Thu Jan 30 13:40:51 UTC 2025 I: starting to build sepp/unstable/armhf on jenkins on '2025-01-30 13:40' Thu Jan 30 13:40:51 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_3/13027/console.log Thu Jan 30 13:40:51 UTC 2025 I: Downloading source for unstable/sepp=4.5.5+dfsg-1 --2025-01-30 13:40:51-- http://deb.debian.org/debian/pool/main/s/sepp/sepp_4.5.5%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2129 (2.1K) [text/prs.lines.tag] Saving to: ‘sepp_4.5.5+dfsg-1.dsc’ 0K .. 100% 331M=0s 2025-01-30 13:40:51 (331 MB/s) - ‘sepp_4.5.5+dfsg-1.dsc’ saved [2129/2129] Thu Jan 30 13:40:51 UTC 2025 I: sepp_4.5.5+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sepp Binary: sepp Architecture: any Version: 4.5.5+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Pierre Gruet Homepage: https://github.com/smirarab/sepp/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/sepp Vcs-Git: https://salsa.debian.org/med-team/sepp.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-dendropy, ant, libjenkins-json-java, libgoogle-gson-java, ncbi-blast+ , pplacer , hmmer Package-List: sepp deb science optional arch=any Checksums-Sha1: b3e537772b20e6d05c959fdcd74db17a2dacc25c 4311920 sepp_4.5.5+dfsg.orig.tar.xz 50e566075afd138ed7b5c484d0de6c8baf4262e3 12476 sepp_4.5.5+dfsg-1.debian.tar.xz Checksums-Sha256: 5914da6499ad9a1e1a48068ac0eba44d8cbd53809a6b4d749094ee455d013e59 4311920 sepp_4.5.5+dfsg.orig.tar.xz 02e538c4842e2e9ef272ae2dff7bb0f01076e782f3b925044ed5b734df638e29 12476 sepp_4.5.5+dfsg-1.debian.tar.xz Files: 07ae330f5e190f7254f4e5983d599095 4311920 sepp_4.5.5+dfsg.orig.tar.xz 898d7b9928c1d4a4515f0e8ad416adcf 12476 sepp_4.5.5+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmb68+cACgkQYAMWptwn dHYynBAAo+JPbP7xzhG4Mj1llmmCTbETJwa9f5i19pxfk/denCSnhp0hYT+eZ0Fo rKUSWin1Gno/A7LVpi+fGjhEW36az5RN1WEKEUpwpd90BEozcK4YfVYZw/cspgsz YuuTR6MVhoQlbTn90MRBz4hVrhehuYjz/mwWExIL6nrRl7HAD8rHKis1geRMiHld btotuU09mVhsU1a3GYAPW6BT1RR8lXsYaGhsV/qwXiDx1Pbb1xP9TCcNVUdrimqC ybDtgphL5uLNVx31hsWamfCdj9Md92ZfwCxRJ75naqh9lsdTeHPMde/n8xeXeyVX Bfh+SKNWhrRqMJz2PyJNkbICPAWHl5n5Z1bbHtk6/PM5FcOJywycPj0fp0yjjWAh 7Avsg0XY8Xr15g+9XXc7qM6rgb9N8MB7CvRHNL+mb2A6aDonR5zPLegFUdE81pDg O0WgtafEvkslSR8wooHQf9WAQHatdHuJyycsB3ZUTGUefhTQDIg/Od1JcXJABF6U 34h0KD/S2JUP+gEgVSGH11FYz77dYtU7lQ4q0LxL31RBtJXxj6f566c55RsP/02x OlU73+zRN4dD5lgp8OJ6J9a+u8HU8UU46ka3nLiOIahZSB0GKLLDfX6u6CITdmGG cOswNUmTbPzn9kFzu+PSpQ2lHXOc5skhn+GTOWPTZI6lJ7E/WDU= =Bg8a -----END PGP SIGNATURE----- Thu Jan 30 13:40:51 UTC 2025 I: Checking whether the package is not for us Thu Jan 30 13:40:51 UTC 2025 I: Starting 1st build on remote node ff4a-armhf-rb.debian.net. Thu Jan 30 13:40:51 UTC 2025 I: Preparing to do remote build '1' on ff4a-armhf-rb.debian.net. Thu Jan 30 13:42:46 UTC 2025 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 30 01:40:58 -12 2025 I: pbuilder-time-stamp: 1738244458 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 [sepp_4.5.5+dfsg-1.dsc] I: copying [./sepp_4.5.5+dfsg.orig.tar.xz] I: copying [./sepp_4.5.5+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./sepp_4.5.5+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting sepp in sepp-4.5.5+dfsg dpkg-source: info: unpacking sepp_4.5.5+dfsg.orig.tar.xz dpkg-source: info: unpacking sepp_4.5.5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying setup.patch dpkg-source: info: applying use_debian_packaged_guppy_from_pplacer.patch dpkg-source: info: applying change_java_version_for_ant.patch dpkg-source: info: applying java_build.patch dpkg-source: info: applying configuration_files_in_etc_and_per_user.patch dpkg-source: info: applying deactivating_log_test.patch dpkg-source: info: applying using_python3_interpreter.patch dpkg-source: info: applying hmmbuild_path_for_testUPP.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/23739/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='baba14a86a9b41a6ba91252f5b320590' 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='23739' 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.BoG5QyWZ/pbuilderrc_P0Kg --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.BoG5QyWZ/b1 --logfile b1/build.log sepp_4.5.5+dfsg-1.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 ff4a 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/23739/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-dendropy, ant, libjenkins-json-java, libgoogle-gson-java, ncbi-blast+, pplacer, hmmer dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19567 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-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on ant; however: Package ant is not installed. pbuilder-satisfydepends-dummy depends on libjenkins-json-java; however: Package libjenkins-json-java is not installed. pbuilder-satisfydepends-dummy depends on libgoogle-gson-java; however: Package libgoogle-gson-java is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on pplacer; however: Package pplacer is not installed. pbuilder-satisfydepends-dummy depends on hmmer; however: Package hmmer 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: ant{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} java-common{a} libapache-pom-java{a} libarchive-zip-perl{a} libcommons-beanutils-java{a} libcommons-collections3-java{a} libcommons-lang-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgoogle-gson-java{a} libicu72{a} libjenkins-json-java{a} libjpeg62-turbo{a} liblcms2-2{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} openjdk-21-jre-headless{a} openssl{a} po-debconf{a} python3{a} python3-autocommand{a} python3-dendropy{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ant-optional curl groovy junit4 libarchive-cpio-perl libasound2t64 libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b liblog4j1.2-java libltdl-dev libmail-sendmail-perl liboss4-salsa-asound2 libxom-java lynx wget 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 87.7 MB of archives. After unpacking 361 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: pplacer which is a virtual package and is not provided by any available package Depends: hmmer 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: ant{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} java-common{a} libapache-pom-java{a} libarchive-zip-perl{a} libcommons-beanutils-java{a} libcommons-collections3-java{a} libcommons-lang-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgoogle-gson-java{a} libicu72{a} libjenkins-json-java{a} libjpeg62-turbo{a} liblcms2-2{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} openjdk-21-jre-headless{a} openssl{a} po-debconf{a} python3{a} python3-autocommand{a} python3-dendropy{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ant-optional curl groovy junit4 libarchive-cpio-perl libasound2t64 libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b liblog4j1.2-java libltdl-dev libmail-sendmail-perl liboss4-salsa-asound2 libxom-java lynx wget 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 87.7 MB of archives. After unpacking 361 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/23739 and its subdirectories Thu Jan 30 13:42:48 UTC 2025 W: No second build log, what happened? Thu Jan 30 13:42:49 UTC 2025 W: Downloading the build dependencies failed Thu Jan 30 13:42:49 UTC 2025 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Thu Jan 30 13:42:49 UTC 2025 W: Network problems are automatically rescheduled after some hours.