Fri Oct 25 01:42:05 UTC 2024 I: starting to build paleomix/unstable/armhf on jenkins on '2024-10-25 01:41' Fri Oct 25 01:42:05 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_20/5000/console.log Fri Oct 25 01:42:05 UTC 2024 I: Downloading source for unstable/paleomix=1.3.8-2 --2024-10-25 01:42:05-- http://deb.debian.org/debian/pool/main/p/paleomix/paleomix_1.3.8-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2466 (2.4K) [text/prs.lines.tag] Saving to: ‘paleomix_1.3.8-2.dsc’ 0K .. 100% 300M=0s 2024-10-25 01:42:05 (300 MB/s) - ‘paleomix_1.3.8-2.dsc’ saved [2466/2466] Fri Oct 25 01:42:05 UTC 2024 I: paleomix_1.3.8-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: paleomix Binary: paleomix Architecture: any Version: 1.3.8-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://geogenetics.ku.dk/publications/paleomix Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/paleomix Vcs-Git: https://salsa.debian.org/med-team/paleomix.git Testsuite: autopkgtest Testsuite-Triggers: python3-pytest Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-pytest , python3-coloredlogs , python3-configargparse , python3-ruamel.yaml , python3-pysam , python3-setproctitle , default-jre-headless , bowtie2, rsync, examl, picard-tools Package-List: paleomix deb science optional arch=any Checksums-Sha1: 9f201401a7f59b6e213ee8ff2bf264fd19177e37 1137201 paleomix_1.3.8.orig.tar.gz 4e4bc8a54120091e4c8a4d776cc97757344d596d 11348 paleomix_1.3.8-2.debian.tar.xz Checksums-Sha256: 7bead15d96027aecea8462ea1a219f4a7c5356536679118140ad6390e01413ca 1137201 paleomix_1.3.8.orig.tar.gz 2b4a90dc51a3cdc9813fc150a76b7d655d03ffed8acd2966cd7261a887fd2fc4 11348 paleomix_1.3.8-2.debian.tar.xz Files: 6e07794044685a77751e6552c52fa7dc 1137201 paleomix_1.3.8.orig.tar.gz cd313700945545f833137174259dec19 11348 paleomix_1.3.8-2.debian.tar.xz Dgit: 2b1bd97ccd5b63e5ba6262700de9199e3af853d8 debian archive/debian/1.3.8-2 https://git.dgit.debian.org/paleomix -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcGqmQUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoqaBAAv7PKwZwnYPMZHPkAvifa/VZux3Zc 7XyqTsPuKmPc5qO55fB2Kqwby4FGQ4diQTx6BA5TH1Va/A+a7cFuQqIWrK/WSQiI JAjAwr31fb7f+hLB/28Q80w536Ub8VTBaffxJ5ZXq87JwDDv5OExOMY/0Ja1H1j8 ae/Cep+u4ql8apIs8pcrkR2OgKFDimI4V2XZBgfC/GSWq/zu3exBv9dv/y3PzXLP ZPZR0Kzsx7nwEbvZCPLe6O+01/Bnvzc5TYQ5s6WyK0OFYVucwNKDQZQr/KRyih8z MJ04XanLGZ1EpMgjmSH2k2Fl7tMjTnMy/QgIfXmhxEvGvoQ4Gj/QixfdKmVLQMgw PeuzS/jyM6gBe930QSmDcGUPg2sEdt/Fb7Q0QU8Y7avlJT4grE563/JTloa5Qu8p VIIWwn8HQHFrTzAZ05l2I5Ug+WD9EbDzduD9sfOJuo/0p4Kpa8dRdI0Xgkg0TGM4 16k4SKieuttahd3azJuUpjaQWyFxzOK5RfXCkXpdvilw7C+vjTFNC4FG25UL8LOp V4m9w9I/uINuO4eRVWLbl1KWoUsD8G4r4VgXGL0UWZmwrZNoqzsHx+qciLpZEXMN UjpaFsGtaqU5ZvlPcsNhXv1MovQVOIdTaWCVCuz8ahQzo+wOVDOdLEhjzxE+nHt4 YmCAhhbjQSkTVEQ= =q9MK -----END PGP SIGNATURE----- Fri Oct 25 01:42:05 UTC 2024 I: Checking whether the package is not for us Fri Oct 25 01:42:05 UTC 2024 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Fri Oct 25 01:42:05 UTC 2024 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Fri Oct 25 01:42:46 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 24 13:42:13 -12 2024 I: pbuilder-time-stamp: 1729820533 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 [paleomix_1.3.8-2.dsc] I: copying [./paleomix_1.3.8.orig.tar.gz] I: copying [./paleomix_1.3.8-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Oct 9 16:08:04 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 ./paleomix_1.3.8-2.dsc: no acceptable signature found dpkg-source: info: extracting paleomix in paleomix-1.3.8 dpkg-source: info: unpacking paleomix_1.3.8.orig.tar.gz dpkg-source: info: unpacking paleomix_1.3.8-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying xfail_command_tests.patch dpkg-source: info: applying python3.11.patch dpkg-source: info: applying shlex.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14377/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='cc0140b3f0c543c5a9736fabaacf0696' 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='14377' 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.dOdoqgHL/pbuilderrc_Umvl --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.dOdoqgHL/b1 --logfile b1/build.log paleomix_1.3.8-2.dsc' SUDO_GID='113' SUDO_UID='107' 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 virt64c 6.1.0-26-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) 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/14377/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), dh-python, python3, python3-setuptools, python3-pytest, python3-coloredlogs, python3-configargparse, python3-ruamel.yaml, python3-pysam, python3-setproctitle, default-jre-headless, bowtie2, rsync, examl, picard-tools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19667 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; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-coloredlogs; however: Package python3-coloredlogs is not installed. pbuilder-satisfydepends-dummy depends on python3-configargparse; however: Package python3-configargparse is not installed. pbuilder-satisfydepends-dummy depends on python3-ruamel.yaml; however: Package python3-ruamel.yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-setproctitle; however: Package python3-setproctitle is not installed. pbuilder-satisfydepends-dummy depends on default-jre-headless; however: Package default-jre-headless is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on rsync; however: Package rsync is not installed. pbuilder-satisfydepends-dummy depends on examl; however: Package examl is not installed. pbuilder-satisfydepends-dummy depends on picard-tools; however: Package picard-tools 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} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} examl{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} java-common{a} libapparmor1{a} libarchive-zip-perl{a} libasound2-data{a} libasound2t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbrotli1{a} libcbor0.10{a} libcom-err2{a} libcups2t64{a} libcurl3t64-gnutls{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnl-3-200{a} libnl-route-3-200{a} libnsl2{a} libnspr4{a} libnss3{a} libopenmpi3t64{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpng16-16t64{a} libpopt0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} librdmacm1t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} man-db{a} media-types{a} netbase{a} ocl-icd-libopencl1{a} openjdk-21-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} po-debconf{a} python3{a} python3-autocommand{a} python3-coloredlogs{a} python3-configargparse{a} python3-humanfriendly{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pysam{a} python3-pytest{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3-setproctitle{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} rsync{a} sensible-utils{a} shared-mime-info{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl ibverbs-providers krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-pygments wget xauth xdg-user-dirs 0 packages upgraded, 151 newly installed, 0 to remove and 0 not upgraded. Need to get 85.5 MB of archives. After unpacking 352 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: picard-tools but it is not installable Unable to resolve dependencies! Giving up... The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} examl{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} java-common{a} libapparmor1{a} libarchive-zip-perl{a} libasound2-data{a} libasound2t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbrotli1{a} libcbor0.10{a} libcom-err2{a} libcups2t64{a} libcurl3t64-gnutls{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnl-3-200{a} libnl-route-3-200{a} libnsl2{a} libnspr4{a} libnss3{a} libopenmpi3t64{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpng16-16t64{a} libpopt0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} librdmacm1t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} man-db{a} media-types{a} netbase{a} ocl-icd-libopencl1{a} openjdk-21-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} po-debconf{a} python3{a} python3-autocommand{a} python3-coloredlogs{a} python3-configargparse{a} python3-humanfriendly{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pysam{a} python3-pytest{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3-setproctitle{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} rsync{a} sensible-utils{a} shared-mime-info{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl ibverbs-providers krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-pygments wget xauth xdg-user-dirs 0 packages upgraded, 151 newly installed, 0 to remove and 0 not upgraded. Need to get 85.5 MB of archives. After unpacking 352 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/14377 and its subdirectories Fri Oct 25 01:42:49 UTC 2024 W: No second build log, what happened? Fri Oct 25 01:42:49 UTC 2024 W: Downloading the build dependencies failed Fri Oct 25 01:42:49 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Fri Oct 25 01:42:49 UTC 2024 W: Network problems are automatically rescheduled after some hours.