I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 23 00:45:06 +14 2024
I: pbuilder-time-stamp: 1719053106
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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-run-alignment-clustalw-perl_1.7.4-3.dsc]
I: copying [./libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz]
I: copying [./libbio-tools-run-alignment-clustalw-perl_1.7.4-3.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun May 29 00:09:42 2022 +14
gpgv: using RSA key B23862C415D6565A4E86CBD7579C160D4C9E23E8
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libbio-tools-run-alignment-clustalw-perl_1.7.4-3.dsc: no acceptable signature found
dpkg-source: info: extracting libbio-tools-run-alignment-clustalw-perl in libbio-tools-run-alignment-clustalw-perl-1.7.4
dpkg-source: info: unpacking libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz
dpkg-source: info: unpacking libbio-tools-run-alignment-clustalw-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/29221/tmp/hooks/D01_modify_environment starting
debug: Running on ionos16-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jun 23 00:45 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/29221/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/29221/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.15(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 '
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=84bd0f3f007e4fcfa0de36bc240e5879
LANG=C
LANGUAGE=de_CH:de
LC_ALL=C
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
MACHTYPE=i686-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=29221
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.5SCf1TRT/pbuilderrc_OhIB --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5SCf1TRT/b2 --logfile b2/build.log --extrapackages usrmerge libbio-tools-run-alignment-clustalw-perl_1.7.4-3.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://85.184.249.68:3128
I: uname -a
Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 21 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 21 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 6 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 21 2022 date
-rwxr-xr-x 1 root root 100364 Sep 21 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 21 2022 df
-rwxr-xr-x 1 root root 162152 Sep 21 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount
-rwxr-xr-x 1 root root 218680 Jan 25 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 21 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 24 2023 login
-rwxr-xr-x 1 root root 162152 Sep 21 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 24 2023 more
-rwsr-xr-x 1 root root 58912 Mar 24 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 21 2022 mv
lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 21 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 6 2023 sed
lrwxrwxrwx 1 root root 9 Jun 23 00:45 sh -> /bin/bash
-rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 21 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 24 2023 su
-rwxr-xr-x 1 root root 38792 Sep 21 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 7 2023 tar
-rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 21 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 21 2022 true
-rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 24 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 10 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 10 2022 znew
I: user script /srv/workspace/pbuilder/29221/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), clustalw, libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, 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 ... 19604 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.
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} libelf1{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} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{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, 39 newly installed, 0 to remove and 0 not upgraded.
Need to get 23.1 MB of archives. After unpacking 85.4 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 clustalw i386 2.1+lgpl-7 [302 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 22 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 24 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libio-string-perl all 1.08-4 [12.1 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libdata-stag-perl all 0.14-3 [448 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libio-pty-perl i386 1:1.17-1 [36.5 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 libipc-run-perl all 20220807.0-1 [104 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libfile-sort-perl all 1.01-3 [21.3 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 libbio-perl-run-perl all 1.7.3-9 [605 kB]
Get: 39 http://deb.debian.org/debian bookworm/main i386 libdevel-checkbin-perl all 0.04-3 [5228 B]
Fetched 23.1 MB in 0s (70.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(Reading database ... 60%
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19604 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_i386.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ...
Unpacking libmagic1:i386 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ...
Unpacking libuchardet0:i386 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_i386.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_i386.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package clustalw.
Preparing to unpack .../15-clustalw_2.1+lgpl-7_i386.deb ...
Unpacking clustalw (2.1+lgpl-7) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
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I: Running cd /build/libbio-tools-run-alignment-clustalw-perl-1.7.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbio-tools-run-alignment-clustalw-perl_1.7.4-3_source.changes
dpkg-buildpackage: info: source package libbio-tools-run-alignment-clustalw-perl
dpkg-buildpackage: info: source version 1.7.4-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Debian Janitor <janitor@jelmer.uk>
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 -ffile-prefix-map=/build/libbio-tools-run-alignment-clustalw-perl-1.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/libbio-tools-run-alignment-clustalw-perl-1.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro"
Locating bin:clustalw... found at /usr/bin/clustalw.
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Tools::Run::Alignment::Clustalw
Writing MYMETA.yml and MYMETA.json
dh_auto_build
make -j15
make[1]: Entering directory '/build/libbio-tools-run-alignment-clustalw-perl-1.7.4'
cp lib/Bio/Tools/Run/Alignment/Clustalw.pm blib/lib/Bio/Tools/Run/Alignment/Clustalw.pm
Manifying 1 pod document
make[1]: Leaving directory '/build/libbio-tools-run-alignment-clustalw-perl-1.7.4'
dh_auto_test
make -j15 test TEST_VERBOSE=1
make[1]: Entering directory '/build/libbio-tools-run-alignment-clustalw-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/Clustalw.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
t/Clustalw.t .............
ok 1 - Found input file
ok 2 - Found profile1 file
ok 3 - Found profile2 file
ok 4 - An object of class 'Bio::Tools::Run::Alignment::Clustalw' isa 'Bio::Tools::Run::Alignment::Clustalw'
ok 5 - program_dir returned correct default
ok 6 - error_string returned correct default
ok 7 - outfile_name returned correct default
ok 8 - bootstrap returned correct default
ok 9 - Correct exe default name
ok 10 - check clustalw version 2.1 is less than 1.8
ok 11 - No error occured
ok 12 - outfile_name returned something
ok 13 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 14 - Correct number of seqs returned
ok 15 - Score
ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 17 - Correct number of seqs returned
ok 18 - Got correct sequence by position
ok 19 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree'
ok 20 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 21 - Correct number of seqs returned
ok 22 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 23 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree'
ok 24 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 25 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree'
ok 26 - footprinting worked
ok 27 - Got correct sequence by position
ok 28 - Got correct sequence by position
ok 29 - Set and got ktuple correctly
ok 30 - Set and got topdiags correctly
ok 31 - Set and got window correctly
ok 32 - Set and got pairgap correctly
ok 33 - Set and got fixedgap correctly
ok 34 - Set and got floatgap correctly
ok 35 - Set and got matrix correctly
ok 36 - Set and got type correctly
ok 37 - Set and got output correctly
ok 38 - Set and got outfile correctly
ok 39 - set and got quiet correctly
ok 40 - set and got bootstrap correctly
1..40
ok
All tests successful.
Files=7, Tests=41, 1 wallclock secs ( 0.02 usr 0.00 sys + 1.06 cusr 0.08 csys = 1.16 CPU)
Result: PASS
make[1]: Leaving directory '/build/libbio-tools-run-alignment-clustalw-perl-1.7.4'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/libbio-tools-run-alignment-clustalw-perl/
make -j15 install DESTDIR=/build/libbio-tools-run-alignment-clustalw-perl-1.7.4/debian/libbio-tools-run-alignment-clustalw-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[1]: Entering directory '/build/libbio-tools-run-alignment-clustalw-perl-1.7.4'
Manifying 1 pod document
Installing /build/libbio-tools-run-alignment-clustalw-perl-1.7.4/debian/libbio-tools-run-alignment-clustalw-perl/usr/share/perl5/Bio/Tools/Run/Alignment/Clustalw.pm
Installing /build/libbio-tools-run-alignment-clustalw-perl-1.7.4/debian/libbio-tools-run-alignment-clustalw-perl/usr/share/man/man3/Bio::Tools::Run::Alignment::Clustalw.3pm
make[1]: Leaving directory '/build/libbio-tools-run-alignment-clustalw-perl-1.7.4'
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dpkg-deb: building package 'libbio-tools-run-alignment-clustalw-perl' in '../libbio-tools-run-alignment-clustalw-perl_1.7.4-3_all.deb'.
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dpkg-genchanges --build=binary -O../libbio-tools-run-alignment-clustalw-perl_1.7.4-3_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
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I: Current time: Sun Jun 23 00:45:26 +14 2024
I: pbuilder-time-stamp: 1719053126