Running as unit: rb-build-arm64_7-45274.service ==================================================================================== Thu Nov 21 06:05:27 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_7) on jenkins, called using "codethink02-arm64 codethink03-arm64" as arguments. Thu Nov 21 06:05:27 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-n03FLqUA" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 06:05:27 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Thu Nov 21 06:05:27 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-SQRtB5' Thu Nov 21 06:05:28 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Thu Nov 21 06:05:28 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-u4CtZV' ok, let's check if psortb is building anywhere yet… ok, psortb is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of psortb in unstable on arm64 on jenkins now. 1st build will be done on codethink02-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Thu Nov 21 06:05:51 UTC 2024 I: starting to build psortb/unstable/arm64 on jenkins on '2024-11-21 06:05' Thu Nov 21 06:05:51 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/45274/console.log 1732169151 arm64 unstable psortb Thu Nov 21 06:05:51 UTC 2024 I: Downloading source for unstable/psortb=3.0.6+dfsg-4 --2024-11-21 06:05:51-- 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% 321M=0s 2024-11-21 06:05:51 (321 MB/s) - ‘psortb_3.0.6+dfsg-4.dsc’ saved [2254/2254] --2024-11-21 06:05:51-- 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% 321M=0s 2024-11-21 06:05:51 (321 MB/s) - ‘psortb_3.0.6+dfsg-4.dsc’ saved [2254/2254] Thu Nov 21 06:05:51 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 Nov 21 06:05:51 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 06:05:51 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Thu Nov 21 06:05:51 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Thu Nov 21 06:05:51 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Thu Nov 21 06:05:51 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-hrGrr4' ==================================================================================== Thu Nov 21 06:05:53 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "1 psortb unstable /srv/reproducible-results/rbuild-debian/r-b-build.3R92BKpH 3.0.6+dfsg-4" as arguments. Thu Nov 21 06:05:53 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-mNVg590c" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 06:05:53 UTC 2024 I: Downloading source for unstable/psortb=3.0.6+dfsg-4 Reading package lists... NOTICE: 'psortb' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/psortb.git Please use: git clone https://salsa.debian.org/med-team/psortb.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 17.0 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main psortb 3.0.6+dfsg-4 (dsc) [2254 B] Get:2 http://deb.debian.org/debian unstable/main psortb 3.0.6+dfsg-4 (tar) [17.0 MB] Get:3 http://deb.debian.org/debian unstable/main psortb 3.0.6+dfsg-4 (diff) [7480 B] Fetched 17.0 MB in 0s (50.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'psortb' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/psortb.git Please use: git clone https://salsa.debian.org/med-team/psortb.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 17.0 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main psortb 3.0.6+dfsg-4 (dsc) [2254 B] Get:2 http://deb.debian.org/debian unstable/main psortb 3.0.6+dfsg-4 (tar) [17.0 MB] Get:3 http://deb.debian.org/debian unstable/main psortb 3.0.6+dfsg-4 (diff) [7480 B] Fetched 17.0 MB in 0s (50.5 MB/s) Download complete and in download only mode ============================================================================= Building psortb in unstable on arm64 on codethink02-arm64 now. Date: Thu Nov 21 06:05:53 GMT 2024 Date UTC: Thu Nov 21 06:05:54 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Nov 20 18:05:54 -12 2024 I: pbuilder-time-stamp: 1732169154 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-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/2455983/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='e151c4704eff4bc18a5cf98c23554e0b' 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='2455983' 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.3R92BKpH/pbuilderrc_rdpJ --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.3R92BKpH/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 codethink02-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2455983/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 ... 20084 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} libcom-err2{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodhmm-dev{a} libmodhmm0{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-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} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{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} python3.12{a} python3.12-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 krb5-locales 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, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 48.8 MB of archives. After unpacking 221 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} libcom-err2{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodhmm-dev{a} libmodhmm0{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-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} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{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} python3.12{a} python3.12-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 krb5-locales 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, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 48.8 MB of archives. After unpacking 221 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/2455983 and its subdirectories Starting cleanup. All cleanup done. Thu Nov 21 06:06:12 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-mNVg590c, removing. /srv/reproducible-results/rbuild-debian/r-b-build.3R92BKpH: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 06:06 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 06:05 b2 -rw-r--r-- 1 jenkins jenkins 2254 May 26 08:02 psortb_3.0.6+dfsg-4.dsc -rw------- 1 jenkins jenkins 3383 Nov 21 06:05 rbuildlog.tKHONk9 /srv/reproducible-results/rbuild-debian/r-b-build.3R92BKpH/b1: total 12 -rw-r--r-- 1 jenkins jenkins 12106 Nov 21 06:06 build.log /srv/reproducible-results/rbuild-debian/r-b-build.3R92BKpH/b2: total 0 Thu Nov 21 06:06:13 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Nov 20 18:05:54 -12 2024 I: pbuilder-time-stamp: 1732169154 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-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/2455983/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='e151c4704eff4bc18a5cf98c23554e0b' 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='2455983' 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.3R92BKpH/pbuilderrc_rdpJ --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.3R92BKpH/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 codethink02-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2455983/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 ... 20084 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} libcom-err2{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodhmm-dev{a} libmodhmm0{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-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} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{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} python3.12{a} python3.12-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 krb5-locales 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, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 48.8 MB of archives. After unpacking 221 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} libcom-err2{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodhmm-dev{a} libmodhmm0{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-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} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{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} python3.12{a} python3.12-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 krb5-locales 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, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 48.8 MB of archives. After unpacking 221 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/2455983 and its subdirectories psortb failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/psortb_3.0.6+dfsg-4.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/psortb_3.0.6+dfsg-4.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/psortb_3.0.6+dfsg-4.build1.log.gz' Thu Nov 21 06:06:14 UTC 2024 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 71.4% -- replaced with stdout Thu Nov 21 06:06:14 UTC 2024 W: Downloading the build dependencies failed Thu Nov 21 06:06:14 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 Nov 21 06:06:14 UTC 2024 W: Network problems are automatically rescheduled after some hours. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-21 06:06:15] INFO: Starting at 2024-11-21 06:06:15.329712 [2024-11-21 06:06:15] INFO: Generating the pages of 1 package(s) [2024-11-21 06:06:16] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/psortb didn't produce a buildlog, even though it has been built. [2024-11-21 06:06:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/psortb_3.0.6+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/psortb_3.0.6+dfsg-4.diff.gz is missing [2024-11-21 06:06:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/psortb_3.0.6+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/psortb_3.0.6+dfsg-4.diff.gz is missing [2024-11-21 06:06:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/psortb_3.0.6+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/psortb_3.0.6+dfsg-3.diff.gz is missing [2024-11-21 06:06:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/psortb_3.0.6+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/psortb_3.0.6+dfsg-3.diff.gz is missing [2024-11-21 06:06:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/psortb_3.0.6+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/psortb_3.0.6+dfsg-3.diff.gz is missing [2024-11-21 06:06:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/arm64/psortb_3.0.6+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/arm64/psortb_3.0.6+dfsg-2.diff.gz is missing [2024-11-21 06:06:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/psortb_3.0.6+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/psortb_3.0.6+dfsg-2.diff.gz is missing [2024-11-21 06:06:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/psortb_3.0.6+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/psortb_3.0.6+dfsg-2.diff.gz is missing [2024-11-21 06:06:16] INFO: Finished at 2024-11-21 06:06:16.661515, took: 0:00:01.331807 Thu Nov 21 06:06:16 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/psortb.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/psortb_3.0.6+dfsg-4.rbuild.log: 66.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/psortb_3.0.6+dfsg-4.rbuild.log.gz [2024-11-21 06:06:17] INFO: Starting at 2024-11-21 06:06:17.099397 [2024-11-21 06:06:17] INFO: Generating the pages of 1 package(s) [2024-11-21 06:06:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/psortb_3.0.6+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/psortb_3.0.6+dfsg-4.diff.gz is missing [2024-11-21 06:06:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/psortb_3.0.6+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/psortb_3.0.6+dfsg-4.diff.gz is missing [2024-11-21 06:06:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/psortb_3.0.6+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/psortb_3.0.6+dfsg-4.diff.gz is missing [2024-11-21 06:06:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/psortb_3.0.6+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/psortb_3.0.6+dfsg-3.diff.gz is missing [2024-11-21 06:06:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/psortb_3.0.6+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/psortb_3.0.6+dfsg-3.diff.gz is missing [2024-11-21 06:06:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/psortb_3.0.6+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/psortb_3.0.6+dfsg-3.diff.gz is missing [2024-11-21 06:06:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/arm64/psortb_3.0.6+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/arm64/psortb_3.0.6+dfsg-2.diff.gz is missing [2024-11-21 06:06:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/psortb_3.0.6+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/psortb_3.0.6+dfsg-2.diff.gz is missing [2024-11-21 06:06:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/psortb_3.0.6+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/psortb_3.0.6+dfsg-2.diff.gz is missing [2024-11-21 06:06:18] INFO: Finished at 2024-11-21 06:06:18.667900, took: 0:00:01.568513 All cleanup done. Thu Nov 21 06:06:18 UTC 2024 - total duration: 0h 0m 47s. Thu Nov 21 06:06:18 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-n03FLqUA, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 51.610s CPU time consumed: 6.750s