Tue Apr 2 14:15:33 UTC 2024 I: starting to build virulencefinder/trixie/i386 on jenkins on '2024-04-02 14:15' Tue Apr 2 14:15:33 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_1/20486/console.log Tue Apr 2 14:15:33 UTC 2024 I: Downloading source for trixie/virulencefinder=2.0.5-1 --2024-04-02 14:15:34-- http://deb.debian.org/debian/pool/main/v/virulencefinder/virulencefinder_2.0.5-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2395 (2.3K) [text/prs.lines.tag] Saving to: ‘virulencefinder_2.0.5-1.dsc’ 0K .. 100% 24.5M=0s 2024-04-02 14:15:34 (24.5 MB/s) - ‘virulencefinder_2.0.5-1.dsc’ saved [2395/2395] Tue Apr 2 14:15:34 UTC 2024 I: virulencefinder_2.0.5-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: virulencefinder Binary: virulencefinder, virulencefinder-examples Architecture: all Version: 2.0.5-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://bitbucket.org/genomicepidemiology/virulencefinder Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/virulencefinder Vcs-Git: https://salsa.debian.org/med-team/virulencefinder.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-tabulate, python3-cgecore, ncbi-blast+ Package-List: virulencefinder deb science optional arch=all virulencefinder-examples deb science optional arch=all Checksums-Sha1: bc65078a3362b49d9d8cc60845fffbd38fdd5a38 263880 virulencefinder_2.0.5.orig.tar.xz ca96264a1855817fb2f15c6a15974a80111351e0 6092 virulencefinder_2.0.5-1.debian.tar.xz Checksums-Sha256: 2936d46e9db0d239294463919b34ae8f57acf0784e82f136010a8654cf00529f 263880 virulencefinder_2.0.5.orig.tar.xz 90f2b8328f42193daacbb52468f0f7c62ad6213538be1e23a7acc4f49826e53d 6092 virulencefinder_2.0.5-1.debian.tar.xz Files: 641ff0055d0c9b7ad332254e16608999 263880 virulencefinder_2.0.5.orig.tar.xz dba0bf1a9f21514bbb8df50035c566e6 6092 virulencefinder_2.0.5-1.debian.tar.xz Dgit: d824513c431858a934172129517b51f93bdc3f77 debian archive/debian/2.0.5-1 https://git.dgit.debian.org/virulencefinder -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmXSMpYUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoxfg//RUCQjakNGggM5beiVSqpmRhTQueB 5nmgVrkNSV+U+cyqbl5mVN5EYk8WyKRsAhQmUr/zJr/sI/csvEh1X/h6u5HtOKSx q+rDQPVplyQO30k/nhkO4BnwkyIQek0zBBuXwpfjVZTAulJt0rtJ8nNkB+98P+/O wlBxTisC9kmuaHspB6zamDbus4xeMpDwYj/oq4gcTO//wpFCPYSDkriM7fKayiIa e+4rpwktfZF0ObI/diK/fxkLn3kUvBohGVSCgo/5u6ujtOhQpQdWbryF6Rq8sExM CzWth66Sg9oRIIXGuxdw32aZlNhEdcRCSCa+STsPY+folCnOXx7YORYztnB0JLTh G8uQ2KaIB1g0LNYOrFjG2R/MRwAqTS9ycKRF6taJlYzU2GlegfVRpNHnXfEqlBS3 ONPLjYFON+05VTGMcs0epmpZfZa1GcPAuIVibATx2sfDIFEzakmRWGOQ3OE/T7dA bCnn7uDfuowi8qU5qiEo8M6apa4U7d29pbD8c80Q8DS+vmgnLppFrJZ8CRabEWLS CFrvdwXRy4+mBfiGQL2XwD/eCGLD7YydFenXmEauWHLYQpYGGub/MPoZVsT3zP4c l4YR6Uf+2wmxmmA45mw5ozUR4APdOjoXw3ZaQu8QZwrUswdt6CY/ekDdLzFwvuOY +H/yNDi+GjOLkBQ= =UNbJ -----END PGP SIGNATURE----- Tue Apr 2 14:15:34 UTC 2024 I: Checking whether the package is not for us Tue Apr 2 14:15:34 UTC 2024 I: Starting 1st build on remote node ionos2-i386.debian.net. Tue Apr 2 14:15:34 UTC 2024 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Tue Apr 2 14:19:31 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 2 02:15:36 -12 2024 I: pbuilder-time-stamp: 1712067336 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 [virulencefinder_2.0.5-1.dsc] I: copying [./virulencefinder_2.0.5.orig.tar.xz] I: copying [./virulencefinder_2.0.5-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 18 16:38:46 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./virulencefinder_2.0.5-1.dsc: no acceptable signature found dpkg-source: info: extracting virulencefinder in virulencefinder-2.0.5 dpkg-source: info: unpacking virulencefinder_2.0.5.orig.tar.xz dpkg-source: info: unpacking virulencefinder_2.0.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible_build.patch dpkg-source: info: applying python3.12.patch dpkg-source: info: applying adjust-reference-data.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/19993/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=8 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='8d182e55a9e94b528dddbab9cf96be3b' 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='19993' 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.4iugzOhd/pbuilderrc_LYyk --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.4iugzOhd/b1 --logfile b1/build.log virulencefinder_2.0.5-1.dsc' SUDO_GID='112' SUDO_UID='107' 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 ionos2-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 1 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/19993/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 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), dh-sequence-python3, python3, python3-tabulate, python3-cgecore, ncbi-blast+ dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19876 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-tabulate; however: Package python3-tabulate is not installed. pbuilder-satisfydepends-dummy depends on python3-cgecore; however: Package python3-cgecore is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ 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-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-extra{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblcms2-2{a} liblerc4{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8{a} libsharpyuv0{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} po-debconf{a} python3{a} python3-biopython{a} python3-cairo{a} python3-cgecore{a} python3-chardet{a} python3-distutils{a} python3-freetype{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-tabulate{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx python-biopython-doc python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 116 newly installed, 0 to remove and 0 not upgraded. Need to get 86.3 MB of archives. After unpacking 323 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.5.0-2+b2 [104 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-3 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libreadline8 i386 8.2-3+b1 [171 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 13 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.2-1 [807 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.2-1 [2244 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 python3-distutils all 3.11.5-1 [131 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20240310 [106 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libpng16-16 i386 1.6.43-1 [285 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.2+dfsg-1+b1 [449 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23 [252 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 62 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-extra all 2.37-8 [1792 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1 [822 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.0-1+b1 [587 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240201-3 [733 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libglib2.0-0 i386 2.78.4-1 [1520 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 8.3.0-2 [2234 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libimagequant0 i386 2.18.0-1 [35.6 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 liblmdb0 i386 0.9.31-1+b1 [46.4 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libmbedcrypto7 i386 2.28.7-1 [295 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libmbedx509-1 i386 2.28.7-1 [131 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libmbedtls14 i386 2.28.7-1 [169 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.0-2+b2 [197 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.2-1 [1927 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.3.2-0.4 [107 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.3.2-0.4 [314 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libwebpdemux2 i386 1.3.2-0.4 [108 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libwebpmux3 i386 1.3.2-0.4 [121 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 ncbi-blast+ i386 2.12.0+ds-4 [13.4 MB] Get: 104 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.2-1 [653 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:1.24.2-2 [4879 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 python3-pil i386 10.2.0-1 [526 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 python3-cairo i386 1.25.1-2 [142 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 python3-freetype all 2.4.0-1 [80.3 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 111 http://deb.debian.org/debian trixie/main i386 python3-reportlab all 4.1.0-1 [674 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 w3c-sgml-lib all 1.3-3 [273 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 python3-biopython i386 1.81+dfsg-3 [1616 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 python3-cgecore all 1.5.6+ds-1 [28.7 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 python3-tabulate all 0.8.10-1 [38.8 kB] Fetched 86.3 MB in 1s (64.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19876 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-2+b2_i386.deb ... Unpacking libexpat1:i386 (2.5.0-2+b2) ... Selecting previously unselected package python3.11-minimal. 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Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 2 14:16:45 UTC 2024. Universal Time is now: Tue Apr 2 14:16:45 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:i386 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libjpeg62-turbo:i386 (1:2.1.5-2+b2) ... Setting up libmbedcrypto7:i386 (2.28.7-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:i386 (1.0.13-3+b1) ... Setting up libimagequant0:i386 (2.18.0-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:i386 (1.6.43-1) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:i386 (14-20240201-3) ... Setting up autoconf (2.71-3) ... 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Setting up libfontconfig1:i386 (2.15.0-1.1) ... Setting up libpython3.12-stdlib:i386 (3.12.2-1) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.8-1) ... Setting up python3.12 (3.12.2-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.18.0-1+b1) ... Setting up libraqm0:i386 (0.10.1-1+b1) ... Setting up libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up ncbi-blast+ (2.12.0+ds-4) ... Setting up python3-pil:i386 (10.2.0-1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-cairo (1.25.1-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-tabulate (0.8.10-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-reportlab (4.1.0-1) ... Setting up dh-python (6.20240310) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.81+dfsg-3) ... Setting up python3-cgecore (1.5.6+ds-1) ... /usr/lib/python3/dist-packages/cgecore/cgefinder.py:242: SyntaxWarning: invalid escape sequence '\w' start = re.search("^-*(\w+)", align_query).start(1) /usr/lib/python3/dist-packages/cgecore/cgefinder.py:243: SyntaxWarning: invalid escape sequence '\w' end = re.search("\w+(-*)$", align_query).start(1) /usr/lib/python3/dist-packages/cgecore/utility.py:137: SyntaxWarning: invalid escape sequence '\{' """ /usr/lib/python3/dist-packages/cgecore/utility.py:491: SyntaxWarning: invalid escape sequence '\w' src = re.sub('[^\w/\-\.\*]', '', src) /usr/lib/python3/dist-packages/cgecore/utility.py:492: SyntaxWarning: invalid escape sequence '\w' dst = re.sub('[^\w/\-\.\*]', '', dst) /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W' if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5: /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W' if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5: /usr/lib/python3/dist-packages/cgecore/utility.py:520: SyntaxWarning: invalid escape sequence '\w' invalid_chars = re.findall('[^\w/\-\.\*]', os.path.basename(file_)) /usr/lib/python3/dist-packages/cgecore/utility.py:539: SyntaxWarning: invalid escape sequence '\w' src = re.sub('[^\w/\-\.\*]', '', src) /usr/lib/python3/dist-packages/cgecore/utility.py:540: SyntaxWarning: invalid escape sequence '\w' dst = re.sub('[^\w/\-\.\*]', '', dst) /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W' if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5: /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W' if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5: 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/virulencefinder-2.0.5/ && 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 > ../virulencefinder_2.0.5-1_source.changes dpkg-buildpackage: info: source package virulencefinder dpkg-buildpackage: info: source version 2.0.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:305: rm -rf test/Hit_in_genome_seq.fsa test/Virulence_genes.fsa test/data.json test/tmp test/results_tab.tsv test/results.txt dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild W: pybuild base:335: missing command (plugin=custom, method=configure, interpreter=python3.11, version=3.11) dh_auto_build -O--buildsystem=pybuild W: pybuild base:335: missing command (plugin=custom, method=build, interpreter=python3.11, version=3.11) debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/virulencefinder-2.0.5' ./virulencefinder.py -i test/test.fsa -o test/ -p test/database/ -mp blastn -x -q ; \ file=test/results_tab.tsv ; \ DIFF=$(diff "$file" test/test_results.tsv) ; \ if [ "$DIFF" = "" ] && [ -s "$file" ] ; then \ echo "TEST SUCCEEDED" ; \ else \ echo "TEST FAILED"; \ fi TEST SUCCEEDED make[1]: Leaving directory '/build/reproducible-path/virulencefinder-2.0.5' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild W: pybuild base:335: missing command (plugin=custom, method=install, interpreter=python3.11, version=3.11) dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/virulencefinder-2.0.5' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/virulencefinder-2.0.5' dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:113: replacing shebang in debian/virulencefinder/usr/share/virulencefinder/virulencefinder.py dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'virulencefinder' in '../virulencefinder_2.0.5-1_all.deb'. dpkg-deb: building package 'virulencefinder-examples' in '../virulencefinder-examples_2.0.5-1_all.deb'. dpkg-genbuildinfo --build=binary -O../virulencefinder_2.0.5-1_i386.buildinfo dpkg-genchanges --build=binary -O../virulencefinder_2.0.5-1_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: including full 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/19993 and its subdirectories I: Current time: Tue Apr 2 02:19:30 -12 2024 I: pbuilder-time-stamp: 1712067570 Tue Apr 2 14:19:32 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Tue Apr 2 14:19:32 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Tue Apr 2 14:20:53 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Tue Apr 2 14:20:53 UTC 2024 I: virulencefinder_2.0.5-1_i386.changes: Format: 1.8 Date: Sun, 18 Feb 2024 17:34:35 +0100 Source: virulencefinder Binary: virulencefinder virulencefinder-examples Architecture: all Version: 2.0.5-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: virulencefinder - identify virulence genes in total or partial sequenced isolates o virulencefinder-examples - example data for virulencefinder Changes: virulencefinder (2.0.5-1) unstable; urgency=medium . * New upstream version 2.0.5 * reproducible_build.patch: refresh. * python3.12.patch: refresh. * adjust-reference-data.patch: new. This patch fixes an autopkgtest failure due to the last line of the reference data not being present in the virulencefinder output. Checksums-Sha1: 727d3126e7e1074062bd75a4c2c8eeb2a372b304 372572 virulencefinder-examples_2.0.5-1_all.deb 9785cbdf3e289031acd5217887429ac35220a4b7 13432 virulencefinder_2.0.5-1_all.deb 18abd46946366b2e1c49a741f4f1ba53558dd4ae 8063 virulencefinder_2.0.5-1_i386.buildinfo Checksums-Sha256: 7801b977ca03f552e77bb67bd83e0fe3eeb800d286cc42246a8673aad46ad475 372572 virulencefinder-examples_2.0.5-1_all.deb c23f3038b9b4712400c01e4c2404269d7bb23a5aa995d3f070f6b737bd5a796e 13432 virulencefinder_2.0.5-1_all.deb 256e07773d12c0af010f2b33c05ffbb91779df891bbd87867780317e8c87e635 8063 virulencefinder_2.0.5-1_i386.buildinfo Files: 503521cc8b5f685a31333da12730546e 372572 science optional virulencefinder-examples_2.0.5-1_all.deb 2bdeb3568e55a821d69e4f93583cf934 13432 science optional virulencefinder_2.0.5-1_all.deb b641084331b852e322e807a70b173457 8063 science optional virulencefinder_2.0.5-1_i386.buildinfo Tue Apr 2 14:20:54 UTC 2024 I: diffoscope 262 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_1-20486.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.4iugzOhd/virulencefinder_2.0.5-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.4iugzOhd/virulencefinder_2.0.5-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.4iugzOhd/virulencefinder_2.0.5-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.4iugzOhd/b1/virulencefinder_2.0.5-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.4iugzOhd/b2/virulencefinder_2.0.5-1_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: 0.326s) 0.326s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.019s) 0.019s 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: 622ms CPU time consumed: 621ms Tue Apr 2 14:20:55 UTC 2024 I: diffoscope 262 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 2 14:20:55 UTC 2024 I: virulencefinder from trixie built successfully and reproducibly on i386. Tue Apr 2 14:20:57 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 2 14:20:57 UTC 2024 I: Submitting 12K b1/virulencefinder_2.0.5-1_i386.buildinfo.asc Tue Apr 2 14:20:58 UTC 2024 I: Submitting 12K b2/virulencefinder_2.0.5-1_i386.buildinfo.asc Tue Apr 2 14:20:58 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 2 14:20:58 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 2 14:20:58 UTC 2024 I: Removing signed virulencefinder_2.0.5-1_i386.buildinfo.asc files: removed './b1/virulencefinder_2.0.5-1_i386.buildinfo.asc' removed './b2/virulencefinder_2.0.5-1_i386.buildinfo.asc'