Thu May 9 01:20:35 UTC 2024 I: starting to build r-bioc-variantannotation/trixie/armhf on jenkins on '2024-05-09 01:20' Thu May 9 01:20:35 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_29/8263/console.log Thu May 9 01:20:35 UTC 2024 I: Downloading source for trixie/r-bioc-variantannotation=1.48.1-1 --2024-05-09 01:20:35-- http://deb.debian.org/debian/pool/main/r/r-bioc-variantannotation/r-bioc-variantannotation_1.48.1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2587 (2.5K) [text/prs.lines.tag] Saving to: ‘r-bioc-variantannotation_1.48.1-1.dsc’ 0K .. 100% 326M=0s 2024-05-09 01:20:35 (326 MB/s) - ‘r-bioc-variantannotation_1.48.1-1.dsc’ saved [2587/2587] Thu May 9 01:20:35 UTC 2024 I: r-bioc-variantannotation_1.48.1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: r-bioc-variantannotation Binary: r-bioc-variantannotation Architecture: any Version: 1.48.1-1 Maintainer: Debian R Packages Maintainers Uploaders: Andreas Tille Homepage: https://bioconductor.org/packages/VariantAnnotation/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-variantannotation Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-variantannotation.git Testsuite: autopkgtest-pkg-r Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-biocgenerics (>= 0.37.0), r-bioc-matrixgenerics, r-bioc-genomeinfodb, r-bioc-genomicranges, r-bioc-summarizedexperiment, r-bioc-rsamtools, r-cran-dbi, r-bioc-zlibbioc, r-bioc-biobase, r-bioc-s4vectors, r-bioc-iranges, r-bioc-xvector, r-bioc-biostrings, r-bioc-annotationdbi, r-bioc-rtracklayer, r-bioc-bsgenome, r-bioc-genomicfeatures, r-bioc-rhtslib (>= 1.99.3), libcurl4-openssl-dev | libcurl4-dev Package-List: r-bioc-variantannotation deb gnu-r optional arch=any Checksums-Sha1: 70c1ec99d741dbb32bc6ce25eef242dc0cdf41dd 1886512 r-bioc-variantannotation_1.48.1.orig.tar.gz 27464073d1f480def0c2dbce807fa62f878b5a47 7900 r-bioc-variantannotation_1.48.1-1.debian.tar.xz Checksums-Sha256: 2af6d1164152f9722fc83cfe16cf43e1a83ba5c9d133d9663175b0ac779e3d51 1886512 r-bioc-variantannotation_1.48.1.orig.tar.gz e051c58f3ed58f8a0e61142e226a059c8e02c71ae1e0ad472bb60b8905aaccf2 7900 r-bioc-variantannotation_1.48.1-1.debian.tar.xz Files: 39b6f4907fe37495a903c338e6d4cc73 1886512 r-bioc-variantannotation_1.48.1.orig.tar.gz 426993cec6182545dabd4954316fa108 7900 r-bioc-variantannotation_1.48.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCgAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVproEOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtHa5w//Vx0Y2fDfLt6nwzNjC+eJ+FvFOhjxI997vKK8 kBnuocbnvX9d+GEpB50wB86lhi/jB1eY4OoppGZ2mqlg/y3fCSpU47wBZIJD0LfE ayn25vGf7FqroMZpq2V9ZKSFWpdUrhOfEDdFjj4Z0vv5/rua9BHjBk/wtvQUyOkn l009PwvkZIBLlVZmHYltpR41BOnNbqvOKy/ONh1VLtI0gIKOL+Ts6Khz5cXfUZGp 64oX5IzQeroPFN0zm/HoSRuriJdkD+etS4oP6EZzq5I0Rh7+4WlMx5Em6s0VAKvQ mQtIGVtGaoliaY47NAJscUw2YVS06zUHeWx0gotw7zgtUItX/vyqHojOKjqK4JAH 5muWfjPgzXYlnnUDbRsnbkV8p3PfkKjCRgwnKE633A7o+p8fM2nWgGpKYiJtiej7 7Ko3Mt8+q64m0W1zT1fuSj0cj/1hM58Vxbm5sAdU3oeP0q/EbX4aa/mPSj8Uijf6 h90Kl/I0l8zFS5WTASQ1uxHQuwV+59Hq6eId054gKB5w2ZxvoKwCqJkmOEMEAZjD UALOeFJTFmf7yn8SHQOOH6dmdXii4ah9h3B1okL7duwXapA1aq51vC/HDzVkSXAy bDjwMDuLxPHM0DrCUhDGB/YDkGpgUf/Z/BCbjJcGcSv8lrgYia73NKbxSjaCp0C8 KfEJURY= =RckZ -----END PGP SIGNATURE----- Thu May 9 01:20:35 UTC 2024 I: Checking whether the package is not for us Thu May 9 01:20:35 UTC 2024 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Thu May 9 01:20:35 UTC 2024 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Thu May 9 01:21:13 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 8 13:20:43 -12 2024 I: pbuilder-time-stamp: 1715217643 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 [r-bioc-variantannotation_1.48.1-1.dsc] I: copying [./r-bioc-variantannotation_1.48.1.orig.tar.gz] I: copying [./r-bioc-variantannotation_1.48.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 1 09:59:29 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./r-bioc-variantannotation_1.48.1-1.dsc: no acceptable signature found dpkg-source: info: extracting r-bioc-variantannotation in r-bioc-variantannotation-1.48.1 dpkg-source: info: unpacking r-bioc-variantannotation_1.48.1.orig.tar.gz dpkg-source: info: unpacking r-bioc-variantannotation_1.48.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop_tests_requiring_large_data_sets.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29266/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='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='bd35dda3d78f48849917a6ea42d3aa98' 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='29266' 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.lLj7WC34/pbuilderrc_HEd7 --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.lLj7WC34/b1 --logfile b1/build.log r-bioc-variantannotation_1.48.1-1.dsc' SUDO_GID='110' SUDO_UID='103' 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 virt32z 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 7 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/29266/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-r, r-base-dev, r-bioc-biocgenerics (>= 0.37.0), r-bioc-matrixgenerics, r-bioc-genomeinfodb, r-bioc-genomicranges, r-bioc-summarizedexperiment, r-bioc-rsamtools, r-cran-dbi, r-bioc-zlibbioc, r-bioc-biobase, r-bioc-s4vectors, r-bioc-iranges, r-bioc-xvector, r-bioc-biostrings, r-bioc-annotationdbi, r-bioc-rtracklayer, r-bioc-bsgenome, r-bioc-genomicfeatures, r-bioc-rhtslib (>= 1.99.3), libcurl4-openssl-dev | libcurl4-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19444 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-r; however: Package dh-r is not installed. pbuilder-satisfydepends-dummy depends on r-base-dev; however: Package r-base-dev is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biocgenerics (>= 0.37.0); however: Package r-bioc-biocgenerics is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-matrixgenerics; however: Package r-bioc-matrixgenerics is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomeinfodb; however: Package r-bioc-genomeinfodb is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomicranges; however: Package r-bioc-genomicranges is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-summarizedexperiment; however: Package r-bioc-summarizedexperiment is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-rsamtools; however: Package r-bioc-rsamtools is not installed. pbuilder-satisfydepends-dummy depends on r-cran-dbi; however: Package r-cran-dbi is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-zlibbioc; however: Package r-bioc-zlibbioc is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biobase; however: Package r-bioc-biobase is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-s4vectors; however: Package r-bioc-s4vectors is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-iranges; however: Package r-bioc-iranges is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-xvector; however: Package r-bioc-xvector is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biostrings; however: Package r-bioc-biostrings is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-annotationdbi; however: Package r-bioc-annotationdbi is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-rtracklayer; however: Package r-bioc-rtracklayer is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-bsgenome; however: Package r-bioc-bsgenome is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomicfeatures; however: Package r-bioc-genomicfeatures is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-rhtslib (>= 1.99.3); however: Package r-bioc-rhtslib is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-openssl-dev | libcurl4-dev; however: Package libcurl4-openssl-dev is not installed. Package libcurl4-dev 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} librtmp1{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx publicsuffix wget 0 packages upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 20.5 MB of archives. After unpacking 73.8 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: dh-r but it is not installable Depends: r-base-dev but it is not installable Depends: r-bioc-biocgenerics (>= 0.37.0) but it is not installable Depends: r-bioc-matrixgenerics but it is not installable Depends: r-bioc-genomeinfodb but it is not installable Depends: r-bioc-genomicranges but it is not installable Depends: r-bioc-summarizedexperiment but it is not installable Depends: r-bioc-rsamtools which is a virtual package and is not provided by any available package Depends: r-cran-dbi but it is not installable Depends: r-bioc-zlibbioc but it is not installable Depends: r-bioc-biobase but it is not installable Depends: r-bioc-s4vectors but it is not installable Depends: r-bioc-iranges but it is not installable Depends: r-bioc-xvector but it is not installable Depends: r-bioc-biostrings but it is not installable Depends: r-bioc-annotationdbi but it is not installable Depends: r-bioc-rtracklayer which is a virtual package and is not provided by any available package Depends: r-bioc-bsgenome but it is not installable Depends: r-bioc-genomicfeatures but it is not installable Depends: r-bioc-rhtslib (>= 1.99.3) 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} 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} libarchive-zip-perl{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} librtmp1{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx publicsuffix wget 0 packages upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 20.5 MB of archives. After unpacking 73.8 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/29266 and its subdirectories Thu May 9 01:21:16 UTC 2024 W: No second build log, what happened? Thu May 9 01:21:16 UTC 2024 W: Downloading the build dependencies failed Thu May 9 01:21:16 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 May 9 01:21:16 UTC 2024 W: Network problems are automatically rescheduled after some hours.