Mon Dec 2 07:40:01 UTC 2024 I: starting to build kraken/bookworm/i386 on jenkins on '2024-12-02 07:39' Mon Dec 2 07:40:01 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/31869/console.log Mon Dec 2 07:40:01 UTC 2024 I: Downloading source for bookworm/kraken=1.1.1-4 --2024-12-02 07:40:01-- http://cdn-fastly.deb.debian.org/debian/pool/main/k/kraken/kraken_1.1.1-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1953 (1.9K) [text/prs.lines.tag] Saving to: ‘kraken_1.1.1-4.dsc’ 0K . 100% 255M=0s 2024-12-02 07:40:01 (255 MB/s) - ‘kraken_1.1.1-4.dsc’ saved [1953/1953] Mon Dec 2 07:40:01 UTC 2024 I: kraken_1.1.1-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: kraken Binary: kraken Architecture: any Version: 1.1.1-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://ccb.jhu.edu/software/kraken/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/kraken Vcs-Git: https://salsa.debian.org/med-team/kraken.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), jellyfish1 Package-List: kraken deb science optional arch=any Checksums-Sha1: 56e70d9b6a9d90bdabfb76f6bd5c14bb92f7bd82 76541 kraken_1.1.1.orig.tar.gz e44a12a51c7affa05d7605fc38bd6981e069d8b0 337236 kraken_1.1.1-4.debian.tar.xz Checksums-Sha256: 73e48f40418f92b8cf036ca1da727ca3941da9b78d4c285b81ba3267326ac4ee 76541 kraken_1.1.1.orig.tar.gz b3adb7c91b18d79310d4610d15df87c875ad4a5ec0db7ef90fa7072f7fb0f00e 337236 kraken_1.1.1-4.debian.tar.xz Files: 91b988e05ffaa128c7bf28816a41a910 76541 kraken_1.1.1.orig.tar.gz 59fcafd28b74c88dacd83b1a76cb4d20 337236 kraken_1.1.1-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmNm0K0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFBWRAAiiTM5dOVYShdnRiH8LSmszuMSvm+6XsL /sOkULU6QfXyFpiHL6liqUmPSBTQC+PxsisRV+2DGroIjbwyX2YKIMkVKwh0Mvug 3Xzu2/3MXf1BJtu0d9hrcbnFNSCEuExG7lcGoK3dzUHgw3AS5QeCt934jRUcRlWz 7luAtVvExWQXoG78xs/zEu+2y1P+XPF1diooDlc6TMBHykq3pLultqxnY4bwG4gn ZzZFSP7qsX6LjN8ON9lLYt08Da01gVtOJMXEeQRynqZUx0vrnCLAwyVXX8R6lxrF C8JmbE9YwBIb0dagDRIeNSA8tfgTGfnf4k1cMwNM+uK4jbBklA1nS7y2i3r2JyGt YPK5caZreQSu/yzzHV1vDiicY9BqWGYKFF2OjpRn7boaeZE7yu6sKPsJLIqsc8y0 c7fjTiyq41gb24/OqVqeTD7anfR9K9Z6JjJRPoJnnJBScGF1KHrGWau92XDOQXy1 Xq2vTP9d0F5fpGWUYct06lLwDIYzW8TyY/pyqLu1ZKtq+iqBHWjPPL32lEUohJJR xzteDtAPBtgK2zmL+T0i3qJDTxvihaHJkGYwfK+vwKRlDBPOjK9Hlrhr7KJkYJ75 EaeGKh8z6IeIGiXnJCGNqCvCNTOXrEzdQZoXLlqjSaIjj+TQlhkhaAQtTffVFX1t vhiXp1Vx4Q4= =ke2l -----END PGP SIGNATURE----- Mon Dec 2 07:40:01 UTC 2024 I: Checking whether the package is not for us Mon Dec 2 07:40:01 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Mon Dec 2 07:40:01 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Mon Dec 2 07:40:24 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 1 19:40:03 -12 2024 I: pbuilder-time-stamp: 1733125203 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: using eatmydata during job I: Copying source file I: copying [kraken_1.1.1-4.dsc] I: copying [./kraken_1.1.1.orig.tar.gz] I: copying [./kraken_1.1.1-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 5 09:07:57 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 ./kraken_1.1.1-4.dsc: no acceptable signature found dpkg-source: info: extracting kraken in kraken-1.1.1 dpkg-source: info: unpacking kraken_1.1.1.orig.tar.gz dpkg-source: info: unpacking kraken_1.1.1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_jellyfish1.patch dpkg-source: info: applying kraken_tmp_dir.patch dpkg-source: info: applying fix_reading_fasta.patch dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/24194/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=11 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='895d7f8ab1354a1cb1391ecddd7db9cb' 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='24194' 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.wdzRi6F2/pbuilderrc_GDsF --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.wdzRi6F2/b1 --logfile b1/build.log kraken_1.1.1-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Mar 29 2024 bash -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 38404 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 38404 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 17892 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 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Oct 18 00:56 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 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Oct 18 00:56 findmnt -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 218680 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 100952 Apr 9 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 22 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Oct 18 00:56 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Oct 18 00:56 more -rwsr-xr-x 1 root root 58912 Oct 18 00:56 mount -rwxr-xr-x 1 root root 13856 Oct 18 00:56 mountpoint -rwxr-xr-x 1 root root 157932 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 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Mar 29 2024 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Oct 18 00:56 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Jan 19 2024 tar -rwxr-xr-x 1 root root 13860 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Oct 18 00:56 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Oct 18 00:56 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/24194/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), jellyfish1 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19554 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 jellyfish1; however: Package jellyfish1 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-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} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.0 MB of archives. After unpacking 72.7 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: jellyfish1 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-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} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.0 MB of archives. After unpacking 72.7 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/24194 and its subdirectories Mon Dec 2 07:40:25 UTC 2024 W: No second build log, what happened? Mon Dec 2 07:40:25 UTC 2024 W: Downloading the build dependencies failed Mon Dec 2 07:40:25 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Mon Dec 2 07:40:25 UTC 2024 W: Network problems are automatically rescheduled after some hours.