@@ -99,12 +100,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 69 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 70 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 69 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 70 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -156,7 +157,7 @@ Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- liblzma5 libmagic1 libncurses5 libpipeline1 libtinfo-dev libtinfo5
+ liblzma5 libmagic1 libncurses5 libpcre3 libpipeline1 libtinfo-dev libtinfo5
libunistring0 libxml2 man-db ncurses-bin po-debconf zlib1g
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
@@ -168,13 +169,13 @@ Recommended packages:
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
The following packages will be upgraded:
liblzma5 libncurses5 libtinfo5 ncurses-bin zlib1g
-5 upgraded, 25 newly installed, 0 to remove and 64 not upgraded.
-Need to get 11.4 MB of archives.
-After this operation, 28.9 MB of additional disk space will be used.
+5 upgraded, 26 newly installed, 0 to remove and 65 not upgraded.
+Need to get 11.7 MB of archives.
+After this operation, 29.3 MB of additional disk space will be used.
Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin mips 5.9-10 [331 kB]
Get:2 http://mirror-ubc.debian.org/debian/ unstable/main liblzma5 mips 5.1.1alpha+20120614-1 [209 kB]
Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 mips 5.9-10 [268 kB]
@@ -183,57 +184,60 @@ Get:5 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g mips 1:1.2.7.dfs
Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.1-1 [36.7 kB]
Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 mips 0.18.1.1-9 [26.7 kB]
Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.11-2 [201 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.8.0+dfsg1-5 [869 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.32.3-1 [1991 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.5-1 [140 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 mips 0.18.1.1-9 [139 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.3 [208 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-9 [1156 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.2-1 [1029 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.11-2 [51.5 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-9 [141 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-9 [1918 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-3 [28.7 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev mips 5.9-10 [104 kB]
-Get:28 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-10 [223 kB]
-Get:29 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:30 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.7.dfsg-13 [213 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 1:8.30-5 [245 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.8.0+dfsg1-5 [869 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.32.3-1 [1991 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.5-1 [140 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 mips 0.18.1.1-9 [139 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.3 [208 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-9 [1156 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.2-1 [1029 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.11-2 [51.5 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-9 [141 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-9 [1918 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-3 [28.7 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev mips 5.9-10 [104 kB]
+Get:29 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-10 [223 kB]
+Get:30 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:31 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.4 MB in 5s (2267 kB/s)
-(Reading database ... 10730 files and directories currently installed.)
+Fetched 11.7 MB in 5s (2208 kB/s)
+(Reading database ... 10710 files and directories currently installed.)
Preparing to replace ncurses-bin 5.9-8 (using .../ncurses-bin_5.9-10_mips.deb) ...
Unpacking replacement ncurses-bin ...
Setting up ncurses-bin (5.9-10) ...
-(Reading database ... 10730 files and directories currently installed.)
+(Reading database ... 10710 files and directories currently installed.)
Preparing to replace liblzma5:mips 5.1.1alpha+20110809-3 (using .../liblzma5_5.1.1alpha+20120614-1_mips.deb) ...
Unpacking replacement liblzma5:mips ...
Setting up liblzma5:mips (5.1.1alpha+20120614-1) ...
-(Reading database ... 10730 files and directories currently installed.)
+(Reading database ... 10710 files and directories currently installed.)
Preparing to replace libtinfo5:mips 5.9-8 (using .../libtinfo5_5.9-10_mips.deb) ...
Unpacking replacement libtinfo5:mips ...
Setting up libtinfo5:mips (5.9-10) ...
-(Reading database ... 10730 files and directories currently installed.)
+(Reading database ... 10710 files and directories currently installed.)
Preparing to replace libncurses5:mips 5.9-8 (using .../libncurses5_5.9-10_mips.deb) ...
Unpacking replacement libncurses5:mips ...
Setting up libncurses5:mips (5.9-10) ...
-(Reading database ... 10730 files and directories currently installed.)
+(Reading database ... 10710 files and directories currently installed.)
Preparing to replace zlib1g:mips 1:1.2.7.dfsg-11 (using .../zlib1g_1%3a1.2.7.dfsg-13_mips.deb) ...
Unpacking replacement zlib1g:mips ...
Setting up zlib1g:mips (1:1.2.7.dfsg-13) ...
Selecting previously unselected package libpipeline1:mips.
-(Reading database ... 10730 files and directories currently installed.)
+(Reading database ... 10710 files and directories currently installed.)
Unpacking libpipeline1:mips (from .../libpipeline1_1.2.1-1_mips.deb) ...
Selecting previously unselected package libasprintf0c2:mips.
Unpacking libasprintf0c2:mips (from .../libasprintf0c2_0.18.1.1-9_mips.deb) ...
Selecting previously unselected package libmagic1:mips.
Unpacking libmagic1:mips (from .../libmagic1_5.11-2_mips.deb) ...
+Selecting previously unselected package libpcre3:mips.
+Unpacking libpcre3:mips (from .../libpcre3_1%3a8.30-5_mips.deb) ...
Selecting previously unselected package libxml2:mips.
Unpacking libxml2:mips (from .../libxml2_2.8.0+dfsg1-5_mips.deb) ...
Selecting previously unselected package libffi5:mips.
@@ -281,6 +285,7 @@ Unpacking zlib1g-dev:mips (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mips.deb) ...
Setting up libpipeline1:mips (1.2.1-1) ...
Setting up libasprintf0c2:mips (0.18.1.1-9) ...
Setting up libmagic1:mips (5.11-2) ...
+Setting up libpcre3:mips (1:8.30-5) ...
Setting up libxml2:mips (2.8.0+dfsg1-5) ...
Setting up libffi5:mips (3.0.10-3) ...
Setting up libglib2.0-0:mips (2.32.3-1) ...
@@ -311,11 +316,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 65 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 3.2.0-0.bpo.1-octeon mips (mips64)
Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.2 g++-4.6_4.6.3-7 gcc-4.6_4.6.3-7 libc6-dev_2.13-33 libstdc++6_4.7.0-12 libstdc++6-4.6-dev_4.6.3-7 linux-libc-dev_3.2.19-1
-Package versions: apt_0.9.5.1 base-files_6.10 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-6 cpp-4.6_4.6.3-7 dash_0.5.7-3 debconf_1.5.43 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.4.2 dpkg-dev_1.16.4.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-6 g++-4.6_4.6.3-7 gcc_4:4.6.3-6 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7-base_4.7.0-12 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-9 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-7 libapt-pkg4.12_0.9.5.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-7 libblkid1_2.20.1-5 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.2 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-1+b1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-12 libgdbm3_1.8.3-10 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.0-12 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-4 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-2 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.2-2 libstdc++6_4.7.0-12 libstdc++6-4.6-dev_4.6.3-7 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.19-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian6 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5 multiarch-support_2.13-33 ncurses-base_5.9-8 ncurses-bin_5.9-10 netbase_5.0 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-11 perl-base_5.14.2-11 perl-modules_5.14.2-11 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.3p2-1.1 sysv-rc_2.88dsf-27 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Package versions: apt_0.9.5.1 base-files_6.10 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-6 cpp-4.6_4.6.3-7 dash_0.5.7-3 debconf_1.5.43 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.4.2 dpkg-dev_1.16.4.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-6 g++-4.6_4.6.3-7 gcc_4:4.6.3-6 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7-base_4.7.0-12 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-9 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-7 libapt-pkg4.12_0.9.5.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-7 libblkid1_2.20.1-5 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.2 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-1+b1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-12 libgdbm3_1.8.3-10 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.0-12 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-4 libsemanage-common_2.1.6-5 libsemanage1_2.1.6-5 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.2-2 libstdc++6_4.7.0-12 libstdc++6-4.6-dev_4.6.3-7 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.19-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian6 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5 multiarch-support_2.13-33 ncurses-base_5.9-8 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-11 perl-base_5.14.2-11 perl-modules_5.14.2-11 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.3p2-1.1 sysv-rc_2.88dsf-26 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -325,13 +330,13 @@ Package versions: apt_0.9.5.1 base-files_6.10 base-passwd_3.5.24 bash_4.2-2 binu
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -344,7 +349,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
@@ -352,25 +357,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -390,10 +395,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -406,12 +411,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -446,8 +451,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -462,10 +467,10 @@ gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=6
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -486,24 +491,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -525,14 +530,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -558,7 +563,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -593,8 +598,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -620,7 +625,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -635,64 +640,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_mips.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org> >../samtools_0.1.18-2_mips.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../samtools_0.1.18-3_mips.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1533
+Build finished at 20120727-1604
-samtools_0.1.18-2_mips.changes:
+samtools_0.1.18-3_mips.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
-Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org>
+Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- 1e6f2e7d1256c1f20d62b8c1dc2aa88284687f8a 525022 samtools_0.1.18-2_mips.deb
- 2103520b2fa9f1081a0452fc08da309a9b12942f 162998 libbam-dev_0.1.18-2_mips.deb
+ b19cd0fcbd83a2600a37b447235b9303c9615e60 525342 samtools_0.1.18-3_mips.deb
+ 1fbd24bf59e3d470f67e6788a151e25233d06090 163210 libbam-dev_0.1.18-3_mips.deb
Checksums-Sha256:
- 254fc1e9ddfd18395a50c6c89c8241431afa69a43f2f069ba6a8428af051a290 525022 samtools_0.1.18-2_mips.deb
- 9632d34be16163f57274720135c8b437c64653ccde8f3e8c396f6339275b8ce4 162998 libbam-dev_0.1.18-2_mips.deb
+ ce993d4a71e36b984a273334831442e7d33018ac1e861bd90894220f2007c945 525342 samtools_0.1.18-3_mips.deb
+ df94beee0cd0c7a2fbfd92a2ca6eae14fcd8f34b53d381236597b62331de7483 163210 libbam-dev_0.1.18-3_mips.deb
Files:
- ac982ec5b317b07ea294b16e52de99d8 525022 science optional samtools_0.1.18-2_mips.deb
- aff061d43305d6b844a16026ddc09eae 162998 libdevel optional libbam-dev_0.1.18-2_mips.deb
+ 866934ed8a0d7da77b303fcfe430dde6 525342 science optional samtools_0.1.18-3_mips.deb
+ fce1cc71ae8f79e4a460f40c6d3bef90 163210 libdevel optional libbam-dev_0.1.18-3_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_mips.deb
+samtools_0.1.18-3_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 525022 bytes: control archive= 1765 bytes.
+ size 525342 bytes: control archive= 1765 bytes.
791 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1106
@@ -708,68 +714,68 @@ samtools_0.1.18-2_mips.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/samtools/
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+drwxr-xr-x root/root 0 2012-07-27 16:02 ./
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7472 2012-07-27 16:03 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9252 2012-07-27 16:03 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 12432 2012-07-27 16:03 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7472 2012-07-27 16:03 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 17692 2012-07-27 16:03 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/bin/
+-rwxr-xr-x root/root 155204 2012-07-27 16:03 ./usr/bin/bcftools
+-rwxr-xr-x root/root 440320 2012-07-27 16:03 ./usr/bin/samtools
+-rwxr-xr-x root/root 29296 2012-07-27 16:03 ./usr/bin/razip
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/samtools/
-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 5778 2012-07-27 15:32 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:31 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:31 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 5778 2012-07-27 16:03 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+drwxr-xr-x root/root 0 2012-07-27 16:02 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2012-07-27 15:50 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2012-07-27 15:19 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1966 2012-07-27 16:03 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2012-07-27 15:32 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/lib/samtools/
--rwxr-xr-x root/root 12432 2012-07-27 15:32 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7472 2012-07-27 15:32 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7472 2012-07-27 15:32 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9252 2012-07-27 15:32 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 17692 2012-07-27 15:32 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/bin/
--rwxr-xr-x root/root 155204 2012-07-27 15:32 ./usr/bin/bcftools
--rwxr-xr-x root/root 440320 2012-07-27 15:32 ./usr/bin/samtools
--rwxr-xr-x root/root 29296 2012-07-27 15:32 ./usr/bin/razip
-lrwxrwxrwx root/root 0 2012-07-27 15:32 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-2_mips.deb
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2012-07-27 16:02 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 16:02 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 16:02 ./usr/share/man/man1/samtools.1.gz
+lrwxrwxrwx root/root 0 2012-07-27 16:03 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-3_mips.deb
────────────────────────────
new debian package, version 2.0.
- size 162998 bytes: control archive= 930 bytes.
+ size 163210 bytes: control archive= 925 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 467
@@ -783,25 +789,25 @@ libbam-dev_0.1.18-2_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/include/samtools/
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/lib/
+-rw-r--r-- root/root 335554 2012-07-27 16:03 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/include/samtools/
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/lib/
--rw-r--r-- root/root 335554 2012-07-27 15:32 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -815,10 +821,8 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-e0fa827d-2930-47ab-919a-e891a4214d2f/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L
+Purging /var/lib/schroot/mount/sid-mips-sbuild-5e383676-c884-4bd9-8f03-7932a12a9603/build/buildd-samtools_0.1.18-3-mips-BQrOiu
Not cleaning session: cloned chroot in use
-Can't open average time db /var/lib/sbuild/avg-build-times
-Can't open average space db /var/lib/sbuild/avg-build-space
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
@@ -826,78 +830,76 @@ Can't open average space db /var/lib/sbuild/avg-build-space
Architecture: mips
Build-Space: 10956
-Build-Time: 1307
+Build-Time: 1302
Distribution: sid
-Install-Time: 81
-Job: samtools_0.1.18-2
+Install-Time: 93
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 1532
-Source-Version: 0.1.18-2
+Package-Time: 1543
+Source-Version: 0.1.18-3
Space: 10956
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1533
-Build needed 00:25:32, 10956k disc space
-Signature with key 'B5319330' requested:
+Finished at 20120727-1604
+Build needed 00:25:43, 10956k disc space
+Signature with key '86ADA8B4' requested:
-From buildd at rem.debian.org Fri Jul 27 15:31:57 2012
-Return-path: <buildd at rem.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at mayer.debian.org Fri Jul 27 15:45:41 2012
+Return-path: <buildd at mayer.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
- id 1SumWC-0001kx-Kx
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:56 +0000
-Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1SumjU-0005sg-GU
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:40 +0000
+Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
- id 1SumWB-00054a-Ja
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:55 +0000
-Received: from buildd by rem.debian.org with local (Exim 4.72)
- (envelope-from <buildd at rem.debian.org>) id 1SumWA-0000eV-1l
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:54 +0000
-Date: Fri, 27 Jul 2012 15:31:54 +0000
-Message-Id: <E1SumWA-0000eV-1l at rem.debian.org>
-From: buildd on rem <buildd at rem.debian.org>
+ CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1SumjS-0001vj-Ou
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:39 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at mayer.debian.org>) id 1SumjQ-0000sF-Fd
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:36 +0000
+Date: Fri, 27 Jul 2012 15:45:36 +0000
+Message-Id: <E1SumjQ-0000sF-Fd at mayer.debian.org>
+From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-3 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (mipsel) 27 Jul 2012 15:23 ║
+║ samtools 0.1.18-3 (mipsel) 27 Jul 2012 15:38 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: mipsel
-Get:1 http://mirror.ayous.org unstable InRelease [249 kB]
-Get:2 http://incoming.debian.org unstable InRelease [249 kB]
-Get:3 http://mirror.ayous.org unstable/main Sources [6317 kB]
+Get:1 http://debian.oregonstate.edu sid InRelease [249 kB]
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:5 http://mirror.ayous.org unstable/contrib Sources [53.9 kB]
-Get:6 http://mirror.ayous.org unstable/non-free Sources [98.1 kB]
-Get:7 http://mirror.ayous.org unstable/main mipsel Packages [5970 kB]
-Get:8 http://mirror.ayous.org unstable/contrib mipsel Packages [38.3 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main mipsel Packages [5971 kB]
-Get:12 http://incoming.debian.org unstable/contrib mipsel Packages [38.3 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [114 kB]
-Fetched 25.6 MB in 1min 10s (361 kB/s)
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://incoming.debian.org Release [1601 B]
+Get:4 http://debian.oregonstate.edu sid/main Sources [6315 kB]
+Hit http://incoming.debian.org sid/main Sources
+Hit http://incoming.debian.org sid/contrib Sources
+Hit http://incoming.debian.org sid/main mipsel Packages
+Hit http://incoming.debian.org sid/contrib mipsel Packages
+Get:5 http://incoming.debian.org Sources [14.5 kB]
+Get:6 http://incoming.debian.org Packages [117 kB]
+Get:7 http://debian.oregonstate.edu sid/contrib Sources [53.9 kB]
+Get:8 http://debian.oregonstate.edu sid/main mipsel Packages [5971 kB]
+Get:9 http://debian.oregonstate.edu sid/contrib mipsel Packages [38.3 kB]
+Fetched 12.8 MB in 35s (359 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -919,10 +921,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (285 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (350 kB/s)
Download complete and in download only mode
Check arch
@@ -942,12 +944,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -997,62 +999,31 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ diffstat file gettext gettext-base groff-base html2text intltool-debian
+ libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0 libmagic1
+ libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
+ devscripts dh-make gettext-doc groff ncurses-doc less www-browser
+ libmail-box-perl procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 18 not upgraded.
-Need to get 10.6 MB of archives.
-After this operation, 29.3 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.1-1 [36.7 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main libasprintf0c2 mipsel 0.18.1.1-9 [26.8 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.11-2 [202 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 1:8.30-5 [245 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.8.0+dfsg1-5 [868 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main libffi5 mipsel 3.0.10-3 [22.8 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.32.3-1 [1985 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.5-1 [139 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main libgettextpo0 mipsel 0.18.1.1-9 [139 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 9.0.3 [207 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-9 [1143 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.2-1 [1029 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.11-2 [51.5 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-9 [140 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-9 [1918 kB]
-Get:19 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.55-3 [28.8 kB]
-Get:23 http://mirror.ayous.org/debian/ unstable/main libtinfo-dev mipsel 5.9-10 [102 kB]
-Get:24 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.9-10 [221 kB]
-Get:25 http://mirror.ayous.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.7.dfsg-13 [215 kB]
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0 libxml2
+ man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.6 MB in 6s (1600 kB/s)
+0 upgraded, 24 newly installed, 0 to remove and 17 not upgraded.
+Need to get 0 B/10.2 MB of archives.
+After this operation, 28.3 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1:mipsel.
-(Reading database ... 10726 files and directories currently installed.)
+(Reading database ... 10891 files and directories currently installed.)
Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
Selecting previously unselected package libasprintf0c2:mipsel.
Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-9_mipsel.deb) ...
Selecting previously unselected package libmagic1:mipsel.
Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
-Selecting previously unselected package libpcre3:mipsel.
-Unpacking libpcre3:mipsel (from .../libpcre3_1%3a8.30-5_mipsel.deb) ...
Selecting previously unselected package libxml2:mipsel.
Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-5_mipsel.deb) ...
Selecting previously unselected package libffi5:mipsel.
@@ -1065,8 +1036,6 @@ Selecting previously unselected package libunistring0:mipsel.
Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
Selecting previously unselected package libgettextpo0:mipsel.
Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-9_mipsel.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_mipsel.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
Selecting previously unselected package man-db.
@@ -1100,7 +1069,6 @@ Unpacking zlib1g-dev:mipsel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mipsel.deb) .
Setting up libpipeline1:mipsel (1.2.1-1) ...
Setting up libasprintf0c2:mipsel (0.18.1.1-9) ...
Setting up libmagic1:mipsel (5.11-2) ...
-Setting up libpcre3:mipsel (1:8.30-5) ...
Setting up libxml2:mipsel (2.8.0+dfsg1-5) ...
Setting up libffi5:mipsel (3.0.10-3) ...
Setting up libglib2.0-0:mipsel (2.32.3-1) ...
@@ -1108,9 +1076,6 @@ No schema files found: doing nothing.
Setting up libcroco3:mipsel (0.6.5-1) ...
Setting up libunistring0:mipsel (0.9.3-5) ...
Setting up libgettextpo0:mipsel (0.18.1.1-9) ...
-Setting up bsdmainutils (9.0.3) ...
-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 groff-base (1.21-9) ...
Setting up man-db (2.6.2-1) ...
Building database of manual pages ...
@@ -1131,11 +1096,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012d-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1146,12 +1111,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -1164,7 +1129,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
@@ -1172,25 +1137,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -1210,10 +1175,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -1226,12 +1191,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -1266,8 +1231,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -1282,10 +1247,10 @@ gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=6
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -1306,24 +1271,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -1345,14 +1310,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -1378,7 +1343,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -1413,8 +1378,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -1440,7 +1405,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -1452,67 +1417,70 @@ dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.18-2_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-3_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1531
+Build finished at 20120727-1545
-samtools_0.1.18-2_mipsel.changes:
+samtools_0.1.18-3_mipsel.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- a504d15f054ac891b1ba7284434385f36055c933 528714 samtools_0.1.18-2_mipsel.deb
- c66e727d2352afe7ef3951ed955346b8b00545c0 165552 libbam-dev_0.1.18-2_mipsel.deb
+ fbdad8c7b943d06b23a609601851719c79ae8249 528128 samtools_0.1.18-3_mipsel.deb
+ 0c31cedee12156cdaf9a3243b6979cdec73f0c43 165534 libbam-dev_0.1.18-3_mipsel.deb
Checksums-Sha256:
- 04d6a9bd7c5cd26399e5f857a9926d84e9bf8129e5fff69a8050f7bbfce89503 528714 samtools_0.1.18-2_mipsel.deb
- 9cac6f06e69744fb5e0d00a5ec86244df335296c8f0a9aac5b1a3c8156dd41ec 165552 libbam-dev_0.1.18-2_mipsel.deb
+ 10eff2a972b78b93caaa55f5fc7de3b34299ece6a0741d144d069d7c70ce2170 528128 samtools_0.1.18-3_mipsel.deb
+ b2a1d344243fe3d3d9aed637f9f5570911f574b48b3923db3bf28fa67f94276e 165534 libbam-dev_0.1.18-3_mipsel.deb
Files:
- c813d9138d332a5252f94c369916b746 528714 science optional samtools_0.1.18-2_mipsel.deb
- 4529f73dd815a7c74c6b207ac6d3a174 165552 libdevel optional libbam-dev_0.1.18-2_mipsel.deb
+ 366461221d46aa8a679a50c0e0cfe449 528128 science optional samtools_0.1.18-3_mipsel.deb
+ 0a5933504f5a307ad579a6a7de287738 165534 libdevel optional libbam-dev_0.1.18-3_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_mipsel.deb
+samtools_0.1.18-3_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 528714 bytes: control archive= 1765 bytes.
+ size 528128 bytes: control archive= 1760 bytes.
793 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1106
@@ -1528,68 +1496,68 @@ samtools_0.1.18-2_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/samtools/
--rwxr-xr-x root/root 9252 2012-07-27 15:31 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7472 2012-07-27 15:31 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 17692 2012-07-27 15:31 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 12432 2012-07-27 15:31 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7472 2012-07-27 15:31 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:31 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:31 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2012-07-27 15:31 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2012-07-27 15:30 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 1966 2012-07-27 15:31 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2012-07-27 15:44 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1966 2012-07-27 15:44 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/bin/
--rwxr-xr-x root/root 440320 2012-07-27 15:31 ./usr/bin/samtools
--rwxr-xr-x root/root 155204 2012-07-27 15:31 ./usr/bin/bcftools
--rwxr-xr-x root/root 29168 2012-07-27 15:31 ./usr/bin/razip
-lrwxrwxrwx root/root 0 2012-07-27 15:31 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-2_mipsel.deb
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:44 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:44 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2012-07-27 15:44 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/bin/
+-rwxr-xr-x root/root 155204 2012-07-27 15:44 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29168 2012-07-27 15:44 ./usr/bin/razip
+-rwxr-xr-x root/root 440320 2012-07-27 15:44 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17692 2012-07-27 15:44 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7472 2012-07-27 15:44 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7472 2012-07-27 15:44 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 12432 2012-07-27 15:44 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9252 2012-07-27 15:44 ./usr/lib/samtools/md5sum-lite
+lrwxrwxrwx root/root 0 2012-07-27 15:44 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-3_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 165552 bytes: control archive= 927 bytes.
+ size 165534 bytes: control archive= 922 bytes.
675 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 467
@@ -1603,25 +1571,25 @@ libbam-dev_0.1.18-2_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/include/samtools/
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/
--rw-r--r-- root/root 335626 2012-07-27 15:31 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/
+-rw-r--r-- root/root 335626 2012-07-27 15:44 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/include/samtools/
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1635,27 +1603,76 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-a7bf88ef-1513-4495-9eba-fbb46666b629/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-94144eca-09d3-4eb1-9fdc-0354750509b2/build/buildd-samtools_0.1.18-3-mipsel-zDspvi
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
+ html2text* intltool-debian* libasprintf0c2* libcroco3* libffi5*
+ libgettextpo0* libglib2.0-0* libmagic1* libncurses5-dev* libpipeline1*
+ libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 24 to remove and 17 not upgraded.
+After this operation, 28.3 MB disk space will be freed.
+(Reading database ... 12379 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libasprintf0c2:mipsel ...
+Removing libcroco3:mipsel ...
+Purging configuration files for libcroco3:mipsel ...
+Removing libglib2.0-0:mipsel ...
+Purging configuration files for libglib2.0-0:mipsel ...
+Removing libffi5:mipsel ...
+Purging configuration files for libffi5:mipsel ...
+Removing libgettextpo0:mipsel ...
+Removing libmagic1:mipsel ...
+Purging configuration files for libmagic1:mipsel ...
+Removing libncurses5-dev ...
+Removing libpipeline1:mipsel ...
+Purging configuration files for libpipeline1:mipsel ...
+Removing libtinfo-dev:mipsel ...
+Removing libunistring0:mipsel ...
+Purging configuration files for libunistring0:mipsel ...
+Removing libxml2:mipsel ...
+Purging configuration files for libxml2:mipsel ...
+Removing zlib1g-dev:mipsel ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10952
-Build-Time: 295
+Build-Space: 10956
+Build-Time: 309
Distribution: sid
-Install-Time: 72
-Job: samtools_0.1.18-2
+Install-Time: 48
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 471
-Source-Version: 0.1.18-2
-Space: 10952
+Package-Time: 428
+Source-Version: 0.1.18-3
+Space: 10956
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1531
-Build needed 00:07:51, 10952k disc space
-Signature with key 'BDA682F0' requested:
+Finished at 20120727-1545
+Build needed 00:07:08, 10956k disc space
+Signature with key '8C9FAB20' requested:
diff --git a/mipsel.log b/mipsel.log
index 994c654..92e8f50 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,60 +1,58 @@
-From buildd at rem.debian.org Fri Jul 27 15:31:57 2012
-Return-path: <buildd at rem.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at mayer.debian.org Fri Jul 27 15:45:41 2012
+Return-path: <buildd at mayer.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
- id 1SumWC-0001kx-Kx
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:56 +0000
-Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1SumjU-0005sg-GU
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:40 +0000
+Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
- id 1SumWB-00054a-Ja
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:55 +0000
-Received: from buildd by rem.debian.org with local (Exim 4.72)
- (envelope-from <buildd at rem.debian.org>) id 1SumWA-0000eV-1l
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:54 +0000
-Date: Fri, 27 Jul 2012 15:31:54 +0000
-Message-Id: <E1SumWA-0000eV-1l at rem.debian.org>
-From: buildd on rem <buildd at rem.debian.org>
+ CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1SumjS-0001vj-Ou
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:39 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at mayer.debian.org>) id 1SumjQ-0000sF-Fd
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:36 +0000
+Date: Fri, 27 Jul 2012 15:45:36 +0000
+Message-Id: <E1SumjQ-0000sF-Fd at mayer.debian.org>
+From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-3 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (mipsel) 27 Jul 2012 15:23 ║
+║ samtools 0.1.18-3 (mipsel) 27 Jul 2012 15:38 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: mipsel
-Get:1 http://mirror.ayous.org unstable InRelease [249 kB]
-Get:2 http://incoming.debian.org unstable InRelease [249 kB]
-Get:3 http://mirror.ayous.org unstable/main Sources [6317 kB]
+Get:1 http://debian.oregonstate.edu sid InRelease [249 kB]
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:5 http://mirror.ayous.org unstable/contrib Sources [53.9 kB]
-Get:6 http://mirror.ayous.org unstable/non-free Sources [98.1 kB]
-Get:7 http://mirror.ayous.org unstable/main mipsel Packages [5970 kB]
-Get:8 http://mirror.ayous.org unstable/contrib mipsel Packages [38.3 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main mipsel Packages [5971 kB]
-Get:12 http://incoming.debian.org unstable/contrib mipsel Packages [38.3 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [114 kB]
-Fetched 25.6 MB in 1min 10s (361 kB/s)
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://incoming.debian.org Release [1601 B]
+Get:4 http://debian.oregonstate.edu sid/main Sources [6315 kB]
+Hit http://incoming.debian.org sid/main Sources
+Hit http://incoming.debian.org sid/contrib Sources
+Hit http://incoming.debian.org sid/main mipsel Packages
+Hit http://incoming.debian.org sid/contrib mipsel Packages
+Get:5 http://incoming.debian.org Sources [14.5 kB]
+Get:6 http://incoming.debian.org Packages [117 kB]
+Get:7 http://debian.oregonstate.edu sid/contrib Sources [53.9 kB]
+Get:8 http://debian.oregonstate.edu sid/main mipsel Packages [5971 kB]
+Get:9 http://debian.oregonstate.edu sid/contrib mipsel Packages [38.3 kB]
+Fetched 12.8 MB in 35s (359 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,10 +74,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (285 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (350 kB/s)
Download complete and in download only mode
Check arch
@@ -99,12 +97,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -154,62 +152,31 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ diffstat file gettext gettext-base groff-base html2text intltool-debian
+ libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0 libmagic1
+ libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
+ devscripts dh-make gettext-doc groff ncurses-doc less www-browser
+ libmail-box-perl procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 18 not upgraded.
-Need to get 10.6 MB of archives.
-After this operation, 29.3 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.1-1 [36.7 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main libasprintf0c2 mipsel 0.18.1.1-9 [26.8 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.11-2 [202 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 1:8.30-5 [245 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.8.0+dfsg1-5 [868 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main libffi5 mipsel 3.0.10-3 [22.8 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.32.3-1 [1985 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.5-1 [139 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main libgettextpo0 mipsel 0.18.1.1-9 [139 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 9.0.3 [207 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-9 [1143 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.2-1 [1029 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.11-2 [51.5 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-9 [140 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-9 [1918 kB]
-Get:19 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.55-3 [28.8 kB]
-Get:23 http://mirror.ayous.org/debian/ unstable/main libtinfo-dev mipsel 5.9-10 [102 kB]
-Get:24 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.9-10 [221 kB]
-Get:25 http://mirror.ayous.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.7.dfsg-13 [215 kB]
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0 libxml2
+ man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.6 MB in 6s (1600 kB/s)
+0 upgraded, 24 newly installed, 0 to remove and 17 not upgraded.
+Need to get 0 B/10.2 MB of archives.
+After this operation, 28.3 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1:mipsel.
-(Reading database ... 10726 files and directories currently installed.)
+(Reading database ... 10891 files and directories currently installed.)
Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
Selecting previously unselected package libasprintf0c2:mipsel.
Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-9_mipsel.deb) ...
Selecting previously unselected package libmagic1:mipsel.
Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
-Selecting previously unselected package libpcre3:mipsel.
-Unpacking libpcre3:mipsel (from .../libpcre3_1%3a8.30-5_mipsel.deb) ...
Selecting previously unselected package libxml2:mipsel.
Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-5_mipsel.deb) ...
Selecting previously unselected package libffi5:mipsel.
@@ -222,8 +189,6 @@ Selecting previously unselected package libunistring0:mipsel.
Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
Selecting previously unselected package libgettextpo0:mipsel.
Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-9_mipsel.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_mipsel.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
Selecting previously unselected package man-db.
@@ -257,7 +222,6 @@ Unpacking zlib1g-dev:mipsel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mipsel.deb) .
Setting up libpipeline1:mipsel (1.2.1-1) ...
Setting up libasprintf0c2:mipsel (0.18.1.1-9) ...
Setting up libmagic1:mipsel (5.11-2) ...
-Setting up libpcre3:mipsel (1:8.30-5) ...
Setting up libxml2:mipsel (2.8.0+dfsg1-5) ...
Setting up libffi5:mipsel (3.0.10-3) ...
Setting up libglib2.0-0:mipsel (2.32.3-1) ...
@@ -265,9 +229,6 @@ No schema files found: doing nothing.
Setting up libcroco3:mipsel (0.6.5-1) ...
Setting up libunistring0:mipsel (0.9.3-5) ...
Setting up libgettextpo0:mipsel (0.18.1.1-9) ...
-Setting up bsdmainutils (9.0.3) ...
-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 groff-base (1.21-9) ...
Setting up man-db (2.6.2-1) ...
Building database of manual pages ...
@@ -288,11 +249,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012d-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -303,12 +264,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -321,7 +282,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
@@ -329,25 +290,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -367,10 +328,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -383,12 +344,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -423,8 +384,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -439,10 +400,10 @@ gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=6
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -463,24 +424,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -502,14 +463,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -535,7 +496,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -570,8 +531,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -597,7 +558,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -609,67 +570,70 @@ dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.18-2_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-3_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1531
+Build finished at 20120727-1545
-samtools_0.1.18-2_mipsel.changes:
+samtools_0.1.18-3_mipsel.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- a504d15f054ac891b1ba7284434385f36055c933 528714 samtools_0.1.18-2_mipsel.deb
- c66e727d2352afe7ef3951ed955346b8b00545c0 165552 libbam-dev_0.1.18-2_mipsel.deb
+ fbdad8c7b943d06b23a609601851719c79ae8249 528128 samtools_0.1.18-3_mipsel.deb
+ 0c31cedee12156cdaf9a3243b6979cdec73f0c43 165534 libbam-dev_0.1.18-3_mipsel.deb
Checksums-Sha256:
- 04d6a9bd7c5cd26399e5f857a9926d84e9bf8129e5fff69a8050f7bbfce89503 528714 samtools_0.1.18-2_mipsel.deb
- 9cac6f06e69744fb5e0d00a5ec86244df335296c8f0a9aac5b1a3c8156dd41ec 165552 libbam-dev_0.1.18-2_mipsel.deb
+ 10eff2a972b78b93caaa55f5fc7de3b34299ece6a0741d144d069d7c70ce2170 528128 samtools_0.1.18-3_mipsel.deb
+ b2a1d344243fe3d3d9aed637f9f5570911f574b48b3923db3bf28fa67f94276e 165534 libbam-dev_0.1.18-3_mipsel.deb
Files:
- c813d9138d332a5252f94c369916b746 528714 science optional samtools_0.1.18-2_mipsel.deb
- 4529f73dd815a7c74c6b207ac6d3a174 165552 libdevel optional libbam-dev_0.1.18-2_mipsel.deb
+ 366461221d46aa8a679a50c0e0cfe449 528128 science optional samtools_0.1.18-3_mipsel.deb
+ 0a5933504f5a307ad579a6a7de287738 165534 libdevel optional libbam-dev_0.1.18-3_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_mipsel.deb
+samtools_0.1.18-3_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 528714 bytes: control archive= 1765 bytes.
+ size 528128 bytes: control archive= 1760 bytes.
793 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1106
@@ -685,68 +649,68 @@ samtools_0.1.18-2_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/samtools/
--rwxr-xr-x root/root 9252 2012-07-27 15:31 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7472 2012-07-27 15:31 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 17692 2012-07-27 15:31 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 12432 2012-07-27 15:31 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7472 2012-07-27 15:31 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:31 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:31 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2012-07-27 15:31 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2012-07-27 15:30 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 1966 2012-07-27 15:31 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2012-07-27 15:44 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1966 2012-07-27 15:44 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/bin/
--rwxr-xr-x root/root 440320 2012-07-27 15:31 ./usr/bin/samtools
--rwxr-xr-x root/root 155204 2012-07-27 15:31 ./usr/bin/bcftools
--rwxr-xr-x root/root 29168 2012-07-27 15:31 ./usr/bin/razip
-lrwxrwxrwx root/root 0 2012-07-27 15:31 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-2_mipsel.deb
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:44 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:44 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2012-07-27 15:44 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/bin/
+-rwxr-xr-x root/root 155204 2012-07-27 15:44 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29168 2012-07-27 15:44 ./usr/bin/razip
+-rwxr-xr-x root/root 440320 2012-07-27 15:44 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17692 2012-07-27 15:44 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7472 2012-07-27 15:44 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7472 2012-07-27 15:44 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 12432 2012-07-27 15:44 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9252 2012-07-27 15:44 ./usr/lib/samtools/md5sum-lite
+lrwxrwxrwx root/root 0 2012-07-27 15:44 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-3_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 165552 bytes: control archive= 927 bytes.
+ size 165534 bytes: control archive= 922 bytes.
675 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 467
@@ -760,25 +724,25 @@ libbam-dev_0.1.18-2_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/include/samtools/
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/
--rw-r--r-- root/root 335626 2012-07-27 15:31 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/
+-rw-r--r-- root/root 335626 2012-07-27 15:44 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/include/samtools/
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -792,27 +756,76 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-a7bf88ef-1513-4495-9eba-fbb46666b629/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-94144eca-09d3-4eb1-9fdc-0354750509b2/build/buildd-samtools_0.1.18-3-mipsel-zDspvi
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
+ html2text* intltool-debian* libasprintf0c2* libcroco3* libffi5*
+ libgettextpo0* libglib2.0-0* libmagic1* libncurses5-dev* libpipeline1*
+ libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 24 to remove and 17 not upgraded.
+After this operation, 28.3 MB disk space will be freed.
+(Reading database ... 12379 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libasprintf0c2:mipsel ...
+Removing libcroco3:mipsel ...
+Purging configuration files for libcroco3:mipsel ...
+Removing libglib2.0-0:mipsel ...
+Purging configuration files for libglib2.0-0:mipsel ...
+Removing libffi5:mipsel ...
+Purging configuration files for libffi5:mipsel ...
+Removing libgettextpo0:mipsel ...
+Removing libmagic1:mipsel ...
+Purging configuration files for libmagic1:mipsel ...
+Removing libncurses5-dev ...
+Removing libpipeline1:mipsel ...
+Purging configuration files for libpipeline1:mipsel ...
+Removing libtinfo-dev:mipsel ...
+Removing libunistring0:mipsel ...
+Purging configuration files for libunistring0:mipsel ...
+Removing libxml2:mipsel ...
+Purging configuration files for libxml2:mipsel ...
+Removing zlib1g-dev:mipsel ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10952
-Build-Time: 295
+Build-Space: 10956
+Build-Time: 309
Distribution: sid
-Install-Time: 72
-Job: samtools_0.1.18-2
+Install-Time: 48
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 471
-Source-Version: 0.1.18-2
-Space: 10952
+Package-Time: 428
+Source-Version: 0.1.18-3
+Space: 10956
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1531
-Build needed 00:07:51, 10952k disc space
-Signature with key 'BDA682F0' requested:
+Finished at 20120727-1545
+Build needed 00:07:08, 10956k disc space
+Signature with key '8C9FAB20' requested:
diff --git a/powerpc.log b/powerpc.log
index a9a9be8..de49be6 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,61 +1,62 @@
-From buildd at praetorius.debian.org Fri Jul 27 15:10:54 2012
-Return-path: <buildd at praetorius.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at poulenc.debian.org Fri Jul 27 15:43:22 2012
+Return-path: <buildd at poulenc.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
- id 1SumBp-0002aq-Tf
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:10:54 +0000
-Received: from [2001:6b0:e:2a18:214:5eff:fe97:268a]
- (helo=praetorius.debian.org)
+ (Exim 4.72) (envelope-from <buildd at poulenc.debian.org>)
+ id 1SumhF-0005Dv-RK
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:43:21 +0000
+Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
+ helo=poulenc.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=praetorius.debian.org,
- EMAIL=hostmaster at praetorius.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
- id 1SumBo-00043a-7w; Fri, 27 Jul 2012 15:10:52 +0000
-Received: from buildd by praetorius.debian.org with local (Exim 4.72)
- (envelope-from <buildd at praetorius.debian.org>)
- id 1SumBm-0003zD-Ln; Fri, 27 Jul 2012 15:10:50 +0000
-Date: Fri, 27 Jul 2012 15:10:50 +0000
-Message-Id: <E1SumBm-0003zD-Ln at praetorius.debian.org>
-From: buildd on praetorius <buildd at praetorius.debian.org>
-To: wouter at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on powerpc (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
+ CN=poulenc.debian.org, EMAIL=hostmaster at poulenc.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at poulenc.debian.org>)
+ id 1SumhE-0001pt-RZ; Fri, 27 Jul 2012 15:43:20 +0000
+Received: from buildd by poulenc.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at poulenc.debian.org>)
+ id 1SumhE-0008KF-Dq; Fri, 27 Jul 2012 15:43:20 +0000
+Message-Id: <E1SumhE-0008KF-Dq at poulenc.debian.org>
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Fri, 27 Jul 2012 15:43:20 +0000
+From: buildd on poulenc <buildd at poulenc.debian.org>
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.18-3 on powerpc (dist=sid)
+Key-Id: 050CE77C
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on praetorius.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on poulenc.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (powerpc) 27 Jul 2012 15:07 ║
+║ samtools 0.1.18-3 (powerpc) 27 Jul 2012 15:40 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: powerpc
-Get:1 http://ftp.se.debian.org unstable InRelease [249 kB]
-Get:2 http://ftp.se.debian.org unstable/main Sources [6317 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [249 kB]
+Get:2 http://ftp.uk.debian.org unstable/main Sources [6315 kB]
Get:3 http://incoming.debian.org unstable InRelease [249 kB]
-Get:4 http://ftp.se.debian.org unstable/contrib Sources [53.9 kB]
-Get:5 http://ftp.se.debian.org unstable/non-free Sources [98.1 kB]
-Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [6016 kB]
+Get:4 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
+Get:5 http://ftp.uk.debian.org unstable/non-free Sources [98.1 kB]
+Get:6 http://ftp.uk.debian.org unstable/main powerpc Packages [6016 kB]
Ign http://incoming.debian.org InRelease
-Get:7 http://ftp.se.debian.org unstable/contrib powerpc Packages [37.7 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:7 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:8 http://ftp.uk.debian.org unstable/contrib powerpc Packages [37.7 kB]
Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
Get:11 http://incoming.debian.org unstable/main powerpc Packages [6016 kB]
Get:12 http://incoming.debian.org unstable/contrib powerpc Packages [37.7 kB]
Get:13 http://incoming.debian.org Release.gpg [836 B]
Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 25.7 MB in 21s (1178 kB/s)
+Get:15 http://incoming.debian.org Sources [14.5 kB]
+Get:16 http://incoming.debian.org Packages [117 kB]
+Fetched 25.7 MB in 30s (836 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -77,10 +78,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (234 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 2s (144 kB/s)
Download complete and in download only mode
Check arch
@@ -100,12 +101,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 34 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 34 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -119,7 +120,7 @@ base-passwd: already installed (3.5.26)
bash: already installed (4.2-2)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.1)
+debianutils: already installed (4.3.2)
diffutils: already installed (1:3.2-6)
dpkg: already installed (1.16.4.3)
e2fsprogs: already installed (1.42.4-3)
@@ -127,8 +128,8 @@ findutils: already installed (4.4.2-4)
grep: already installed (2.12-2)
gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
-ncurses-base: already installed (5.9-9)
-ncurses-bin: already installed (5.9-9)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
perl-base: already installed (5.14.2-12)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
@@ -157,70 +158,53 @@ Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libncurses5 libpcre3 libpipeline1 libtinfo-dev libtinfo5
- libunistring0 libxml2 man-db ncurses-bin po-debconf
+ libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-The following packages will be upgraded:
- libncurses5 libtinfo5 ncurses-bin
-3 upgraded, 26 newly installed, 0 to remove and 31 not upgraded.
-Need to get 11.5 MB of archives.
+0 upgraded, 26 newly installed, 0 to remove and 28 not upgraded.
+Need to get 10.8 MB of archives.
After this operation, 28.9 MB of additional disk space will be used.
-Get:1 http://ftp.se.debian.org/debian/ unstable/main ncurses-bin powerpc 5.9-10 [333 kB]
-Get:2 http://ftp.se.debian.org/debian/ unstable/main libtinfo5 powerpc 5.9-10 [272 kB]
-Get:3 http://ftp.se.debian.org/debian/ unstable/main libncurses5 powerpc 5.9-10 [104 kB]
-Get:4 http://ftp.se.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.1-1 [38.5 kB]
-Get:5 http://ftp.se.debian.org/debian/ unstable/main libasprintf0c2 powerpc 0.18.1.1-9 [27.0 kB]
-Get:6 http://ftp.se.debian.org/debian/ unstable/main libmagic1 powerpc 5.11-2 [201 kB]
-Get:7 http://ftp.se.debian.org/debian/ unstable/main libpcre3 powerpc 1:8.30-5 [240 kB]
-Get:8 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.8.0+dfsg1-5 [851 kB]
-Get:9 http://ftp.se.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
-Get:10 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.32.3-1 [2044 kB]
-Get:11 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.5-1 [143 kB]
-Get:12 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
-Get:13 http://ftp.se.debian.org/debian/ unstable/main libgettextpo0 powerpc 0.18.1.1-9 [137 kB]
-Get:14 http://ftp.se.debian.org/debian/ unstable/main bsdmainutils powerpc 9.0.3 [208 kB]
-Get:15 http://ftp.se.debian.org/debian/ unstable/main groff-base powerpc 1.21-9 [1179 kB]
-Get:16 http://ftp.se.debian.org/debian/ unstable/main man-db powerpc 2.6.2-1 [1062 kB]
-Get:17 http://ftp.se.debian.org/debian/ unstable/main file powerpc 5.11-2 [51.7 kB]
-Get:18 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-9 [131 kB]
-Get:19 http://ftp.se.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:20 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:21 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-9 [1929 kB]
-Get:22 http://ftp.se.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp.se.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp.se.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:25 http://ftp.se.debian.org/debian/ unstable/main diffstat powerpc 1.55-3 [29.2 kB]
-Get:26 http://ftp.se.debian.org/debian/ unstable/main libtinfo-dev powerpc 5.9-10 [105 kB]
-Get:27 http://ftp.se.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-10 [211 kB]
-Get:28 http://ftp.se.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:29 http://ftp.se.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.7.dfsg-13 [213 kB]
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.1-1 [38.5 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 powerpc 0.18.1.1-9 [27.0 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.11-2 [201 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 1:8.30-5 [240 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.8.0+dfsg1-5 [851 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.32.3-1 [2044 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.5-1 [143 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 powerpc 0.18.1.1-9 [137 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 9.0.3 [208 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-9 [1179 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.2-1 [1062 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.11-2 [51.7 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-9 [131 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-9 [1929 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.55-3 [29.2 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev powerpc 5.9-10 [105 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-10 [211 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.5 MB in 2s (5676 kB/s)
-(Reading database ... 10745 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.9-9 (using .../ncurses-bin_5.9-10_powerpc.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-10) ...
-(Reading database ... 10745 files and directories currently installed.)
-Preparing to replace libtinfo5:powerpc 5.9-9 (using .../libtinfo5_5.9-10_powerpc.deb) ...
-Unpacking replacement libtinfo5:powerpc ...
-Setting up libtinfo5:powerpc (5.9-10) ...
-(Reading database ... 10745 files and directories currently installed.)
-Preparing to replace libncurses5:powerpc 5.9-9 (using .../libncurses5_5.9-10_powerpc.deb) ...
-Unpacking replacement libncurses5:powerpc ...
-Setting up libncurses5:powerpc (5.9-10) ...
+Fetched 10.8 MB in 3s (3574 kB/s)
Selecting previously unselected package libpipeline1:powerpc.
-(Reading database ... 10745 files and directories currently installed.)
+(Reading database ... 10700 files and directories currently installed.)
Unpacking libpipeline1:powerpc (from .../libpipeline1_1.2.1-1_powerpc.deb) ...
Selecting previously unselected package libasprintf0c2:powerpc.
Unpacking libasprintf0c2:powerpc (from .../libasprintf0c2_0.18.1.1-9_powerpc.deb) ...
@@ -306,11 +290,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 31 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-33 libstdc++6_4.7.1-2 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-2
-Package versions: apt_0.9.6 base-files_6.11 base-passwd_3.5.26 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-2 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.6 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.3 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-2 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.4-3 libstdc++6_4.7.1-2 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-33 ncurses-base_5.9-9 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.3p2-1.1 sysv-rc_2.88dsf-27 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Package versions: apt_0.9.6 base-files_6.11 base-passwd_3.5.26 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-2 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.6 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.3 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-2 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.4-3 libstdc++6_4.7.1-2 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-33 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.3p2-1.1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -321,12 +305,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -339,7 +323,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
@@ -347,25 +331,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -385,10 +369,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -401,12 +385,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -441,8 +425,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -457,10 +441,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -481,24 +465,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -520,14 +504,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -553,7 +537,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -588,8 +572,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -615,7 +599,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -627,67 +611,70 @@ dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_powerpc.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../samtools_0.1.18-2_powerpc.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../samtools_0.1.18-3_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1510
+Build finished at 20120727-1543
-samtools_0.1.18-2_powerpc.changes:
+samtools_0.1.18-3_powerpc.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org>
+Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- 526e893c91a8c60e7379b4bb2ead4c2371a49812 513788 samtools_0.1.18-2_powerpc.deb
- a1d4325586bf89cbc9e97e1be73bd0ae128c36a5 150414 libbam-dev_0.1.18-2_powerpc.deb
+ 201aa0d6e1cc27d7bdd24748bec86638e73a77db 513056 samtools_0.1.18-3_powerpc.deb
+ 8c590ff0ae64ab17f3590dbaf616af5246ea439f 149972 libbam-dev_0.1.18-3_powerpc.deb
Checksums-Sha256:
- 24e3c29d3ae4f99efb75dee2648f1990e2b704d2c8bfcb832fe94cc01e987c17 513788 samtools_0.1.18-2_powerpc.deb
- 03a4fb47ea65f56b8358f36590aea108c1129e0892bb80d4bd03876b243b2185 150414 libbam-dev_0.1.18-2_powerpc.deb
+ 9dced67a3b8160cbd39cf8f0bb1da3fe7593a9b3596ad8785c26875659004e3c 513056 samtools_0.1.18-3_powerpc.deb
+ e7e63cedf73288e26dbe039cdf5f85999412efa73404c856c7090cfcc2b388cf 149972 libbam-dev_0.1.18-3_powerpc.deb
Files:
- 60a3c941233db871ec58cb293307936d 513788 science optional samtools_0.1.18-2_powerpc.deb
- ace1b0d9145133516849a955abc2dd39 150414 libdevel optional libbam-dev_0.1.18-2_powerpc.deb
+ 78ad583f99e101926045d97bc30ac0be 513056 science optional samtools_0.1.18-3_powerpc.deb
+ f749f74ac053d1d83c8077ae9c3438d1 149972 libdevel optional libbam-dev_0.1.18-3_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_powerpc.deb
+samtools_0.1.18-3_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 513788 bytes: control archive= 1763 bytes.
+ size 513056 bytes: control archive= 1764 bytes.
794 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1013
@@ -703,68 +690,68 @@ samtools_0.1.18-2_powerpc.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/bin/
--rwxr-xr-x root/root 130976 2012-07-27 15:10 ./usr/bin/bcftools
--rwxr-xr-x root/root 25484 2012-07-27 15:10 ./usr/bin/razip
--rwxr-xr-x root/root 375080 2012-07-27 15:10 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/lib/samtools/
--rwxr-xr-x root/root 7348 2012-07-27 15:10 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 11080 2012-07-27 15:10 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 18528 2012-07-27 15:10 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7348 2012-07-27 15:10 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8036 2012-07-27 15:10 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2012-07-27 15:10 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2012-07-27 15:10 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2012-07-27 15:43 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2012-07-27 15:43 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/samtools/
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 5778 2012-07-27 15:43 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1966 2012-07-27 15:43 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2012-07-27 15:10 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 126609 2012-07-27 15:42 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 1966 2012-07-27 15:10 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/samtools/
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 5778 2012-07-27 15:10 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-lrwxrwxrwx root/root 0 2012-07-27 15:10 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-2_powerpc.deb
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7348 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11080 2012-07-27 15:43 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8036 2012-07-27 15:43 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7348 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 18528 2012-07-27 15:43 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/bin/
+-rwxr-xr-x root/root 375080 2012-07-27 15:43 ./usr/bin/samtools
+-rwxr-xr-x root/root 25484 2012-07-27 15:43 ./usr/bin/razip
+-rwxr-xr-x root/root 130976 2012-07-27 15:43 ./usr/bin/bcftools
+lrwxrwxrwx root/root 0 2012-07-27 15:43 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-3_powerpc.deb
───────────────────────────────
new debian package, version 2.0.
- size 150414 bytes: control archive= 926 bytes.
+ size 149972 bytes: control archive= 928 bytes.
676 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 409
@@ -778,25 +765,25 @@ libbam-dev_0.1.18-2_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/lib/
--rw-r--r-- root/root 276222 2012-07-27 15:10 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/include/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/samtools/
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
+-rw-r--r-- root/root 276222 2012-07-27 15:43 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -810,7 +797,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-105a1aa5-a0a8-46f0-a2ca-b14adcdb81dc/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-d948fd80-97e7-4ef9-88d6-d6707400a517/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -819,17 +806,17 @@ Not cleaning session: cloned chroot in use
Architecture: powerpc
Build-Space: 10504
-Build-Time: 86
+Build-Time: 81
Distribution: sid
-Install-Time: 79
-Job: samtools_0.1.18-2
+Install-Time: 49
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 207
-Source-Version: 0.1.18-2
+Package-Time: 177
+Source-Version: 0.1.18-3
Space: 10504
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1510
-Build needed 00:03:27, 10504k disc space
-
+Finished at 20120727-1543
+Build needed 00:02:57, 10504k disc space
+Signature with key '050CE77C' requested:
diff --git a/s390.log b/s390.log
index 127fbd5..26f4ee3 100644
--- a/s390.log
+++ b/s390.log
@@ -1,62 +1,61 @@
-From buildd at zandonai.debian.org Fri Jul 27 15:06:52 2012
-Return-path: <buildd at zandonai.debian.org>
+From buildd at zappa.debian.org Fri Jul 27 15:46:08 2012
+Return-path: <buildd at zappa.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1Sum7w-0001fy-9h
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:06:52 +0000
-Received: from zandonai.debian.org ([80.245.147.46])
+ (Exim 4.72) (envelope-from <buildd at zappa.debian.org>)
+ id 1Sumjw-00062B-5r
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:46:08 +0000
+Received: from [148.100.96.103] (helo=zappa.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=zandonai.debian.org,
- EMAIL=hostmaster at zandonai.debian.org (verified)
+ CN=zappa.debian.org, EMAIL=hostmaster at zappa.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1Sum7v-00008M-8I; Fri, 27 Jul 2012 15:06:51 +0000
-Received: from buildd by zandonai.debian.org with local (Exim 4.72)
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- id 1Sum7u-0003mU-9i; Fri, 27 Jul 2012 15:06:50 +0000
-Message-Id: <E1Sum7u-0003mU-9i at zandonai.debian.org>
+ (Exim 4.72) (envelope-from <buildd at zappa.debian.org>)
+ id 1Sumju-0001zC-Us; Fri, 27 Jul 2012 15:46:07 +0000
+Received: from buildd by zappa.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zappa.debian.org>)
+ id 1Sumjt-0007cl-KT; Fri, 27 Jul 2012 15:46:05 +0000
+Message-Id: <E1Sumjt-0007cl-KT at zappa.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:06:50 +0000
-From: buildd on zandonai <buildd at zandonai.debian.org>
+Date: Fri, 27 Jul 2012 15:46:05 +0000
+From: buildd on zappa <buildd at zappa.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-2 on s390 (dist=sid)
-Key-Id: E7C67939
+Subject: Log for successful build of samtools_0.1.18-3 on s390 (dist=sid)
+Key-Id: 0C4D1E93
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zappa.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (s390) 27 Jul 2012 15:05 ║
+║ samtools 0.1.18-3 (s390) 27 Jul 2012 15:42 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: s390
-Hit http://ftp.de.debian.org unstable InRelease
-Hit http://ftp.de.debian.org unstable/main Sources
-Hit http://ftp.de.debian.org unstable/contrib Sources
-Hit http://ftp.de.debian.org unstable/non-free Sources
-Hit http://ftp.de.debian.org unstable/main s390 Packages
-Hit http://ftp.de.debian.org unstable/contrib s390 Packages
-Hit http://incoming.debian.org unstable InRelease
+Get:1 http://incoming.debian.org unstable InRelease [249 kB]
+Get:2 http://ftp.us.debian.org unstable InRelease [249 kB]
Ign http://incoming.debian.org InRelease
-Hit http://incoming.debian.org unstable/main Sources
-Hit http://incoming.debian.org unstable/contrib Sources
-Hit http://incoming.debian.org unstable/non-free Sources
-Hit http://incoming.debian.org unstable/main s390 Packages
-Hit http://incoming.debian.org unstable/contrib s390 Packages
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Get:2 http://incoming.debian.org Release [1601 B]
-Get:3 http://incoming.debian.org Sources [14.3 kB]
-Get:4 http://incoming.debian.org Packages [113 kB]
-Fetched 129 kB in 2s (55.0 kB/s)
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1601 B]
+Get:5 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:6 http://ftp.us.debian.org unstable/main Sources [6315 kB]
+Get:7 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:8 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
+Get:9 http://incoming.debian.org unstable/main s390 Packages [5930 kB]
+Get:10 http://incoming.debian.org unstable/contrib s390 Packages [37.5 kB]
+Get:11 http://incoming.debian.org Sources [14.5 kB]
+Get:12 http://incoming.debian.org Packages [117 kB]
+Get:13 http://ftp.us.debian.org unstable/contrib Sources [53.9 kB]
+Get:14 http://ftp.us.debian.org unstable/non-free Sources [98.1 kB]
+Get:15 http://ftp.us.debian.org unstable/main s390 Packages [5930 kB]
+Get:16 http://ftp.us.debian.org unstable/contrib s390 Packages [37.5 kB]
+Fetched 25.5 MB in 53s (476 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -74,14 +73,13 @@ Download source files with APT
Reading package lists...
Building dependency tree...
-Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (287 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 0s (523 kB/s)
Download complete and in download only mode
Check arch
@@ -100,13 +98,11 @@ Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -117,7 +113,7 @@ Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diff
Checking for already installed dependencies...
base-files: already installed (6.11)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-3)
+bash: already installed (4.2-4)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
debianutils: already installed (4.3.2)
@@ -154,7 +150,6 @@ Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
-Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
@@ -172,39 +167,39 @@ The following NEW packages will be installed:
html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 26 newly installed, 0 to remove and 14 not upgraded.
Need to get 11.0 MB of archives.
After this operation, 29.1 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.1-1 [40.0 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 s390 0.18.1.1-9 [26.8 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.11-2 [205 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 1:8.30-5 [248 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.8.0+dfsg1-5 [892 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.32.3-1 [2122 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.5-1 [150 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 s390 0.18.1.1-9 [146 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 9.0.3 [213 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-9 [1148 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.2-1 [1074 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main file s390 5.11-2 [52.0 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-9 [152 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-9 [1959 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.55-3 [29.8 kB]
-Get:23 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev s390 5.9-10 [113 kB]
-Get:24 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-10 [213 kB]
-Get:25 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.7.dfsg-13 [215 kB]
+Get:1 http://ftp.us.debian.org/debian/ unstable/main libpipeline1 s390 1.2.1-1 [40.0 kB]
+Get:2 http://ftp.us.debian.org/debian/ unstable/main libasprintf0c2 s390 0.18.1.1-9 [26.8 kB]
+Get:3 http://ftp.us.debian.org/debian/ unstable/main libmagic1 s390 5.11-2 [205 kB]
+Get:4 http://ftp.us.debian.org/debian/ unstable/main libpcre3 s390 1:8.30-5 [248 kB]
+Get:5 http://ftp.us.debian.org/debian/ unstable/main libxml2 s390 2.8.0+dfsg1-5 [892 kB]
+Get:6 http://ftp.us.debian.org/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
+Get:7 http://ftp.us.debian.org/debian/ unstable/main libglib2.0-0 s390 2.32.3-1 [2122 kB]
+Get:8 http://ftp.us.debian.org/debian/ unstable/main libcroco3 s390 0.6.5-1 [150 kB]
+Get:9 http://ftp.us.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
+Get:10 http://ftp.us.debian.org/debian/ unstable/main libgettextpo0 s390 0.18.1.1-9 [146 kB]
+Get:11 http://ftp.us.debian.org/debian/ unstable/main bsdmainutils s390 9.0.3 [213 kB]
+Get:12 http://ftp.us.debian.org/debian/ unstable/main groff-base s390 1.21-9 [1148 kB]
+Get:13 http://ftp.us.debian.org/debian/ unstable/main man-db s390 2.6.2-1 [1074 kB]
+Get:14 http://ftp.us.debian.org/debian/ unstable/main file s390 5.11-2 [52.0 kB]
+Get:15 http://ftp.us.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-9 [152 kB]
+Get:16 http://ftp.us.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://ftp.us.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:18 http://ftp.us.debian.org/debian/ unstable/main gettext s390 0.18.1.1-9 [1959 kB]
+Get:19 http://ftp.us.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://ftp.us.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://ftp.us.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://ftp.us.debian.org/debian/ unstable/main diffstat s390 1.55-3 [29.8 kB]
+Get:23 http://ftp.us.debian.org/debian/ unstable/main libtinfo-dev s390 5.9-10 [113 kB]
+Get:24 http://ftp.us.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-10 [213 kB]
+Get:25 http://ftp.us.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://ftp.us.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.0 MB in 5s (2080 kB/s)
+Fetched 11.0 MB in 10s (1056 kB/s)
Selecting previously unselected package libpipeline1:s390.
-(Reading database ... 10663 files and directories currently installed.)
+(Reading database ... 10773 files and directories currently installed.)
Unpacking libpipeline1:s390 (from .../libpipeline1_1.2.1-1_s390.deb) ...
Selecting previously unselected package libasprintf0c2:s390.
Unpacking libasprintf0c2:s390 (from .../libasprintf0c2_0.18.1.1-9_s390.deb) ...
@@ -290,11 +285,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-1 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-3 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-3 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-5 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
+Package versions: apt_0.9.7.2 base-files_6.11 base-passwd_3.5.26 bash_4.2-4 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-5 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.2 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-5 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-5 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-5 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -305,12 +300,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -323,7 +318,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
@@ -331,25 +326,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -369,10 +364,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -385,12 +380,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -419,8 +414,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -435,10 +430,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -459,24 +454,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -490,14 +485,14 @@ gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-s
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -523,7 +518,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -558,8 +553,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -585,7 +580,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -597,67 +592,70 @@ dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_s390.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_s390.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.18-2_s390.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_s390.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zappa) <buildd_s390x-zappa at buildd.debian.org> >../samtools_0.1.18-3_s390.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1506
+Build finished at 20120727-1546
-samtools_0.1.18-2_s390.changes:
+samtools_0.1.18-3_s390.changes:
Format: 1.8
-Date: Thu, 26 Jul 2012 18:30:48 -0400
+Date: Fri, 27 Jul 2012 11:11:41 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.18-2
+Version: 0.1.18-3
Distribution: sid
Urgency: low
-Maintainer: s390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
+Maintainer: s390/s390x Build Daemon (zappa) <buildd_s390x-zappa at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 544976 671524
+Closes: 653042 671524
Changes:
- samtools (0.1.18-2) unstable; urgency=low
+ samtools (0.1.18-3) unstable; urgency=low
.
- * added patch to fix segfault in mpileup (Closes: #544976)
+ * upload 0.1.18-2 closed the wrong bug, correction:
+ * added patch to fix segfault in mpileup (Closes: #653042)
* added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- 76f21c3aa163dae86db10c87248a6e3cefa425cf 529036 samtools_0.1.18-2_s390.deb
- 6d62763947814acc48fa0d228b35a2f95bc77ae6 156454 libbam-dev_0.1.18-2_s390.deb
+ 74aa8dc71998f8a42c8b5730f792b94475cb662d 529586 samtools_0.1.18-3_s390.deb
+ e0b19292c1b93779765175ae1d06a2a7f0d53f12 156030 libbam-dev_0.1.18-3_s390.deb
Checksums-Sha256:
- 230fcce76704d86173deab1a84cb78e18611e1754887ec9b2daf3b549b6d2047 529036 samtools_0.1.18-2_s390.deb
- 030cdbfdaf16e414a85a8964304a707e1e08cfa430d2ba837066eced8acd0e64 156454 libbam-dev_0.1.18-2_s390.deb
+ b9c1ec4654d69578c24bae721ec1a86561fcde67134949adc18b8f20fa8933d6 529586 samtools_0.1.18-3_s390.deb
+ 4f61616acf2511127ed0a6a80d3948b88d3b79352d753e8d2245fc393f6d8e80 156030 libbam-dev_0.1.18-3_s390.deb
Files:
- 965800e9f5c5a9738b63dc7097a12951 529036 science optional samtools_0.1.18-2_s390.deb
- b0304fea00da983af8345be33bef5ee0 156454 libdevel optional libbam-dev_0.1.18-2_s390.deb
+ 0de00d985611b9e54e5e79dd80d363aa 529586 science optional samtools_0.1.18-3_s390.deb
+ ae7354bcaa605dc1430e6cc33d386000 156030 libdevel optional libbam-dev_0.1.18-3_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-2_s390.deb
+samtools_0.1.18-3_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 529036 bytes: control archive= 1759 bytes.
+ size 529586 bytes: control archive= 1762 bytes.
791 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1066
@@ -673,68 +671,68 @@ samtools_0.1.18-2_s390.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/bin/
--rwxr-xr-x root/root 141452 2012-07-27 15:06 ./usr/bin/bcftools
--rwxr-xr-x root/root 416680 2012-07-27 15:06 ./usr/bin/samtools
--rwxr-xr-x root/root 27584 2012-07-27 15:06 ./usr/bin/razip
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/lib/samtools/
--rwxr-xr-x root/root 11488 2012-07-27 15:06 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7596 2012-07-27 15:06 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7596 2012-07-27 15:06 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8424 2012-07-27 15:06 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 17340 2012-07-27 15:06 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2012-07-27 15:06 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2012-07-27 15:06 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/samtools/
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5778 2012-07-27 15:06 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/doc/samtools/
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/bin/
+-rwxr-xr-x root/root 27584 2012-07-27 15:45 ./usr/bin/razip
+-rwxr-xr-x root/root 416680 2012-07-27 15:45 ./usr/bin/samtools
+-rwxr-xr-x root/root 141452 2012-07-27 15:45 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:45 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:45 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1966 2012-07-27 15:45 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2012-07-27 15:06 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2012-07-27 15:06 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-lrwxrwxrwx root/root 0 2012-07-27 15:06 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2012-07-27 15:45 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2012-07-27 15:45 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11488 2012-07-27 15:45 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7596 2012-07-27 15:45 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8424 2012-07-27 15:45 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 17340 2012-07-27 15:45 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7596 2012-07-27 15:45 ./usr/lib/samtools/maq2sam-long
+lrwxrwxrwx root/root 0 2012-07-27 15:45 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.18-2_s390.deb
+libbam-dev_0.1.18-3_s390.deb
────────────────────────────
new debian package, version 2.0.
- size 156454 bytes: control archive= 922 bytes.
+ size 156030 bytes: control archive= 925 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-2
+ Version: 0.1.18-3
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 421
@@ -748,25 +746,25 @@ libbam-dev_0.1.18-2_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/include/samtools/
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/lib/
--rw-r--r-- root/root 288978 2012-07-27 15:06 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/include/samtools/
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/lib/
+-rw-r--r-- root/root 288978 2012-07-27 15:45 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -780,7 +778,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-f8862312-c6fc-4cdf-9518-200305394bf9/build/buildd-samtools_0.1.18-2-s390-QXGKh8
+Purging /var/lib/schroot/mount/sid-s390-sbuild-ead94a4a-16f2-48ac-80e6-fb156be5d852/build/buildd-samtools_0.1.18-3-s390-vNgSph
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -788,22 +786,22 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 11272
-Build-Time: 33
+Build-Space: 11100
+Build-Time: 135
Distribution: sid
-Install-Time: 10
-Job: samtools_0.1.18-2
+Install-Time: 27
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 57
-Source-Version: 0.1.18-2
-Space: 11272
+Package-Time: 228
+Source-Version: 0.1.18-3
+Space: 11100
Status: successful
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1506
-Build needed 00:00:57, 11272k disc space
-Signature with key 'E7C67939' requested:
-From buildd at zandonai.debian.org Fri Jul 27 15:11:58 2012
+Finished at 20120727-1546
+Build needed 00:03:48, 11100k disc space
+Signature with key '0C4D1E93' requested:
+From buildd at zandonai.debian.org Fri Jul 27 15:45:49 2012
Return-path: <buildd at zandonai.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -811,38 +809,38 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1SumCr-0002yt-TQ
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:11:58 +0000
+ id 1Sumjd-0005vy-HI
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:49 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1SumCq-000498-VX; Fri, 27 Jul 2012 15:11:57 +0000
+ id 1Sumjc-0005mz-GL; Fri, 27 Jul 2012 15:45:48 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1SumCq-0005Vc-IP; Fri, 27 Jul 2012 15:11:56 +0000
-Message-Id: <E1SumCq-0005Vc-IP at zandonai.debian.org>
+ id 1Sumjc-0006Qk-2Q; Fri, 27 Jul 2012 15:45:48 +0000
+Message-Id: <E1Sumjc-0006Qk-2Q at zandonai.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:11:56 +0000
+Date: Fri, 27 Jul 2012 15:45:48 +0000
From: buildd on zandonai <buildd at zandonai.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.18-2 on s390x (dist=sid)
+Subject: Log for attempted build of samtools_0.1.18-3 on s390x (dist=sid)
Key-Id: BE1C5586
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (s390x) 27 Jul 2012 15:09 ║
+║ samtools 0.1.18-3 (s390x) 27 Jul 2012 15:43 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: s390x
Get:1 http://ftp.de.debian.org unstable InRelease [249 kB]
Get:2 http://incoming.debian.org unstable InRelease [249 kB]
@@ -859,9 +857,9 @@ Get:11 http://incoming.debian.org unstable/main s390x Packages [5879 kB]
Get:12 http://incoming.debian.org unstable/contrib s390x Packages [37.0 kB]
Get:13 http://incoming.debian.org Release.gpg [836 B]
Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 25.4 MB in 24s (1028 kB/s)
+Get:15 http://incoming.debian.org Sources [14.5 kB]
+Get:16 http://incoming.debian.org Packages [117 kB]
+Fetched 25.4 MB in 22s (1140 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -883,10 +881,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (286 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (288 kB/s)
Download complete and in download only mode
Check arch
@@ -983,7 +981,7 @@ Get:24 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390x 5.9-
Get:25 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
Get:26 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.1 MB in 5s (2157 kB/s)
+Fetched 11.1 MB in 5s (2127 kB/s)
Selecting previously unselected package libpipeline1:s390x.
(Reading database ... 10787 files and directories currently installed.)
Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.1-1_s390x.deb) ...
@@ -1086,12 +1084,529 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying fix_coverage_cap.patch
+
+Check disc space
+────────────────
+
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package samtools
+dpkg-buildpackage: source version 0.1.18-3
+ dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: host architecture s390x
+ fakeroot debian/rules clean
+test -x debian/rules
+dh_testroot
+rm -f debian/stamp-makefile-build debian/stamp-makefile-install
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
+rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+rm -f debian/stamp-makefile-check
+dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch fix_coverage_cap.patch
+Restoring bam2depth.c
+
+Removing patch fix_segfault_with_small_ref.patch
+Restoring bam_plcmd.c
+
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
+rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+ debian/rules build-arch
+test -x debian/rules
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Applying patch fix_segfault_with_small_ref.patch
+patching file bam_plcmd.c
+
+Applying patch fix_coverage_cap.patch
+patching file bam2depth.c
+
+Now at patch fix_coverage_cap.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
+touch debian/stamp-makefile-build
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/examples'
+../samtools faidx ex1.fa
+../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
+[sam_header_read2] 2 sequences loaded.
+../samtools index ex1.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+[samopen] SAM header is present: 2 sequences.
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+[samopen] SAM header is present: 2 sequences.
+(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
+../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
+make[1]: *** [ex1f.bam] Killed
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/examples'
+make: *** [debian/stamp-makefile-check] Error 2
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20120727-1545
+FAILED [dpkg-buildpackage died]
+────────────────────────────────────────────────────────────────────────────────
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-80ba5657-d6f5-4ca2-931a-cbd3940fc021/sid-s390x-sbuild/build/buildd-samtools_0.1.18-3-s390x-8JKR6G
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: s390x
+Build-Space: 9780
+Build-Time: 109
+Distribution: sid
+Fail-Stage: build
+Install-Time: 11
+Job: samtools_0.1.18-3
+Package: samtools
+Package-Time: 154
+Source-Version: 0.1.18-3
+Space: 9780
+Status: attempted
+Version: 0.1.18-3
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20120727-1545
+Build needed 00:02:34, 9780k disc space
+From buildd at zandonai.debian.org Wed Aug 29 03:08:35 2012
+Return-path: <buildd at zandonai.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1T6Ydv-00050a-Mz
+ for logs at buildd.debian.org; Wed, 29 Aug 2012 03:08:35 +0000
+Received: from zandonai.debian.org ([80.245.147.46])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=zandonai.debian.org,
+ EMAIL=hostmaster at zandonai.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1T6Ydu-0004Un-M2; Wed, 29 Aug 2012 03:08:34 +0000
+Received: from buildd by zandonai.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zandonai.debian.org>)
+ id 1T6Ydu-0003zo-1b; Wed, 29 Aug 2012 03:08:34 +0000
+Message-Id: <E1T6Ydu-0003zo-1b at zandonai.debian.org>
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Wed, 29 Aug 2012 03:08:33 +0000
+From: buildd on zandonai <buildd at zandonai.debian.org>
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.18-3 on s390x (dist=sid)
+Key-Id: BE1C5586
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 0.1.18-3 (s390x) 29 Aug 2012 03:06 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 0.1.18-3
+Source Version: 0.1.18-3
+Architecture: s390x
+Get:1 http://ftp.de.debian.org unstable InRelease [257 kB]
+Get:2 http://incoming.debian.org unstable InRelease [257 kB]
+Hit http://ftp.de.debian.org unstable/main Sources
+Hit http://ftp.de.debian.org unstable/contrib Sources
+Hit http://ftp.de.debian.org unstable/non-free Sources
+Hit http://ftp.de.debian.org unstable/main s390x Packages
+Hit http://ftp.de.debian.org unstable/contrib s390x Packages
+Ign http://incoming.debian.org InRelease
+Get:3 http://incoming.debian.org unstable/main Sources [6331 kB]
+Get:4 http://incoming.debian.org unstable/contrib Sources [53.6 kB]
+Get:5 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
+Get:6 http://incoming.debian.org unstable/main s390x Packages [5891 kB]
+Get:7 http://incoming.debian.org unstable/contrib s390x Packages [36.8 kB]
+Get:8 http://incoming.debian.org Release.gpg [836 B]
+Get:9 http://incoming.debian.org Release [1141 B]
+Get:10 http://incoming.debian.org Sources [23.8 kB]
+Get:11 http://incoming.debian.org Packages [284 kB]
+Fetched 13.2 MB in 24s (537 kB/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 390 kB of source archives.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 0s (849 kB/s)
+Download complete and in download only mode
+
+Check arch
+──────────
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5+b1)
+fakeroot: already installed (1.18.4-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
+Checking for already installed dependencies...
+libc6-dev: already installed (2.13-34)
+gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+debhelper: missing
+Using default version 9.20120608
+cdbs: missing
+quilt: missing
+libncurses5-dev: missing
+zlib1g-dev: missing
+Checking for dependency conflicts...
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
+ po-debconf
+Suggested packages:
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
+ mail-transport-agent
+Recommended packages:
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
+The following NEW packages will be installed:
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 38 not upgraded.
+Need to get 11.1 MB of archives.
+After this operation, 30.7 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390x 1.2.1-1 [40.5 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-9 [26.8 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390x 1:8.30-5 [254 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-5 [901 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390x 2.32.3-1 [2105 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390x 0.6.5-1 [151 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-9 [158 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main man-db s390x 2.6.2-1 [1069 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390x 0.18.1.1-9 [156 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.117 [79.9 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main gettext s390x 0.18.1.1-9 [2037 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://ftp.de.debian.org/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
+Get:25 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.1 MB in 6s (1846 kB/s)
+Selecting previously unselected package libpipeline1:s390x.
+(Reading database ... 10787 files and directories currently installed.)
+Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.1-1_s390x.deb) ...
+Selecting previously unselected package libasprintf0c2:s390x.
+Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-9_s390x.deb) ...
+Selecting previously unselected package libmagic1:s390x.
+Unpacking libmagic1:s390x (from .../libmagic1_5.11-2_s390x.deb) ...
+Selecting previously unselected package libpcre3:s390x.
+Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.30-5_s390x.deb) ...
+Selecting previously unselected package libxml2:s390x.
+Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-5_s390x.deb) ...
+Selecting previously unselected package libffi5:s390x.
+Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
+Selecting previously unselected package libglib2.0-0:s390x.
+Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.32.3-1_s390x.deb) ...
+Selecting previously unselected package libcroco3:s390x.
+Unpacking libcroco3:s390x (from .../libcroco3_0.6.5-1_s390x.deb) ...
+Selecting previously unselected package libunistring0:s390x.
+Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
+Selecting previously unselected package libgettextpo0:s390x.
+Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-9_s390x.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.2-1_s390x.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../archives/file_5.11-2_s390x.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_s390x.deb) ...
+Selecting previously unselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.117_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_s390x.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_s390x.deb) ...
+Selecting previously unselected package libtinfo-dev:s390x.
+Unpacking libtinfo-dev:s390x (from .../libtinfo-dev_5.9-10_s390x.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_s390x.deb) ...
+Selecting previously unselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Selecting previously unselected package zlib1g-dev:s390x.
+Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
+Setting up libpipeline1:s390x (1.2.1-1) ...
+Setting up libasprintf0c2:s390x (0.18.1.1-9) ...
+Setting up libmagic1:s390x (5.11-2) ...
+Setting up libpcre3:s390x (1:8.30-5) ...
+Setting up libxml2:s390x (2.8.0+dfsg1-5) ...
+Setting up libffi5:s390x (3.0.10-3+b1) ...
+Setting up libglib2.0-0:s390x (2.32.3-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:s390x (0.6.5-1) ...
+Setting up libunistring0:s390x (0.9.3-5+b1) ...
+Setting up libgettextpo0:s390x (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+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 groff-base (1.21-9) ...
+Setting up man-db (2.6.2-1) ...
+Building database of manual pages ...
+Setting up file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up cdbs (0.4.117) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up gettext (0.18.1.1-9) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:s390x (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.32-5-s390x s390x (s390x)
+Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
+Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.117 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-3 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-3 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -1104,7 +1619,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture s390x
fakeroot debian/rules clean
@@ -1112,25 +1627,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -1150,10 +1665,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -1166,12 +1681,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -1200,8 +1715,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -1216,10 +1731,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -1240,24 +1755,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -1271,14 +1786,14 @@ gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-s
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -1289,3 +1804,34 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtoo
[samopen] SAM header is present: 2 sequences.
(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
+make[1]: *** [ex1f.bam] Killed
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/examples'
+make: *** [debian/stamp-makefile-check] Error 2
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20120829-0308
+FAILED [dpkg-buildpackage died]
+────────────────────────────────────────────────────────────────────────────────
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-fcd0e2de-81bc-415a-8d68-06cb3cc50741/sid-s390x-sbuild/build/buildd-samtools_0.1.18-3-s390x-mBlLZO
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: s390x
+Build-Space: 9780
+Build-Time: 67
+Distribution: sid
+Fail-Stage: build
+Install-Time: 11
+Job: samtools_0.1.18-3
+Package: samtools
+Package-Time: 113
+Source-Version: 0.1.18-3
+Space: 9780
+Status: attempted
+Version: 0.1.18-3
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20120829-0308
+Build needed 00:01:53, 9780k disc space
diff --git a/s390x.log b/s390x.log
index 759d351..e69de29 100644
--- a/s390x.log
+++ b/s390x.log
@@ -1,486 +0,0 @@
-From buildd at zandonai.debian.org Fri Jul 27 15:11:58 2012
-Return-path: <buildd at zandonai.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1SumCr-0002yt-TQ
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:11:58 +0000
-Received: from zandonai.debian.org ([80.245.147.46])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=zandonai.debian.org,
- EMAIL=hostmaster at zandonai.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1SumCq-000498-VX; Fri, 27 Jul 2012 15:11:57 +0000
-Received: from buildd by zandonai.debian.org with local (Exim 4.72)
- (envelope-from <buildd at zandonai.debian.org>)
- id 1SumCq-0005Vc-IP; Fri, 27 Jul 2012 15:11:56 +0000
-Message-Id: <E1SumCq-0005Vc-IP at zandonai.debian.org>
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:11:56 +0000
-From: buildd on zandonai <buildd at zandonai.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.18-2 on s390x (dist=sid)
-Key-Id: BE1C5586
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (s390x) 27 Jul 2012 15:09 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
-Architecture: s390x
-Get:1 http://ftp.de.debian.org unstable InRelease [249 kB]
-Get:2 http://incoming.debian.org unstable InRelease [249 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [6315 kB]
-Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:5 http://ftp.de.debian.org unstable/contrib Sources [53.9 kB]
-Get:6 http://ftp.de.debian.org unstable/non-free Sources [98.1 kB]
-Get:7 http://ftp.de.debian.org unstable/main s390x Packages [5879 kB]
-Get:8 http://ftp.de.debian.org unstable/contrib s390x Packages [37.0 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main s390x Packages [5879 kB]
-Get:12 http://incoming.debian.org unstable/contrib s390x Packages [37.0 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 25.4 MB in 24s (1028 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (286 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5+b1)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-libc6-dev: already installed (2.13-34)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120608
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 23 not upgraded.
-Need to get 11.1 MB of archives.
-After this operation, 30.7 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390x 1.2.1-1 [40.5 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-9 [26.8 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390x 1:8.30-5 [254 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-5 [901 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390x 2.32.3-1 [2105 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390x 0.6.5-1 [151 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-9 [158 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main man-db s390x 2.6.2-1 [1069 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390x 0.18.1.1-9 [156 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main gettext s390x 0.18.1.1-9 [2037 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://ftp.de.debian.org/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
-Get:23 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
-Get:24 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
-Get:25 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.1 MB in 5s (2157 kB/s)
-Selecting previously unselected package libpipeline1:s390x.
-(Reading database ... 10787 files and directories currently installed.)
-Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.1-1_s390x.deb) ...
-Selecting previously unselected package libasprintf0c2:s390x.
-Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-9_s390x.deb) ...
-Selecting previously unselected package libmagic1:s390x.
-Unpacking libmagic1:s390x (from .../libmagic1_5.11-2_s390x.deb) ...
-Selecting previously unselected package libpcre3:s390x.
-Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.30-5_s390x.deb) ...
-Selecting previously unselected package libxml2:s390x.
-Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-5_s390x.deb) ...
-Selecting previously unselected package libffi5:s390x.
-Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
-Selecting previously unselected package libglib2.0-0:s390x.
-Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.32.3-1_s390x.deb) ...
-Selecting previously unselected package libcroco3:s390x.
-Unpacking libcroco3:s390x (from .../libcroco3_0.6.5-1_s390x.deb) ...
-Selecting previously unselected package libunistring0:s390x.
-Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
-Selecting previously unselected package libgettextpo0:s390x.
-Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-9_s390x.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_s390x.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_s390x.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_s390x.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_s390x.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_s390x.deb) ...
-Selecting previously unselected package libtinfo-dev:s390x.
-Unpacking libtinfo-dev:s390x (from .../libtinfo-dev_5.9-10_s390x.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_s390x.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev:s390x.
-Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
-Setting up libpipeline1:s390x (1.2.1-1) ...
-Setting up libasprintf0c2:s390x (0.18.1.1-9) ...
-Setting up libmagic1:s390x (5.11-2) ...
-Setting up libpcre3:s390x (1:8.30-5) ...
-Setting up libxml2:s390x (2.8.0+dfsg1-5) ...
-Setting up libffi5:s390x (3.0.10-3+b1) ...
-Setting up libglib2.0-0:s390x (2.32.3-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:s390x (0.6.5-1) ...
-Setting up libunistring0:s390x (0.9.3-5+b1) ...
-Setting up libgettextpo0:s390x (0.18.1.1-9) ...
-Setting up bsdmainutils (9.0.3) ...
-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 groff-base (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
-Building database of manual pages ...
-Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
-Setting up html2text (1.3.2a-15+b1) ...
-Setting up gettext (0.18.1.1-9) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:s390x (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-3 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-3 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
- dpkg-source --before-build samtools-0.1.18
-dpkg-buildpackage: host architecture s390x
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch no-pileup-tests.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'bgzf_close':
-bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
-seqtk.c: In function 'stk_comp':
-seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
diff --git a/sparc.log b/sparc.log
index 8bacb06..93377c3 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,62 +1,62 @@
-From buildd at stadler.debian.org Fri Jul 27 15:18:18 2012
-Return-path: <buildd at stadler.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at lebrun.debian.org Fri Jul 27 15:45:27 2012
+Return-path: <buildd at lebrun.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at stadler.debian.org>)
- id 1SumJ0-0004ng-D1
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:18:18 +0000
-Received: from stadler.debian.org ([2a02:16a8:dc41:100::ffff])
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1SumjH-0005oK-6F
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:27 +0000
+Received: from [2001:b68:ff:5:203:baff:fe59:abad] (helo=lebrun.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=stadler.debian.org, EMAIL=hostmaster at stadler.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at stadler.debian.org>)
- id 1SumIz-0004O4-FU
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:18:17 +0000
-Received: from buildd by stadler.debian.org with local (Exim 4.72)
- (envelope-from <buildd at stadler.debian.org>)
- id 1SumIx-0008Bn-Jr; Fri, 27 Jul 2012 15:18:15 +0000
-Message-Id: <E1SumIx-0008Bn-Jr at stadler.debian.org>
+ CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1SumjG-0001sq-3e
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:26 +0000
+Received: from buildd by lebrun.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at lebrun.debian.org>)
+ id 1SumjE-0002pT-2f; Fri, 27 Jul 2012 15:45:24 +0000
+Message-Id: <E1SumjE-0002pT-2f at lebrun.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:18:15 +0000
-From: buildd on stadler <buildd at stadler.debian.org>
-To: logs at buildd.debian.org,buildd-admin at stadler.debian.org
-Subject: Log for attempted build of samtools_0.1.18-2 on sparc (dist=sid)
-Key-Id: F53143B2
+Date: Fri, 27 Jul 2012 15:45:23 +0000
+From: buildd on lebrun <buildd at lebrun.debian.org>
+To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
+Subject: Log for attempted build of samtools_0.1.18-3 on sparc (dist=sid)
+Key-Id: E1D842D6
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on stadler.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-2 (sparc) 27 Jul 2012 15:09 ║
+║ samtools 0.1.18-3 (sparc) 27 Jul 2012 15:40 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-2
-Source Version: 0.1.18-2
+Version: 0.1.18-3
+Source Version: 0.1.18-3
Architecture: sparc
-Get:1 http://debian.inode.at unstable InRelease [249 kB]
+Get:1 http://debian.carnet.hr unstable InRelease [249 kB]
Get:2 http://incoming.debian.org unstable InRelease [249 kB]
-Get:3 http://debian.inode.at unstable/main Sources [6317 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [6315 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
Get:5 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:6 http://debian.inode.at unstable/contrib Sources [53.9 kB]
-Get:7 http://debian.inode.at unstable/non-free Sources [98.1 kB]
-Get:8 http://debian.inode.at unstable/main sparc Packages [5980 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main sparc Packages [5980 kB]
-Get:12 http://debian.inode.at unstable/contrib sparc Packages [37.8 kB]
+Get:6 http://debian.carnet.hr unstable/contrib Sources [53.9 kB]
+Get:7 http://debian.carnet.hr unstable/non-free Sources [98.1 kB]
+Get:8 http://debian.carnet.hr unstable/main sparc Packages [5980 kB]
+Get:9 http://debian.carnet.hr unstable/contrib sparc Packages [37.8 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
+Get:12 http://incoming.debian.org unstable/main sparc Packages [5980 kB]
Get:13 http://incoming.debian.org unstable/contrib sparc Packages [37.8 kB]
Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.3 kB]
-Get:16 http://incoming.debian.org Packages [113 kB]
-Fetched 25.6 MB in 2min 36s (163 kB/s)
+Get:15 http://incoming.debian.org Sources [14.5 kB]
+Get:16 http://incoming.debian.org Packages [117 kB]
+Fetched 25.6 MB in 59s (431 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,10 +78,10 @@ Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
-Fetched 390 kB in 1s (297 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
+Fetched 390 kB in 1s (261 kB/s)
Download complete and in download only mode
Check arch
@@ -176,36 +176,36 @@ The following NEW packages will be installed:
0 upgraded, 26 newly installed, 0 to remove and 25 not upgraded.
Need to get 10.5 MB of archives.
After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://debian.inode.at/debian/ unstable/main libpipeline1 sparc 1.2.1-1 [35.8 kB]
-Get:2 http://debian.inode.at/debian/ unstable/main libasprintf0c2 sparc 0.18.1.1-9 [26.5 kB]
-Get:3 http://debian.inode.at/debian/ unstable/main libmagic1 sparc 5.11-2 [197 kB]
-Get:4 http://debian.inode.at/debian/ unstable/main libpcre3 sparc 1:8.30-5 [246 kB]
-Get:5 http://debian.inode.at/debian/ unstable/main libxml2 sparc 2.8.0+dfsg1-5 [826 kB]
-Get:6 http://debian.inode.at/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
-Get:7 http://debian.inode.at/debian/ unstable/main libglib2.0-0 sparc 2.32.3-1 [1926 kB]
-Get:8 http://debian.inode.at/debian/ unstable/main libcroco3 sparc 0.6.5-1 [135 kB]
-Get:9 http://debian.inode.at/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
-Get:10 http://debian.inode.at/debian/ unstable/main libgettextpo0 sparc 0.18.1.1-9 [129 kB]
-Get:11 http://debian.inode.at/debian/ unstable/main bsdmainutils sparc 9.0.3 [206 kB]
-Get:12 http://debian.inode.at/debian/ unstable/main groff-base sparc 1.21-9 [1133 kB]
-Get:13 http://debian.inode.at/debian/ unstable/main man-db sparc 2.6.2-1 [1032 kB]
-Get:14 http://debian.inode.at/debian/ unstable/main file sparc 5.11-2 [51.1 kB]
-Get:15 http://debian.inode.at/debian/ unstable/main gettext-base sparc 0.18.1.1-9 [148 kB]
-Get:16 http://debian.inode.at/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://debian.inode.at/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:18 http://debian.inode.at/debian/ unstable/main gettext sparc 0.18.1.1-9 [1893 kB]
-Get:19 http://debian.inode.at/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://debian.inode.at/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://debian.inode.at/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://debian.inode.at/debian/ unstable/main diffstat sparc 1.55-3 [28.6 kB]
-Get:23 http://debian.inode.at/debian/ unstable/main libtinfo-dev sparc 5.9-10 [97.5 kB]
-Get:24 http://debian.inode.at/debian/ unstable/main libncurses5-dev sparc 5.9-10 [204 kB]
-Get:25 http://debian.inode.at/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://debian.inode.at/debian/ unstable/main zlib1g-dev sparc 1:1.2.7.dfsg-13 [211 kB]
+Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.1-1 [35.8 kB]
+Get:2 http://debian.carnet.hr/debian/ unstable/main libasprintf0c2 sparc 0.18.1.1-9 [26.5 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.11-2 [197 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 1:8.30-5 [246 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.8.0+dfsg1-5 [826 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.32.3-1 [1926 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.5-1 [135 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:10 http://debian.carnet.hr/debian/ unstable/main libgettextpo0 sparc 0.18.1.1-9 [129 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 9.0.3 [206 kB]
+Get:12 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-9 [1133 kB]
+Get:13 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.2-1 [1032 kB]
+Get:14 http://debian.carnet.hr/debian/ unstable/main file sparc 5.11-2 [51.1 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-9 [148 kB]
+Get:16 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:18 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-9 [1893 kB]
+Get:19 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://debian.carnet.hr/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.55-3 [28.6 kB]
+Get:23 http://debian.carnet.hr/debian/ unstable/main libtinfo-dev sparc 5.9-10 [97.5 kB]
+Get:24 http://debian.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-10 [204 kB]
+Get:25 http://debian.carnet.hr/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.7.dfsg-13 [211 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.5 MB in 10s (979 kB/s)
+Fetched 10.5 MB in 10s (1006 kB/s)
Selecting previously unselected package libpipeline1:sparc.
-(Reading database ... 11051 files and directories currently installed.)
+(Reading database ... 11055 files and directories currently installed.)
Unpacking libpipeline1:sparc (from .../libpipeline1_1.2.1-1_sparc.deb) ...
Selecting previously unselected package libasprintf0c2:sparc.
Unpacking libasprintf0c2:sparc (from .../libasprintf0c2_0.18.1.1-9_sparc.deb) ...
@@ -306,12 +306,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 13:09:06 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-2.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -324,7 +324,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-2
+dpkg-buildpackage: source version 0.1.18-3
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
@@ -332,25 +332,25 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -370,10 +370,10 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -386,12 +386,12 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -426,8 +426,8 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -442,10 +442,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -466,24 +466,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -505,27 +505,27 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
make[1]: *** [ex1.bam] Bus error
make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1518
+Build finished at 20120727-1545
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-6973a6e3-efb0-4bfc-ba6f-7c96b1af3c3a/build/buildd-samtools_0.1.18-2-sparc-HSj7IP
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-c0dfe45e-ca10-47f2-a0e7-42a63dbea57a/build/buildd-samtools_0.1.18-3-sparc-Dzk96g
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -533,18 +533,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 6704
-Build-Time: 267
+Build-Space: 6800
+Build-Time: 139
Distribution: sid
Fail-Stage: build
-Install-Time: 87
-Job: samtools_0.1.18-2
+Install-Time: 76
+Job: samtools_0.1.18-3
Package: samtools
-Package-Time: 542
-Source-Version: 0.1.18-2
-Space: 6704
+Package-Time: 296
+Source-Version: 0.1.18-3
+Space: 6800
Status: attempted
-Version: 0.1.18-2
+Version: 0.1.18-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1518
-Build needed 00:09:02, 6704k disc space
+Finished at 20120727-1545
+Build needed 00:04:56, 6800k disc space
--
Processing of sequence alignments in SAM and BAM formats.
More information about the debian-med-commit
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