[Debian-med-packaging] mafft_6.857-1_amd64.changes ACCEPTED into unstable
Charles Plessy
plessy at debian.org
Fri Aug 5 01:40:10 UTC 2011
Le Fri, Aug 05, 2011 at 01:18:26AM +0000, Debian FTP Masters a écrit :
>
> Accepted:
> mafft_6.857-1.debian.tar.gz
> to main/m/mafft/mafft_6.857-1.debian.tar.gz
> mafft_6.857-1.dsc
> to main/m/mafft/mafft_6.857-1.dsc
> mafft_6.857-1_amd64.deb
> to main/m/mafft/mafft_6.857-1_amd64.deb
> mafft_6.857.orig.tar.gz
> to main/m/mafft/mafft_6.857.orig.tar.gz
>
>
> Override entries for your package:
> mafft_6.857-1.dsc - source science
> mafft_6.857-1_amd64.deb - optional science
>
> Announcing to debian-devel-changes at lists.debian.org
> Closing bugs: 636634
Build logs attached.
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
-------------- next part --------------
sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on aqwa.igloo
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? mafft 6.857-1 (amd64) 05 août 2011 09:58 ?
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Package: mafft
Version: 6.857-1
Source Version: 6.857-1
Distribution: unstable
Architecture: amd64
I: NOTICE: Log filtering will replace 'build/mafft-dlwV1T/mafft-6.857' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/mafft-dlwV1T' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-90edc9c8-55f4-4843-bc39-270b82bc40f6' with '«CHROOT»'
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? Update chroot ?
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Hit ftp://ftp.jaist.ac.jp sid InRelease
Hit ftp://ftp.jaist.ac.jp sid/main Sources/DiffIndex
Hit ftp://ftp.jaist.ac.jp sid/main amd64 Packages/DiffIndex
Hit ftp://ftp.jaist.ac.jp sid/main TranslationIndex
Hit ftp://ftp.jaist.ac.jp sid/main Translation-fr
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
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? Fetch source files ?
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Local sources
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mafft_6.857-1.dsc exists in .; copying to chroot
Check arch
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-DjuQmj/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
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? Install core build dependencies (apt-based resolver) ?
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Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/718 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously deselected package sbuild-build-depends-core-dummy.
(Reading database ... 10847 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, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), quilt (>= 0.47)
Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), quilt (>= 0.47)
dpkg-deb: building package `sbuild-build-depends-mafft-dummy' in `/«BUILDDIR»/resolver-odNR3q/apt_archive/sbuild-build-depends-mafft-dummy.deb'.
OK
Reading package lists...
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? Install mafft build dependencies (apt-based resolver) ?
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Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl procmail graphviz
Recommended packages:
curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
sbuild-build-depends-mafft-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/9594 kB of archives.
After this operation, 28.0 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
(Reading database ... 10847 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ...
Selecting previously deselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_amd64.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_amd64.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_amd64.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_amd64.deb) ...
Selecting previously deselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_amd64.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.9.3_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_amd64.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package sbuild-build-depends-mafft-dummy.
Unpacking sbuild-build-depends-mafft-dummy (from .../sbuild-build-depends-mafft-dummy.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up bsdmainutils (8.2.3) ...
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 (1.21-6) ...
Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.9.3) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up sbuild-build-depends-mafft-dummy (0.invalid.0) ...
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? Build environment ?
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Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
Toolchain package versions: binutils_2.21.53.20110729-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-5 gcc-4.6_4.6.1-5 libc6-dev_2.13-13 libstdc++6_4.6.1-5 libstdc++6-4.6-dev_4.6.1-5 linux-libc-dev_3.0.0-1
Package versions: apt_0.8.15.5 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110729-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-5 dash_0.5.5.1-7.4 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.3 debian-archive-keyring_2010.08.28 debianutils_4.0.2 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_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-5 gcc_4:4.6.1-2 gcc-4.6_4.6.1-5 gcc-4.6-base_4.6.1-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-6 libc-bin_2.13-13 libc-dev-bin_2.13-13 libc6_2.13-13 libc6-dev_2.13-13 libclass-isa-perl_0.36-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.7_4.7.25-20 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-5 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-5 liblocale-gettext-perl_1.05-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-5 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libpod-plainer-perl_1.03-1 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-5 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-5 libstdc++6-4.6-dev_4.6.1-5 libswitch-perl_2.16-2 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 libusb-0.1-4_2:0.1.12-18 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-13 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-2 perl-base_5.12.4-2 perl-modules_5.12.4-2 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mafft-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-5 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3
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? Build ?
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Unpack source
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dpkg-source: warning: extracting unsigned source package (mafft_6.857-1.dsc)
dpkg-source: info: extracting mafft in mafft-6.857
dpkg-source: info: unpacking mafft_6.857.orig.tar.gz
dpkg-source: info: unpacking mafft_6.857-1.debian.tar.gz
Check disc space
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Sufficient free space for build
User Environment
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HOME=/sbuild-nonexistent
LOGNAME=charles
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
SCHROOT_SESSION_ID=sid-amd64-sbuild-90edc9c8-55f4-4843-bc39-270b82bc40f6
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
TERM=xterm
USER=charles
USERNAME=charles
dpkg-buildpackage
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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 mafft
dpkg-buildpackage: source version 6.857-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
dpkg-source --before-build mafft-6.857
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
dh clean --with quilt
dh_testdir
dh_auto_clean
dh_quilt_unpatch
No patch removed
debian/rules override_dh_clean
make[1]: Entering directory `/«PKGBUILDDIR»'
[ ! -f core/Makefile ] || /usr/bin/make -C core clean
make[2]: Entering directory `/«PKGBUILDDIR»/core'
rm -f *.o *.a *.exe *~ dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu mafft mafft-homologs.rb
make[2]: Leaving directory `/«PKGBUILDDIR»/core'
rm -rf binaries/* scripts/*
dh_clean
make[1]: Leaving directory `/«PKGBUILDDIR»'
dpkg-source -b mafft-6.857
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building mafft using existing ./mafft_6.857.orig.tar.gz
dpkg-source: info: building mafft in mafft_6.857-1.debian.tar.gz
dpkg-source: info: building mafft in mafft_6.857-1.dsc
debian/rules build
dh build --with quilt
dh_testdir
dh_quilt_patch
No patches in series
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory `/«PKGBUILDDIR»'
/usr/bin/make -C core PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft
make[2]: Entering directory `/«PKGBUILDDIR»/core'
gcc -Denablemultithread -O3 -c mtxutl.c
gcc -Denablemultithread -O3 -c io.c
gcc -Denablemultithread -O3 -c mltaln9.c
gcc -Denablemultithread -O3 -c tddis.c
gcc -Denablemultithread -O3 -c constants.c
gcc -Denablemultithread -O3 -c nj.c
gcc -Denablemultithread -O3 -c partQalignmm.c
gcc -Denablemultithread -O3 -c partSalignmm.c
gcc -Denablemultithread -O3 -c Lalignmm.c
gcc -Denablemultithread -O3 -c rna.c
gcc -Denablemultithread -O3 -c Salignmm.c
gcc -Denablemultithread -O3 -c Ralignmm.c
gcc -Denablemultithread -O3 -c Qalignmm.c
gcc -Denablemultithread -O3 -c Halignmm.c
gcc -Denablemultithread -O3 -c Falign.c
gcc -Denablemultithread -O3 -c Falign_localhom.c
gcc -Denablemultithread -O3 -c Galign11.c
gcc -Denablemultithread -O3 -c MSalignmm.c
gcc -Denablemultithread -O3 -c fftFunctions.c
gcc -Denablemultithread -O3 -c fft.c
gcc -Denablemultithread -O3 -c tditeration.c
gcc -Denablemultithread -O3 -c dvtditr.c
gcc -Denablemultithread -O3 -c defs.c
gcc -Denablemultithread -O3 -c SAalignmm.c -o SAalignmm.o
gcc -Denablemultithread -O3 -c treeOperation.c
gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c dndfast7.c
gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c dndblast.c
gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c sextet5.c
gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c mafft-distance.c
gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c MSalign11.c
gcc -Denablemultithread -O3 -c suboptalign11.c
gcc -Denablemultithread -O3 -c genGalign11.c
gcc -Denablemultithread -O3 -c genalign11.c
gcc -Denablemultithread -O3 -c Lalign11.c
gcc -Denablemultithread -O3 -c pairlocalalign.c
gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c pair2hat3s.c
gcc -o pair2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o pair2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c multi2hat3s.c
gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c rnatest.c
gcc -o rnatest mtxutl.o io.o mltaln9.o tddis.o constants.o Lalignmm.o rna.o rnatest.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c pairash.c
gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c splittbfast.c
gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c disttbfast.c
gcc -Denablemultithread -O3 -c addfunctions.c
gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c tbfast.c
gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c mafft-profile.c
gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c f2cl.c
gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c mccaskillwrap.c
gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c contrafoldwrap.c
gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c countlen.c
gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c seq2regtable.c
gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c regtable2seq.c
gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c score.c
gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c getlag.c
gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c dndpre.c
gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c dndpre2.c
gcc -o dndpre2 dndpre2.o io.o constants.o mtxutl.o mltaln9.o defs.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c setcore.c
gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c replaceu.c
gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread
gcc -Denablemultithread -O3 -c restoreu.c
gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread
sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft
sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb
cp mafft mafft-homologs.rb ../scripts
chmod 755 ../scripts/*
cp dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu ../binaries
chmod 755 ../binaries/*
cp mafft.1 mafft-homologs.1 ../binaries
done.
make[2]: Leaving directory `/«PKGBUILDDIR»/core'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test
fakeroot debian/rules binary
dh binary --with quilt
dh_testroot
dh_prep
dh_installdirs
dh_auto_install
debian/rules override_dh_install
make[1]: Entering directory `/«PKGBUILDDIR»'
/usr/bin/make -C core PREFIX=/«PKGBUILDDIR»/debian/mafft/usr/lib/mafft MANDIR=/«PKGBUILDDIR»/debian/mafft/usr/share/man/man1 LIBDIR=/«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft install
make[2]: Entering directory `/«PKGBUILDDIR»/core'
cp mafft mafft-homologs.rb ../scripts
chmod 755 ../scripts/*
cp dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu ../binaries
chmod 755 ../binaries/*
cp mafft.1 mafft-homologs.1 ../binaries
done.
mkdir -p /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft
chmod 755 /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft
mkdir -p /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/bin
chmod 755 /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/bin
chmod 755 mafft mafft-homologs.rb
install mafft mafft-homologs.rb /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/bin
chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu
install dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft
install -m 644 mafft.1 mafft-homologs.1 /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft
( cd /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/bin; \
rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \
ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
ln -s mafft einsi; \
ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
rm -f mafft-profile mafft-profile.exe; ln -s /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft/mafft-profile .; \
rm -f mafft-distance mafft-distance.exe; ln -s /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft/mafft-distance . )
mkdir -p /«PKGBUILDDIR»/debian/mafft/usr/share/man/man1
chmod 755 /«PKGBUILDDIR»/debian/mafft/usr/share/man/man1
install -m 644 mafft.1 mafft-homologs.1 /«PKGBUILDDIR»/debian/mafft/usr/share/man/man1
make[2]: Leaving directory `/«PKGBUILDDIR»/core'
rm /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft/*.1
# Testing Mafft?
MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft test/sample | diff test/sample.fftns2 -
nthread = 0
done.
scoremtx = 1
Gap Penalty = -1.53, +0.00, +0.00
Making a distance matrix ..
1 / 36
11 / 36
21 / 36
31 / 36
done.
Constructing a UPGMA tree ...
0 / 36
10 / 36
20 / 36
30 / 36
done.
Progressive alignment ...
STEP 1 / 35 f
STEP 2 / 35 f
STEP 3 / 35 f
STEP 4 / 35 f
STEP 5 / 35 f
STEP 6 / 35 f
STEP 7 / 35 f
STEP 8 / 35 f
STEP 9 / 35 f
STEP 10 / 35 f
STEP 11 / 35 f
STEP 12 / 35 f
STEP 13 / 35 f
STEP 14 / 35 f
STEP 15 / 35 f
STEP 16 / 35 f
STEP 17 / 35 f
STEP 18 / 35 f
STEP 19 / 35 f
STEP 20 / 35 f
STEP 21 / 35 f
STEP 22 / 35 f
STEP 23 / 35 d
STEP 24 / 35 f
STEP 25 / 35 d
STEP 26 / 35 f
STEP 27 / 35 d
STEP 28 / 35 d
STEP 29 / 35 f
STEP 30 / 35 d
STEP 31 / 35 d
STEP 32 / 35 d
STEP 33 / 35 d
STEP 34 / 35 d
Reallocating..done. *alloclen = 2119
STEP 35 / 35 d
done.
disttbfast (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
nthread = 0
blosum 62 / kimura 200
done.
scoremtx = 1
Gap Penalty = -1.53, +0.00, +0.00
Making a distance matrix ..
0 / 35
10 / 35
20 / 35
30 / 35
done.
Constructing a UPGMA tree ...
0 / 36
10 / 36
20 / 36
30 / 36
done.
Progressive alignment ...
STEP 1 /35 f
STEP 2 /35 f
STEP 3 /35 f
STEP 4 /35 f
STEP 5 /35 f
STEP 6 /35 f
STEP 7 /35 f
STEP 8 /35 f
STEP 9 /35 f
STEP 10 /35 f
STEP 11 /35 f
STEP 12 /35 f
STEP 13 /35 f
STEP 14 /35 f
STEP 15 /35 f
STEP 16 /35 f
STEP 17 /35 f
STEP 18 /35 f
STEP 19 /35 f
STEP 20 /35 f
STEP 21 /35 f
STEP 22 /35 f
STEP 23 /35 d
STEP 24 /35 f
STEP 25 /35 f
STEP 26 /35 f
STEP 27 /35 d
STEP 28 /35 d
STEP 29 /35 f
STEP 30 /35 f
STEP 31 /35 d
STEP 32 /35 d
STEP 33 /35 d
STEP 34 /35 d
STEP 35 /35 d
done.
tbfast (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
Strategy:
FFT-NS-2 (Fast but rough)
Progressive method (guide trees were built 2 times.)
If unsure which option to use, try 'mafft --auto input > output'.
If the possibility of long gaps can be excluded, add '--ep 0.123'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.
MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --maxiterate 100 test/sample | diff test/sample.fftnsi -
nthread = 0
done.
scoremtx = 1
Gap Penalty = -1.53, +0.00, +0.00
Making a distance matrix ..
1 / 36
11 / 36
21 / 36
31 / 36
done.
Constructing a UPGMA tree ...
0 / 36
10 / 36
20 / 36
30 / 36
done.
Progressive alignment ...
STEP 1 / 35 f
STEP 2 / 35 f
STEP 3 / 35 f
STEP 4 / 35 f
STEP 5 / 35 f
STEP 6 / 35 f
STEP 7 / 35 f
STEP 8 / 35 f
STEP 9 / 35 f
STEP 10 / 35 f
STEP 11 / 35 f
STEP 12 / 35 f
STEP 13 / 35 f
STEP 14 / 35 f
STEP 15 / 35 f
STEP 16 / 35 f
STEP 17 / 35 f
STEP 18 / 35 f
STEP 19 / 35 f
STEP 20 / 35 f
STEP 21 / 35 f
STEP 22 / 35 f
STEP 23 / 35 d
STEP 24 / 35 f
STEP 25 / 35 d
STEP 26 / 35 f
STEP 27 / 35 d
STEP 28 / 35 d
STEP 29 / 35 f
STEP 30 / 35 d
STEP 31 / 35 d
STEP 32 / 35 d
STEP 33 / 35 d
STEP 34 / 35 d
Reallocating..done. *alloclen = 2119
STEP 35 / 35 d
done.
disttbfast (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
nthread = 0
blosum 62 / kimura 200
done.
scoremtx = 1
Gap Penalty = -1.53, +0.00, +0.00
Making a distance matrix ..
0 / 35
10 / 35
20 / 35
30 / 35
done.
Constructing a UPGMA tree ...
0 / 36
10 / 36
20 / 36
30 / 36
done.
Progressive alignment ...
STEP 1 /35 f
STEP 2 /35 f
STEP 3 /35 f
STEP 4 /35 f
STEP 5 /35 f
STEP 6 /35 f
STEP 7 /35 f
STEP 8 /35 f
STEP 9 /35 f
STEP 10 /35 f
STEP 11 /35 f
STEP 12 /35 f
STEP 13 /35 f
STEP 14 /35 f
STEP 15 /35 f
STEP 16 /35 f
STEP 17 /35 f
STEP 18 /35 f
STEP 19 /35 f
STEP 20 /35 f
STEP 21 /35 f
STEP 22 /35 f
STEP 23 /35 d
STEP 24 /35 f
STEP 25 /35 f
STEP 26 /35 f
STEP 27 /35 d
STEP 28 /35 d
STEP 29 /35 f
STEP 30 /35 f
STEP 31 /35 d
STEP 32 /35 d
STEP 33 /35 d
STEP 34 /35 d
STEP 35 /35 d
done.
tbfast (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
nthread = 0
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 16
done.
scoremtx = 1
0 / 36
10 / 36
20 / 36
30 / 36
Segment 1/ 1 1- 712
STEP 001-001-0 identical.
STEP 001-001-1 identical.
STEP 001-002-0 identical.
STEP 001-002-1 identical.
STEP 001-003-0 identical.
STEP 001-003-1 identical.
STEP 001-004-0 identical.
STEP 001-004-1 identical.
STEP 001-005-0 identical.
STEP 001-005-1 identical.
STEP 001-006-0 identical.
STEP 001-006-1 identical.
STEP 001-007-0 rejected.
STEP 001-007-1 identical.
STEP 001-008-0 identical.
STEP 001-008-1 identical.
STEP 001-009-0 rejected.
STEP 001-009-1 rejected.
STEP 001-010-0 rejected.
STEP 001-010-1 identical.
STEP 001-011-0 identical.
STEP 001-011-1 identical.
STEP 001-012-0 identical.
STEP 001-012-1 identical.
STEP 001-013-0 identical.
STEP 001-013-1 identical.
STEP 001-014-0 identical.
STEP 001-014-1 accepted.
STEP 001-015-0 identical.
STEP 001-015-1 identical.
STEP 001-016-0 identical.
STEP 001-016-1 accepted.
STEP 001-017-0 identical.
STEP 001-017-1 identical.
STEP 001-018-0 identical.
STEP 001-018-1 identical.
STEP 001-019-0 rejected.
STEP 001-019-1 rejected.
STEP 001-020-0 accepted.
STEP 001-020-1 rejected.
STEP 001-021-0 rejected.
STEP 001-021-1 rejected.
STEP 001-022-0 rejected.
STEP 001-022-1 rejected.
STEP 001-023-0 rejected.
STEP 001-023-1 identical.
STEP 001-024-0 rejected.
STEP 001-024-1 rejected.
STEP 001-025-0 identical.
STEP 001-025-1 accepted.
STEP 001-026-0 identical.
STEP 001-026-1 rejected.
STEP 001-027-0 rejected.
STEP 001-027-1 identical.
STEP 001-028-0 identical.
STEP 001-028-1 rejected.
STEP 001-029-0 accepted.
STEP 001-029-1 accepted.
STEP 001-030-0 accepted.
STEP 001-030-1 rejected.
STEP 001-031-0 identical.
STEP 001-031-1 rejected.
STEP 001-032-0 rejected.
STEP 001-032-1 identical.
STEP 001-033-0 accepted.
STEP 001-033-1 rejected.
STEP 001-034-0 rejected.
STEP 001-034-1 rejected.
STEP 001-035-1 rejected.
STEP 002-035-1 rejected.
STEP 002-034-0 rejected.
STEP 002-034-1 rejected.
STEP 002-033-0 identical.
STEP 002-033-1 rejected.
STEP 002-032-0 rejected.
STEP 002-032-1 identical.
STEP 002-031-0 identical.
STEP 002-031-1 rejected.
STEP 002-030-0 accepted.
STEP 002-030-1 rejected.
STEP 002-029-0 rejected.
STEP 002-029-1 accepted.
STEP 002-028-0 identical.
STEP 002-028-1 rejected.
STEP 002-027-0 rejected.
STEP 002-027-1 identical.
STEP 002-026-0 identical.
STEP 002-026-1 rejected.
STEP 002-025-0 identical.
STEP 002-025-1 rejected.
STEP 002-024-0 rejected.
STEP 002-024-1 rejected.
STEP 002-023-0 rejected.
STEP 002-023-1 identical.
STEP 002-022-0 rejected.
STEP 002-022-1 rejected.
STEP 002-021-0 rejected.
STEP 002-021-1 rejected.
STEP 002-020-0 identical.
STEP 002-020-1 rejected.
STEP 002-019-0 rejected.
STEP 002-019-1 rejected.
STEP 002-018-0 identical.
STEP 002-018-1 identical.
STEP 002-017-0 identical.
STEP 002-017-1 identical.
STEP 002-016-0 identical.
STEP 002-016-1 identical.
STEP 002-015-0 identical.
STEP 002-015-1 identical.
STEP 002-014-0 identical.
STEP 002-014-1 identical.
STEP 002-013-0 identical.
STEP 002-013-1 accepted.
STEP 002-012-0 identical.
STEP 002-012-1 identical.
STEP 002-011-0 identical.
STEP 002-011-1 identical.
STEP 002-010-0 accepted.
STEP 002-010-1 identical.
STEP 002-009-0 identical.
STEP 002-009-1 accepted.
STEP 002-008-0 identical.
STEP 002-008-1 identical.
STEP 002-007-0 identical.
STEP 002-007-1 identical.
STEP 002-006-0 identical.
STEP 002-006-1 identical.
STEP 002-005-0 identical.
STEP 002-005-1 identical.
STEP 002-004-0 identical.
STEP 002-004-1 identical.
STEP 002-003-0 identical.
STEP 002-003-1 identical.
STEP 002-002-0 identical.
STEP 002-002-1 identical.
STEP 002-001-0 identical.
STEP 002-001-1 identical.
STEP 003-001-0 identical.
STEP 003-001-1 identical.
STEP 003-002-0 identical.
STEP 003-002-1 identical.
STEP 003-003-0 identical.
STEP 003-003-1 identical.
STEP 003-004-0 identical.
STEP 003-004-1 identical.
STEP 003-005-0 identical.
STEP 003-005-1 identical.
STEP 003-006-0 identical.
STEP 003-006-1 identical.
STEP 003-007-0 identical.
STEP 003-007-1 identical.
STEP 003-008-0 identical.
STEP 003-008-1 identical.
STEP 003-009-0 identical.
STEP 003-009-1 identical.
STEP 003-010-0 identical.
STEP 003-010-1 identical.
STEP 003-011-0 identical.
STEP 003-011-1 identical.
STEP 003-012-0 identical.
STEP 003-012-1 identical.
STEP 003-013-0 identical.
STEP 003-013-1 identical.
STEP 003-014-0 identical.
STEP 003-014-1 identical.
STEP 003-015-0 identical.
STEP 003-015-1 identical.
STEP 003-016-0 identical.
STEP 003-016-1 identical.
STEP 003-017-0 identical.
STEP 003-017-1 identical.
STEP 003-018-0 identical.
STEP 003-018-1 identical.
STEP 003-019-0 rejected.
STEP 003-019-1 rejected.
STEP 003-020-0 identical.
STEP 003-020-1 rejected.
STEP 003-021-0 rejected.
STEP 003-021-1 rejected.
STEP 003-022-0 rejected.
STEP 003-022-1 rejected.
STEP 003-023-0 rejected.
STEP 003-023-1 identical.
STEP 003-024-0 rejected.
STEP 003-024-1 rejected.
STEP 003-025-0 identical.
STEP 003-025-1 rejected.
STEP 003-026-0 identical.
STEP 003-026-1 rejected.
STEP 003-027-0 rejected.
STEP 003-027-1 identical.
STEP 003-028-0 identical.
STEP 003-028-1 rejected.
Converged.
done
dvtditr (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
Strategy:
FFT-NS-i (Accurate but slow)
Iterative refinement method (max. 16 iterations)
If unsure which option to use, try 'mafft --auto input > output'.
If the possibility of long gaps can be excluded, add '--ep 0.123'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.
MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --globalpair test/sample | diff test/sample.gins1 -
nthread = 0
done.
scoremtx = 1
Gap Penalty = -2.00, -0.10, +0.10
0 / 36
1 / 36
2 / 36
3 / 36
4 / 36
5 / 36
6 / 36
7 / 36
8 / 36
9 / 36
10 / 36
11 / 36
12 / 36
13 / 36
14 / 36
15 / 36
16 / 36
17 / 36
18 / 36
19 / 36
20 / 36
21 / 36
22 / 36
23 / 36
24 / 36
25 / 36
26 / 36
27 / 36
28 / 36
29 / 36
30 / 36
31 / 36
32 / 36
33 / 36
34 / 36
##### writing hat3
pairlocalalign (aa) Version 6.857b alg=A, model=BLOSUM62, 2.000, -0.099, +0.100
0 thread(s)
nthread = 0
blosum 62 / kimura 200
Loading 'hat3' ...
done.
done.
scoremtx = 1
Gap Penalty = -1.53, +0.00, +0.00
Loading 'hat2' ... done.
Constructing a UPGMA tree ...
0 / 36
10 / 36
20 / 36
30 / 36
done.
Progressive alignment ...
STEP 1 /35 c
STEP 2 /35 c
STEP 3 /35 c
STEP 4 /35 c
STEP 5 /35 c
STEP 6 /35 c
STEP 7 /35 c
STEP 8 /35 c
STEP 9 /35 c
STEP 10 /35 c
STEP 11 /35 c
STEP 12 /35 c
STEP 13 /35 c
STEP 14 /35 c
STEP 15 /35 c
STEP 16 /35 c
STEP 17 /35 c
STEP 18 /35 c
STEP 19 /35 c
STEP 20 /35 c
STEP 21 /35 c
STEP 22 /35 c
STEP 23 /35 c
STEP 24 /35 c
STEP 25 /35 c
STEP 26 /35 c
STEP 27 /35 c
STEP 28 /35 c
STEP 29 /35 c
STEP 30 /35 c
STEP 31 /35 c
STEP 32 /35 c
STEP 33 /35 c
STEP 34 /35 c
Reallocating..done. *alloclen = 2116
STEP 35 /35 c
done.
tbfast (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
Strategy:
G-INS-1 (Not tested.)
Progressive method incorporating GLOBAL pairwise alignment information
If unsure which option to use, try 'mafft --auto input > output'.
If the possibility of long gaps can be excluded, add '--ep 0.123'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.
MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --globalpair --maxiterate 100 test/sample | diff test/sample.ginsi -
nthread = 0
done.
scoremtx = 1
Gap Penalty = -2.00, -0.10, +0.10
0 / 36
1 / 36
2 / 36
3 / 36
4 / 36
5 / 36
6 / 36
7 / 36
8 / 36
9 / 36
10 / 36
11 / 36
12 / 36
13 / 36
14 / 36
15 / 36
16 / 36
17 / 36
18 / 36
19 / 36
20 / 36
21 / 36
22 / 36
23 / 36
24 / 36
25 / 36
26 / 36
27 / 36
28 / 36
29 / 36
30 / 36
31 / 36
32 / 36
33 / 36
34 / 36
##### writing hat3
pairlocalalign (aa) Version 6.857b alg=A, model=BLOSUM62, 2.000, -0.099, +0.100
0 thread(s)
nthread = 0
blosum 62 / kimura 200
Loading 'hat3' ...
done.
done.
scoremtx = 1
Gap Penalty = -1.53, +0.00, +0.00
Loading 'hat2' ... done.
Constructing a UPGMA tree ...
0 / 36
10 / 36
20 / 36
30 / 36
done.
Progressive alignment ...
STEP 1 /35 c
STEP 2 /35 c
STEP 3 /35 c
STEP 4 /35 c
STEP 5 /35 c
STEP 6 /35 c
STEP 7 /35 c
STEP 8 /35 c
STEP 9 /35 c
STEP 10 /35 c
STEP 11 /35 c
STEP 12 /35 c
STEP 13 /35 c
STEP 14 /35 c
STEP 15 /35 c
STEP 16 /35 c
STEP 17 /35 c
STEP 18 /35 c
STEP 19 /35 c
STEP 20 /35 c
STEP 21 /35 c
STEP 22 /35 c
STEP 23 /35 c
STEP 24 /35 c
STEP 25 /35 c
STEP 26 /35 c
STEP 27 /35 c
STEP 28 /35 c
STEP 29 /35 c
STEP 30 /35 c
STEP 31 /35 c
STEP 32 /35 c
STEP 33 /35 c
STEP 34 /35 c
Reallocating..done. *alloclen = 2116
STEP 35 /35 c
done.
tbfast (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
nthread = 0
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 16
Loading 'hat3' ... done.
done.
scoremtx = 1
0 / 36
10 / 36
20 / 36
30 / 36
Segment 1/ 1 1- 710
STEP 001-001-0 identical.
STEP 001-001-1 identical.
STEP 001-002-0 identical.
STEP 001-002-1 identical.
STEP 001-003-0 identical.
STEP 001-003-1 identical.
STEP 001-004-0 identical.
STEP 001-004-1 identical.
STEP 001-005-0 identical.
STEP 001-005-1 identical.
STEP 001-006-0 accepted.
STEP 001-006-1 accepted.
STEP 001-007-0 identical.
STEP 001-007-1 identical.
STEP 001-008-0 identical.
STEP 001-008-1 identical.
STEP 001-009-0 identical.
STEP 001-009-1 identical.
STEP 001-010-0 identical.
STEP 001-010-1 identical.
STEP 001-011-0 identical.
STEP 001-011-1 accepted.
STEP 001-012-0 identical.
STEP 001-012-1 identical.
STEP 001-013-0 identical.
STEP 001-013-1 accepted.
STEP 001-014-0 identical.
STEP 001-014-1 rejected.
STEP 001-015-0 identical.
STEP 001-015-1 identical.
STEP 001-016-0 identical.
STEP 001-016-1 identical.
STEP 001-017-0 identical.
STEP 001-017-1 identical.
STEP 001-018-0 identical.
STEP 001-018-1 identical.
STEP 001-019-0 identical.
STEP 001-019-1 rejected.
STEP 001-020-0 accepted.
STEP 001-020-1 identical.
STEP 001-021-0 identical.
STEP 001-021-1 identical.
STEP 001-022-0 accepted.
STEP 001-022-1 rejected.
STEP 001-023-0 identical.
STEP 001-023-1 rejected.
STEP 001-024-0 accepted.
STEP 001-024-1 accepted.
STEP 001-025-0 accepted.
STEP 001-025-1 accepted.
STEP 001-026-0 identical.
STEP 001-026-1 accepted.
STEP 001-027-0 rejected.
STEP 001-027-1 identical.
STEP 001-028-0 identical.
STEP 001-028-1 identical.
STEP 001-029-0 accepted.
STEP 001-029-1 accepted.
STEP 001-030-0 rejected.
STEP 001-030-1 accepted.
STEP 001-031-0 identical.
STEP 001-031-1 accepted.
STEP 001-032-0 accepted.
STEP 001-032-1 rejected.
STEP 001-033-0 rejected.
STEP 001-033-1 rejected.
STEP 001-034-0 rejected.
STEP 001-034-1 rejected.
STEP 001-035-1 accepted.
STEP 002-035-1 identical.
STEP 002-034-0 accepted.
STEP 002-034-1 rejected.
STEP 002-033-0 rejected.
STEP 002-033-1 rejected.
STEP 002-032-0 rejected.
STEP 002-032-1 rejected.
STEP 002-031-0 rejected.
STEP 002-031-1 accepted.
STEP 002-030-0 identical.
STEP 002-030-1 rejected.
STEP 002-029-0 rejected.
STEP 002-029-1 rejected.
STEP 002-028-0 accepted.
STEP 002-028-1 rejected.
STEP 002-027-0 identical.
STEP 002-027-1 identical.
STEP 002-026-0 identical.
STEP 002-026-1 identical.
STEP 002-025-0 identical.
STEP 002-025-1 identical.
STEP 002-024-0 identical.
STEP 002-024-1 accepted.
STEP 002-023-0 rejected.
STEP 002-023-1 identical.
STEP 002-022-0 identical.
STEP 002-022-1 accepted.
STEP 002-021-0 identical.
STEP 002-021-1 identical.
STEP 002-020-0 identical.
STEP 002-020-1 identical.
STEP 002-019-0 identical.
STEP 002-019-1 identical.
STEP 002-018-0 identical.
STEP 002-018-1 identical.
STEP 002-017-0 accepted.
STEP 002-017-1 identical.
STEP 002-016-0 identical.
STEP 002-016-1 identical.
STEP 002-015-0 identical.
STEP 002-015-1 identical.
STEP 002-014-0 identical.
STEP 002-014-1 accepted.
STEP 002-013-0 identical.
STEP 002-013-1 identical.
STEP 002-012-0 identical.
STEP 002-012-1 identical.
STEP 002-011-0 identical.
STEP 002-011-1 identical.
STEP 002-010-0 identical.
STEP 002-010-1 identical.
STEP 002-009-0 identical.
STEP 002-009-1 identical.
STEP 002-008-0 identical.
STEP 002-008-1 identical.
STEP 002-007-0 identical.
STEP 002-007-1 identical.
STEP 002-006-0 rejected.
STEP 002-006-1 accepted.
STEP 002-005-0 identical.
STEP 002-005-1 identical.
STEP 002-004-0 identical.
STEP 002-004-1 identical.
STEP 002-003-0 identical.
STEP 002-003-1 identical.
STEP 002-002-0 identical.
STEP 002-002-1 identical.
STEP 002-001-0 identical.
STEP 002-001-1 identical.
STEP 003-001-0 identical.
STEP 003-001-1 identical.
STEP 003-002-0 identical.
STEP 003-002-1 identical.
STEP 003-003-0 identical.
STEP 003-003-1 identical.
STEP 003-004-0 identical.
STEP 003-004-1 identical.
STEP 003-005-0 identical.
STEP 003-005-1 identical.
STEP 003-006-0 rejected.
STEP 003-006-1 identical.
STEP 003-007-0 identical.
STEP 003-007-1 identical.
STEP 003-008-0 identical.
STEP 003-008-1 identical.
STEP 003-009-0 identical.
STEP 003-009-1 identical.
STEP 003-010-0 identical.
STEP 003-010-1 identical.
STEP 003-011-0 identical.
STEP 003-011-1 identical.
STEP 003-012-0 identical.
STEP 003-012-1 identical.
STEP 003-013-0 identical.
STEP 003-013-1 identical.
STEP 003-014-0 identical.
STEP 003-014-1 identical.
STEP 003-015-0 identical.
STEP 003-015-1 identical.
STEP 003-016-0 identical.
STEP 003-016-1 identical.
STEP 003-017-0 identical.
STEP 003-017-1 identical.
STEP 003-018-0 identical.
STEP 003-018-1 identical.
STEP 003-019-0 identical.
STEP 003-019-1 identical.
STEP 003-020-0 identical.
STEP 003-020-1 identical.
STEP 003-021-0 identical.
STEP 003-021-1 identical.
STEP 003-022-0 identical.
STEP 003-022-1 identical.
STEP 003-023-0 rejected.
STEP 003-023-1 identical.
STEP 003-024-0 identical.
STEP 003-024-1 identical.
STEP 003-025-0 identical.
STEP 003-025-1 identical.
STEP 003-026-0 identical.
STEP 003-026-1 rejected.
STEP 003-027-0 identical.
STEP 003-027-1 identical.
STEP 003-028-0 identical.
STEP 003-028-1 rejected.
STEP 003-029-0 rejected.
STEP 003-029-1 rejected.
STEP 003-030-0 identical.
STEP 003-030-1 identical.
STEP 003-031-0 rejected.
STEP 003-031-1 rejected.
Converged.
done
dvtditr (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
Strategy:
G-INS-i (Suitable for sequences of similar lengths, very slow)
Iterative refinement method (<16) with GLOBAL pairwise alignment information
If unsure which option to use, try 'mafft --auto input > output'.
If the possibility of long gaps can be excluded, add '--ep 0.123'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.
MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --localpair test/sample | diff test/sample.lins1 -
nthread = 0
done.
scoremtx = 1
Gap Penalty = -2.00, -0.10, +0.10
0 / 36
1 / 36
2 / 36
3 / 36
4 / 36
5 / 36
6 / 36
7 / 36
8 / 36
9 / 36
10 / 36
11 / 36
12 / 36
13 / 36
14 / 36
15 / 36
16 / 36
17 / 36
18 / 36
19 / 36
20 / 36
21 / 36
22 / 36
23 / 36
24 / 36
25 / 36
26 / 36
27 / 36
28 / 36
29 / 36
30 / 36
31 / 36
32 / 36
33 / 36
34 / 36
##### writing hat3
pairlocalalign (aa) Version 6.857b alg=L, model=BLOSUM62, 2.000, -0.099, +0.100
0 thread(s)
nthread = 0
blosum 62 / kimura 200
Loading 'hat3' ...
done.
done.
scoremtx = 1
Gap Penalty = -1.53, +0.00, +0.00
Loading 'hat2' ... done.
Constructing a UPGMA tree ...
0 / 36
10 / 36
20 / 36
30 / 36
done.
Progressive alignment ...
STEP 1 /35 c
STEP 2 /35 c
STEP 3 /35 c
STEP 4 /35 c
STEP 5 /35 c
STEP 6 /35 c
STEP 7 /35 c
STEP 8 /35 c
STEP 9 /35 c
STEP 10 /35 c
STEP 11 /35 c
STEP 12 /35 c
STEP 13 /35 c
STEP 14 /35 c
STEP 15 /35 c
STEP 16 /35 c
STEP 17 /35 c
STEP 18 /35 c
STEP 19 /35 c
STEP 20 /35 c
STEP 21 /35 c
STEP 22 /35 c
STEP 23 /35 c
STEP 24 /35 c
STEP 25 /35 c
STEP 26 /35 c
STEP 27 /35 c
STEP 28 /35 c
STEP 29 /35 c
STEP 30 /35 c
STEP 31 /35 c
STEP 32 /35 c
STEP 33 /35 c
STEP 34 /35 c
Reallocating..done. *alloclen = 2097
STEP 35 /35 c
done.
tbfast (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
Strategy:
L-INS-1 (Not tested.)
Progressive method incorporating LOCAL pairwise alignment information
If unsure which option to use, try 'mafft --auto input > output'.
If the possibility of long gaps can be excluded, add '--ep 0.123'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.
MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --localpair --maxiterate 100 test/sample | diff test/sample.linsi -
nthread = 0
done.
scoremtx = 1
Gap Penalty = -2.00, -0.10, +0.10
0 / 36
1 / 36
2 / 36
3 / 36
4 / 36
5 / 36
6 / 36
7 / 36
8 / 36
9 / 36
10 / 36
11 / 36
12 / 36
13 / 36
14 / 36
15 / 36
16 / 36
17 / 36
18 / 36
19 / 36
20 / 36
21 / 36
22 / 36
23 / 36
24 / 36
25 / 36
26 / 36
27 / 36
28 / 36
29 / 36
30 / 36
31 / 36
32 / 36
33 / 36
34 / 36
##### writing hat3
pairlocalalign (aa) Version 6.857b alg=L, model=BLOSUM62, 2.000, -0.099, +0.100
0 thread(s)
nthread = 0
blosum 62 / kimura 200
Loading 'hat3' ...
done.
done.
scoremtx = 1
Gap Penalty = -1.53, +0.00, +0.00
Loading 'hat2' ... done.
Constructing a UPGMA tree ...
0 / 36
10 / 36
20 / 36
30 / 36
done.
Progressive alignment ...
STEP 1 /35 c
STEP 2 /35 c
STEP 3 /35 c
STEP 4 /35 c
STEP 5 /35 c
STEP 6 /35 c
STEP 7 /35 c
STEP 8 /35 c
STEP 9 /35 c
STEP 10 /35 c
STEP 11 /35 c
STEP 12 /35 c
STEP 13 /35 c
STEP 14 /35 c
STEP 15 /35 c
STEP 16 /35 c
STEP 17 /35 c
STEP 18 /35 c
STEP 19 /35 c
STEP 20 /35 c
STEP 21 /35 c
STEP 22 /35 c
STEP 23 /35 c
STEP 24 /35 c
STEP 25 /35 c
STEP 26 /35 c
STEP 27 /35 c
STEP 28 /35 c
STEP 29 /35 c
STEP 30 /35 c
STEP 31 /35 c
STEP 32 /35 c
STEP 33 /35 c
STEP 34 /35 c
Reallocating..done. *alloclen = 2097
STEP 35 /35 c
done.
tbfast (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
nthread = 0
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 16
Loading 'hat3' ... done.
done.
scoremtx = 1
0 / 36
10 / 36
20 / 36
30 / 36
Segment 1/ 1 1- 691
STEP 001-001-0 identical.
STEP 001-001-1 identical.
STEP 001-002-0 identical.
STEP 001-002-1 identical.
STEP 001-003-0 identical.
STEP 001-003-1 identical.
STEP 001-004-0 identical.
STEP 001-004-1 identical.
STEP 001-005-0 identical.
STEP 001-005-1 identical.
STEP 001-006-0 rejected.
STEP 001-006-1 identical.
STEP 001-007-0 identical.
STEP 001-007-1 identical.
STEP 001-008-0 identical.
STEP 001-008-1 identical.
STEP 001-009-0 identical.
STEP 001-009-1 identical.
STEP 001-010-0 identical.
STEP 001-010-1 identical.
STEP 001-011-0 identical.
STEP 001-011-1 accepted.
STEP 001-012-0 rejected.
STEP 001-012-1 identical.
STEP 001-013-0 identical.
STEP 001-013-1 rejected.
STEP 001-014-0 identical.
STEP 001-014-1 identical.
STEP 001-015-0 identical.
STEP 001-015-1 identical.
STEP 001-016-0 identical.
STEP 001-016-1 identical.
STEP 001-017-0 identical.
STEP 001-017-1 identical.
STEP 001-018-0 identical.
STEP 001-018-1 identical.
STEP 001-019-0 rejected.
STEP 001-019-1 accepted.
STEP 001-020-0 accepted.
STEP 001-020-1 identical.
STEP 001-021-0 identical.
STEP 001-021-1 identical.
STEP 001-022-0 rejected.
STEP 001-022-1 rejected.
STEP 001-023-0 rejected.
STEP 001-023-1 accepted.
STEP 001-024-0 rejected.
STEP 001-024-1 accepted.
STEP 001-025-0 identical.
STEP 001-025-1 accepted.
STEP 001-026-0 identical.
STEP 001-026-1 rejected.
STEP 001-027-0 identical.
STEP 001-027-1 identical.
STEP 001-028-0 rejected.
STEP 001-028-1 rejected.
STEP 001-029-0 accepted.
STEP 001-029-1 accepted.
STEP 001-030-0 rejected.
STEP 001-030-1 accepted.
STEP 001-031-0 rejected.
STEP 001-031-1 rejected.
STEP 001-032-0 accepted.
STEP 001-032-1 rejected.
STEP 001-033-0 accepted.
STEP 001-033-1 rejected.
STEP 001-034-0 rejected.
STEP 001-034-1 rejected.
STEP 001-035-1 accepted.
STEP 002-035-1 identical.
STEP 002-034-0 rejected.
STEP 002-034-1 rejected.
STEP 002-033-0 identical.
STEP 002-033-1 rejected.
STEP 002-032-0 identical.
STEP 002-032-1 rejected.
STEP 002-031-0 rejected.
STEP 002-031-1 accepted.
STEP 002-030-0 rejected.
STEP 002-030-1 rejected.
STEP 002-029-0 accepted.
STEP 002-029-1 rejected.
STEP 002-028-0 accepted.
STEP 002-028-1 accepted.
STEP 002-027-0 identical.
STEP 002-027-1 identical.
STEP 002-026-0 identical.
STEP 002-026-1 accepted.
STEP 002-025-0 identical.
STEP 002-025-1 identical.
STEP 002-024-0 accepted.
STEP 002-024-1 rejected.
STEP 002-023-0 accepted.
STEP 002-023-1 rejected.
STEP 002-022-0 accepted.
STEP 002-022-1 accepted.
STEP 002-021-0 identical.
STEP 002-021-1 identical.
STEP 002-020-0 identical.
STEP 002-020-1 rejected.
STEP 002-019-0 identical.
STEP 002-019-1 accepted.
STEP 002-018-0 identical.
STEP 002-018-1 identical.
STEP 002-017-0 accepted.
STEP 002-017-1 identical.
STEP 002-016-0 identical.
STEP 002-016-1 accepted.
STEP 002-015-0 identical.
STEP 002-015-1 identical.
STEP 002-014-0 identical.
STEP 002-014-1 identical.
STEP 002-013-0 identical.
STEP 002-013-1 rejected.
STEP 002-012-0 identical.
STEP 002-012-1 identical.
STEP 002-011-0 identical.
STEP 002-011-1 identical.
STEP 002-010-0 identical.
STEP 002-010-1 identical.
STEP 002-009-0 identical.
STEP 002-009-1 identical.
STEP 002-008-0 identical.
STEP 002-008-1 identical.
STEP 002-007-0 identical.
STEP 002-007-1 identical.
STEP 002-006-0 identical.
STEP 002-006-1 identical.
STEP 002-005-0 identical.
STEP 002-005-1 identical.
STEP 002-004-0 identical.
STEP 002-004-1 identical.
STEP 002-003-0 identical.
STEP 002-003-1 identical.
STEP 002-002-0 identical.
STEP 002-002-1 identical.
STEP 002-001-0 identical.
STEP 002-001-1 identical.
STEP 003-001-0 identical.
STEP 003-001-1 identical.
STEP 003-002-0 identical.
STEP 003-002-1 identical.
STEP 003-003-0 identical.
STEP 003-003-1 identical.
STEP 003-004-0 identical.
STEP 003-004-1 identical.
STEP 003-005-0 identical.
STEP 003-005-1 identical.
STEP 003-006-0 identical.
STEP 003-006-1 identical.
STEP 003-007-0 identical.
STEP 003-007-1 identical.
STEP 003-008-0 identical.
STEP 003-008-1 identical.
STEP 003-009-0 identical.
STEP 003-009-1 identical.
STEP 003-010-0 identical.
STEP 003-010-1 identical.
STEP 003-011-0 identical.
STEP 003-011-1 identical.
STEP 003-012-0 identical.
STEP 003-012-1 identical.
STEP 003-013-0 identical.
STEP 003-013-1 rejected.
STEP 003-014-0 identical.
STEP 003-014-1 identical.
STEP 003-015-0 identical.
STEP 003-015-1 identical.
STEP 003-016-0 identical.
STEP 003-016-1 identical.
STEP 003-017-0 identical.
STEP 003-017-1 identical.
STEP 003-018-0 identical.
STEP 003-018-1 identical.
STEP 003-019-0 identical.
STEP 003-019-1 identical.
STEP 003-020-0 identical.
STEP 003-020-1 rejected.
STEP 003-021-0 identical.
STEP 003-021-1 identical.
Converged.
done
dvtditr (aa) Version 6.857b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000
0 thread(s)
Strategy:
L-INS-i (Probably most accurate, very slow)
Iterative refinement method (<16) with LOCAL pairwise alignment information
If unsure which option to use, try 'mafft --auto input > output'.
If the possibility of long gaps can be excluded, add '--ep 0.123'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_installcatalogs
dh_installcron
dh_installdebconf
dh_installemacsen
dh_installifupdown
dh_installinfo
dh_installinit
dh_installmenu
dh_installmime
dh_installmodules
dh_installlogcheck
dh_installlogrotate
dh_installpam
dh_installppp
dh_installudev
dh_installwm
dh_installxfonts
dh_installgsettings
dh_bugfiles
dh_ucf
dh_lintian
dh_gconf
dh_icons
dh_perl
dh_usrlocal
dh_link
dh_compress
dh_fixperms
dh_strip
dh_makeshlibs
dh_shlibdeps
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package `mafft' in `../mafft_6.857-1_amd64.deb'.
dpkg-genchanges >../mafft_6.857-1_amd64.changes
dpkg-genchanges: including full source code in upload
dpkg-source --after-build mafft-6.857
dpkg-buildpackage: full upload (original source is included)
????????????????????????????????????????????????????????????????????????????????
Build finished at 20110805-1000
Finished
????????
I: Built successfully
????????????????????????????????????????????????????????????????????????????????
? Changes ?
????????????????????????????????????????????????????????????????????????????????
mafft_6.857-1_amd64.changes:
????????????????????????????
Format: 1.8
Date: Fri, 05 Aug 2011 09:54:09 +0900
Source: mafft
Binary: mafft
Architecture: source amd64
Version: 6.857-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
mafft - Multiple alignment program for amino acid or nucleotide sequences
Closes: 636634
Changes:
mafft (6.857-1) unstable; urgency=low
.
* New upstream version.
* Enable multithread, correct FHS path (debian/rules).
* Removed extra manpage copies instead of patching Makefile and
installing via debhleper (debian/patches, debian/rules, debian/manpages).
* Removed debian/dirs, not needed anymore.
* Run the tests after installation, and allow them to fail (debian/rules).
* Build when running debian/rules build (override typo, Closes: #636634).
* Corrected VCS fields in debian/control.
* Incremented Standards-Version to reflect conformance wiht Policy 3.9.2
(debian/control, no changes needed).
Checksums-Sha1:
e515ce9717df03bdc41e01f495264d311a2572f3 1071 mafft_6.857-1.dsc
95789a1e770f27051c87fe8378fa57992cdb7397 384084 mafft_6.857.orig.tar.gz
f5b838fa0c51137c40c87099017894f1cec4981c 4981 mafft_6.857-1.debian.tar.gz
4ed9abdf470251dc2ebd089ba2126b43ccc4edf9 3437470 mafft_6.857-1_amd64.deb
Checksums-Sha256:
948744a7514f280a115859fe79c132c28310a8a42e5a1b089f1f610a1737fd80 1071 mafft_6.857-1.dsc
ef671432e94b475c34a50fa34c98b2612bbdd52bb16f95bfff57cbf9974a30e5 384084 mafft_6.857.orig.tar.gz
3063f27497fa41f6b914ee0bd09c7b6749de34635a263e6df70d69d948278505 4981 mafft_6.857-1.debian.tar.gz
4974d8d45993543ce85162a5bfe2ad2a0e470e5e40c4336e01cb5dea82503c88 3437470 mafft_6.857-1_amd64.deb
Files:
e40cfb2a178b3262e11c72e23c37b5a4 1071 science optional mafft_6.857-1.dsc
85ef7cbe13fe3e51b004ad9267215f48 384084 science optional mafft_6.857.orig.tar.gz
1ed8e4199c52d390aca476b2a72e73f1 4981 science optional mafft_6.857-1.debian.tar.gz
1affcfece9fd5aea9d558f9204f6c326 3437470 science optional mafft_6.857-1_amd64.deb
????????????????????????????????????????????????????????????????????????????????
? Package contents ?
????????????????????????????????????????????????????????????????????????????????
mafft_6.857-1_amd64.deb
???????????????????????
new debian package, version 2.0.
size 3437470 bytes: control archive= 2129 bytes.
1368 bytes, 30 lines control
3205 bytes, 46 lines md5sums
Package: mafft
Version: 6.857-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 7844
Depends: libc6 (>= 2.7)
Recommends: blast2, lynx, ruby
Enhances: t-coffee
Section: science
Priority: optional
Homepage: http://align.bmr.kyushu-u.ac.jp/mafft/software/
Description: Multiple alignment program for amino acid or nucleotide sequences
MAFFT is a multiple sequence alignment program which offers three
accuracy-oriented methods:
* L-INS-i (probably most accurate; recommended for <200 sequences;
iterative refinement method incorporating local pairwise alignment
information),
* G-INS-i (suitable for sequences of similar lengths; recommended for
<200 sequences; iterative refinement method incorporating global
pairwise alignment information),
* E-INS-i (suitable for sequences containing large unalignable regions;
recommended for <200 sequences),
and five speed-oriented methods:
* FFT-NS-i (iterative refinement method; two cycles only),
* FFT-NS-i (iterative refinement method; max. 1000 iterations),
* FFT-NS-2 (fast; progressive method),
* FFT-NS-1 (very fast; recommended for >2000 sequences; progressive
method with a rough guide tree),
* NW-NS-PartTree-1 (recommended for ?50,000 sequences; progressive
method with the PartTree algorithm).
drwxr-xr-x root/root 0 2011-08-05 09:59 ./
drwxr-xr-x root/root 0 2011-08-05 10:00 ./usr/
drwxr-xr-x root/root 0 2011-08-05 09:59 ./usr/lib/
drwxr-xr-x root/root 0 2011-08-05 09:59 ./usr/lib/mafft/
drwxr-xr-x root/root 0 2011-08-05 09:59 ./usr/lib/mafft/lib/
drwxr-xr-x root/root 0 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/
-rwxr-xr-x root/root 236400 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/dndblast
-rwxr-xr-x root/root 220176 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/dndpre
-rwxr-xr-x root/root 219984 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/dndpre2
-rwxr-xr-x root/root 74384 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/countlen
-rwxr-xr-x root/root 465040 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/pairlocalalign
-rwxr-xr-x root/root 232816 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/sextet5
-rwxr-xr-x root/root 462832 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/pairash
-rwxr-xr-x root/root 462288 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/splittbfast
-rwxr-xr-x root/root 459632 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/tbfast
-rwxr-xr-x root/root 224144 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/mccaskillwrap
-rwxr-xr-x root/root 151696 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/f2cl
-rwxr-xr-x root/root 221232 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/contrafoldwrap
-rwxr-xr-x root/root 236400 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/dndfast7
-rwxr-xr-x root/root 433008 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/getlag
-rwxr-xr-x root/root 144352 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/restoreu
-rwxr-xr-x root/root 268368 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/rnatest
-rwxr-xr-x root/root 244560 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/multi2hat3s
-rwxr-xr-x root/root 244560 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/pair2hat3s
-rwxr-xr-x root/root 145712 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/regtable2seq
-rwxr-xr-x root/root 74576 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/seq2regtable
-rwxr-xr-x root/root 454864 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/disttbfast
-rwxr-xr-x root/root 433008 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/mafft-profile
-rwxr-xr-x root/root 143936 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/replaceu
-rwxr-xr-x root/root 233616 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/mafft-distance
-rwxr-xr-x root/root 218416 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/score
-rwxr-xr-x root/root 432080 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/setcore
-rwxr-xr-x root/root 478192 2011-08-05 10:00 ./usr/lib/mafft/lib/mafft/dvtditr
drwxr-xr-x root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/
-rwxr-xr-x root/root 58436 2011-08-05 09:59 ./usr/lib/mafft/bin/mafft
-rwxr-xr-x root/root 8263 2011-08-05 09:59 ./usr/lib/mafft/bin/mafft-homologs.rb
drwxr-xr-x root/root 0 2011-08-05 09:59 ./usr/share/
drwxr-xr-x root/root 0 2011-08-05 09:59 ./usr/share/doc/
drwxr-xr-x root/root 0 2011-08-05 10:00 ./usr/share/doc/mafft/
drwxr-xr-x root/root 0 2011-08-05 10:00 ./usr/share/doc/mafft/test/
-rw-r--r-- root/root 7202 2011-03-30 06:57 ./usr/share/doc/mafft/test/sample.fftnsi.gz
-rw-r--r-- root/root 6763 2007-04-05 15:00 ./usr/share/doc/mafft/test/sample.gz
-rw-r--r-- root/root 1916 2007-11-28 20:14 ./usr/share/doc/mafft/test/samplerna.xinsi
-rw-r--r-- root/root 7518 2009-03-16 19:16 ./usr/share/doc/mafft/test/sample.dpparttree.gz
-rw-r--r-- root/root 7191 2009-03-16 19:14 ./usr/share/doc/mafft/test/sample.ginsi.gz
-rw-r--r-- root/root 7186 2009-03-16 19:14 ./usr/share/doc/mafft/test/sample.linsi.gz
-rw-r--r-- root/root 7257 2009-03-16 19:13 ./usr/share/doc/mafft/test/sample.gins1.gz
-rw-r--r-- root/root 7255 2009-03-16 19:15 ./usr/share/doc/mafft/test/sample.lins1.gz
-rw-r--r-- root/root 7452 2009-03-16 19:16 ./usr/share/doc/mafft/test/sample.parttree.gz
-rw-r--r-- root/root 7203 2010-10-06 08:20 ./usr/share/doc/mafft/test/sample.fftns2.gz
-rw-r--r-- root/root 1502 2007-11-28 20:13 ./usr/share/doc/mafft/test/samplerna
-rw-r--r-- root/root 1916 2007-11-28 20:15 ./usr/share/doc/mafft/test/samplerna.qinsi
-rw-r--r-- root/root 1011 2009-12-14 14:15 ./usr/share/doc/mafft/README.Debian
-rw-r--r-- root/root 2009 2011-08-05 09:18 ./usr/share/doc/mafft/copyright
-rw-r--r-- root/root 1607 2011-08-05 09:54 ./usr/share/doc/mafft/changelog.Debian.gz
drwxr-xr-x root/root 0 2011-08-05 09:59 ./usr/share/man/
drwxr-xr-x root/root 0 2011-08-05 10:00 ./usr/share/man/man1/
-rw-r--r-- root/root 4420 2011-08-05 09:59 ./usr/share/man/man1/mafft.1.gz
-rw-r--r-- root/root 2130 2011-08-05 09:59 ./usr/share/man/man1/mafft-homologs.1.gz
drwxr-xr-x root/root 0 2011-08-05 10:00 ./usr/bin/
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/ginsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/mafft-nwnsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/mafft-qinsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/mafft-einsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/einsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/nwns -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/nwnsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/mafft-ginsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 09:59 ./usr/lib/mafft/bin/mafft-fftns -> mafft
lrwxrwxrwx root/root 0 2011-08-05 09:59 ./usr/lib/mafft/bin/fftns -> mafft
lrwxrwxrwx root/root 0 2011-08-05 09:59 ./usr/lib/mafft/bin/mafft-nwns -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/mafft-profile -> ../lib/mafft/mafft-profile
lrwxrwxrwx root/root 0 2011-08-05 09:59 ./usr/lib/mafft/bin/mafft-linsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 09:59 ./usr/lib/mafft/bin/mafft-fftnsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 09:59 ./usr/lib/mafft/bin/mafft-xinsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/lib/mafft/bin/mafft-distance -> ../lib/mafft/mafft-distance
lrwxrwxrwx root/root 0 2011-08-05 09:59 ./usr/lib/mafft/bin/fftnsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 09:59 ./usr/lib/mafft/bin/linsi -> mafft
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/mafft-profile.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/fftnsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/mafft-einsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/mafft-linsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/mafft-fftnsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/ginsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/linsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/mafft-ginsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/fftns.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/mafft-fftns.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/share/man/man1/einsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/bin/mafft-homologs -> ../lib/mafft/bin/mafft-homologs.rb
lrwxrwxrwx root/root 0 2011-08-05 10:00 ./usr/bin/mafft -> ../lib/mafft/bin/mafft
????????????????????????????????????????????????????????????????????????????????
? Post Build ?
????????????????????????????????????????????????????????????????????????????????
lintian
???????
P: mafft source: unneeded-build-dep-on-quilt
P: mafft: no-upstream-changelog
I: mafft: hyphen-used-as-minus-sign usr/share/man/man1/mafft-homologs.1.gz:52
I: Lintian run was successful.
????????????????????????????????????????????????????????????????????????????????
? Cleanup ?
????????????????????????????????????????????????????????????????????????????????
Purging /«BUILDDIR»
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
bsdmainutils* debhelper* diffstat* file* gettext* gettext-base* groff-base*
html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpcre3*
libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt*
sbuild-build-depends-core-dummy* sbuild-build-depends-mafft-dummy*
0 upgraded, 0 newly installed, 21 to remove and 0 not upgraded.
After this operation, 28.0 MB disk space will be freed.
(Reading database ... 12244 files and directories currently installed.)
Removing sbuild-build-depends-mafft-dummy ...
Removing debhelper ...
Removing man-db ...
Purging configuration files for man-db ...
Removing bsdmainutils ...
Purging configuration files for bsdmainutils ...
Removing quilt ...
Purging configuration files for quilt ...
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 libcroco3 ...
Purging configuration files for libcroco3 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
Purging configuration files for libunistring0 ...
Removing libxml2 ...
Purging configuration files for libxml2 ...
Removing sbuild-build-depends-core-dummy ...
????????????????????????????????????????????????????????????????????????????????
? Summary ?
????????????????????????????????????????????????????????????????????????????????
Architecture: amd64
Build-Space: 32704
Build-Time: 70
Distribution: unstable
Install-Time: 12
Job: mafft_6.857-1.dsc
Lintian: pass
Package: mafft
Package-Time: 85
Source-Version: 6.857-1
Space: 32704
Status: successful
Version: 6.857-1
????????????????????????????????????????????????????????????????????????????????
Finished at 20110805-1000
Build needed 00:01:25, 32704k disc space
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