Sat Dec 14 08:43:02 UTC 2024 I: starting to build proteinortho/bookworm/armhf on jenkins on '2024-12-14 08:42' Sat Dec 14 08:43:02 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_18/9189/console.log Sat Dec 14 08:43:02 UTC 2024 I: Downloading source for bookworm/proteinortho=6.1.7+dfsg-1 --2024-12-14 08:43:03-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/proteinortho/proteinortho_6.1.7%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2161 (2.1K) [text/prs.lines.tag] Saving to: ‘proteinortho_6.1.7+dfsg-1.dsc’ 0K .. 100% 294M=0s 2024-12-14 08:43:03 (294 MB/s) - ‘proteinortho_6.1.7+dfsg-1.dsc’ saved [2161/2161] Sat Dec 14 08:43:03 UTC 2024 I: proteinortho_6.1.7+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: proteinortho Binary: proteinortho Architecture: any Version: 6.1.7+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://gitlab.com/paulklemm_PHD/proteinortho Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/proteinortho Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper Package-List: proteinortho deb science optional arch=any Checksums-Sha1: 29811b2acf3417951bb5d028320c29aa3412425f 361184 proteinortho_6.1.7+dfsg.orig.tar.xz 55358cf9e5a4c831b806e57840d50f495242603b 7532 proteinortho_6.1.7+dfsg-1.debian.tar.xz Checksums-Sha256: 14edfb3dd8dff76bc2f6ce544c8885a0babf59f63a5098e3e35d25e62b88b392 361184 proteinortho_6.1.7+dfsg.orig.tar.xz bef72174cd12b03b3961f1fbf33e4b4fd99f774a1189deeaf5588f9726604435 7532 proteinortho_6.1.7+dfsg-1.debian.tar.xz Files: 6c9a51302f1b8d4d6f7d77176af5e918 361184 proteinortho_6.1.7+dfsg.orig.tar.xz 2963ebab45b9cb2ac2e1fe392483d653 7532 proteinortho_6.1.7+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPGvpcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEMjw//aZZhe2STeHHAs+p1Vtuvv8vz76NVPzmm CxiW8Aq6Plj3CP3rgvFomgngVVdrHxBtqUoXN2pMBsw3jzlYd9MqqJ0NXwZT3M2G 57xVuFt+cHRlPt+MJhCma73qFqlyyD3zeNkAsGD0mMR443HOJtvufH39OgLgbAMm XrI01mWP24Usgxc8jNfoHEOEw1xZ2hEYkehqe9hqa1SrBHRKLS/77XB/1KGe9N/U cQYWWWGzvC72pvV+B3BlPxFpwT1HDyV6qS6dTqrg6DpTpEG7T4qSoTk8hB49+z3A AosdVgJs+PxJ4DknkfeqIqBLPgEuEDDlu1E7uT9E3fWHKvPULbs5CRnM3rbNXw20 5utaWgo/fYe7/Q4RVgc77x+P8Wn/EaSEGsRlD0SX3nSpmj0uaYBp3mW9GsVQEltp /PFgfYVOHU8VOG8wCmCxlujmhZrWCquhUWTg1Ykk9CKgPOj320wIMA2vH7/K1fwR 0HRTJBpz48j2TVAhNzrpU0jwhLHdKh5O7vmM5QJxKo9m2eJTB6I7TIdm6f5x7CZI hI3m5BAcTJlKqR9PuB62xEB/yDUQQ2osxZfMwdYmWG5E2CmS7qm0Pizh9o5aRvL4 wxqsxz7Dwyy6expO8WsBuoBTPBhShixYKmWJ8z7z0FCIQwVBKhTOytENes7jv++G mw/hxsJzgLE= =MJIM -----END PGP SIGNATURE----- Sat Dec 14 08:43:03 UTC 2024 I: Checking whether the package is not for us Sat Dec 14 08:43:03 UTC 2024 I: Starting 1st build on remote node ff64a-armhf-rb.debian.net. Sat Dec 14 08:43:03 UTC 2024 I: Preparing to do remote build '1' on ff64a-armhf-rb.debian.net. Sat Dec 14 08:44:21 UTC 2024 I: Deleting $TMPDIR on ff64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 13 20:43:11 -12 2024 I: pbuilder-time-stamp: 1734165791 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 [proteinortho_6.1.7+dfsg-1.dsc] I: copying [./proteinortho_6.1.7+dfsg.orig.tar.xz] I: copying [./proteinortho_6.1.7+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jan 17 03:28:23 2023 -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 ./proteinortho_6.1.7+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting proteinortho in proteinortho-6.1.7+dfsg dpkg-source: info: unpacking proteinortho_6.1.7+dfsg.orig.tar.xz dpkg-source: info: unpacking proteinortho_6.1.7+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying deb_diamond dpkg-source: info: applying ignore-warnings.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5630/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=5 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='31b90502730b463aa4d934cd130571d0' 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='5630' 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.PUONndYE/pbuilderrc_Nx07 --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.PUONndYE/b1 --logfile b1/build.log proteinortho_6.1.7+dfsg-1.dsc' SUDO_GID='114' SUDO_UID='109' 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 ff64a 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin total 4964 -rwxr-xr-x 1 root root 838488 Mar 29 2024 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 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 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 Oct 18 00:56 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 Oct 18 00:56 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 Oct 18 00:56 more -rwsr-xr-x 1 root root 38496 Oct 18 00:56 mount -rwxr-xr-x 1 root root 9824 Oct 18 00:56 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 Mar 29 2024 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 Oct 18 00:56 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Jan 19 2024 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 Oct 18 00:56 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 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/5630/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), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19279 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 ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev | libatlas-base-dev | liblapack.so; however: Package liblapack-dev is not installed. Package libatlas-base-dev is not installed. Package liblapack.so is not installed. pbuilder-satisfydepends-dummy depends on diamond-aligner (>= 2.0.10~); however: Package diamond-aligner is not installed. pbuilder-satisfydepends-dummy depends on procps; however: Package procps is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack-dev{a} liblapack3{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libpcre3{a} libpipeline1{a} libproc2-0{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} ncbi-blast+{a} ncbi-data{a} po-debconf{a} procps{a} python3{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 psmisc wget 0 packages upgraded, 55 newly installed, 0 to remove and 0 not upgraded. Need to get 42.6 MB of archives. After unpacking 172 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: diamond-aligner (>= 2.0.10~) 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} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack-dev{a} liblapack3{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libpcre3{a} libpipeline1{a} libproc2-0{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} ncbi-blast+{a} ncbi-data{a} po-debconf{a} procps{a} python3{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 psmisc wget 0 packages upgraded, 55 newly installed, 0 to remove and 0 not upgraded. Need to get 42.6 MB of archives. After unpacking 172 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/5630 and its subdirectories Sat Dec 14 08:44:24 UTC 2024 W: No second build log, what happened? Sat Dec 14 08:44:24 UTC 2024 W: Downloading the build dependencies failed Sat Dec 14 08:44:24 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Sat Dec 14 08:44:24 UTC 2024 W: Network problems are automatically rescheduled after some hours.