Sun May 19 00:31:36 UTC 2024 I: starting to build srst2/bookworm/armhf on jenkins on '2024-05-19 00:31' Sun May 19 00:31:36 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_9/5859/console.log Sun May 19 00:31:36 UTC 2024 I: Downloading source for bookworm/srst2=0.2.0-9 --2024-05-19 00:31:37-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/srst2/srst2_0.2.0-9.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2155 (2.1K) [text/prs.lines.tag] Saving to: ‘srst2_0.2.0-9.dsc’ 0K .. 100% 314M=0s 2024-05-19 00:31:37 (314 MB/s) - ‘srst2_0.2.0-9.dsc’ saved [2155/2155] Sun May 19 00:31:37 UTC 2024 I: srst2_0.2.0-9.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: srst2 Binary: srst2 Architecture: any Version: 0.2.0-9 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://katholt.github.io/srst2/ Standards-Version: 4.6.0 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-python, python3, python3-setuptools, markdown, dos2unix, python3-mock , python3-scipy , bowtie2 , samtools Package-List: srst2 deb science optional arch=any Checksums-Sha1: b10c53e3a16271e4506ce253200410884b02679a 1380071 srst2_0.2.0.orig.tar.gz 07a8d1c8c6607cebf58c4c301255c625866de36e 17972 srst2_0.2.0-9.debian.tar.xz Checksums-Sha256: 352c59bdf00039dfa5610a4b88049a0eb114d7c2a305d4924b6e605cc6d15123 1380071 srst2_0.2.0.orig.tar.gz 19636b8ce6330f0aa92f1d8c0bdc23b40916ed52fd7cb7cd111f3d88431d7efc 17972 srst2_0.2.0-9.debian.tar.xz Files: ef447fc394d2f60adc2a32edd6ebe374 1380071 srst2_0.2.0.orig.tar.gz fb750f2c65bbd89be359e27e28ae0e0d 17972 srst2_0.2.0-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmEvncARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFLMg//eRToUE4vpoNk+Xp/EspySUv8o1zaMTUA 3xVq2VGwxXFLE/axwO7+WS997qyr35hPKiY5qmoEDwC12iye+FwphMAD30CLIOGB 8yGCmrMoMlVUhG0pIwxpTnRfme021Aum0iEswNR6p8KAbcGpIJ3iW+fVMqM30L02 azbY3DL85Bvw20nDk9SScACsC2Kz4PU9bixCkAEgM66k6IKRuIbmCa9bywgSo/NR Vel1uPN7fUWZcHWAjLrJ+Us+VOlXq+Wj7FQHYbm+KGvtbAd4dPCyFVfsNrZH1uF3 jYRDecXTUywevJ3fcrm8KU8kISisFRL+LkgaqW/wUecZ7ewbHRg/THQD0sxt3TnU Y6X2RwjWErprrVIhmD7njUhKBf+GAJA1UD0i6e3pLE1xs6jA1sogVPO//uqN4YwT tKB479NPzJTy1AWVxpdOFSxZJ4GRvEo95VAavBQyeKYjDcQ1lZm9aPpkrWVnOyxh 7RDT0AoUG0+afFgnUTxpGi+VhkalEBqv4Zvf/3Wqm6I47MVK3B4/+RmXhk+NytEp H350y2/DqsjQkN1oroJUGyAqOqKsJ+Ma/RGoNYe//SOac3IJRcQGO7iNfjYW9y+0 jgAVBf0jlvCj907S0iBJnlfGeIOQcwxQ28pxbjijuSEg7X6iR9DVs8CVYGsJjOdG WI6cVe6qhg0= =+U3S -----END PGP SIGNATURE----- Sun May 19 00:31:37 UTC 2024 I: Checking whether the package is not for us Sun May 19 00:31:37 UTC 2024 I: Starting 1st build on remote node virt32a-armhf-rb.debian.net. Sun May 19 00:31:37 UTC 2024 I: Preparing to do remote build '1' on virt32a-armhf-rb.debian.net. Sun May 19 00:32:19 UTC 2024 I: Deleting $TMPDIR on virt32a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 18 12:31:44 -12 2024 I: pbuilder-time-stamp: 1716078704 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [srst2_0.2.0-9.dsc] I: copying [./srst2_0.2.0.orig.tar.gz] I: copying [./srst2_0.2.0-9.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Sep 1 03:35:28 2021 -12 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_0.2.0-9.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_0.2.0-9.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/4346/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='d1b61cb6bb6f4172bac7b241cae0a629' 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='4346' 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.t7apLJKD/pbuilderrc_8cVS --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.t7apLJKD/b1 --logfile b1/build.log srst2_0.2.0-9.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32a 6.1.0-21-armmp-lpae #1 SMP Debian 6.1.90-1 (2024-05-03) armv7l GNU/Linux I: ls -l /bin total 4964 -rwxr-xr-x 1 root root 838488 Apr 23 2023 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 2023 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 2022 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 2023 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 2023 more -rwsr-xr-x 1 root root 38496 Mar 22 2023 mount -rwxr-xr-x 1 root root 9824 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 14152 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 2023 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Jan 19 21:27 tar -rwxr-xr-x 1 root root 9800 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 2023 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/4346/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: armhf 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-python, python3, python3-setuptools, markdown, dos2unix, python3-mock, 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 ... 19288 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-python; however: Package dh-python 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-mock; however: Package python3-mock 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} 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} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhts3{a} libhtscodecs2{a} libicu72{a} liblapack3{a} liblbfgsb0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} markdown{a} media-types{a} po-debconf{a} python3{a} python3-decorator{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-mock{a} python3-numpy{a} python3-pbr{a} python3-pkg-resources{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-pil wget 0 packages upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 47.3 MB of archives. After unpacking 179 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: bowtie2 which is a virtual package and is not provided by any available package Unable to resolve dependencies! Giving up... 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} 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} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhts3{a} libhtscodecs2{a} libicu72{a} liblapack3{a} liblbfgsb0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} markdown{a} media-types{a} po-debconf{a} python3{a} python3-decorator{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-mock{a} python3-numpy{a} python3-pbr{a} python3-pkg-resources{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-pil wget 0 packages upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 47.3 MB of archives. After unpacking 179 MB will be used. Abort. E: pbuilder-satisfydepends failed. 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/4346 and its subdirectories Sun May 19 00:32:22 UTC 2024 W: No second build log, what happened? Sun May 19 00:32:22 UTC 2024 W: Downloading the build dependencies failed Sun May 19 00:32:22 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Sun May 19 00:32:22 UTC 2024 W: Network problems are automatically rescheduled after some hours.