Thu Jun 20 06:29:55 UTC 2024 I: starting to build psortb/trixie/arm64 on jenkins on '2024-06-20 06:29' Thu Jun 20 06:29:55 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/24239/console.log Thu Jun 20 06:29:55 UTC 2024 I: Downloading source for trixie/psortb=3.0.6+dfsg-4 --2024-06-20 06:29:56-- http://deb.debian.org/debian/pool/main/p/psortb/psortb_3.0.6%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2254 (2.2K) [text/prs.lines.tag] Saving to: ‘psortb_3.0.6+dfsg-4.dsc’ 0K .. 100% 257M=0s 2024-06-20 06:29:56 (257 MB/s) - ‘psortb_3.0.6+dfsg-4.dsc’ saved [2254/2254] Thu Jun 20 06:29:56 UTC 2024 I: psortb_3.0.6+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: psortb Binary: psortb Architecture: any Version: 3.0.6+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://www.psort.org/ Standards-Version: 4.7.0 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, pkgconf, pftools Package-List: psortb deb science optional arch=any Checksums-Sha1: c47d0ec328df75f2151dd6d5b5840768006519f8 17036876 psortb_3.0.6+dfsg.orig.tar.xz c10819ffb3b3d31ca99a66f9768493ed46e5a541 7480 psortb_3.0.6+dfsg-4.debian.tar.xz Checksums-Sha256: ed32aa0240bb03daed228b32614a53c146afba6ca66fd087702315d75e23f751 17036876 psortb_3.0.6+dfsg.orig.tar.xz fc09ccbf18a26cefd75e8c6030e192878b94b251a6a3206614931820ef6344d0 7480 psortb_3.0.6+dfsg-4.debian.tar.xz Files: c4feab06d3031fecac1ab90258550209 17036876 psortb_3.0.6+dfsg.orig.tar.xz dbe47096a741a5132191480aa07bb7d4 7480 psortb_3.0.6+dfsg-4.debian.tar.xz Dgit: 4806a2aae47b085aac7d4851a89b803020876c96 debian archive/debian/3.0.6+dfsg-4 https://git.dgit.debian.org/psortb -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmZS6scUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdry2hAAiLUm7A9Zl9L7P13u8spjnNXnKq4o lnUhE1DiKRk798zry3EmPP7q7rynIQJuDoeGNwIRNlNblDxsy7dydcglnUY40uXk qk2rHKooIryioJPSjJdxBElF7+EW70ajIidgWpzR3BNfyVIVF5ivpcIjfrSzmpvf 8GjEO4H9YBnl2AvBWo+wYi+1YYEC1zneDXyOtQ7c1sjEvNXoex0Ud2DEQ2cD+iBq FROVjIN+UUaU0aqxUWd5z+y4mZkM8zW6/VEepv9a4oxb3lIqAZ5Q/1tWxgm0Ww9B I2AMiJNMOd74NsMGKa7eRqYYOXDMVzDUihqBjuPZlAEmQ44ulSvnwNHUs7jRdYM6 lq6hk+w+pTGEeMP3CwkOls77C4QvHTuap/Mk+T5M99cINNWPXMjNmZ1PGvwbIs12 QmeKh+uoQiYRk7RyljqLyVFMrlczC5Pdk9bsLyJm+fQer3ePV32GxQw02ok1ymje OdNvyUFCuBwpHQto53DzRfaTXVkrMGIv1XsHlutIX5CTaXNL74gYAcSiZdCswNhj cZyyVCDmEeuhuIJKsw8rv9X9G/8OMRzRFNrttzz/lWqUQd+aK8/F7eQdYjA8TOaa UrmWZYcKWcmFlq4AD4OCILT4+KB9LY93sj2Ap382mDf+Z+Y2MGVI038u5pokY0cq NULN/MYhxVzrWxE= =bHrm -----END PGP SIGNATURE----- Thu Jun 20 06:29:56 UTC 2024 I: Checking whether the package is not for us Thu Jun 20 06:29:56 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Thu Jun 20 06:29:56 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu Jun 20 06:30:18 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 19 18:29:58 -12 2024 I: pbuilder-time-stamp: 1718864998 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 [psortb_3.0.6+dfsg-4.dsc] I: copying [./psortb_3.0.6+dfsg.orig.tar.xz] I: copying [./psortb_3.0.6+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun May 26 07:54:47 2024 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-4.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-4.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 dpkg-source: info: applying add_missing_header.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1041803/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='fdbec16a392e4024a5bc787af8a177e6' 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='1041803' 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.jVxHTzUS/pbuilderrc_uRUR --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.jVxHTzUS/b1 --logfile b1/build.log psortb_3.0.6+dfsg-4.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 Jun 5 22:35 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1041803/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), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkgconf, 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 ... 19760 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 pkgconf; however: Package pkgconf 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-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} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsquid-dev{a} libsquid1t64{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} 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, 77 newly installed, 0 to remove and 0 not upgraded. Need to get 44.3 MB of archives. After unpacking 200 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-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} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsquid-dev{a} libsquid1t64{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} 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, 77 newly installed, 0 to remove and 0 not upgraded. Need to get 44.3 MB of archives. After unpacking 200 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/1041803 and its subdirectories Thu Jun 20 06:30:20 UTC 2024 W: No second build log, what happened? Thu Jun 20 06:30:20 UTC 2024 W: Downloading the build dependencies failed Thu Jun 20 06:30:20 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 Jun 20 06:30:20 UTC 2024 W: Network problems are automatically rescheduled after some hours.