Thu May 9 23:17:25 UTC 2024 I: starting to build srst2/trixie/amd64 on jenkins on '2024-05-09 23:17' Thu May 9 23:17:25 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_33/11683/console.log Thu May 9 23:17:25 UTC 2024 I: Downloading source for trixie/srst2=0.2.0-11 --2024-05-09 23:17:25-- http://deb.debian.org/debian/pool/main/s/srst2/srst2_0.2.0-11.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2144 (2.1K) [text/prs.lines.tag] Saving to: ‘srst2_0.2.0-11.dsc’ 0K .. 100% 305M=0s 2024-05-09 23:17:25 (305 MB/s) - ‘srst2_0.2.0-11.dsc’ saved [2144/2144] Thu May 9 23:17:25 UTC 2024 I: srst2_0.2.0-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: srst2 Binary: srst2 Architecture: any Version: 0.2.0-11 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://katholt.github.io/srst2/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/srst2 Vcs-Git: https://salsa.debian.org/med-team/srst2.git Testsuite: autopkgtest Testsuite-Triggers: python3-mock Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-setuptools, markdown, dos2unix, python3-scipy , bowtie2 , samtools Package-List: srst2 deb science optional arch=any Checksums-Sha1: b10c53e3a16271e4506ce253200410884b02679a 1380071 srst2_0.2.0.orig.tar.gz dd754c8ca69cb4c92edb9dea046e56d2e6867de3 17856 srst2_0.2.0-11.debian.tar.xz Checksums-Sha256: 352c59bdf00039dfa5610a4b88049a0eb114d7c2a305d4924b6e605cc6d15123 1380071 srst2_0.2.0.orig.tar.gz 7d35f7b9174088b01c02a5e97d408b799a3bfd1fc7747c0d5a7c3d8718cf4309 17856 srst2_0.2.0-11.debian.tar.xz Files: ef447fc394d2f60adc2a32edd6ebe374 1380071 srst2_0.2.0.orig.tar.gz b2325945b181585b3b7436ce098de40f 17856 srst2_0.2.0-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWph6cRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFI8w//e/qOWUOwbKRq0n9EZRiBljSyRSCVJA6z hAYU5DHyKHxHWHWRSg3MfF47ZaTYsdlt0xgMHKUtO/vHSHmO3sjWC2rHX1gsjofR mLjyPn4VFLX+pxOa7nr60cdb/rdgLQ0k8KGKMbQOWqDQYgsWvtFFbI3boiQXDE3t ZfK4BedgIZ4shiCoG0tZheKvXfvquC9V06k0c3yYVX01loc4hNS4kp17NhJtdBL9 wr5mpjnxfDGLR5ycfuTSUbrtD9rA5INBcS622X8fzwMHKPVPVXnsp+kZzjZea+B5 y/dostNE2eC2f/tH2otiMBxJmS7/QiCThOHQc2opXtaZclyQ+Mpd9MJjsaluKQ/P sm+neHmCKZ0PjTvvLdSbXrDCl2ciyBwBs1lcjopIX33M+nllo8dVj7lV08zq/ia1 naeHmzdWLSpeAOc9tlpKxdNv0VxmHDrw+2A/XvuULkL8Y2XP6vlZ/Q8Slm+PuqX5 IHbXdm0t7Vf/th7MfxE016meHTGBJIHRUpvHTHJS/hnJuhqFlDCnl9caoRGo+sdo Lz5lbJH8uSSFtKZZCE4P9kpWGJ1SvmVUj2quS3YWnwMuMvwGKUKGbbx9/7U0uYcV EWh7LCRMzJpANYtcR2k+QBa+rqkAjaqhptCtLEK/fPcPj5UZyhtNcQzveMID9TBI 1FXO686J0Ps= =M8gR -----END PGP SIGNATURE----- Thu May 9 23:17:25 UTC 2024 I: Checking whether the package is not for us Thu May 9 23:17:25 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Thu May 9 23:17:25 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Thu May 9 23:19:00 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 9 11:17:28 -12 2024 I: pbuilder-time-stamp: 1715296648 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: Copying source file I: copying [srst2_0.2.0-11.dsc] I: copying [./srst2_0.2.0.orig.tar.gz] I: copying [./srst2_0.2.0-11.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 18 20:18:47 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./srst2_0.2.0-11.dsc: no acceptable signature found dpkg-source: info: extracting srst2 in srst2-0.2.0 dpkg-source: info: unpacking srst2_0.2.0.orig.tar.gz dpkg-source: info: unpacking srst2_0.2.0-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying check_command_line_arguments.patch dpkg-source: info: applying add_usr_bin_python_to_scripts.patch dpkg-source: info: applying fix_test.patch dpkg-source: info: applying fix_grep_call.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying biopython-1.78.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3034051/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='00f65aa5c98c46cfba55f13cf66767a8' 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='3034051' 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.ngj5Bt23/pbuilderrc_ew6Y --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.ngj5Bt23/b1 --logfile b1/build.log srst2_0.2.0-11.dsc' SUDO_GID='109' 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 infom01-amd64 6.1.0-21-cloud-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 May 8 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3034051/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), dh-sequence-python3, python3, python3-setuptools, markdown, dos2unix, python3-scipy, bowtie2, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 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-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on markdown; however: Package markdown is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} bowtie2{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dos2unix{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} markdown{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-decorator{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-scipy{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-pil wget 0 packages upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 59.6 MB of archives. After unpacking 269 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 bowtie2 amd64 2.5.3-1 [1438 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240422 [107 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dos2unix amd64 7.5.2-1 [518 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 57 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-3 [432 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 markdown all 1.0.1-12 [17.7 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get: 78 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Fetched 59.6 MB in 1s (60.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu May 9 23:18:34 UTC 2024. Universal Time is now: Thu May 9 23:18:34 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.4+20240414-1) ... Setting up autopoint (0.21-14) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up dos2unix (7.5.2-1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up markdown (1.0.1-12) ... 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 liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-3) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up samtools (1.19.2-1+b1) ... Setting up bowtie2 (2.5.3-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up dh-python (6.20240422) ... Setting up python3-scipy (1.11.4-6) ... Processing triggers for libc-bin (2.38-7) ... 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/srst2-0.2.0/ && 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 > ../srst2_0.2.0-11_source.changes dpkg-buildpackage: info: source package srst2 dpkg-buildpackage: info: source version 0.2.0-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.11 setup.py clean 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it 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 I: pybuild base:311: python3.11 setup.py config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build markdown README.md > README.html markdown database_clustering/README.md > database_clustering_README.html make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' cd tests && python3 test_slurm_srst2.py && python3 test_srst2.py ........... ---------------------------------------------------------------------- Ran 11 tests in 0.033s OK ................. ---------------------------------------------------------------------- Ran 17 tests in 0.039s OK make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/srst2/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/srst2-0.2.0/debian/srst2 /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_install mv debian/srst2/usr/lib/*/dist-packages/srst2/* debian/srst2/usr/share/srst2 rm -rf debian/*/usr/bin/*.py debian/srst2/usr/lib/*/dist-packages/ # fix line endings to make sure Python3 interpreter will be found find debian/*/usr/share -name "VFDB*" -exec dos2unix \{\} \; dos2unix: converting file debian/srst2/usr/share/srst2/database_clustering/VFDB_cdhit_to_csv.py to Unix format... dos2unix: converting file debian/srst2/usr/share/srst2/database_clustering/VFDBgenus.py to Unix format... sed -i '1s:^#!/usr/local.*python[.0-9]*$:#!/usr/bin/python3:' debian/srst2/usr/share/srst2/qsub_srst2.py find debian -name __pycache__ -type d | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_installdocs sed -i "s?sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__).*scripts.*?sys.path.append(os.path.abspath('/usr/share/srst2'))?" debian/srst2/usr/share/doc/srst2/tests/*.py make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild 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 debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_fixperms chmod +x debian/srst2/usr/share/srst2/database_clustering/get_genus_vfdb.sh chmod +x debian/srst2/usr/share/srst2/database_clustering/get_all_vfdb.sh chmod -x debian/srst2/usr/share/srst2/database_clustering/align_plot_tree_min3.py for py in `find debian -name "*.py"` ; do \ if head -n 1 $py | grep -q '^#! */usr/bin/.*python' ; then chmod +x $py ; fi ; \ done make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -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 'srst2' in '../srst2_0.2.0-11_amd64.deb'. dpkg-genbuildinfo --build=binary -O../srst2_0.2.0-11_amd64.buildinfo dpkg-genchanges --build=binary -O../srst2_0.2.0-11_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/3034051 and its subdirectories I: Current time: Thu May 9 11:18:59 -12 2024 I: pbuilder-time-stamp: 1715296739 Thu May 9 23:19:01 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Thu May 9 23:19:01 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Thu May 9 23:20:16 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Thu May 9 23:20:16 UTC 2024 I: srst2_0.2.0-11_amd64.changes: Format: 1.8 Date: Thu, 18 Jan 2024 21:10:58 +0100 Source: srst2 Binary: srst2 Architecture: amd64 Version: 0.2.0-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: srst2 - Short Read Sequence Typing for Bacterial Pathogens Changes: srst2 (0.2.0-11) unstable; urgency=medium . [ Alexandre Detiste ] * remove dependency on python3-mock . [ Andreas Tille ] * Add support for loong64 for autopkgtest * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) Checksums-Sha1: 18830701b1a2961da7390b90b6442f6f84aef6d9 6534 srst2_0.2.0-11_amd64.buildinfo ae350171e395dcf1adea7eed8882cb2ca96434dd 61028 srst2_0.2.0-11_amd64.deb Checksums-Sha256: 67547cd804f4f6157dc0ae44324c1a549cbfd2be68285ccee15d14ee0c353d58 6534 srst2_0.2.0-11_amd64.buildinfo 9417c14da2103013e63244832d1a5d017bbe3eb04f4870e435947f1adf64e176 61028 srst2_0.2.0-11_amd64.deb Files: 7e5477bec3898b8dea5cf276911c7b7c 6534 science optional srst2_0.2.0-11_amd64.buildinfo f295a5d7d0022a6b7e8ef9d697c3d5a8 61028 science optional srst2_0.2.0-11_amd64.deb Thu May 9 23:20:17 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_33-11683.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ngj5Bt23/srst2_0.2.0-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ngj5Bt23/srst2_0.2.0-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ngj5Bt23/srst2_0.2.0-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ngj5Bt23/b1/srst2_0.2.0-11_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ngj5Bt23/b2/srst2_0.2.0-11_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: 0.383s) 0.383s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.017s) 0.017s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 745ms CPU time consumed: 740ms Thu May 9 23:20:19 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 9 23:20:19 UTC 2024 I: srst2 from trixie built successfully and reproducibly on amd64. Thu May 9 23:20:22 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 9 23:20:22 UTC 2024 I: Submitting 8.0K b1/srst2_0.2.0-11_amd64.buildinfo.asc Thu May 9 23:20:23 UTC 2024 I: Submitting 8.0K b2/srst2_0.2.0-11_amd64.buildinfo.asc Thu May 9 23:20:24 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 9 23:20:24 UTC 2024 I: Done submitting .buildinfo files. Thu May 9 23:20:24 UTC 2024 I: Removing signed srst2_0.2.0-11_amd64.buildinfo.asc files: removed './b1/srst2_0.2.0-11_amd64.buildinfo.asc' removed './b2/srst2_0.2.0-11_amd64.buildinfo.asc'