Thu May 16 00:39:12 UTC 2024 I: starting to build minimac4/trixie/arm64 on jenkins on '2024-05-16 00:39' Thu May 16 00:39:12 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_24/35892/console.log Thu May 16 00:39:12 UTC 2024 I: Downloading source for trixie/minimac4=4.1.6-1 --2024-05-16 00:39:12-- http://deb.debian.org/debian/pool/main/m/minimac4/minimac4_4.1.6-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2288 (2.2K) [text/prs.lines.tag] Saving to: ‘minimac4_4.1.6-1.dsc’ 0K .. 100% 359M=0s 2024-05-16 00:39:12 (359 MB/s) - ‘minimac4_4.1.6-1.dsc’ saved [2288/2288] Thu May 16 00:39:12 UTC 2024 I: minimac4_4.1.6-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: minimac4 Binary: minimac4 Architecture: any Version: 4.1.6-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi , Étienne Mollier Homepage: https://genome.sph.umich.edu/wiki/Minimac4 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/minimac4 Vcs-Git: https://salsa.debian.org/med-team/minimac4.git Testsuite: autopkgtest Testsuite-Triggers: bcftools Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libstatgen-dev, libshrinkwrap-dev, libsavvy-dev, libomp-jonathonl-dev, liblzma-dev, libzstd-dev, bcftools Package-List: minimac4 deb science optional arch=any Checksums-Sha1: 190a527edb4cf800a0c3b6ed2cc732442c10ef72 53460 minimac4_4.1.6.orig.tar.gz 8104bc421b8d4b717ca4608f39775675dda37d23 5368 minimac4_4.1.6-1.debian.tar.xz Checksums-Sha256: 0bce8d6edbf5d5d944b19c4e36403d0bc1d18f2d6003d88e01086488c3eb9333 53460 minimac4_4.1.6.orig.tar.gz 994819c4e4ff50247f6f7420ed438e7cd802baaa445beecf3f581ef8ef346b2c 5368 minimac4_4.1.6-1.debian.tar.xz Files: e7c0cfe90add2248fc79824add76253a 53460 minimac4_4.1.6.orig.tar.gz 86de610bf26bb05bae065ea9149df3d1 5368 minimac4_4.1.6-1.debian.tar.xz Dgit: f06073708f98230727f744ec1f0ae2b7a82b38c1 debian archive/debian/4.1.6-1 https://git.dgit.debian.org/minimac4 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmVzCnkUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoxww//VN8VG/iYLukZlL/mut4jDnSvmKn7 HZGN2OojXPMtzVlI7yCROdWICQXaNkzntWKNoP6fc5c6X15lrANtWNziLVHw3fKa RVnN8Z9uEL6QHVHPh+zfXa6sje4nrMiU7Fr5biaXCyeUS0ht30nX/M3L695CQF7b SppP3j4AX0gPpFaj8k/6onJZPbGaNIDj/sTgl67DLsE8k6ht9GJtvyuJs3IGbLg5 ZndqE3I1UQdSzwHs7SXia+kimXN848bUEBfoNi/FBBEpAX11eAEoX75ShKuLcjTW v6mXVQBoUZ99C6oOlqSHLTmPoOD/CuDab8YfIM4OIf7dpcjSdXEL/xQ5TGjnoMGn ncSsDMNqL+fNjWrYN/8LN5YTewK6g5qwxEtpAARdTu6NYfzWW9p2LT6Th+VNvk+o hY8SeYQGNqeOKjcRRD2V1RpRmc5mrq2eAcQ6gIYs0zypq4fozM1rqmcIIKYecago wFtcjn0VEGrPC6PhYjXAAS3DOeBWlRT2luw5mM6uu4zBSyTkpu4EdT4kTemUqO8+ f8mFIZ6fPER9n9Rer50I3IFSVkxn1mb2kHv76jJ1FiOHI7Q9WDEo5h2oiSdSjrZ/ iLAjZHB/Buu9O3cwlnVC6Xz6JxZtmhdp14kaLPkfF1c2Qo+T7MLMNd9uayUJM9b2 qrkjd+gngOl7TF8= =Hdso -----END PGP SIGNATURE----- Thu May 16 00:39:12 UTC 2024 I: Checking whether the package is not for us Thu May 16 00:39:12 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Thu May 16 00:39:12 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu May 16 00:39:36 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 15 12:39:14 -12 2024 I: pbuilder-time-stamp: 1715819954 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [minimac4_4.1.6-1.dsc] I: copying [./minimac4_4.1.6.orig.tar.gz] I: copying [./minimac4_4.1.6-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 8 12:22:17 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./minimac4_4.1.6-1.dsc: no acceptable signature found dpkg-source: info: extracting minimac4 in minimac4-4.1.6 dpkg-source: info: unpacking minimac4_4.1.6.orig.tar.gz dpkg-source: info: unpacking minimac4_4.1.6-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Use_shared_zlib.patch dpkg-source: info: applying lzma.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2825995/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='015efa1045d14c88913ff464f069c5cd' 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='2825995' 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.pf2k7p8D/pbuilderrc_QP19 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pf2k7p8D/b1 --logfile b1/build.log minimac4_4.1.6-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 14 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2825995/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: arm64 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), cmake, zlib1g-dev, libstatgen-dev, libshrinkwrap-dev, libsavvy-dev, libomp-jonathonl-dev, liblzma-dev, libzstd-dev, bcftools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19744 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libstatgen-dev; however: Package libstatgen-dev is not installed. pbuilder-satisfydepends-dummy depends on libshrinkwrap-dev; however: Package libshrinkwrap-dev is not installed. pbuilder-satisfydepends-dummy depends on libsavvy-dev; however: Package libsavvy-dev is not installed. pbuilder-satisfydepends-dummy depends on libomp-jonathonl-dev; however: Package libomp-jonathonl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools 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} bcftools{a} blt{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libomp-jonathonl-dev{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsavvy-dev{a} libsharpyuv0{a} libshrinkwrap-dev{a} libssh2-1t64{a} libsub-override-perl{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-appdirs{a} python3-argcomplete{a} python3-argh{a} python3-attr{a} python3-biopython{a} python3-brotli{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-gffutils{a} python3-importlib-metadata{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pyfaidx{a} python3-pyparsing{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-simplejson{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-unicodedata2{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bs4 python3-cssselect python3-html5lib python3-olefile python3-pybedtools shared-mime-info wget xdg-user-dirs 0 packages upgraded, 177 newly installed, 0 to remove and 0 not upgraded. Need to get 126 MB of archives. After unpacking 535 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libstatgen-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} bcftools{a} blt{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libomp-jonathonl-dev{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsavvy-dev{a} libsharpyuv0{a} libshrinkwrap-dev{a} libssh2-1t64{a} libsub-override-perl{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-appdirs{a} python3-argcomplete{a} python3-argh{a} python3-attr{a} python3-biopython{a} python3-brotli{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-gffutils{a} python3-importlib-metadata{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pyfaidx{a} python3-pyparsing{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-simplejson{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-unicodedata2{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bs4 python3-cssselect python3-html5lib python3-olefile python3-pybedtools shared-mime-info wget xdg-user-dirs 0 packages upgraded, 177 newly installed, 0 to remove and 0 not upgraded. Need to get 126 MB of archives. After unpacking 535 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/2825995 and its subdirectories Thu May 16 00:39:38 UTC 2024 W: No second build log, what happened? Thu May 16 00:39:38 UTC 2024 W: Downloading the build dependencies failed Thu May 16 00:39:38 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Thu May 16 00:39:38 UTC 2024 W: Network problems are automatically rescheduled after some hours.