I: pbuilder: network access will be disabled during build
I: Current time: Tue Mar 31 21:07:12 -12 2026
I: pbuilder-time-stamp: 1775034432
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc]
I: copying [./libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz]
I: copying [./libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc: unsupported subcommand
dpkg-source: info: extracting libbio-tools-run-alignment-tcoffee-perl in libbio-tools-run-alignment-tcoffee-perl-1.7.4
dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz
dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying doc-typos.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1548921/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='ac46fbdb26c144379f2fdb382c783bd1'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='1548921'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.km0GK649/pbuilderrc_nIpH --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.km0GK649/b1 --logfile b1/build.log libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos15-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1548921/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), clustalw, libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libtest-exception-perl, perl, t-coffee
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19778 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on clustalw; however:
Package clustalw is not installed.
pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however:
Package libbio-perl-perl is not installed.
pbuilder-satisfydepends-dummy depends on libbio-perl-run-perl; however:
Package libbio-perl-run-perl is not installed.
pbuilder-satisfydepends-dummy depends on libdevel-checkbin-perl; however:
Package libdevel-checkbin-perl is not installed.
pbuilder-satisfydepends-dummy depends on libtest-exception-perl; however:
Package libtest-exception-perl is not installed.
pbuilder-satisfydepends-dummy depends on t-coffee; however:
Package t-coffee is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-checkbin-perl{a} libelf1t64{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libicu72{a} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-uplevel-perl{a} libtest-exception-perl{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} t-coffee{a}
The following packages are RECOMMENDED but will NOT be installed:
amap-align clustalo curl dialign-tx fsa kalign libace-perl libalgorithm-diff-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx mafft muscle mustang ncbi-blast+ perl-tk poa prank probcons proda tm-align wget
0 packages upgraded, 42 newly installed, 0 to remove and 0 not upgraded.
Need to get 25.7 MB of archives. After unpacking 93.4 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
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Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
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Get: 17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
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Get: 20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
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Get: 24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libfile-sort-perl all 1.01-3 [21.3 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libbio-perl-run-perl all 1.7.3-13 [528 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libdevel-checkbin-perl all 0.04-3 [5228 B]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [1032 kB]
Fetched 25.7 MB in 3s (8740 kB/s)
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update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
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Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
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Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_source.changes
dpkg-buildpackage: info: source package libbio-tools-run-alignment-tcoffee-perl
dpkg-buildpackage: info: source version 1.7.4-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Jelmer Vernooij <jelmer@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
/usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro"
Locating bin:t_coffee... found at /usr/bin/t_coffee.
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Tools::Run::Alignment::TCoffee
Writing MYMETA.yml and MYMETA.json
dh_auto_build
make -j42
make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4'
cp lib/Bio/Tools/Run/Alignment/TCoffee.pm blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm
Manifying 1 pod document
make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4'
dh_auto_test
make -j42 test TEST_VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4'
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t
t/00-compile.t ...........
1..1
ok 1 - Bio/Tools/Run/Alignment/TCoffee.pm loaded ok
ok
t/author-eol.t ........... skipped: these tests are for testing by the author
t/author-mojibake.t ...... skipped: these tests are for testing by the author
t/author-no-tabs.t ....... skipped: these tests are for testing by the author
t/author-pod-coverage.t .. skipped: these tests are for testing by the author
t/author-pod-syntax.t .... skipped: these tests are for testing by the author
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t/TCoffee.t ..............
ok 1 - An object of class 'Bio::Tools::Run::Alignment::TCoffee' isa 'Bio::Tools::Run::Alignment::TCoffee'
ok 2 - set factory parameter
ok 3 - get factory parameter
ok 4 - Code tested only on t_coffee versions > 1.22
#Single Thread
ok 5
ok 6
#Single Thread
ok 7
#Single Thread
#Single Thread
#Single Thread
#Single Thread
#Single Thread
ok 8
ok 9 - no T-COFFEE errors
ok 10
ok 11
ok 12
#Single Thread
#Single Thread
ok 13
ok 14
ok 15
#Single Thread
#Single Thread
ok 16
ok 17 - expect 21 >= val >= 23
ok 18 - expect 47 or 48
#Single Thread
ok 19 - simple generic run
ok 20
#Single Thread
#Single Thread
#Single Thread
#Single Thread
#Single Thread
ok 21
ok 22 - no T-COFFEE errors
ok 23
ok 24 - expect 13 or 14
ok 25 - expect 41 or 42
1..25
rmdir /tmp/I1pieY9hhz
ok
All tests successful.
Files=7, Tests=26, 10 wallclock secs ( 0.03 usr 0.02 sys + 4.97 cusr 5.57 csys = 10.59 CPU)
Result: PASS
make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/libbio-tools-run-alignment-tcoffee-perl/
make -j42 install DESTDIR=/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4'
Manifying 1 pod document
Installing /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm
Installing /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/man/man3/Bio::Tools::Run::Alignment::TCoffee.3pm
make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4'
dh_installdocs
dh_installchangelogs
dh_installman
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
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dpkg-deb: building package 'libbio-tools-run-alignment-tcoffee-perl' in '../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb'.
dpkg-genbuildinfo --build=binary -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_amd64.buildinfo
dpkg-genchanges --build=binary -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/1548921 and its subdirectories
I: Current time: Tue Mar 31 21:07:49 -12 2026
I: pbuilder-time-stamp: 1775034469