Tue Jun 25 12:22:09 UTC 2024 I: starting to build virulencefinder/unstable/i386 on jenkins on '2024-06-25 12:21' Tue Jun 25 12:22:09 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_17/7521/console.log Tue Jun 25 12:22:09 UTC 2024 I: Downloading source for unstable/virulencefinder=2.0.5-2 --2024-06-25 12:22:09-- http://deb.debian.org/debian/pool/main/v/virulencefinder/virulencefinder_2.0.5-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2395 (2.3K) [text/prs.lines.tag] Saving to: ‘virulencefinder_2.0.5-2.dsc’ 0K .. 100% 275M=0s 2024-06-25 12:22:09 (275 MB/s) - ‘virulencefinder_2.0.5-2.dsc’ saved [2395/2395] Tue Jun 25 12:22:09 UTC 2024 I: virulencefinder_2.0.5-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: virulencefinder Binary: virulencefinder, virulencefinder-examples Architecture: all Version: 2.0.5-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://bitbucket.org/genomicepidemiology/virulencefinder Standards-Version: 4.7.0 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 ec013f4e8d77e59079693eaeb9bda3422604a4be 6144 virulencefinder_2.0.5-2.debian.tar.xz Checksums-Sha256: 2936d46e9db0d239294463919b34ae8f57acf0784e82f136010a8654cf00529f 263880 virulencefinder_2.0.5.orig.tar.xz 64ab0a80d01bafaf831070f7678169880be6e405d08128880f2dd29974c7fbbd 6144 virulencefinder_2.0.5-2.debian.tar.xz Files: 641ff0055d0c9b7ad332254e16608999 263880 virulencefinder_2.0.5.orig.tar.xz ca07e5311107f325f2f688ecae36697a 6144 virulencefinder_2.0.5-2.debian.tar.xz Dgit: a3ba065aa7c12b2931475a4c33078c400d9f85ca debian archive/debian/2.0.5-2 https://git.dgit.debian.org/virulencefinder -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmZN0XAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqDOBAAwO72XNQ8519J5o4uRBCyaHj6Kymx yjXEKYwh/fIo55EAyPiAJutEFI3mnF3Ol2v4WP27QEmDKUdZlxC8616fZReF9Wtq JUcH7ufrfOF2cbZocn+YGHRpo1y3z+vcLT4p0OiCpZZ9kglLJBB7TTEc27wohrCo 1mR1GUOdn5IR6+Rk4E3iJlMkRj7A0is99zgkYQ+O0q034Vb4llUFGKvtI+pjqzRj IeP2Zry5jSwi+9dU0jVRjrJzukmXkiDsuojNWJHlSZUmjLIfoBIQOnMj4ZNKj3Dc wZbhP/2OLNgqQhX8gdlUEKYTYButzZ66BwNTZmwUjejowFTl62HqRNXmk0JGrRlx iLuODiA/LLpBDRYF54w4lHVJjiggBZf5Gu2IWiJv7j8Gf20MoGVqHTEj4NC+bRtK ujWSXe2yaqu3Mmz7K7uretLFxw5jRODmz2VoTy8k/AHGhxNd5qN8SqlqHov18RHo OwxNUNZ0Z0oCDpfnpgzyZDoUtVoMEdHBlRUOX8u52cm8d18449mTQtfykGSpcfEw BFp0vuldECQJ+xLT29isA7VV1LbjcRq2ieoOZjt9llTBc3vE15qAP2MZQMFZhk7/ ipjy/33H+7gd/s98v3QbN+5gdWrcEeA/WrPzUsGyqpJcxK/w2r7HkWyIlRJxB09P DfqIqpb8tBnLNo8= =S6MV -----END PGP SIGNATURE----- Tue Jun 25 12:22:09 UTC 2024 I: Checking whether the package is not for us Tue Jun 25 12:22:09 UTC 2024 I: Starting 1st build on remote node infom07-i386.debian.net. Tue Jun 25 12:22:09 UTC 2024 I: Preparing to do remote build '1' on infom07-i386.debian.net. Tue Jun 25 12:23:54 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 25 00:22:13 -12 2024 I: pbuilder-time-stamp: 1719318133 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [virulencefinder_2.0.5-2.dsc] I: copying [./virulencefinder_2.0.5.orig.tar.xz] I: copying [./virulencefinder_2.0.5-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed May 22 11:05:20 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_2.0.5-2.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_2.0.5-2.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/29963/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='c2e2089943e34d5eb0d9db8dd5bbbce0' 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='29963' 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.Vn8rfk71/pbuilderrc_RisK --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Vn8rfk71/b1 --logfile b1/build.log virulencefinder_2.0.5-2.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom07-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 22:35 /bin -> usr/bin I: user script /srv/workspace/pbuilder/29963/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 ... 19557 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-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} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{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} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{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} python3.12{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 fonts-dejavu-extra 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, 109 newly installed, 0 to remove and 0 not upgraded. Need to get 80.8 MB of archives. After unpacking 305 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.4-1 [811 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.4-1 [2218 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.2-1 [26.5 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.4-1 [1947 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.4-1 [664 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.2-1 [9436 B] Get: 13 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.2-1 [27.5 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-1 [200 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-4 [1194 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.1-9 [101 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-2 [1421 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-1 [723 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.16 [88.6 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 36 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg-3 [704 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-1 [1624 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 debhelper all 13.16 [891 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 python3-lib2to3 all 3.12.3-3.1 [77.7 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 python3-distutils all 3.12.3-3.1 [131 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240422 [107 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.2+dfsg-1+b4 [449 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23 [252 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 59 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2 [148 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2 [116 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2 [105 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b1 [28.8 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.0-3+b1 [588 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.1.0-2 [734 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.80.3-1 [1555 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 8.3.0-2+b1 [2234 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b1 [35.9 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3 [169 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 liblmdb0 i386 0.9.31-1+b1 [46.4 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libmbedcrypto7t64 i386 2.28.8-1 [299 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libmbedx509-1t64 i386 2.28.8-1 [133 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libmbedtls14t64 i386 2.28.8-1 [171 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1 [113 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1 [318 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.4.0-0.1 [111 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.4.0-0.1 [125 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 ncbi-blast+ i386 2.12.0+ds-4+b1 [13.4 MB] Get: 98 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-10 [5468 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 python3-pil i386 10.3.0-2 [566 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 python3-cairo i386 1.26.0-1 [142 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 python3-freetype all 2.4.0-2 [78.6 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 104 http://deb.debian.org/debian unstable/main i386 python3-reportlab all 4.2.0-2 [1149 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 w3c-sgml-lib all 1.3-3 [273 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 python3-biopython i386 1.83+dfsg1-3 [1627 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 python3-cgecore all 1.5.6+ds-1 [28.7 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 python3-tabulate all 0.9.0-1 [45.9 kB] Fetched 80.8 MB in 4s (21.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 19557 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.4-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.4-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. 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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../6-libpython3.12-stdlib_3.12.4-1_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.4-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../7-python3.12_3.12.4-1_i386.deb ... Unpacking python3.12 (3.12.4-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.12.2-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.2-1) ... Setting up python3-minimal (3.12.2-1) ... Selecting previously unselected package python3. (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 ... 20879 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.2-1_i386.deb ... Unpacking python3 (3.12.2-1) ... Selecting previously unselected package sgml-base. 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Preparing to unpack .../62-libgfortran5_14.1.0-2_i386.deb ... Unpacking libgfortran5:i386 (14.1.0-2) ... Selecting previously unselected package libglib2.0-0t64:i386. Preparing to unpack .../63-libglib2.0-0t64_2.80.3-1_i386.deb ... Unpacking libglib2.0-0t64:i386 (2.80.3-1) ... Selecting previously unselected package libgraphite2-3:i386. Preparing to unpack .../64-libgraphite2-3_1.3.14-2_i386.deb ... Unpacking libgraphite2-3:i386 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:i386. Preparing to unpack .../65-libharfbuzz0b_8.3.0-2+b1_i386.deb ... Unpacking libharfbuzz0b:i386 (8.3.0-2+b1) ... Selecting previously unselected package libimagequant0:i386. Preparing to unpack .../66-libimagequant0_2.18.0-1+b1_i386.deb ... Unpacking libimagequant0:i386 (2.18.0-1+b1) ... Selecting previously unselected package libjbig0:i386. Preparing to unpack .../67-libjbig0_2.1-6.1+b1_i386.deb ... Unpacking libjbig0:i386 (2.1-6.1+b1) ... Selecting previously unselected package libjpeg62-turbo:i386. Preparing to unpack .../68-libjpeg62-turbo_1%3a2.1.5-3_i386.deb ... Unpacking libjpeg62-turbo:i386 (1:2.1.5-3) ... Selecting previously unselected package liblapack3:i386. Preparing to unpack .../69-liblapack3_3.12.0-3_i386.deb ... Unpacking liblapack3:i386 (3.12.0-3) ... Selecting previously unselected package liblcms2-2:i386. Preparing to unpack .../70-liblcms2-2_2.14-2+b1_i386.deb ... Unpacking liblcms2-2:i386 (2.14-2+b1) ... Selecting previously unselected package liblerc4:i386. Preparing to unpack .../71-liblerc4_4.0.0+ds-4+b1_i386.deb ... Unpacking liblerc4:i386 (4.0.0+ds-4+b1) ... Selecting previously unselected package liblmdb0:i386. Preparing to unpack .../72-liblmdb0_0.9.31-1+b1_i386.deb ... Unpacking liblmdb0:i386 (0.9.31-1+b1) ... Selecting previously unselected package libmbedcrypto7t64:i386. Preparing to unpack .../73-libmbedcrypto7t64_2.28.8-1_i386.deb ... Unpacking libmbedcrypto7t64:i386 (2.28.8-1) ... 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Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.26.4+ds-10) ... Setting up python3-reportlab (4.2.0-2) ... Setting up dh-python (6.20240422) ... Processing triggers for libc-bin (2.38-13) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-3) ... 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_2.0.5-2_source.changes dpkg-buildpackage: info: source package virulencefinder dpkg-buildpackage: info: source version 2.0.5-2 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:311: 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:341: missing command (plugin=custom, method=configure, interpreter=python3.12, version=3.12) dh_auto_build -O--buildsystem=pybuild W: pybuild base:341: missing command (plugin=custom, method=build, interpreter=python3.12, version=3.12) 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:341: missing command (plugin=custom, method=install, interpreter=python3.12, version=3.12) 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-examples' in '../virulencefinder-examples_2.0.5-2_all.deb'. dpkg-deb: building package 'virulencefinder' in '../virulencefinder_2.0.5-2_all.deb'. dpkg-genbuildinfo --build=binary -O../virulencefinder_2.0.5-2_i386.buildinfo dpkg-genchanges --build=binary -O../virulencefinder_2.0.5-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/29963 and its subdirectories I: Current time: Tue Jun 25 00:23:52 -12 2024 I: pbuilder-time-stamp: 1719318232 Tue Jun 25 12:23:56 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom08-i386.debian.net. Tue Jun 25 12:23:56 UTC 2024 I: Preparing to do remote build '2' on infom08-i386.debian.net. Tue Jun 25 12:25:09 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. Tue Jun 25 12:25:10 UTC 2024 I: virulencefinder_2.0.5-2_i386.changes: Format: 1.8 Date: Wed, 22 May 2024 13:00:29 +0200 Source: virulencefinder Binary: virulencefinder virulencefinder-examples Architecture: all Version: 2.0.5-2 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 Closes: 1066004 Changes: virulencefinder (2.0.5-2) unstable; urgency=medium . * d/control: remove stray dependency on python3-distutils. (Closes: #1066004) * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: 41177e0dba67cef6cd0c21f717bd6dd750109c94 372580 virulencefinder-examples_2.0.5-2_all.deb c8cd86b9051f955dcdb7814dceb2d55c3a209009 13472 virulencefinder_2.0.5-2_all.deb a91a62ce82bf2fdab0838bedeb573eccff4ec737 7439 virulencefinder_2.0.5-2_i386.buildinfo Checksums-Sha256: 4b3e9167b652889a2a3df313c902f1adad07937e17d1e2dc25abb00a8afed342 372580 virulencefinder-examples_2.0.5-2_all.deb 1a19f507fabec8b19b3e6678938e78da3358805f0ed0c28b6f6d36e7f29fe75e 13472 virulencefinder_2.0.5-2_all.deb 696525bac47a8aa57708add8fc4fbf03ccc9f3ed88b814650634bfd854126784 7439 virulencefinder_2.0.5-2_i386.buildinfo Files: 418d1af146526b1664b99c9c5d917ebb 372580 science optional virulencefinder-examples_2.0.5-2_all.deb 0b48bd4d070c0e41227e2f44b79da7bd 13472 science optional virulencefinder_2.0.5-2_all.deb e801cc6487733002a4572ecb5047278c 7439 science optional virulencefinder_2.0.5-2_i386.buildinfo Tue Jun 25 12:25:11 UTC 2024 I: diffoscope 271 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_17-7521.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Vn8rfk71/virulencefinder_2.0.5-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Vn8rfk71/virulencefinder_2.0.5-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Vn8rfk71/virulencefinder_2.0.5-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Vn8rfk71/b1/virulencefinder_2.0.5-2_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.Vn8rfk71/b2/virulencefinder_2.0.5-2_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: 0.428s) 0.428s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.024s) 0.024s 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: 810ms CPU time consumed: 805ms Tue Jun 25 12:25:12 UTC 2024 I: diffoscope 271 found no differences in the changes files, and a .buildinfo file also exists. Tue Jun 25 12:25:12 UTC 2024 I: virulencefinder from unstable built successfully and reproducibly on i386. Tue Jun 25 12:25:14 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Jun 25 12:25:14 UTC 2024 I: Submitting 12K b1/virulencefinder_2.0.5-2_i386.buildinfo.asc Tue Jun 25 12:25:15 UTC 2024 I: Submitting 12K b2/virulencefinder_2.0.5-2_i386.buildinfo.asc Tue Jun 25 12:25:15 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jun 25 12:25:15 UTC 2024 I: Done submitting .buildinfo files. Tue Jun 25 12:25:15 UTC 2024 I: Removing signed virulencefinder_2.0.5-2_i386.buildinfo.asc files: removed './b1/virulencefinder_2.0.5-2_i386.buildinfo.asc' removed './b2/virulencefinder_2.0.5-2_i386.buildinfo.asc'