Thu Dec 26 13:26:09 UTC 2024 I: starting to build circlator/unstable/arm64 on jenkins on '2024-12-26 13:25' Thu Dec 26 13:26:09 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_9/54199/console.log Thu Dec 26 13:26:09 UTC 2024 I: Downloading source for unstable/circlator=1.5.6-12 --2024-12-26 13:26:09-- http://deb.debian.org/debian/pool/main/c/circlator/circlator_1.5.6-12.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2302 (2.2K) [text/prs.lines.tag] Saving to: ‘circlator_1.5.6-12.dsc’ 0K .. 100% 281M=0s 2024-12-26 13:26:09 (281 MB/s) - ‘circlator_1.5.6-12.dsc’ saved [2302/2302] Thu Dec 26 13:26:09 UTC 2024 I: circlator_1.5.6-12.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: circlator Binary: circlator Architecture: all Version: 1.5.6-12 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://sanger-pathogens.github.io/circlator/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/circlator Vcs-Git: https://salsa.debian.org/med-team/circlator.git Testsuite: autopkgtest Testsuite-Triggers: python3-all, python3-pytest, spades Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, python3-packaging, python3-openpyxl, python3-jdcal, python3-pysam, python3-pymummer, python3-pytest , fastaq , spades , bwa , prodigal , canu Package-List: circlator deb science optional arch=all Checksums-Sha1: 4b152777c1f475f34867b6014f04efc69d467eb2 5724413 circlator_1.5.6.orig.tar.gz 8c666d8432a682488651f0fc7133df882308ece5 6412 circlator_1.5.6-12.debian.tar.xz Checksums-Sha256: 1c6ea4f3dfd726cf798b7b3a23e1cb02ade0471597c412b119de8be73db804b6 5724413 circlator_1.5.6.orig.tar.gz 2c7f8e3b403602aa47c43d5920e019d40f84d7c348c1f5c5f2688467cef0ed66 6412 circlator_1.5.6-12.debian.tar.xz Files: dbb1ab9bf8d9834fa9106dc99e85d76e 5724413 circlator_1.5.6.orig.tar.gz a80bc843b6b229b8242cb235d7c496fc 6412 circlator_1.5.6-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdSyZwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGq7Q/+KkBrvMURFVPnMPXUkKZRkd1O0cb33jti q+l14mnTt1VpO64BBlontT6ITZ+56xoRbhv7bdKSet6/CyaBIZ1XdbT0LP/98Xjc RHMBdQNm2R5rjKd/g5UwKHGK9UOnEInIv3XTY4D6ZKbPxHFGBZ0A2sZFoHEjbGZT Pizbt7rPpNOXDS9eb9ULGS2LbTlPeeKHEgWB/VXaQctqEafsofxL3w3CN9D6bfoR m+MPjiafNSvus3Wb9BN7uH5/f3yqBeTssRWZ1fHh9wgn0AgDQLHSy98hfgHMUzwj ZCtoOojQvGon368TadAGg7AbSLWCzPgqSAzAz73cUxmGBp+2HxYs/Odp6+8E2Zld M1KccDhUSc+VTfjBvt8fb4d7V+v6tkSs7xrp0rEmpga5Xtor51RTTN5snw21pOb9 vCx0m/uqkHzCXIDYLI3EE6GIZj8nyvuLLVJvzzQroWIDQUllWaDg1qDv7Q7vEEK0 Nh19larSaKc/g01RI0MEzsid3LUO2WZH+EzAX78Ypp0ixWr8RMX8f0i9Ku2cnZs/ rvMdDm0jZovB1kMvUEA4VCGhaiFFpo0O7xA+YppPSdSTySXlt7MCPQ5EW0Btf42K 3DpT1CrTMhy5s0Qons1brGft1dAVt2pFo7LFSPazON6NLx4Smof08eM3v6uFZvQn oT303iX2/CA= =6u37 -----END PGP SIGNATURE----- Thu Dec 26 13:26:09 UTC 2024 I: Checking whether the package is not for us Thu Dec 26 13:26:09 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Thu Dec 26 13:26:09 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Thu Dec 26 13:26:33 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jan 28 07:49:11 -12 2026 I: pbuilder-time-stamp: 1769629751 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [circlator_1.5.6-12.dsc] I: copying [./circlator_1.5.6.orig.tar.gz] I: copying [./circlator_1.5.6-12.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-12.dsc: unsupported subcommand dpkg-source: info: extracting circlator in circlator-1.5.6 dpkg-source: info: unpacking circlator_1.5.6.orig.tar.gz dpkg-source: info: unpacking circlator_1.5.6-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_canu_detection.patch dpkg-source: info: applying switch-to-pytest.patch dpkg-source: info: applying split_canu_tests dpkg-source: info: applying remove-distutils.patch dpkg-source: info: applying python3.12-syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3501837/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='6c87540752b24618b31599919bb2d85b' 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='3501837' 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.2rmTNz94/pbuilderrc_eMrL --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2rmTNz94/b1 --logfile b1/build.log circlator_1.5.6-12.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 codethink03-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3501837/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), dh-sequence-python3, python3-all, python3-setuptools, python3-packaging, python3-openpyxl, python3-jdcal, python3-pysam, python3-pymummer, python3-pytest, fastaq, spades, bwa, prodigal, canu dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19975 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-openpyxl; however: Package python3-openpyxl is not installed. pbuilder-satisfydepends-dummy depends on python3-jdcal; however: Package python3-jdcal is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-pymummer; however: Package python3-pymummer is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on fastaq; however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on spades; however: Package spades is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on prodigal; however: Package prodigal is not installed. pbuilder-satisfydepends-dummy depends on canu; however: Package canu 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: aglfn{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} bwa{a} ca-certificates{a} ca-certificates-java{a} canu{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gawk{a} gettext{a} gettext-base{a} gnuplot-data{a} gnuplot-nox{a} groff-base{a} intltool-debian{a} jaligner{a} jarwrapper{a} java-common{a} libabsl20230802{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libatinject-jsr330-api-java{a} libavif16{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcommons-codec-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-parent-java{a} libcurl3t64-gnutls{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} liberror-prone-java{a} libexpat1{a} libfastutil-java{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfilesys-df-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgcrypt20{a} libgd3{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libguava-java{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libnspr4{a} libnss3{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsigsegv2{a} libsnappy1v5{a} libssh2-1t64{a} libssw-java{a} libsvtav1enc2{a} libtasn1-6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxpm4{a} libxrender1{a} libxslt1.1{a} libyuv0{a} m4{a} man-db{a} media-types{a} mhap{a} mummer{a} netbase{a} openjdk-21-jre-headless{a} openssl{a} po-debconf{a} prodigal{a} python3{a} python3-all{a} python3-autocommand{a} python3-et-xmlfile{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jdcal{a} python3-lxml{a} python3-minimal{a} python3-more-itertools{a} python3-openpyxl{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pymummer{a} python3-pysam{a} python3-pytest{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-liberation groff krb5-locales libarchive-cpio-perl libasound2t64 libcups2t64 libglib2.0-data libgpg-error-l10n libgpm2 libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmail-sendmail-perl liboss4-salsa-asound2 libsasl2-modules lynx publicsuffix python3-bs4 python3-cssselect python3-html5lib python3-pil python3-pygments shared-mime-info wget xdg-user-dirs 0 packages upgraded, 195 newly installed, 0 to remove and 0 not upgraded. Need to get 134 MB of archives. After unpacking 541 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: spades 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: aglfn{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} bwa{a} ca-certificates{a} ca-certificates-java{a} canu{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gawk{a} gettext{a} gettext-base{a} gnuplot-data{a} gnuplot-nox{a} groff-base{a} intltool-debian{a} jaligner{a} jarwrapper{a} java-common{a} libabsl20230802{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libatinject-jsr330-api-java{a} libavif16{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcommons-codec-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-parent-java{a} libcurl3t64-gnutls{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} liberror-prone-java{a} libexpat1{a} libfastutil-java{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfilesys-df-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgcrypt20{a} libgd3{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libguava-java{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libnspr4{a} libnss3{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsigsegv2{a} libsnappy1v5{a} libssh2-1t64{a} libssw-java{a} libsvtav1enc2{a} libtasn1-6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxpm4{a} libxrender1{a} libxslt1.1{a} libyuv0{a} m4{a} man-db{a} media-types{a} mhap{a} mummer{a} netbase{a} openjdk-21-jre-headless{a} openssl{a} po-debconf{a} prodigal{a} python3{a} python3-all{a} python3-autocommand{a} python3-et-xmlfile{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jdcal{a} python3-lxml{a} python3-minimal{a} python3-more-itertools{a} python3-openpyxl{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pymummer{a} python3-pysam{a} python3-pytest{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-liberation groff krb5-locales libarchive-cpio-perl libasound2t64 libcups2t64 libglib2.0-data libgpg-error-l10n libgpm2 libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmail-sendmail-perl liboss4-salsa-asound2 libsasl2-modules lynx publicsuffix python3-bs4 python3-cssselect python3-html5lib python3-pil python3-pygments shared-mime-info wget xdg-user-dirs 0 packages upgraded, 195 newly installed, 0 to remove and 0 not upgraded. Need to get 134 MB of archives. After unpacking 541 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/3501837 and its subdirectories Thu Dec 26 13:26:34 UTC 2024 W: No second build log, what happened? Thu Dec 26 13:26:34 UTC 2024 W: Downloading the build dependencies failed Thu Dec 26 13:26:34 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 Dec 26 13:26:34 UTC 2024 W: Network problems are automatically rescheduled after some hours.