Wed Nov 20 02:32:44 UTC 2024 I: starting to build r-bioc-genelendatabase/trixie/i386 on jenkins on '2024-11-20 02:32' Wed Nov 20 02:32:44 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_13/50915/console.log Wed Nov 20 02:32:44 UTC 2024 I: Downloading source for trixie/r-bioc-genelendatabase=1.40.1-1 --2024-11-20 02:32:44-- http://deb.debian.org/debian/pool/main/r/r-bioc-genelendatabase/r-bioc-genelendatabase_1.40.1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2242 (2.2K) [text/prs.lines.tag] Saving to: ‘r-bioc-genelendatabase_1.40.1-1.dsc’ 0K .. 100% 305M=0s 2024-11-20 02:32:44 (305 MB/s) - ‘r-bioc-genelendatabase_1.40.1-1.dsc’ saved [2242/2242] Wed Nov 20 02:32:44 UTC 2024 I: r-bioc-genelendatabase_1.40.1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: r-bioc-genelendatabase Binary: r-bioc-genelendatabase Architecture: all Version: 1.40.1-1 Maintainer: Debian R Packages Maintainers Uploaders: Andreas Tille Homepage: https://bioconductor.org/packages/data/experiment/geneLenDataBase/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-genelendatabase Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-genelendatabase.git Testsuite: autopkgtest-pkg-r Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-rtracklayer (>= 1.64.0), r-bioc-genomicfeatures (>= 1.56.0), r-bioc-txdbmaker Package-List: r-bioc-genelendatabase deb gnu-r optional arch=all Checksums-Sha1: a1640c1727942d04411af4016b54ba80c6ba2ee5 100438279 r-bioc-genelendatabase_1.40.1.orig.tar.gz a481392c49e0b4abe847566831838884c86ea85c 4928 r-bioc-genelendatabase_1.40.1-1.debian.tar.xz Checksums-Sha256: 689efdfe8d896720a2d43162ea8d877f6cced7efa9c5a4b760f9bcfcb0060e31 100438279 r-bioc-genelendatabase_1.40.1.orig.tar.gz f79047a6d64157d82e297cf2493fe33b39a4a4ff377ad3eca97ed724f87c8c8c 4928 r-bioc-genelendatabase_1.40.1-1.debian.tar.xz Files: a5b4f62fdd6d45a9f8e59575266961cc 100438279 r-bioc-genelendatabase_1.40.1.orig.tar.gz cc63ab26f56c4104fc974e1fd5ca68db 4928 r-bioc-genelendatabase_1.40.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmbBzTwACgkQPCZ2P2xn 5uKWyA/+MDxguA+mPIWK5fJ/tDc7OwVN/WnIitZ5C5GClorZSWcv+yo7x8hg056s zNIsHe/JdEg5xNgE+/ecpr2RvbcNHvNT7cN4n7SXsnM7xTWp7FsHaUEONljIlQbQ 54pXgblX3Qb9+t64Avc3YM+FQNOknUji+FOe6EczBG4iTP59NzsH35gC9bLU/YKS 8tNb62s52SdmtN3eDoxWjuZBWnSHgdKeL+zZ5+6VAhYKjD+j6dY0ekccNb57Sbdz LkmWXx6dLC0DNKqe/ja6k7+t5tR/KCO+qrfafTEMmo9/mSZqNgQP8iE8voKtCe0w AqbaqaDFPr3pBh+JGwa4myltELTaHHBtK6eQOE4wRriFYm5h44IhUA1E5F3ZdhPE uZXIgiq9kvC0d0REYU0N4I8GnO+RCi/Aq2UHbNzeSAaWSs8SkpoWY2cp2xFgKgiA ixGf61tcIXve+4XSZiWFuCH/1665/komGAk/5hIgBzXw26ENv8fjOlkD+J+g3QEy 1s4ThNPCKSRb5V+/qJapxtIvGS7rcr3q+y9gFx1a243lSNunkhXAE4hUoGg5gMDs Va40lV0T1n2vME1zYd8kdjQzpX5bsYoSKt6Gsknt9x2wcQbmWcy+AKY2U/uVtNHy 2H7FskUZ+eXQS0yhTOrzVEn4LT1VrY7fy9ZM/7EkQ+etO0RKV9w= =kGYY -----END PGP SIGNATURE----- Wed Nov 20 02:32:44 UTC 2024 I: Checking whether the package is not for us Wed Nov 20 02:32:44 UTC 2024 I: Starting 1st build on remote node infom07-i386.debian.net. Wed Nov 20 02:32:44 UTC 2024 I: Preparing to do remote build '1' on infom07-i386.debian.net. Wed Nov 20 02:33:12 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Nov 19 14:32:48 -12 2024 I: pbuilder-time-stamp: 1732069968 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: using eatmydata during job I: Copying source file I: copying [r-bioc-genelendatabase_1.40.1-1.dsc] I: copying [./r-bioc-genelendatabase_1.40.1.orig.tar.gz] I: copying [./r-bioc-genelendatabase_1.40.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 18 10:30:20 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./r-bioc-genelendatabase_1.40.1-1.dsc: no acceptable signature found dpkg-source: info: extracting r-bioc-genelendatabase in r-bioc-genelendatabase-1.40.1 dpkg-source: info: unpacking r-bioc-genelendatabase_1.40.1.orig.tar.gz dpkg-source: info: unpacking r-bioc-genelendatabase_1.40.1-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/23030/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='853f04aa04374cd6a0b6da94225e2298' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='23030' 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.o6WQAzZ0/pbuilderrc_Zh84 --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.o6WQAzZ0/b1 --logfile b1/build.log r-bioc-genelendatabase_1.40.1-1.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom07-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/23030/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: i386 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-rtracklayer (>= 1.64.0), r-bioc-genomicfeatures (>= 1.56.0), r-bioc-txdbmaker dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19956 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-rtracklayer (>= 1.64.0); however: Package r-bioc-rtracklayer is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomicfeatures (>= 1.56.0); however: Package r-bioc-genomicfeatures is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-txdbmaker; however: Package r-bioc-txdbmaker 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} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-r{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-i686-linux-gnu{a} gfortran-i686-linux-gnu{a} groff-base{a} icu-devtools{a} intltool-debian{a} libalgorithm-c3-perl{a} libarchive-zip-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libclass-c3-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclone-perl{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-optlist-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libeval-closure-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran-14-dev{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhttp-date-perl{a} libhttp-message-perl{a} libice6{a} libicu-dev{a} libicu72{a} libio-html-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblwp-mediatypes-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmodule-implementation-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoose-perl{a} libmro-compat-perl{a} libnamespace-clean-perl{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-classify-perl{a} libparams-util-perl{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libswitch-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libvariable-magic-perl{a} libwebp7{a} libwww-curl-perl{a} libwww-curl-simple-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxmuu1{a} libxrender1{a} libxss1{a} libxt6t64{a} m4{a} man-db{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} r-base-core{a} r-base-dev{a} readline-common{a} sensible-utils{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xauth{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc cme curl devscripts git-buildpackage krb5-locales libarchive-cpio-perl libclass-c3-xs-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libio-compress-brotli-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl lynx publicsuffix r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 185 newly installed, 0 to remove and 0 not upgraded. Need to get 104 MB of archives. After unpacking 320 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: r-bioc-rtracklayer (>= 1.64.0) which is a virtual package and is not provided by any available package Depends: r-bioc-genomicfeatures (>= 1.56.0) but it is not installable Depends: r-bioc-txdbmaker 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} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-r{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-i686-linux-gnu{a} gfortran-i686-linux-gnu{a} groff-base{a} icu-devtools{a} intltool-debian{a} libalgorithm-c3-perl{a} libarchive-zip-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libclass-c3-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclone-perl{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-optlist-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libeval-closure-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran-14-dev{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhttp-date-perl{a} libhttp-message-perl{a} libice6{a} libicu-dev{a} libicu72{a} libio-html-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblwp-mediatypes-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmodule-implementation-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoose-perl{a} libmro-compat-perl{a} libnamespace-clean-perl{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-classify-perl{a} libparams-util-perl{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libswitch-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libvariable-magic-perl{a} libwebp7{a} libwww-curl-perl{a} libwww-curl-simple-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxmuu1{a} libxrender1{a} libxss1{a} libxt6t64{a} m4{a} man-db{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} r-base-core{a} r-base-dev{a} readline-common{a} sensible-utils{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xauth{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc cme curl devscripts git-buildpackage krb5-locales libarchive-cpio-perl libclass-c3-xs-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libio-compress-brotli-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl lynx publicsuffix r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 185 newly installed, 0 to remove and 0 not upgraded. Need to get 104 MB of archives. After unpacking 320 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/23030 and its subdirectories Wed Nov 20 02:33:13 UTC 2024 W: No second build log, what happened? Wed Nov 20 02:33:13 UTC 2024 W: Downloading the build dependencies failed Wed Nov 20 02:33:13 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Wed Nov 20 02:33:13 UTC 2024 W: Network problems are automatically rescheduled after some hours.