Sun Jun 2 15:51:05 UTC 2024 I: starting to build skesa/bookworm/armhf on jenkins on '2024-06-02 15:50' Sun Jun 2 15:51:05 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_11/4230/console.log Sun Jun 2 15:51:05 UTC 2024 I: Downloading source for bookworm/skesa=2.4.0-6 --2024-06-02 15:51:05-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/skesa/skesa_2.4.0-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2099 (2.0K) [text/prs.lines.tag] Saving to: ‘skesa_2.4.0-6.dsc’ 0K .. 100% 246M=0s 2024-06-02 15:51:05 (246 MB/s) - ‘skesa_2.4.0-6.dsc’ saved [2099/2099] Sun Jun 2 15:51:05 UTC 2024 I: skesa_2.4.0-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: skesa Binary: skesa Architecture: any Version: 2.4.0-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Aaron M. Ucko Homepage: https://github.com/ncbi/SKESA Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/skesa Vcs-Git: https://salsa.debian.org/med-team/skesa.git Build-Depends: debhelper-compat (= 13), libboost-dev, libboost-chrono-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-regex-dev, libboost-system-dev, libboost-timer-dev, libncbi-vdb-dev (>= 3), libngs-c++-dev Package-List: skesa deb science optional arch=any Checksums-Sha1: 5f77c432dbc512571a176f3f77fcc1c1cb691b30 138729 skesa_2.4.0.orig.tar.gz d0de656004183a22dbcc4902d7405e3e91016b49 16224 skesa_2.4.0-6.debian.tar.xz Checksums-Sha256: c07b56dfa394c013e519d5a246b7dee03db41d8ac912ab9ca02cf4d20bf13b15 138729 skesa_2.4.0.orig.tar.gz b3a4bd0102dda32f80096da3477a911dff1c680ee1f87610c7dd8e17f88ea3df 16224 skesa_2.4.0-6.debian.tar.xz Files: 0846b4a906285d34e7e45d08b37ba18f 138729 skesa_2.4.0.orig.tar.gz d199516007e792983d6d7a5f0d06805a 16224 skesa_2.4.0-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmPNgfQACgkQHnCRsfFK ZKJ1qw//bPq+nkuQlmlUEj4U88SuWEyH42Befykckye7yXpFyigku1Bg78rViOi1 tyUA9ONjvdtPj60Kz/Z6b7FewFrvtpAWP4WbAkmp/IiVil8YsPGKgrs2NleqUgmJ SYcdTR14UhTEZ5cNuMvkecMfFoDMLvs2WkWUSkjKIm3wVLb4PnYqKLCjzC9qv58R vVqV38+/8gHRvLlQfBnwBg5mPXI/tzUrOb4pj2Kxib+/aeM/DFWBk2oYKjBJ82VZ bkFzd2mx70c6e7XrhmScWjCq08/TexJXzKYvlSwLpi3v7cDMDMSIaukTS7huVDWB meD2X7Z6K4qMzR12tBgdVQGpvV/G74J1czMFPw3WUumvRIlxn1nmCXunAJPS+Eoj z9+O7FNBKqZ/RWeSkhVNxs6i0KHeu1X7OnGwDxvDyZDwjMymkOjvmox/lzBn0UW5 4dOVsvHh52Bh68LxM3oj+H+7CigimCzY4xFI5tOSmFHoboYPhwrgkn+sYe7qwnlQ L0EhoTFp8o9WR5ZR+P4UNYuP5l0eVokacgto/pgSdld4LHj3Oqtqc4BiEHq5YwFK xk6AriE/Ah6V+y5eF+EAU0jfdBVySVYqcZggkR9ur2tXd7ZzIiZzONrUA6ekrORL z7DzMN1mudMoh/+jrAkSHTFwYL2PNmbFepf0ryQ0T5OVd1asT4c= =u/Xz -----END PGP SIGNATURE----- Sun Jun 2 15:51:05 UTC 2024 I: Checking whether the package is not for us Sun Jun 2 15:51:05 UTC 2024 I: Starting 1st build on remote node wbq0-armhf-rb.debian.net. Sun Jun 2 15:51:05 UTC 2024 I: Preparing to do remote build '1' on wbq0-armhf-rb.debian.net. Sun Jun 2 15:53:22 UTC 2024 I: Deleting $TMPDIR on wbq0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 2 03:51:18 -12 2024 I: pbuilder-time-stamp: 1717343478 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 [skesa_2.4.0-6.dsc] I: copying [./skesa_2.4.0.orig.tar.gz] I: copying [./skesa_2.4.0-6.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 22 06:35:32 2023 -12 gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./skesa_2.4.0-6.dsc: no acceptable signature found dpkg-source: info: extracting skesa in skesa-2.4.0 dpkg-source: info: unpacking skesa_2.4.0.orig.tar.gz dpkg-source: info: unpacking skesa_2.4.0-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_ngs-sdk.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying link_boost_dynamically.patch dpkg-source: info: applying no_sse4.2.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25907/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='d4743c50b90441a8bc2460a0d4769412' 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='25907' 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.51bZ4lv5/pbuilderrc_Af46 --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.51bZ4lv5/b1 --logfile b1/build.log skesa_2.4.0-6.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 wbq0 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/25907/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), libboost-dev, libboost-chrono-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-regex-dev, libboost-system-dev, libboost-timer-dev, libncbi-vdb-dev (>= 3), libngs-c++-dev 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 libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-chrono-dev; however: Package libboost-chrono-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-timer-dev; however: Package libboost-timer-dev is not installed. pbuilder-satisfydepends-dummy depends on libncbi-vdb-dev (>= 3); however: Package libncbi-vdb-dev is not installed. pbuilder-satisfydepends-dummy depends on libngs-c++-dev; however: Package libngs-c++-dev 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} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-chrono-dev{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-timer-dev{a} libboost-timer1.74-dev{a} libboost-timer1.74.0{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu-dev{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, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 41.1 MB of archives. After unpacking 283 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libncbi-vdb-dev (>= 3) which is a virtual package and is not provided by any available package Depends: libngs-c++-dev 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} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-chrono-dev{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-timer-dev{a} libboost-timer1.74-dev{a} libboost-timer1.74.0{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu-dev{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, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 41.1 MB of archives. After unpacking 283 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/25907 and its subdirectories Sun Jun 2 15:53:25 UTC 2024 W: No second build log, what happened? Sun Jun 2 15:53:25 UTC 2024 W: Downloading the build dependencies failed Sun Jun 2 15:53:25 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Sun Jun 2 15:53:25 UTC 2024 W: Network problems are automatically rescheduled after some hours.