Sun May 19 00:45:53 UTC 2024 I: starting to build psortb/unstable/armhf on jenkins on '2024-05-19 00:45' Sun May 19 00:45:53 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_16/5996/console.log Sun May 19 00:45:53 UTC 2024 I: Downloading source for unstable/psortb=3.0.6+dfsg-3 --2024-05-19 00:45:54-- http://deb.debian.org/debian/pool/main/p/psortb/psortb_3.0.6%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2217 (2.2K) [text/prs.lines.tag] Saving to: ‘psortb_3.0.6+dfsg-3.dsc’ 0K .. 100% 247M=0s 2024-05-19 00:45:54 (247 MB/s) - ‘psortb_3.0.6+dfsg-3.dsc’ saved [2217/2217] Sun May 19 00:45:54 UTC 2024 I: psortb_3.0.6+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: psortb Binary: psortb Architecture: any Version: 3.0.6+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://www.psort.org/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/psortb Vcs-Git: https://salsa.debian.org/med-team/psortb.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkg-config, pftools Package-List: psortb deb science optional arch=any Checksums-Sha1: c47d0ec328df75f2151dd6d5b5840768006519f8 17036876 psortb_3.0.6+dfsg.orig.tar.xz 3ff44e2646ae0b528bd81be76dee033d507bd6b2 6976 psortb_3.0.6+dfsg-3.debian.tar.xz Checksums-Sha256: ed32aa0240bb03daed228b32614a53c146afba6ca66fd087702315d75e23f751 17036876 psortb_3.0.6+dfsg.orig.tar.xz f844813967c3b4bab7d979cf10a21c23428f28f6484859c0def1c7cc40fcc896 6976 psortb_3.0.6+dfsg-3.debian.tar.xz Files: c4feab06d3031fecac1ab90258550209 17036876 psortb_3.0.6+dfsg.orig.tar.xz 9594c13a92511a5179fa3159c56c810a 6976 psortb_3.0.6+dfsg-3.debian.tar.xz Dgit: a9febf79c415bb81a3b745d1eb0c1b28da1388a4 debian archive/debian/3.0.6+dfsg-3 https://git.dgit.debian.org/psortb -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmJltKYUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpZ1Q/+IGmwP0xHYMzw9TvQh1T1uuH0IqRw ObT48OsOzM7KKvog1sTFfzHABnD9dAZJfGFqWPovbbnDRIbG6iFNa6oOkRGBz5WZ NQLCJr/6rntAVabHlQ/HRJLOs2ze6v47KklLqp7m8SKkPdJzvJAh7Fjyk8bSk/cA IoZ9KPVNTzd57dhbGyHJYW0ZJJaKQClEfjTw+PguZ5kkyHTFYsnyiIYlKae/gBvi iR8EY6EcNL/cGOMDIFnK62+rDBf2J6M2/AA7He5kwCU25B1Nold1WGVxbiF9IffL dhwI18S+joKITcYqxI5ObDiKEDM5nhLOsNcWtb6567C0+tMOWxCJO+10RrdQiBFL 6/dgVXsBEQNEupveBZ96JeudpCqxQFE4GlDevJe96MPr/my/O4ZDD+JlVkdy/E3x epZxyN6tFDNdvHZFALm5LgiWmZFuUCpZ407bFKFpo9lrT3UvyNkGkXE4TrCCMlN8 v0+hCSMK674glsDptVtqHEhaJog3mKJzksPWGko7QdXV5LL0hTG2D8/cKADq/Fpu JK+pmT5Pom2C30g/0pg3RCOSCnQyZwknxo2QVhaGv4NRc2NX76dsZDfJYLT5oq7r vd20fhIw3RpQ3YnezRqk8RfyZ05r2Poi1KgJmtVGq/oEVpfLzxRdXQdUXEDWXefx BkuCPbjiYl+kylg= =OSkL -----END PGP SIGNATURE----- Sun May 19 00:45:54 UTC 2024 I: Checking whether the package is not for us Sun May 19 00:45:54 UTC 2024 I: Starting 1st build on remote node virt32b-armhf-rb.debian.net. Sun May 19 00:45:54 UTC 2024 I: Preparing to do remote build '1' on virt32b-armhf-rb.debian.net. Sun May 19 00:46:56 UTC 2024 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 18 12:46:04 -12 2024 I: pbuilder-time-stamp: 1716079564 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 [psortb_3.0.6+dfsg-3.dsc] I: copying [./psortb_3.0.6+dfsg.orig.tar.xz] I: copying [./psortb_3.0.6+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Apr 24 20:35:50 2022 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 ./psortb_3.0.6+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting psortb in psortb-3.0.6+dfsg dpkg-source: info: unpacking psortb_3.0.6+dfsg.orig.tar.xz dpkg-source: info: unpacking psortb_3.0.6+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying biosquid_includes.patch dpkg-source: info: applying fix_hmmer_interface.patch dpkg-source: info: applying fix_build_Algorithm-SVM.patch dpkg-source: info: applying remove-bundled-party-libsvm.patch dpkg-source: info: applying path_to_conf.patch dpkg-source: info: applying fix_module_path.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/20982/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='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='2364061ff0e14bdfb7bc988658efe6aa' 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='20982' 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.QH3HdwxT/pbuilderrc_8H1h --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.QH3HdwxT/b1 --logfile b1/build.log psortb_3.0.6+dfsg-3.dsc' SUDO_GID='112' SUDO_UID='106' 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 virt32b 6.1.0-21-armmp-lpae #1 SMP Debian 6.1.90-1 (2024-05-03) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 17 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/20982/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), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkg-config, pftools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19463 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 libsvm-dev; however: Package libsvm-dev is not installed. pbuilder-satisfydepends-dummy depends on bioperl; however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+-legacy; however: Package ncbi-blast+-legacy is not installed. pbuilder-satisfydepends-dummy depends on libsquid-dev; however: Package libsquid-dev is not installed. pbuilder-satisfydepends-dummy depends on libhmmer2-dev; however: Package libhmmer2-dev is not installed. pbuilder-satisfydepends-dummy depends on libsvmloc-dev; however: Package libsvmloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libmodhmm-dev; however: Package libmodhmm-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on pftools; however: Package pftools 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} bioperl{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} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbio-perl-perl{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libdata-optlist-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmodhmm-dev{a} libmodhmm0{a} libparams-util-perl{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsquid-dev{a} libsquid1t64{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libsub-uplevel-perl{a} libsvm-dev{a} libsvm3{a} libsvmloc-dev{a} libsvmloc0{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run ca-certificates curl libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libhttp-message-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk wget 0 packages upgraded, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 43.1 MB of archives. After unpacking 166 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: pftools 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} bioperl{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} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbio-perl-perl{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libdata-optlist-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmodhmm-dev{a} libmodhmm0{a} libparams-util-perl{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsquid-dev{a} libsquid1t64{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libsub-uplevel-perl{a} libsvm-dev{a} libsvm3{a} libsvmloc-dev{a} libsvmloc0{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run ca-certificates curl libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libhttp-message-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk wget 0 packages upgraded, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 43.1 MB of archives. After unpacking 166 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/20982 and its subdirectories Sun May 19 00:46:59 UTC 2024 W: No second build log, what happened? Sun May 19 00:46:59 UTC 2024 W: Downloading the build dependencies failed Sun May 19 00:46:59 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 May 19 00:46:59 UTC 2024 W: Network problems are automatically rescheduled after some hours.