I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 4 08:25:27 -12 2024 I: pbuilder-time-stamp: 1720124727 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: using eatmydata during job I: Copying source file I: copying [plasmidid_1.6.5+dfsg-2.dsc] I: copying [./plasmidid_1.6.5+dfsg.orig.tar.xz] I: copying [./plasmidid_1.6.5+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 24 16:34:28 2022 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 ./plasmidid_1.6.5+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting plasmidid in plasmidid-1.6.5+dfsg dpkg-source: info: unpacking plasmidid_1.6.5+dfsg.orig.tar.xz dpkg-source: info: unpacking plasmidid_1.6.5+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fixTests.patch dpkg-source: info: applying AdjustPythonPath.patch dpkg-source: info: applying spelling.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/13124/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='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='24e64abb71484f4da995a48a7b1e7f24' 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='13124' 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.0ozSnr2f/pbuilderrc_YIKr --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.0ozSnr2f/b1 --logfile b1/build.log plasmidid_1.6.5+dfsg-2.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 6.1.0-22-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.94-1 (2024-06-21) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 22:35 /bin -> usr/bin I: user script /srv/workspace/pbuilder/13124/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), dh-python, python3-all, help2man, ncbi-blast+, bedtools, bowtie2, samtools, prokka, cd-hit, mash, circos dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19672 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on prokka; however: Package prokka is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on mash; however: Package mash is not installed. pbuilder-satisfydepends-dummy depends on circos; however: Package circos 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: adwaita-icon-theme{a} aragorn{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} cd-hit{a} circos{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-circos-symbols{a} fonts-cmu{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} help2man{a} hicolor-icon-theme{a} hmmer{a} infernal{a} intltool-debian{a} java-common{a} less{a} libabsl20230802{a} libaom3{a} libarchive-zip-perl{a} libasound2-data{a} libasound2t64{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libbio-searchio-hmmer-perl{a} libbrotli1{a} libcairo2{a} libcarp-always-perl{a} libclone-perl{a} libcom-err2{a} libconfig-general-perl{a} libcups2t64{a} libcurl3t64-gnutls{a} libdata-dumper-simple-perl{a} libdata-stag-perl{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdivsufsort3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-basedir-perl{a} libfile-stripnondeterminism-perl{a} libfont-ttf-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd-perl{a} libgd3{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgetopt-simple-perl{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphics-colornames-perl{a} libgraphics-colorobject-perl{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libio-all-perl{a} libio-string-perl{a} libipc-system-simple-perl{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblist-allutils-perl{a} liblist-someutils-perl{a} liblist-utilsby-perl{a} libllvm17t64{a} liblmdb0{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libmath-bezier-perl{a} libmath-round-perl{a} libmath-vec-perl{a} libmath-vecstat-perl{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmodule-implementation-perl{a} libmodule-runtime-perl{a} libncbi6t64{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libnumber-format-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libparams-validate-perl{a} libpciaccess0{a} libpcsclite1{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} libpython3.12-minimal{a} libpython3.12-stdlib{a} librav1e0{a} libreadline8t64{a} libreadonly-perl{a} libregexp-common-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libset-intspan-perl{a} libsharpyuv0{a} libspiffy-perl{a} libssh2-1t64{a} libstatistics-basic-perl{a} libsvg-perl{a} libswiss-perl{a} libtext-format-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libvulkan1{a} libwebp7{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml2{a} libxpm4{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libyuv0{a} libz3-4{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} ncbi-tools-bin{a} netbase{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} parallel{a} po-debconf{a} procps{a} prodigal{a} prokka{a} python3{a} python3-all{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} shared-mime-info{a} sysstat{a} tzdata{a} ucf{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf bcron bioperl-run circos-tools cron cronie curl dbus fonts-dejavu-extra krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libatk-wrapper-java-jni libbio-asn1-entrezgene-perl libbio-perl-run-perl libcgi-pm-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgail-common libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libgtk2.0-bin libheif-plugin-aomenc libheif-plugin-x265 libhtml-parser-perl libhtml-tableextract-perl libldap-common liblist-moreutils-perl liblist-someutils-xs-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpod-coverage-perl libpostscript-perl librsvg2-common libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libtest-pod-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-expat-perl libxml-sax-writer-perl libxml-twig-perl libxml-writer-perl lynx mesa-vulkan-drivers perl-tk psmisc publicsuffix systemd systemd-cron wget xdg-user-dirs 0 packages upgraded, 259 newly installed, 0 to remove and 0 not upgraded. Need to get 230 MB of archives. After unpacking 1029 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: bowtie2 which is a virtual package and is not provided by any available package Depends: mash 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: adwaita-icon-theme{a} aragorn{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} cd-hit{a} circos{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-circos-symbols{a} fonts-cmu{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} help2man{a} hicolor-icon-theme{a} hmmer{a} infernal{a} intltool-debian{a} java-common{a} less{a} libabsl20230802{a} libaom3{a} libarchive-zip-perl{a} libasound2-data{a} libasound2t64{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libbio-searchio-hmmer-perl{a} libbrotli1{a} libcairo2{a} libcarp-always-perl{a} libclone-perl{a} libcom-err2{a} libconfig-general-perl{a} libcups2t64{a} libcurl3t64-gnutls{a} libdata-dumper-simple-perl{a} libdata-stag-perl{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdivsufsort3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-basedir-perl{a} libfile-stripnondeterminism-perl{a} libfont-ttf-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd-perl{a} libgd3{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgetopt-simple-perl{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphics-colornames-perl{a} libgraphics-colorobject-perl{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libio-all-perl{a} libio-string-perl{a} libipc-system-simple-perl{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblist-allutils-perl{a} liblist-someutils-perl{a} liblist-utilsby-perl{a} libllvm17t64{a} liblmdb0{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libmath-bezier-perl{a} libmath-round-perl{a} libmath-vec-perl{a} libmath-vecstat-perl{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmodule-implementation-perl{a} libmodule-runtime-perl{a} libncbi6t64{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libnumber-format-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libparams-validate-perl{a} libpciaccess0{a} libpcsclite1{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} libpython3.12-minimal{a} libpython3.12-stdlib{a} librav1e0{a} libreadline8t64{a} libreadonly-perl{a} libregexp-common-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libset-intspan-perl{a} libsharpyuv0{a} libspiffy-perl{a} libssh2-1t64{a} libstatistics-basic-perl{a} libsvg-perl{a} libswiss-perl{a} libtext-format-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libvulkan1{a} libwebp7{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml2{a} libxpm4{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libyuv0{a} libz3-4{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} ncbi-tools-bin{a} netbase{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} parallel{a} po-debconf{a} procps{a} prodigal{a} prokka{a} python3{a} python3-all{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} shared-mime-info{a} sysstat{a} tzdata{a} ucf{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf bcron bioperl-run circos-tools cron cronie curl dbus fonts-dejavu-extra krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libatk-wrapper-java-jni libbio-asn1-entrezgene-perl libbio-perl-run-perl libcgi-pm-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgail-common libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libgtk2.0-bin libheif-plugin-aomenc libheif-plugin-x265 libhtml-parser-perl libhtml-tableextract-perl libldap-common liblist-moreutils-perl liblist-someutils-xs-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpod-coverage-perl libpostscript-perl librsvg2-common libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libtest-pod-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-expat-perl libxml-sax-writer-perl libxml-twig-perl libxml-writer-perl lynx mesa-vulkan-drivers perl-tk psmisc publicsuffix systemd systemd-cron wget xdg-user-dirs 0 packages upgraded, 259 newly installed, 0 to remove and 0 not upgraded. Need to get 230 MB of archives. After unpacking 1029 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/13124 and its subdirectories