Mon Apr 17 19:46:23 UTC 2023 I: starting to build libbio-tools-run-alignment-clustalw-perl/bookworm/amd64 on jenkins on '2023-04-17 19:46' Mon Apr 17 19:46:23 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_5/25/console.log Mon Apr 17 19:46:23 UTC 2023 I: Downloading source for bookworm/libbio-tools-run-alignment-clustalw-perl=1.7.4-3 --2023-04-17 19:46:23-- http://cdn-fastly.deb.debian.org/debian/pool/main/libb/libbio-tools-run-alignment-clustalw-perl/libbio-tools-run-alignment-clustalw-perl_1.7.4-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2489 (2.4K) [text/prs.lines.tag] Saving to: ‘libbio-tools-run-alignment-clustalw-perl_1.7.4-3.dsc’ 0K .. 100% 310M=0s 2023-04-17 19:46:23 (310 MB/s) - ‘libbio-tools-run-alignment-clustalw-perl_1.7.4-3.dsc’ saved [2489/2489] Mon Apr 17 19:46:23 UTC 2023 I: libbio-tools-run-alignment-clustalw-perl_1.7.4-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-tools-run-alignment-clustalw-perl Binary: libbio-tools-run-alignment-clustalw-perl Architecture: all Version: 1.7.4-3 Maintainer: Debian Perl Group Uploaders: David Miguel Susano Pinto Homepage: https://metacpan.org/release/Bio-Tools-Run-Alignment-Clustalw Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-clustalw-perl Vcs-Git: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-clustalw-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13) Build-Depends-Indep: clustalw, libbio-perl-perl , libbio-perl-run-perl , libdevel-checkbin-perl, perl Package-List: libbio-tools-run-alignment-clustalw-perl deb science optional arch=all Checksums-Sha1: 926fde7762db2c2e9aa3d94295fb8cf7c9994cc7 30259 libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz 1339ea5f460a1f050d8ff844daaad2b14bb4ebf7 2364 libbio-tools-run-alignment-clustalw-perl_1.7.4-3.debian.tar.xz Checksums-Sha256: 4e322d50fd945257f61609ed6e59c3e6817948166a6230d24d5ca23b507e331e 30259 libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz aa642c8426baa8126efec3c6fa869453d71e02df83f1c9917d5f48c5279c2cb1 2364 libbio-tools-run-alignment-clustalw-perl_1.7.4-3.debian.tar.xz Files: 6820fcb8ca70c5fd75baa4bf979ab274 30259 libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz 0fc63c99dfffcde8c2e7f1afb336ad65 2364 libbio-tools-run-alignment-clustalw-perl_1.7.4-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEsjhixBXWVlpOhsvXV5wWDUyeI+gFAmKR9OYACgkQV5wWDUye I+gxnQ//RcH4vvJQiIM3/sMgMWTyd6lOv3jcrNSj0r6eh0QD8L/com6S1IShhkN3 ya0mRAuiFDj++orvrptvHzyw0jHdx0ce3pzEdsYPDLF18FliYUTQgE2Dto1vO0/z paFU0fHNeL8UjVXlM8WsZyXu79/MgIiNNg14IrduMBZVRmkQYn5lCkUFLmwV9OkV iwKgzVFgSNotYMnEk4mzOhySdAuB+ivzwu9DDjL7Rtl2EfqqP/wVg5nLVp1SHE+r pt9tixnVh3HNVUNwuFLfcfwiBlvrkOZpBAxy3ww0HxbmHiRTGevy4eumA9XXu6MC Bt6iIJgNkqJyxJTajKeHSfdAlfjxMj555jOQ6Wk2MzcBPpu97ggFDkxaczLfbjEX BjRp3tp1MCNqynacs7WoyUiAd7UDOK9Gz2VCEhDAQg226+AwzpjnrCSE48sa7IF9 2bXSY1pDcu/NbxP9X1maQRCt5wX2kiBumP+HFi/U8UyqVshGzuvfiORcCX6X2Nnw knNI0TpMv23FaCyHRY73GIxeSYtVatLPGIIiNpHVwdjBcWne5DEFjYQ01M+vqKaH dAUHRfYepsuB+NdG4gP03MqA4AFMtVEJUTmsCG/SjqhCloismdHaQzm+OdSLiM2X q5YE+5ukWaVpt3zpFzyKVlV4QtjCcDgbm5+jCSPFgat81NEO3KY= =1MJl -----END PGP SIGNATURE----- Mon Apr 17 19:46:23 UTC 2023 I: Checking whether the package is not for us Mon Apr 17 19:46:23 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon Apr 17 19:46:23 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon Apr 17 19:47:28 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 17 07:46:26 -12 2023 I: pbuilder-time-stamp: 1681760786 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: 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 Fri May 27 22:09:42 2022 -12 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/2306057/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='70f45dc848d84f578ea24fc6f01a0347' 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='2306057' 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.QiEZYY2Q/pbuilderrc_0dvo --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QiEZYY2Q/b1 --logfile b1/build.log libbio-tools-run-alignment-clustalw-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://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2306057/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 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 ... 19596 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 22.8 MB of archives. After unpacking 85.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libio-pty-perl amd64 1:1.17-1 [34.9 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libbio-perl-run-perl all 1.7.3-9 [605 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libdevel-checkbin-perl all 0.04-3 [5228 B] Fetched 22.8 MB in 1s (44.2 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% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 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_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... 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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 (1.13.1-1) ... Setting up libbio-perl-run-perl (1.7.3-9) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-8) ... 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/libbio-tools-run-alignment-clustalw-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-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 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 -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=x86_64-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, 4 wallclock secs ( 0.03 usr 0.03 sys + 2.08 cusr 0.24 csys = 2.38 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' 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-run-alignment-clustalw-perl' in '../libbio-tools-run-alignment-clustalw-perl_1.7.4-3_all.deb'. dpkg-genbuildinfo --build=binary -O../libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.buildinfo dpkg-genchanges --build=binary -O../libbio-tools-run-alignment-clustalw-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/2306057 and its subdirectories I: Current time: Mon Apr 17 07:47:27 -12 2023 I: pbuilder-time-stamp: 1681760847 Mon Apr 17 19:47:28 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Mon Apr 17 19:47:28 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Mon Apr 17 19:47:54 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Mon Apr 17 19:47:54 UTC 2023 I: libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.changes: Format: 1.8 Date: Sat, 28 May 2022 11:09:16 +0100 Source: libbio-tools-run-alignment-clustalw-perl Binary: libbio-tools-run-alignment-clustalw-perl Architecture: all Version: 1.7.4-3 Distribution: unstable Urgency: medium Maintainer: Debian Perl Group Changed-By: Debian Janitor Description: libbio-tools-run-alignment-clustalw-perl - Bioperl interface to Clustal W Changes: libbio-tools-run-alignment-clustalw-perl (1.7.4-3) unstable; urgency=medium . * Remove constraints unnecessary since buster: + libbio-tools-run-alignment-clustalw-perl: Drop versioned constraint on libbio-perl-run-perl in Replaces. + libbio-tools-run-alignment-clustalw-perl: Drop versioned constraint on libbio-perl-run-perl in Breaks. Checksums-Sha1: 479b46bbd1cb7d91e3cf9db875d11c1cf4168958 24628 libbio-tools-run-alignment-clustalw-perl_1.7.4-3_all.deb 1d83790c9ec1c497081f4ca6bdf88561e9c56aaf 5285 libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.buildinfo Checksums-Sha256: 6a1564f35c09d9e4ad3445b8f04f6c14bda4b49fb2308095bf44514a7a114238 24628 libbio-tools-run-alignment-clustalw-perl_1.7.4-3_all.deb cd373906701498e55a12bfe8ffae329973b045e659d4d0275b5039f6e2290fc3 5285 libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.buildinfo Files: aab48ccab8e31875f45e6fead543cf39 24628 science optional libbio-tools-run-alignment-clustalw-perl_1.7.4-3_all.deb 6b88c93f08197b81ec8f7eb02b4a7b74 5285 science optional libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.buildinfo Mon Apr 17 19:47:55 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QiEZYY2Q/libbio-tools-run-alignment-clustalw-perl_1.7.4-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QiEZYY2Q/libbio-tools-run-alignment-clustalw-perl_1.7.4-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QiEZYY2Q/libbio-tools-run-alignment-clustalw-perl_1.7.4-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QiEZYY2Q/b1/libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QiEZYY2Q/b2/libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.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: 0.373s) 0.373s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.016s) 0.016s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon Apr 17 19:47:56 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Mon Apr 17 19:47:56 UTC 2023 I: libbio-tools-run-alignment-clustalw-perl from bookworm built successfully and reproducibly on amd64. Mon Apr 17 19:47:58 UTC 2023 I: Submitting .buildinfo files to external archives: Mon Apr 17 19:47:58 UTC 2023 I: Submitting 8.0K b1/libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.buildinfo.asc Mon Apr 17 19:47:58 UTC 2023 I: Submitting 8.0K b2/libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.buildinfo.asc Mon Apr 17 19:47:59 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Apr 17 19:47:59 UTC 2023 I: Done submitting .buildinfo files. Mon Apr 17 19:47:59 UTC 2023 I: Removing signed libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.buildinfo.asc files: removed './b1/libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.buildinfo.asc' removed './b2/libbio-tools-run-alignment-clustalw-perl_1.7.4-3_amd64.buildinfo.asc'