Sat Nov 23 07:14:46 UTC 2024  I: starting to build libbio-tools-phylo-paml-perl/trixie/i386 on jenkins on '2024-11-23 07:14'
Sat Nov 23 07:14:46 UTC 2024  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_18/32057/console.log
Sat Nov 23 07:14:46 UTC 2024  I: Downloading source for trixie/libbio-tools-phylo-paml-perl=1.7.3-4
--2024-11-23 07:14:46--  http://deb.debian.org/debian/pool/main/libb/libbio-tools-phylo-paml-perl/libbio-tools-phylo-paml-perl_1.7.3-4.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2341 (2.3K) [text/prs.lines.tag]
Saving to: ‘libbio-tools-phylo-paml-perl_1.7.3-4.dsc’

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2024-11-23 07:14:46 (318 MB/s) - ‘libbio-tools-phylo-paml-perl_1.7.3-4.dsc’ saved [2341/2341]

Sat Nov 23 07:14:46 UTC 2024  I: libbio-tools-phylo-paml-perl_1.7.3-4.dsc
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Hash: SHA512

Format: 3.0 (quilt)
Source: libbio-tools-phylo-paml-perl
Binary: libbio-tools-phylo-paml-perl
Architecture: all
Version: 1.7.3-4
Maintainer: Debian Perl Group <pkg-perl-maintainers@lists.alioth.debian.org>
Uploaders: David Miguel Susano Pinto <carandraug+dev@gmail.com>
Homepage: https://metacpan.org/release/Bio-Tools-Phylo-PAML
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl
Vcs-Git: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git
Testsuite: autopkgtest-pkg-perl
Build-Depends: debhelper-compat (= 13)
Build-Depends-Indep: libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libio-string-perl, paml, perl
Package-List:
 libbio-tools-phylo-paml-perl deb science optional arch=all
Checksums-Sha1:
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 234b33e8fc175f177e68c60041fa8a1bdabc5f86 2784 libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz
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 424dccca82b61e3daf62f52e33de35efdbe1b69644d07015e987671fa7130cb4 137819 libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz
 f88ff3149e7272680b64d89a0d95890eecebb6497a60a74aa2aa842c325ccee1 2784 libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz
Files:
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Sat Nov 23 07:14:46 UTC 2024  I: Checking whether the package is not for us
Sat Nov 23 07:14:46 UTC 2024  I: Starting 1st build on remote node infom08-i386.debian.net.
Sat Nov 23 07:14:46 UTC 2024  I: Preparing to do remote build '1' on infom08-i386.debian.net.
Sat Nov 23 07:15:13 UTC 2024  I: Deleting $TMPDIR on infom08-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Dec 26 01:37:47 -12 2025
I: pbuilder-time-stamp: 1766756267
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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: using eatmydata during job
I: Copying source file
I: copying [libbio-tools-phylo-paml-perl_1.7.3-4.dsc]
I: copying [./libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz]
I: copying [./libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Oct 14 14:47:44 2022 
gpgv:                using RSA key B23862C415D6565A4E86CBD7579C160D4C9E23E8
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libbio-tools-phylo-paml-perl_1.7.3-4.dsc: no acceptable signature found
dpkg-source: info: extracting libbio-tools-phylo-paml-perl in libbio-tools-phylo-paml-perl-1.7.3
dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz
dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying evolver-program-name.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/9120/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='i386'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 '
  DISTRIBUTION='trixie'
  HOME='/root'
  HOST_ARCH='i386'
  IFS=' 	
  '
  INVOCATION_ID='3952ee23c7724b4a8c300e49096be638'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
  LD_PRELOAD='libeatmydata.so'
  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='9120'
  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.rpv8Y43G/pbuilderrc_LMPR --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rpv8Y43G/b1 --logfile b1/build.log libbio-tools-phylo-paml-perl_1.7.3-4.dsc'
  SUDO_GID='111'
  SUDO_UID='104'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
I: uname -a
  Linux infom08-i386 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Aug  4  2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/9120/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: i386
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), libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libio-string-perl, paml, perl
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19956 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 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 libio-string-perl; however:
  Package libio-string-perl is not installed.
 pbuilder-satisfydepends-dummy depends on paml; however:
  Package paml 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} 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} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} paml{a} po-debconf{a} sensible-utils{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl 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 perl-tk wget 
0 packages upgraded, 38 newly installed, 0 to remove and 0 not upgraded.
Need to get 24.5 MB of archives. After unpacking 90.4 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 libio-string-perl all 1.08-4 [12.1 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 libdata-stag-perl all 0.14-3 [448 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 libio-pty-perl i386 1:1.20-1+b2 [35.8 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 libipc-run-perl all 20231003.0-2 [101 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 libfile-sort-perl all 1.01-3 [21.3 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 libbio-perl-run-perl all 1.7.3-12 [528 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 libdevel-checkbin-perl all 0.04-3 [5228 B]
Get: 38 http://deb.debian.org/debian trixie/main i386 paml i386 4.9j+dfsg-5 [639 kB]
Fetched 24.5 MB in 0s (54.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libio-string-perl.
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Unpacking libio-string-perl (1.08-4) ...
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Preparing to unpack .../30-libdata-stag-perl_0.14-3_all.deb ...
Unpacking libdata-stag-perl (0.14-3) ...
Selecting previously unselected package libbio-perl-perl.
Preparing to unpack .../31-libbio-perl-perl_1.7.8-1_all.deb ...
Unpacking libbio-perl-perl (1.7.8-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../32-libio-pty-perl_1%3a1.20-1+b2_i386.deb ...
Unpacking libio-pty-perl (1:1.20-1+b2) ...
Selecting previously unselected package libipc-run-perl.
Preparing to unpack .../33-libipc-run-perl_20231003.0-2_all.deb ...
Unpacking libipc-run-perl (20231003.0-2) ...
Selecting previously unselected package libfile-sort-perl.
Preparing to unpack .../34-libfile-sort-perl_1.01-3_all.deb ...
Unpacking libfile-sort-perl (1.01-3) ...
Selecting previously unselected package libbio-perl-run-perl.
Preparing to unpack .../35-libbio-perl-run-perl_1.7.3-12_all.deb ...
Unpacking libbio-perl-run-perl (1.7.3-12) ...
Selecting previously unselected package libdevel-checkbin-perl.
Preparing to unpack .../36-libdevel-checkbin-perl_0.04-3_all.deb ...
Unpacking libdevel-checkbin-perl (0.04-3) ...
Selecting previously unselected package paml.
Preparing to unpack .../37-paml_4.9j+dfsg-5_i386.deb ...
Unpacking paml (4.9j+dfsg-5) ...
Setting up libpipeline1:i386 (1.5.8-1) ...
Setting up libicu72:i386 (72.1-5+b1) ...
Setting up bsdextrautils (2.40.2-11) ...
Setting up libdevel-checkbin-perl (0.04-3) ...
Setting up libio-pty-perl (1:1.20-1+b2) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.20) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-2) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up libio-string-perl (1.08-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.22.5-2) ...
Setting up libipc-run-perl (20231003.0-2) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up libdata-stag-perl (0.14-3) ...
Setting up sensible-utils (0.0.24) ...
Setting up paml (4.9j+dfsg-5) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libbio-perl-perl (1.7.8-1) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up libfile-sort-perl (1.01-3) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up libbio-perl-run-perl (1.7.3-12) ...
Setting up gettext (0.22.5-2) ...
Setting up libtool (2.4.7-8) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-5) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.20) ...
Processing triggers for libc-bin (2.40-3) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/ && 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-phylo-paml-perl_1.7.3-4_source.changes
dpkg-buildpackage: info: source package libbio-tools-phylo-paml-perl
dpkg-buildpackage: info: source version 1.7.3-4
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 i386
 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-phylo-paml-perl-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro"
Warning: prerequisite Bio::Tools::Run::Alignment::Clustalw 0 not found.
Warning: prerequisite Bio::Tools::Run::Alignment::TCoffee 0 not found.
Locating bin:basemlg... found at /usr/bin/basemlg.
Locating bin:codeml... found at /usr/bin/codeml.
Locating bin:paml-evolver... found at /usr/bin/paml-evolver.
Locating bin:yn00... found at /usr/bin/yn00.
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Tools::Phylo::PAML
Writing MYMETA.yml and MYMETA.json
   dh_auto_build
	make -j6
make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3'
cp lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm
cp lib/Bio/Tools/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Phylo/PAML/Codeml.pm
cp lib/Bio/Tools/Phylo/PAML.pm blib/lib/Bio/Tools/Phylo/PAML.pm
cp lib/Bio/Tools/Phylo/PAML/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.pm
cp lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
cp lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm
cp lib/Bio/Tools/Phylo/PAML/ModelResult.pm blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm
cp lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
cp bin/bp_pairwise_kaks blib/script/bp_pairwise_kaks
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_pairwise_kaks
Manifying 1 pod document
Manifying 8 pod documents
make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3'
   dh_auto_test
	make -j6 test TEST_VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3'
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..9
ok 1 - Bio/Tools/Phylo/PAML.pm loaded ok
ok 2 - Bio/Tools/Phylo/PAML/Codeml.pm loaded ok
ok 3 - Bio/Tools/Phylo/PAML/ModelResult.pm loaded ok
ok 4 - Bio/Tools/Phylo/PAML/Result.pm loaded ok
ok 5 - Bio/Tools/Run/Phylo/PAML/Baseml.pm loaded ok
ok 6 - Bio/Tools/Run/Phylo/PAML/Codeml.pm loaded ok
ok 7 - Bio/Tools/Run/Phylo/PAML/Evolver.pm loaded ok
ok 8 - Bio/Tools/Run/Phylo/PAML/Yn00.pm loaded ok
ok 9 # skip bin/bp_pairwise_kaks isn't perl
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
t/PAML-parser.t .......... 
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
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ok 161
ok 162 - node\#8 reconstructed seq
ok 163 - ancestral AA
ok 164 - ancestral AA
ok 165 - derived AA
ok 166 - ancestral AA
ok 167 - ancestral AA
ok 168 - derived AA
ok 169 - derived AA
ok 170
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ok 203 - codeml 4.3 runmode=-2
ok 204
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ok 214 - codeml 4.3 two NSSites models
ok 215
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ok 238 - NEB positively selected sites
ok 239
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ok 250 - bug 3040
ok 251 - bug 3365
ok 252 - bug 3366
ok 253 - bug 3367
ok 254 - bug 3332
ok 255 - bug 3331
1..255
ok
t/PAML-run.t ............. 
ok 1
ok 2
ok 3 - got results
ok 4 - got a result
ok 5
ok 6
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ok 14 - got results
ok 15 - got a result
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ok 28 - got results
ok 29
1..29
ok
All tests successful.
Files=8, Tests=293,  2 wallclock secs ( 0.02 usr  0.02 sys +  1.72 cusr  0.14 csys =  1.90 CPU)
Result: PASS
make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install --destdir=debian/libbio-tools-phylo-paml-perl/
	make -j6 install DESTDIR=/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3'
Manifying 1 pod document
Manifying 8 pod documents
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Baseml.pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Evolver.pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Yn00.pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Codeml.pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML.pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/ModelResult.pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Result.pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Codeml.pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man1/bp_pairwise_kaks.1p
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Codeml.3pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML.3pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Evolver.3pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Baseml.3pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Codeml.3pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::ModelResult.3pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Result.3pm
Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks
make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3'
   debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3'
dh_install
sed -i '1s|^#!/usr/bin/env perl|#!/usr/bin/perl|' /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks
make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3'
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_lintian
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'libbio-tools-phylo-paml-perl' in '../libbio-tools-phylo-paml-perl_1.7.3-4_all.deb'.
 dpkg-genbuildinfo --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_i386.buildinfo
 dpkg-genchanges --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_i386.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/9120 and its subdirectories
I: Current time: Fri Dec 26 01:38:12 -12 2025
I: pbuilder-time-stamp: 1766756292
Sat Nov 23 07:15:14 UTC 2024  I: 1st build successful. Starting 2nd build on remote node infom07-i386.debian.net.
Sat Nov 23 07:15:14 UTC 2024  I: Preparing to do remote build '2' on infom07-i386.debian.net.
Sat Nov 23 07:15:50 UTC 2024  I: Deleting $TMPDIR on infom07-i386.debian.net.
Sat Nov 23 07:15:51 UTC 2024  I: libbio-tools-phylo-paml-perl_1.7.3-4_i386.changes:
Format: 1.8
Date: Fri, 14 Oct 2022 15:47:06 +0100
Source: libbio-tools-phylo-paml-perl
Binary: libbio-tools-phylo-paml-perl
Architecture: all
Version: 1.7.3-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Perl Group <pkg-perl-maintainers@lists.alioth.debian.org>
Changed-By: Jelmer Vernooij <jelmer@debian.org>
Description:
 libbio-tools-phylo-paml-perl - Bioperl interface to the PAML suite
Changes:
 libbio-tools-phylo-paml-perl (1.7.3-4) unstable; urgency=medium
 .
   [ Debian Janitor ]
   * Update standards version to 4.5.1, no changes needed.
   * Remove constraints unnecessary since buster
   * Update standards version to 4.6.0, no changes needed.
Checksums-Sha1:
 bdb0a2e9a66d46c5888e4e1820074c3b72eaad98 78500 libbio-tools-phylo-paml-perl_1.7.3-4_all.deb
 1f75881476065aba5e83fac2ebf7c993e765c501 5027 libbio-tools-phylo-paml-perl_1.7.3-4_i386.buildinfo
Checksums-Sha256:
 66a6093f1cb7ffd2ded6fe818f7c3833801075e2e9bee988407aef827164933c 78500 libbio-tools-phylo-paml-perl_1.7.3-4_all.deb
 987dcbc04806f8abf9e7235aeece1ea36c2c6aaedfb39a5cf76b5b61504817d9 5027 libbio-tools-phylo-paml-perl_1.7.3-4_i386.buildinfo
Files:
 1891fafabb7f2c9bf8bfdc5972900129 78500 science optional libbio-tools-phylo-paml-perl_1.7.3-4_all.deb
 375c5ba49617117af1b488148ac58552 5027 science optional libbio-tools-phylo-paml-perl_1.7.3-4_i386.buildinfo
Sat Nov 23 07:15:52 UTC 2024  I: diffoscope 283 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_18-32057.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.rpv8Y43G/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.rpv8Y43G/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.rpv8Y43G/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.rpv8Y43G/b1/libbio-tools-phylo-paml-perl_1.7.3-4_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.rpv8Y43G/b2/libbio-tools-phylo-paml-perl_1.7.3-4_i386.changes

## command (total time: 0.000s)
       0.000s      1 call     cmp (internal)

## has_same_content_as (total time: 0.000s)
       0.000s      1 call     abc.DotChangesFile

## main (total time: 0.368s)
       0.368s      2 calls    outputs
       0.000s      1 call     cleanup

## recognizes (total time: 0.017s)
       0.017s     12 calls    diffoscope.comparators.binary.FilesystemFile

## specialize (total time: 0.000s)
       0.000s      1 call     specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 690ms
CPU time consumed: 689ms
Sat Nov 23 07:15:53 UTC 2024  I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists.
Sat Nov 23 07:15:53 UTC 2024  I: libbio-tools-phylo-paml-perl from trixie built successfully and reproducibly on i386.
Sat Nov 23 07:15:54 UTC 2024  I: Submitting .buildinfo files to external archives:
Sat Nov 23 07:15:54 UTC 2024  I: Submitting 8.0K	b1/libbio-tools-phylo-paml-perl_1.7.3-4_i386.buildinfo.asc
Sat Nov 23 07:15:55 UTC 2024  I: Submitting 8.0K	b2/libbio-tools-phylo-paml-perl_1.7.3-4_i386.buildinfo.asc
Sat Nov 23 07:15:56 UTC 2024  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Nov 23 07:15:56 UTC 2024  I: Done submitting .buildinfo files.
Sat Nov 23 07:15:56 UTC 2024  I: Removing signed libbio-tools-phylo-paml-perl_1.7.3-4_i386.buildinfo.asc files:
removed './b1/libbio-tools-phylo-paml-perl_1.7.3-4_i386.buildinfo.asc'
removed './b2/libbio-tools-phylo-paml-perl_1.7.3-4_i386.buildinfo.asc'