[Debian-med-packaging] FFT-NS-i test data unreproducible with mafft 7.113 on a Debian system.
Charles Plessy
plessy at debian.org
Mon Oct 14 01:38:36 UTC 2013
Dear Dr Katoh,
I was preparing to update MAFFT to version 7.113 in Debian
(packages.debian.org/mafft), but stopped when I realised that, in contrary with
version 7.058, I can not reproduce the reference alignment from the test
directory. I attached the differences produced by the following command.
mafft --thread 0 --maxiterate 100 sample | diff sample.fftnsi - > sample.fftnsi.diff
I also attached the script that we use as regression test in Debian, inspired
by the test commands in MAFFT's readme file.
Just in case you need more details on how I compiled MAFFT, I also attached the
full build log. The key line is probably the following.
/usr/bin/make -C core PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" CPPFLAGS="-D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro"
Have a nice day,
--
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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#!/bin/sh -e
MAFFT="mafft --thread 0"
TESTDATADIR=/usr/share/doc/mafft/test/
$MAFFT $TESTDATADIR/sample | diff $TESTDATADIR/sample.fftns2 -
$MAFFT --maxiterate 100 $TESTDATADIR/sample | diff $TESTDATADIR/sample.fftnsi -
$MAFFT --globalpair $TESTDATADIR/sample | diff $TESTDATADIR/sample.gins1 -
$MAFFT --globalpair --maxiterate 100 $TESTDATADIR/sample | diff $TESTDATADIR/sample.ginsi -
$MAFFT --localpair $TESTDATADIR/sample | diff $TESTDATADIR/sample.lins1 -
$MAFFT --localpair --maxiterate 100 $TESTDATADIR/sample | diff $TESTDATADIR/sample.linsi -
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sbuild (Debian sbuild) 0.64.0 (17 May 2013) on aqwa.igloo
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? mafft 7.113-1 (amd64) 14 oct. 2013 10:31 ?
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Package: mafft
Version: 7.113-1
Source Version: 7.113-1
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
I: NOTICE: Log filtering will replace 'build/mafft-E1XobP/mafft-7.113' with '?PKGBUILDDIR?'
I: NOTICE: Log filtering will replace 'build/mafft-E1XobP' with '?BUILDDIR?'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-a7f8ddd3-2264-4f6c-a850-7dd8ad4b660b' with '?CHROOT?'
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? Update chroot ?
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Hit http://ftp.jp.debian.org unstable InRelease
Hit http://ftp.jp.debian.org unstable/main Sources/DiffIndex
Hit http://ftp.jp.debian.org unstable/main amd64 Packages/DiffIndex
Hit http://ftp.jp.debian.org unstable/main Translation-en/DiffIndex
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_7.113-1.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-Bs3B5Q/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/772 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11125 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, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9)
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9)
dpkg-deb: building package `sbuild-build-depends-mafft-dummy' in `/?BUILDDIR?/resolver-LVrU4Y/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 file gettext gettext-base groff-base intltool-debian
libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1 libpipeline1
libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base intltool-debian
libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1 libpipeline1
libunistring0 libxml2 man-db po-debconf sbuild-build-depends-mafft-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/7971 kB of archives.
After this operation, 24.9 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1:amd64.
(Reading database ... 11125 files and directories currently installed.)
Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.4-1_amd64.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.22.2-3_amd64.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_amd64.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.5-2_amd64.deb) ...
Selecting previously unselected package libasprintf0c2:amd64.
Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.3.1-1_amd64.deb) ...
Selecting previously unselected package libmagic1:amd64.
Unpacking libmagic1:amd64 (from .../libmagic1_1%3a5.14-2_amd64.deb) ...
Selecting previously unselected package libxml2:amd64.
Unpacking libxml2:amd64 (from .../libxml2_2.9.1+dfsg1-3_amd64.deb) ...
Selecting previously unselected package libffi6:amd64.
Unpacking libffi6:amd64 (from .../libffi6_3.0.13-4_amd64.deb) ...
Selecting previously unselected package libglib2.0-0:amd64.
Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.36.4-1_amd64.deb) ...
Selecting previously unselected package libcroco3:amd64.
Unpacking libcroco3:amd64 (from .../libcroco3_0.6.8-2_amd64.deb) ...
Selecting previously unselected package libunistring0:amd64.
Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_1%3a5.14-2_amd64.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.3.1-1_amd64.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.3.1-1_amd64.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_9.20130921_all.deb) ...
Selecting previously unselected package sbuild-build-depends-mafft-dummy.
Unpacking sbuild-build-depends-mafft-dummy (from .../sbuild-build-depends-mafft-dummy.deb) ...
Setting up libpipeline1:amd64 (1.2.4-1) ...
Setting up groff-base (1.22.2-3) ...
Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:amd64 (0.18.3.1-1) ...
Setting up libmagic1:amd64 (1:5.14-2) ...
Setting up libxml2:amd64 (2.9.1+dfsg1-3) ...
Setting up libffi6:amd64 (3.0.13-4) ...
Setting up libglib2.0-0:amd64 (2.36.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3:amd64 (0.6.8-2) ...
Setting up libunistring0:amd64 (0.9.3-5) ...
Setting up file (1:5.14-2) ...
Setting up gettext-base (0.18.3.1-1) ...
Setting up gettext (0.18.3.1-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20130921) ...
Setting up sbuild-build-depends-mafft-dummy (0.invalid.0) ...
Processing triggers for libc-bin ...
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? Build environment ?
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Kernel: Linux 3.10-1-amd64 amd64 (x86_64)
Toolchain package versions: binutils_2.23.90.20130927-1 dpkg-dev_1.17.1 g++-4.8_4.8.1-10 gcc-4.8_4.8.1-10 libc6-dev_2.17-93 libstdc++-4.8-dev_4.8.1-10 libstdc++6_4.8.1-10 linux-libc-dev_3.10.11-1
Package versions: apt_0.9.12 base-files_7.2 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.23.90.20130927-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1 cpp_4:4.8.1-3 cpp-4.8_4.8.1-10 dash_0.5.7-3 debconf_1.5.51 debconf-i18n_1.5.51 debfoster_2.7-1.2 debhelper_9.20130921 debian-archive-keyring_2012.4 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.1 dpkg-dev_1.17.1 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 eatmydata_26-2 fakeroot_1.20-1 file_1:5.14-2 findutils_4.4.2-6 g++_4:4.8.1-3 g++-4.8_4.8.1-10 gcc_4:4.8.1-3 gcc-4.7-base_4.7.3-7 gcc-4.8_4.8.1-10 gcc-4.8-base_4.8.1-10 gettext_0.18.3.1-1 gettext-base_0.18.3.1-1 gnupg_1.4.15-1 gpgv_1.4.15-1 grep_2.14-4 groff-base_1.22.2-3 gzip_1.6-2 hostname_3.14 initscripts_2.88dsf-43 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1 libapt-pkg4.12_0.9.12 libarchive-extract-perl_0.68-1 libasan0_4.8.1-10 libasprintf0c2_0.18.3.1-1 libatomic1_4.8.1-10 libattr1_1:2.4.47-1 libblkid1_2.20.1-5.5 libbz2-1.0_1.0.6-5 libc-bin_2.17-93 libc-dev-bin_2.17-93 libc6_2.17-93 libc6-dev_2.17-93 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.0-2 libcomerr2_1.42.8-1 libcroco3_0.6.8-2 libdb5.1_5.1.29-7 libdpkg-perl_1.17.1 libffi6_3.0.13-4 libgc1c2_1:7.2d-5 libgcc-4.8-dev_4.8.1-10 libgcc1_1:4.8.1-10 libgdbm3_1.8.3-12 libglib2.0-0_2.36.4-1 libgmp10_2:5.1.2+dfsg-3 libgomp1_4.8.1-10 libisl10_0.11.2-1 libitm1_4.8.1-10 liblocale-gettext-perl_1.05-7+b2 liblog-message-simple-perl_0.10-1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmodule-pluggable-perl_4.8-1 libmount1_2.20.1-5.5 libmpc3_1.0.1-1 libmpfr4_3.1.1-2 libncurses5_5.9+20130608-1 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libpod-latex-perl_0.61-1 libquadmath0_4.8.1-10 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.13-3 libsemanage-common_2.1.10-3 libsemanage1_2.1.10-3 libsepol1_2.1.9-2 libslang2_2.2.4-15 libss2_1.42.8-1 libstdc++-4.8-dev_4.8.1-10 libstdc++6_4.8.1-10 libswitch-perl_2.16-2 libterm-ui-perl_0.38-1 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-soundex-perl_3.4-1+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9+20130608-1 libtsan0_4.8.1-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.10.11-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12 make_3.81-8.2 man-db_2.6.5-2 mawk_1.3.3-17 mount_2.20.1-5.5 multiarch-support_2.17-93 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.7.1-3 perl_5.18.1-4 perl-base_5.18.1-4 perl-modules_5.18.1-4 po-debconf_1.0.16+nmu2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mafft-dummy_0.invalid.0 sed_4.2.2-2 sensible-utils_0.0.9 sysv-rc_2.88dsf-43 sysvinit_2.88dsf-43 sysvinit-utils_2.88dsf-43 tar_1.26+dfsg-10 tzdata_2013d-1 util-linux_2.20.1-5.5 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1
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? Build ?
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Unpack source
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dpkg-source: warning: extracting unsigned source package (mafft_7.113-1.dsc)
dpkg-source: info: extracting mafft in mafft-7.113
dpkg-source: info: unpacking mafft_7.113.orig.tar.gz
dpkg-source: info: unpacking mafft_7.113-1.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_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
SCHROOT_SESSION_ID=unstable-amd64-sbuild-a7f8ddd3-2264-4f6c-a850-7dd8ad4b660b
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
TERM=xterm
USER=charles
USERNAME=charles
XDG_RUNTIME_DIR=/run/user/1000
XDG_SESSION_ID=2
dpkg-buildpackage
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dpkg-buildpackage: source package mafft
dpkg-buildpackage: source version 7.113-1
dpkg-buildpackage: source distribution UNRELEASED
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
dpkg-source --before-build mafft-7.113
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
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 *~ mafftash_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version 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-7.113
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building mafft using existing ./mafft_7.113.orig.tar.gz
dpkg-source: info: building mafft in mafft_7.113-1.debian.tar.gz
dpkg-source: info: building mafft in mafft_7.113-1.dsc
debian/rules build
dh build
dh_testdir
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 CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" CPPFLAGS="-D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro"
make[2]: Entering directory `/?PKGBUILDDIR?/core'
cp mafftash_premafft.tmpl mafftash_premafft.pl
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c mtxutl.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c io.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c mltaln9.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c tddis.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c constants.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c nj.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c partQalignmm.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c partSalignmm.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c Lalignmm.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c rna.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c Salignmm.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c Ralignmm.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c Qalignmm.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c Halignmm.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c Falign.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c Falign_localhom.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c Galign11.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c MSalignmm.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c fftFunctions.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c fft.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c tditeration.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c dvtditr.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c defs.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c SAalignmm.c -o SAalignmm.o
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c treeOperation.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c addfunctions.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 addfunctions.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c dndfast7.c
gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c dndblast.c
gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sextet5.c
gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c mafft-distance.c
gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c MSalign11.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c suboptalign11.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c genGalign11.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c genalign11.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c Lalign11.c
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c addsingle.c
gcc -o addsingle 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 addsingle.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c disttbfast.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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c f2cl.c
gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c mccaskillwrap.c
gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c contrafoldwrap.c
gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c countlen.c
gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c seq2regtable.c
gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c regtable2seq.c
gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c score.c
gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c dndpre.c
gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c replaceu.c
gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c restoreu.c
gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c setdirection.c
gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c makedirectionlist.c
gcc -o makedirectionlist 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 makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -lm -lpthread
gcc -o version version.c -Denablemultithread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro
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 mafftash_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version ../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
dh_testroot
dh_prep
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 mafftash_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version ../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 addsingle splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version
install -s dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version /?PKGBUILDDIR?/debian/mafft/usr/lib/mafft/lib/mafft
install mafftash_premafft.pl /?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
make[1]: Leaving directory `/?PKGBUILDDIR?'
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
debian/rules override_dh_compress
make[1]: Entering directory `/?PKGBUILDDIR?'
dh_compress -X test/sample
make[1]: Leaving directory `/?PKGBUILDDIR?'
dh_fixperms
dh_strip
dh_makeshlibs
dh_shlibdeps
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package mafft: unused substitution variable ${perl:Depends}
dh_md5sums
debian/rules override_dh_builddeb
make[1]: Entering directory `/?PKGBUILDDIR?'
dh_builddeb -- -Z xz
dpkg-deb: building package `mafft' in `../mafft_7.113-1_amd64.deb'.
make[1]: Leaving directory `/?PKGBUILDDIR?'
dpkg-genchanges >../mafft_7.113-1_amd64.changes
dpkg-genchanges: including full source code in upload
dpkg-source --after-build mafft-7.113
dpkg-buildpackage: full upload (original source is included)
????????????????????????????????????????????????????????????????????????????????
Build finished at 20131014-1032
Finished
????????
I: Built successfully
????????????????????????????????????????????????????????????????????????????????
? Post Build Chroot ?
????????????????????????????????????????????????????????????????????????????????
lintian
???????
Merged Build-Depends: lintian
Filtered Build-Depends: lintian
dpkg-deb: building package `sbuild-build-depends-lintian-dummy' in `/?BUILDDIR?/resolver-SmbnRw/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
OK
Reading package lists...
????????????????????????????????????????????????????????????????????????????????
? Install lintian build dependencies (apt-based resolver) ?
????????????????????????????????????????????????????????????????????????????????
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat hardening-includes libapt-pkg-perl libarchive-zip-perl
libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl
libfile-basedir-perl libio-pty-perl libio-socket-inet6-perl
libio-socket-ssl-perl libio-string-perl libipc-run-perl
liblist-moreutils-perl libmailtools-perl libnet-dns-perl
libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
libnet-ssleay-perl libparse-debianchangelog-perl libsocket6-perl libssl1.0.0
libsub-name-perl libtext-levenshtein-perl liburi-perl lintian netbase
patchutils t1utils
Suggested packages:
libwww-perl binutils-multiarch libtext-template-perl
Recommended packages:
libauthen-sasl-perl libhtml-parser-perl libhtml-template-perl
libxml-simple-perl libperlio-gzip-perl ifupdown
The following NEW packages will be installed:
diffstat hardening-includes libapt-pkg-perl libarchive-zip-perl
libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl
libfile-basedir-perl libio-pty-perl libio-socket-inet6-perl
libio-socket-ssl-perl libio-string-perl libipc-run-perl
liblist-moreutils-perl libmailtools-perl libnet-dns-perl
libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
libnet-ssleay-perl libparse-debianchangelog-perl libsocket6-perl libssl1.0.0
libsub-name-perl libtext-levenshtein-perl liburi-perl lintian netbase
patchutils sbuild-build-depends-lintian-dummy t1utils
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I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/addsingle
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/contrafoldwrap
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/countlen
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/disttbfast
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/dndblast
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/dndfast7
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/dndpre
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/dvtditr
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/f2cl
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/getlag
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/mafft-distance
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/mafft-profile
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/makedirectionlist
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/mccaskillwrap
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/multi2hat3s
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/pair2hat3s
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/pairash
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/pairlocalalign
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/regtable2seq
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/replaceu
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/restoreu
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/rnatest
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/score
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/seq2regtable
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/setcore
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/setdirection
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/sextet5
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/splittbfast
I: mafft: hardening-no-fortify-functions usr/lib/mafft/lib/mafft/tbfast
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.
????????????????????????????????????????????????????????????????????????????????
? Changes ?
????????????????????????????????????????????????????????????????????????????????
mafft_7.113-1_amd64.changes:
????????????????????????????
Format: 1.8
Date: Mon, 14 Oct 2013 08:41:03 +0900
Source: mafft
Binary: mafft
Architecture: source amd64
Version: 7.113-1
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
Changes:
mafft (7.113-1) UNRELEASED; urgency=low
.
Wait before uploading: on regression test is failing.
.
* New upstream version.
* Correct watch file, which was downloading the non-free version.
This error did not affect the current stable release of Debian.
* debian/tests/with-example-data: disable multithreading to stabilise output.
Checksums-Sha1:
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626206a46f221eeec469f2bf772525c6f792ff5d 5909 mafft_7.113-1.debian.tar.gz
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Files:
cbba2fdd456b7faec57d730e49f842d1 1100 science optional mafft_7.113-1.dsc
b87844de453395eaf24de9201e1169b6 378435 science optional mafft_7.113.orig.tar.gz
e6009c74a1db5cd713df8be986227469 5909 science optional mafft_7.113-1.debian.tar.gz
3b7655de5f03d08cefb6a38f55a264ee 757500 science optional mafft_7.113-1_amd64.deb
????????????????????????????????????????????????????????????????????????????????
? Package contents ?
????????????????????????????????????????????????????????????????????????????????
mafft_7.113-1_amd64.deb
???????????????????????
new debian package, version 2.0.
size 757500 bytes: control archive=2204 bytes.
1362 bytes, 30 lines control
3404 bytes, 49 lines md5sums
Package: mafft
Version: 7.113-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 7577
Depends: libc6 (>= 2.14)
Recommends: blast2, lynx, ruby
Enhances: t-coffee
Section: science
Priority: optional
Homepage: http://mafft.cbrc.jp/alignment/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 2013-10-14 10:32 ./
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/share/
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/share/man/
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/share/man/man1/
-rw-r--r-- root/root 2130 2013-10-14 10:32 ./usr/share/man/man1/mafft-homologs.1.gz
-rw-r--r-- root/root 4420 2013-10-14 10:32 ./usr/share/man/man1/mafft.1.gz
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/share/doc/mafft/
-rw-r--r-- root/root 1961 2013-10-14 08:48 ./usr/share/doc/mafft/copyright
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/share/doc/mafft/test/
-rw-r--r-- root/root 29320 2013-09-28 16:18 ./usr/share/doc/mafft/test/sample.ginsi
-rw-r--r-- root/root 16616 2007-04-05 15:00 ./usr/share/doc/mafft/test/sample
-rw-r--r-- root/root 29140 2013-09-28 16:21 ./usr/share/doc/mafft/test/sample.fftnsi
-rw-r--r-- root/root 29572 2013-09-28 16:20 ./usr/share/doc/mafft/test/sample.dpparttree
-rw-r--r-- root/root 1916 2013-09-28 16:19 ./usr/share/doc/mafft/test/samplerna.xinsi
-rw-r--r-- root/root 1502 2007-11-28 20:13 ./usr/share/doc/mafft/test/samplerna
-rw-r--r-- root/root 29896 2013-09-28 16:18 ./usr/share/doc/mafft/test/sample.gins1
-rw-r--r-- root/root 1916 2007-11-28 20:15 ./usr/share/doc/mafft/test/samplerna.qinsi
-rw-r--r-- root/root 29176 2013-09-28 16:17 ./usr/share/doc/mafft/test/sample.fftns2
-rw-r--r-- root/root 28888 2013-09-28 16:18 ./usr/share/doc/mafft/test/sample.lins1
-rw-r--r-- root/root 29824 2013-09-28 16:18 ./usr/share/doc/mafft/test/sample.linsi
-rw-r--r-- root/root 29608 2013-09-28 16:21 ./usr/share/doc/mafft/test/sample.parttree
-rw-r--r-- root/root 2453 2013-10-14 10:30 ./usr/share/doc/mafft/changelog.Debian.gz
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/lib/
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/lib/mafft/
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/lib/mafft/lib/
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/
-rwxr-xr-x root/root 387480 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/pairash
-rwxr-xr-x root/root 375224 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/makedirectionlist
-rwxr-xr-x root/root 231832 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/rnatest
-rwxr-xr-x root/root 6755 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/mafftash_premafft.pl
-rwxr-xr-x root/root 362904 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/setcore
-rwxr-xr-x root/root 195000 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/mccaskillwrap
-rwxr-xr-x root/root 403928 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/pairlocalalign
-rwxr-xr-x root/root 203160 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/dndfast7
-rwxr-xr-x root/root 362904 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/getlag
-rwxr-xr-x root/root 203128 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/sextet5
-rwxr-xr-x root/root 149960 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/regtable2seq
-rwxr-xr-x root/root 6128 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/version
-rwxr-xr-x root/root 391608 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/splittbfast
-rwxr-xr-x root/root 211352 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/multi2hat3s
-rwxr-xr-x root/root 387576 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/disttbfast
-rwxr-xr-x root/root 211352 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/pair2hat3s
-rwxr-xr-x root/root 76224 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/seq2regtable
-rwxr-xr-x root/root 145864 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/setdirection
-rwxr-xr-x root/root 203128 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/mafft-distance
-rwxr-xr-x root/root 145880 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/replaceu
-rwxr-xr-x root/root 76224 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/countlen
-rwxr-xr-x root/root 149960 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/restoreu
-rwxr-xr-x root/root 203160 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/dndblast
-rwxr-xr-x root/root 395736 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/addsingle
-rwxr-xr-x root/root 362904 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/mafft-profile
-rwxr-xr-x root/root 190840 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/score
-rwxr-xr-x root/root 190840 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/contrafoldwrap
-rwxr-xr-x root/root 190872 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/dndpre
-rwxr-xr-x root/root 121208 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/f2cl
-rwxr-xr-x root/root 412184 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/dvtditr
-rwxr-xr-x root/root 391640 2013-10-14 10:32 ./usr/lib/mafft/lib/mafft/tbfast
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/
-rwxr-xr-x root/root 8263 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-homologs.rb
-rwxr-xr-x root/root 72918 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft
drwxr-xr-x root/root 0 2013-10-14 10:32 ./usr/bin/
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/fftns.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/mafft-fftnsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/mafft-einsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/fftnsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/einsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/mafft-fftns.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/mafft-profile.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/ginsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/mafft-linsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/mafft-ginsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/share/man/man1/linsi.1.gz -> mafft.1.gz
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-qinsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/fftns -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/linsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-xinsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/ginsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-einsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-fftnsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/nwns -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-distance -> ../lib/mafft/mafft-distance
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-fftns -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/nwnsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-linsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/einsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-profile -> ../lib/mafft/mafft-profile
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/fftnsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-nwns -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-nwnsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/lib/mafft/bin/mafft-ginsi -> mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/bin/mafft -> ../lib/mafft/bin/mafft
lrwxrwxrwx root/root 0 2013-10-14 10:32 ./usr/bin/mafft-homologs -> ../lib/mafft/bin/mafft-homologs.rb
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? Post Build ?
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? Cleanup ?
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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*
hardening-includes* intltool-debian* libapt-pkg-perl* libarchive-zip-perl*
libasprintf0c2* libclass-accessor-perl* libclone-perl* libcroco3*
libdigest-hmac-perl* libemail-valid-perl* libffi6* libfile-basedir-perl*
libglib2.0-0* libio-pty-perl* libio-socket-inet6-perl*
libio-socket-ssl-perl* libio-string-perl* libipc-run-perl*
liblist-moreutils-perl* libmagic1* libmailtools-perl* libnet-dns-perl*
libnet-domain-tld-perl* libnet-ip-perl* libnet-smtp-ssl-perl*
libnet-ssleay-perl* libparse-debianchangelog-perl* libpipeline1*
libsocket6-perl* libssl1.0.0* libsub-name-perl* libtext-levenshtein-perl*
libunistring0* liburi-perl* libxml2* lintian* man-db* netbase* patchutils*
po-debconf* sbuild-build-depends-core-dummy*
sbuild-build-depends-lintian-dummy* sbuild-build-depends-mafft-dummy*
t1utils*
0 upgraded, 0 newly installed, 51 to remove and 0 not upgraded.
After this operation, 36.1 MB disk space will be freed.
(Reading database ... 13682 files and directories currently installed.)
Removing sbuild-build-depends-lintian-dummy ...
Removing lintian ...
Purging configuration files for lintian ...
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 diffstat ...
Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
Removing gettext-base ...
Removing groff-base ...
Purging configuration files for groff-base ...
Removing hardening-includes ...
Removing libapt-pkg-perl ...
Removing libarchive-zip-perl ...
Removing libasprintf0c2:amd64 ...
Removing libparse-debianchangelog-perl ...
Removing libclass-accessor-perl ...
Removing libclone-perl ...
Removing libcroco3:amd64 ...
Purging configuration files for libcroco3:amd64 ...
Removing libemail-valid-perl ...
Removing libnet-dns-perl ...
Removing libdigest-hmac-perl ...
Removing libglib2.0-0:amd64 ...
Purging configuration files for libglib2.0-0:amd64 ...
Removing libffi6:amd64 ...
Purging configuration files for libffi6:amd64 ...
Removing libfile-basedir-perl ...
Removing libipc-run-perl ...
Removing libio-pty-perl ...
Removing libio-socket-inet6-perl ...
Removing libmailtools-perl ...
Removing libnet-smtp-ssl-perl ...
Removing libio-socket-ssl-perl ...
Removing libio-string-perl ...
Removing liblist-moreutils-perl ...
Removing libmagic1:amd64 ...
Purging configuration files for libmagic1:amd64 ...
Removing libnet-domain-tld-perl ...
Removing libnet-ip-perl ...
Removing libnet-ssleay-perl ...
Removing libpipeline1:amd64 ...
Purging configuration files for libpipeline1:amd64 ...
Removing libsocket6-perl ...
Removing libssl1.0.0:amd64 ...
Purging configuration files for libssl1.0.0:amd64 ...
Removing libsub-name-perl ...
Removing libtext-levenshtein-perl ...
Removing libunistring0:amd64 ...
Purging configuration files for libunistring0:amd64 ...
Removing liburi-perl ...
Removing libxml2:amd64 ...
Purging configuration files for libxml2:amd64 ...
Removing netbase ...
Purging configuration files for netbase ...
Removing patchutils ...
Removing sbuild-build-depends-core-dummy ...
Removing t1utils ...
Processing triggers for libc-bin ...
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? Summary ?
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Build Architecture: amd64
Build-Space: 65728
Build-Time: 62
Distribution: unstable
Host Architecture: amd64
Install-Time: 16
Job: mafft_7.113-1.dsc
Lintian: pass
Machine Architecture: amd64
Package: mafft
Package-Time: 87
Source-Version: 7.113-1
Space: 65728
Status: successful
Version: 7.113-1
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Finished at 20131014-1032
Build needed 00:01:27, 65728k disc space
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