Tue Jun 18 16:48:45 UTC 2024 I: starting to build seqsero/bookworm/armhf on jenkins on '2024-06-18 16:48' Tue Jun 18 16:48:45 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_35/4204/console.log Tue Jun 18 16:48:45 UTC 2024 I: Downloading source for bookworm/seqsero=1.0.1+dfsg-6 --2024-06-18 16:48:45-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/seqsero/seqsero_1.0.1%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2024 (2.0K) [text/prs.lines.tag] Saving to: ‘seqsero_1.0.1+dfsg-6.dsc’ 0K . 100% 260M=0s 2024-06-18 16:48:45 (260 MB/s) - ‘seqsero_1.0.1+dfsg-6.dsc’ saved [2024/2024] Tue Jun 18 16:48:45 UTC 2024 I: seqsero_1.0.1+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: seqsero Binary: seqsero Architecture: any Version: 1.0.1+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/denglab/SeqSero Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/seqsero Vcs-Git: https://salsa.debian.org/med-team/seqsero.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3, bwa, sra-toolkit Package-List: seqsero deb science optional arch=any Checksums-Sha1: 5531311d55cff8cb84ebade2499ebedf4732a883 355568 seqsero_1.0.1+dfsg.orig.tar.xz 873a8b6a41031621e9c7dd05e2ac890750be0feb 43084 seqsero_1.0.1+dfsg-6.debian.tar.xz Checksums-Sha256: 37f9c68c941b5fe5648d86ad3e89235c3f7455aa3d2d933e75da211a9240bd0a 355568 seqsero_1.0.1+dfsg.orig.tar.xz 8e72e6bf6c087e0d533f1e2d7693686468b8b8820d71d19715783ec82a847156 43084 seqsero_1.0.1+dfsg-6.debian.tar.xz Files: 53cee0dd133a96cf84b614df0ccf72df 355568 seqsero_1.0.1+dfsg.orig.tar.xz 640dc43659231fad76ee23541e5da9e4 43084 seqsero_1.0.1+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmM1n9wRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEzZBAAhws+Q68lNyn8s+h08GKNCdT8TIzEpxzw lUwZyI7Y9lNfu2qSaE+1X6qEVGaw+u5uMtvjqfU6sRu8jX6QtJKDTNXqJfIc15vc g5+3O8ubgAbChCWOxeJdpHHlaWnJ9CWxRld6QXFAWd7m35cSMAbo7s7dgTTpQdi9 dW4ZQ+Uo5AFQyXfXwN1BpeeoUJr9BHReBHb4tbPcxMYqljNc46CsfqpgyK7p2EGt jLatpM2oprHvaSFGaKGzo3leoF/8ClwI4CVFhoEwCESOsOGiZ+gQlUI3WMGS71uZ OUMLaEopUsUg0uByZI8ucRH8GxZ16S3LGUufrbjwAvWjWHfVKObQ0lGNC+PGNIBK V+Du/ztbQDO5SOXADEreCcV5p180GsXSB3XhDWHs3L9NmJb3xfoRfUTra/N/LNas fsI9rsm/rJYrouCtWZ6yDd1PMuJuE3nXbM4Bi+zKMbVWtwUC87BK9OD3VNXphu77 mjswMUyZlUt8vTY2b9pI+8qaUsEgGAsuAeAXqian6wCktTx7th8iaXck8QzrXDjO tj9l5DZLesyHJdpM+fFMFnqcqUvsVKdqTgWLY/wHMT26wGhiahllf2XloaopGSoi SMgR5nXmAj4BIiP3n/rfBrn7GwcknMiuvVnAxg9HpdmSScdNVg9Cs0WJaZk+l/4g ukbSIaL3XEA= =yjHb -----END PGP SIGNATURE----- Tue Jun 18 16:48:45 UTC 2024 I: Checking whether the package is not for us Tue Jun 18 16:48:45 UTC 2024 I: Starting 1st build on remote node cbxi4pro0-armhf-rb.debian.net. Tue Jun 18 16:48:45 UTC 2024 I: Preparing to do remote build '1' on cbxi4pro0-armhf-rb.debian.net. Tue Jun 18 16:50:14 UTC 2024 I: Deleting $TMPDIR on cbxi4pro0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 18 04:48:54 -12 2024 I: pbuilder-time-stamp: 1718729334 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 [seqsero_1.0.1+dfsg-6.dsc] I: copying [./seqsero_1.0.1+dfsg.orig.tar.xz] I: copying [./seqsero_1.0.1+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Sep 29 01:38:36 2022 -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 ./seqsero_1.0.1+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting seqsero in seqsero-1.0.1+dfsg dpkg-source: info: unpacking seqsero_1.0.1+dfsg.orig.tar.xz dpkg-source: info: unpacking seqsero_1.0.1+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_perl_interpreter.patch dpkg-source: info: applying fix_usage.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14516/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='4b57ca6f1b6e4d41a473c2599d0757fe' 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='14516' 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.7veYomrY/pbuilderrc_2t2R --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.7veYomrY/b1 --logfile b1/build.log seqsero_1.0.1+dfsg-6.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 cbxi4pro0 6.1.0-21-armmp #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/14516/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, bwa, sra-toolkit 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 bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on sra-toolkit; however: Package sra-toolkit 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} bwa{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 23.7 MB of archives. After unpacking 88.9 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: sra-toolkit 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} bwa{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 23.7 MB of archives. After unpacking 88.9 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/14516 and its subdirectories Tue Jun 18 16:50:17 UTC 2024 W: No second build log, what happened? Tue Jun 18 16:50:17 UTC 2024 W: Downloading the build dependencies failed Tue Jun 18 16:50:17 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Tue Jun 18 16:50:17 UTC 2024 W: Network problems are automatically rescheduled after some hours.