Running as unit: rb-build-i386_12-30192.service ==================================================================================== Fri Nov 22 14:31:29 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_i386_12) on jenkins, called using "ionos12-i386 ionos16-i386" as arguments. Fri Nov 22 14:31:29 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-9fYqDMxC" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 14:31:29 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos12-i386.debian.net is marked as down. Fri Nov 22 14:31:29 UTC 2024 - checking via ssh if ionos12-i386.debian.net is up. removed '/tmp/read-only-fs-test-ml6bW5' Fri Nov 22 14:31:30 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos16-i386.debian.net is marked as down. Fri Nov 22 14:31:30 UTC 2024 - checking via ssh if ionos16-i386.debian.net is up. removed '/tmp/read-only-fs-test-mSLZbO' ok, let's check if r-bioc-structuralvariantannotation is building anywhere yet… ok, r-bioc-structuralvariantannotation is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of r-bioc-structuralvariantannotation in trixie on i386 on jenkins now. 1st build will be done on ionos12-i386.debian.net. 2nd build will be done on ionos16-i386.debian.net. ============================================================================= Fri Nov 22 14:31:47 UTC 2024 I: starting to build r-bioc-structuralvariantannotation/trixie/i386 on jenkins on '2024-11-22 14:31' Fri Nov 22 14:31:47 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/30192/console.log 1732285907 i386 trixie r-bioc-structuralvariantannotation Fri Nov 22 14:31:47 UTC 2024 I: Downloading source for trixie/r-bioc-structuralvariantannotation=1.20.0+ds-1 --2024-11-22 14:31:47-- http://deb.debian.org/debian/pool/main/r/r-bioc-structuralvariantannotation/r-bioc-structuralvariantannotation_1.20.0%2bds-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2734 (2.7K) [text/prs.lines.tag] Saving to: ‘r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc’ 0K .. 100% 405M=0s 2024-11-22 14:31:47 (405 MB/s) - ‘r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc’ saved [2734/2734] --2024-11-22 14:31:47-- http://deb.debian.org/debian/pool/main/r/r-bioc-structuralvariantannotation/r-bioc-structuralvariantannotation_1.20.0%2bds-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2734 (2.7K) [text/prs.lines.tag] Saving to: ‘r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc’ 0K .. 100% 405M=0s 2024-11-22 14:31:47 (405 MB/s) - ‘r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc’ saved [2734/2734] Fri Nov 22 14:31:47 UTC 2024 I: r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: r-bioc-structuralvariantannotation Binary: r-bioc-structuralvariantannotation Architecture: all Version: 1.20.0+ds-1 Maintainer: Debian R Packages Maintainers Uploaders: Steffen Moeller Homepage: https://bioconductor.org/packages/StructuralVariantAnnotation/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-structuralvariantannotation Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-structuralvariantannotation.git Testsuite: autopkgtest-pkg-r Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-genomicranges (>= 1.56.1), r-bioc-rtracklayer (>= 1.64.0), r-bioc-variantannotation (>= 1.50.0), r-bioc-biocgenerics (>= 0.50.0), r-cran-assertthat, r-bioc-biostrings (>= 2.72.1), r-bioc-pwalign (>= 1.0.0-2~0exp1), r-cran-stringr, r-cran-dplyr, r-cran-rlang, r-bioc-genomicfeatures (>= 1.56.0), r-bioc-iranges (>= 2.38.1), r-bioc-s4vectors (>= 0.42.1), r-bioc-summarizedexperiment (>= 1.34.0), r-bioc-genomeinfodb (>= 1.40.1) Package-List: r-bioc-structuralvariantannotation deb gnu-r optional arch=all Checksums-Sha1: 4babbb8b439f98036abd0710368bf3c7bad64e66 262388 r-bioc-structuralvariantannotation_1.20.0+ds.orig.tar.xz ee7d3360614b09f2448a202f398472a297ab29dd 7220 r-bioc-structuralvariantannotation_1.20.0+ds-1.debian.tar.xz Checksums-Sha256: 185810ad426b57eb7c2da4a84a4a8851377c30823008cb00c8950232109c65c8 262388 r-bioc-structuralvariantannotation_1.20.0+ds.orig.tar.xz fa52b86eb82b253d7a2e3910b20a5c9d77cb57a3b04a7017e31a6d5d10c22c81 7220 r-bioc-structuralvariantannotation_1.20.0+ds-1.debian.tar.xz Files: 7d7a1b4072c77868d7a5334c6ced5e97 262388 r-bioc-structuralvariantannotation_1.20.0+ds.orig.tar.xz ec24476e68b123680366435372d3eda0 7220 r-bioc-structuralvariantannotation_1.20.0+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmbBz8cACgkQPCZ2P2xn 5uLkGRAArUaZUJDMwEQAlsxyxdW5hF+4RqszDZPi3m/OwWN2S86oCqba6bDZxrmE euu2u5N1XS/771k0Sl+NuULxac6guaZuDBCs2XUrD4y48sR8ruguZWs2h8F04uwy mIRl0hVbI9yPdqU4zUSC+y/71SOsFujMxCCY+J8fAu25UBsDWMLjV38uLcF7GIRV 6o1bFwVleCqSQ2Vrw0E1Wlih22M8jVCytxbChedRdsyN82/clOtapVfBz/P1C2ll ULqVVIF+XQKh9PZCB3/jCUfo0UKmTmwhzHua0MZ+1JUIr56p9+/jBBBQOQsAmYwo DudAl1KUJ49jHRRaz+GasaX6y+BtxIhA83DumjEuzUoB7Qyaf/TPYBJcweOEgFBS 9arkywn92fg4fmz3mhr68vMNgfFR5x9BX+F9U0iZxYcZQXccGnD4H1s1P5/wK7i1 xJdrZY2WqEDHpCJNAxmOXmLxcJJlFMjvaYhaqvPVdbK/AI4gmYzqIH9SPeKw/yAD 6a0N31v+bhJ52IGI7SDF6NNZttb5x+awcjvUPMm+6YH5mDPEOVi1Za6epuosRBoL I2rYgCO10Rw9UNrvi565LDZy5Q6OGTnrZmA7CCUcdOLlgybp5HJyA9BcvcvZRzcH 5IqwfZ2vZvltvx+0p784yXmmKKAUOGs/vrxtLUEaEQF1TeTfL/M= =snxM -----END PGP SIGNATURE----- Fri Nov 22 14:31:47 UTC 2024 I: Checking whether the package is not for us Fri Nov 22 14:31:47 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Fri Nov 22 14:31:47 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Fri Nov 22 14:31:47 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos12-i386.debian.net is marked as down. Fri Nov 22 14:31:47 UTC 2024 - checking via ssh if ionos12-i386.debian.net is up. removed '/tmp/read-only-fs-test-p4s0mY' ==================================================================================== Fri Nov 22 14:31:49 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos12-i386, called using "1 r-bioc-structuralvariantannotation trixie /srv/reproducible-results/rbuild-debian/r-b-build.a8RnUObV 1.20.0+ds-1" as arguments. Fri Nov 22 14:31:49 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Eev68zw8" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 14:31:49 UTC 2024 I: Downloading source for trixie/r-bioc-structuralvariantannotation=1.20.0+ds-1 Reading package lists... NOTICE: 'r-bioc-structuralvariantannotation' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-structuralvariantannotation.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-structuralvariantannotation.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 272 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main r-bioc-structuralvariantannotation 1.20.0+ds-1 (dsc) [2734 B] Get:2 http://deb.debian.org/debian trixie/main r-bioc-structuralvariantannotation 1.20.0+ds-1 (tar) [262 kB] Get:3 http://deb.debian.org/debian trixie/main r-bioc-structuralvariantannotation 1.20.0+ds-1 (diff) [7220 B] Fetched 272 kB in 0s (4345 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'r-bioc-structuralvariantannotation' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-structuralvariantannotation.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-structuralvariantannotation.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 272 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main r-bioc-structuralvariantannotation 1.20.0+ds-1 (dsc) [2734 B] Get:2 http://deb.debian.org/debian trixie/main r-bioc-structuralvariantannotation 1.20.0+ds-1 (tar) [262 kB] Get:3 http://deb.debian.org/debian trixie/main r-bioc-structuralvariantannotation 1.20.0+ds-1 (diff) [7220 B] Fetched 272 kB in 0s (4345 kB/s) Download complete and in download only mode ============================================================================= Building r-bioc-structuralvariantannotation in trixie on i386 on ionos12-i386 now. Date: Fri Nov 22 15:31:49 CET 2024 Date UTC: Fri Nov 22 14:31:49 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: Fri Nov 22 02:31:50 -12 2024 I: pbuilder-time-stamp: 1732285910 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-structuralvariantannotation_1.20.0+ds-1.dsc] I: copying [./r-bioc-structuralvariantannotation_1.20.0+ds.orig.tar.xz] I: copying [./r-bioc-structuralvariantannotation_1.20.0+ds-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 18 10:41:11 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting r-bioc-structuralvariantannotation in r-bioc-structuralvariantannotation-1.20.0+ds dpkg-source: info: unpacking r-bioc-structuralvariantannotation_1.20.0+ds.orig.tar.xz dpkg-source: info: unpacking r-bioc-structuralvariantannotation_1.20.0+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_requiring_large_data.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/9080/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=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='269573733fc34f4191d85ab6286b3957' 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='9080' 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.a8RnUObV/pbuilderrc_DaD9 --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.a8RnUObV/b1 --logfile b1/build.log r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-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/9080/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-genomicranges (>= 1.56.1), r-bioc-rtracklayer (>= 1.64.0), r-bioc-variantannotation (>= 1.50.0), r-bioc-biocgenerics (>= 0.50.0), r-cran-assertthat, r-bioc-biostrings (>= 2.72.1), r-bioc-pwalign (>= 1.0.0-2~0exp1), r-cran-stringr, r-cran-dplyr, r-cran-rlang, r-bioc-genomicfeatures (>= 1.56.0), r-bioc-iranges (>= 2.38.1), r-bioc-s4vectors (>= 0.42.1), r-bioc-summarizedexperiment (>= 1.34.0), r-bioc-genomeinfodb (>= 1.40.1) 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-genomicranges (>= 1.56.1); however: Package r-bioc-genomicranges 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-variantannotation (>= 1.50.0); however: Package r-bioc-variantannotation is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biocgenerics (>= 0.50.0); however: Package r-bioc-biocgenerics is not installed. pbuilder-satisfydepends-dummy depends on r-cran-assertthat; however: Package r-cran-assertthat is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biostrings (>= 2.72.1); however: Package r-bioc-biostrings is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-pwalign (>= 1.0.0-2~0exp1); however: Package r-bioc-pwalign is not installed. pbuilder-satisfydepends-dummy depends on r-cran-stringr; however: Package r-cran-stringr is not installed. pbuilder-satisfydepends-dummy depends on r-cran-dplyr; however: Package r-cran-dplyr is not installed. pbuilder-satisfydepends-dummy depends on r-cran-rlang; however: Package r-cran-rlang 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-iranges (>= 2.38.1); however: Package r-bioc-iranges is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-s4vectors (>= 0.42.1); however: Package r-bioc-s4vectors is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-summarizedexperiment (>= 1.34.0); however: Package r-bioc-summarizedexperiment is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomeinfodb (>= 1.40.1); however: Package r-bioc-genomeinfodb 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} r-bioc-biocgenerics{a} r-bioc-s4vectors{a} r-cran-assertthat{a} r-cran-cli{a} r-cran-dplyr{a} r-cran-fansi{a} r-cran-generics{a} r-cran-glue{a} r-cran-lifecycle{a} r-cran-magrittr{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-r6{a} r-cran-rlang{a} r-cran-stringi{a} r-cran-stringr{a} r-cran-tibble{a} r-cran-tidyselect{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-withr{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-cran-bench r-cran-bit64 r-cran-broom r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-formattable r-cran-fs r-cran-ggplot2 r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-lintr r-cran-lobstr r-cran-lubridate r-cran-mockery r-cran-pkgdown r-cran-pkgload r-cran-processx r-cran-ps r-cran-purrr r-cran-rmarkdown r-cran-rmysql r-cran-rpostgresql r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-testthat r-cran-tidyr r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 206 newly installed, 0 to remove and 0 not upgraded. Need to get 117 MB of archives. After unpacking 341 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: r-bioc-genomicranges (>= 1.56.1) which is a virtual package and is not provided by any available package Depends: r-bioc-rtracklayer (>= 1.64.0) which is a virtual package and is not provided by any available package Depends: r-bioc-variantannotation (>= 1.50.0) which is a virtual package and is not provided by any available package Depends: r-bioc-biostrings (>= 2.72.1) which is a virtual package and is not provided by any available package Depends: r-bioc-pwalign (>= 1.0.0-2~0exp1) 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-iranges (>= 2.38.1) which is a virtual package and is not provided by any available package Depends: r-bioc-summarizedexperiment (>= 1.34.0) but it is not installable Depends: r-bioc-genomeinfodb (>= 1.40.1) 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} r-bioc-biocgenerics{a} r-bioc-s4vectors{a} r-cran-assertthat{a} r-cran-cli{a} r-cran-dplyr{a} r-cran-fansi{a} r-cran-generics{a} r-cran-glue{a} r-cran-lifecycle{a} r-cran-magrittr{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-r6{a} r-cran-rlang{a} r-cran-stringi{a} r-cran-stringr{a} r-cran-tibble{a} r-cran-tidyselect{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-withr{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-cran-bench r-cran-bit64 r-cran-broom r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-formattable r-cran-fs r-cran-ggplot2 r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-lintr r-cran-lobstr r-cran-lubridate r-cran-mockery r-cran-pkgdown r-cran-pkgload r-cran-processx r-cran-ps r-cran-purrr r-cran-rmarkdown r-cran-rmysql r-cran-rpostgresql r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-testthat r-cran-tidyr r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 206 newly installed, 0 to remove and 0 not upgraded. Need to get 117 MB of archives. After unpacking 341 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/9080 and its subdirectories Starting cleanup. All cleanup done. Fri Nov 22 14:32:14 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-Eev68zw8, removing. /srv/reproducible-results/rbuild-debian/r-b-build.a8RnUObV: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 14:32 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 14:31 b2 -rw-r--r-- 1 jenkins jenkins 2734 Aug 18 10:46 r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc -rw------- 1 jenkins jenkins 4039 Nov 22 14:31 rbuildlog.PdvWwmO /srv/reproducible-results/rbuild-debian/r-b-build.a8RnUObV/b1: total 20 -rw-r--r-- 1 jenkins jenkins 19117 Nov 22 14:32 build.log /srv/reproducible-results/rbuild-debian/r-b-build.a8RnUObV/b2: total 0 Fri Nov 22 14:32:14 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Nov 22 02:31:50 -12 2024 I: pbuilder-time-stamp: 1732285910 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-structuralvariantannotation_1.20.0+ds-1.dsc] I: copying [./r-bioc-structuralvariantannotation_1.20.0+ds.orig.tar.xz] I: copying [./r-bioc-structuralvariantannotation_1.20.0+ds-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 18 10:41:11 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting r-bioc-structuralvariantannotation in r-bioc-structuralvariantannotation-1.20.0+ds dpkg-source: info: unpacking r-bioc-structuralvariantannotation_1.20.0+ds.orig.tar.xz dpkg-source: info: unpacking r-bioc-structuralvariantannotation_1.20.0+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_requiring_large_data.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/9080/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=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='269573733fc34f4191d85ab6286b3957' 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='9080' 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.a8RnUObV/pbuilderrc_DaD9 --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.a8RnUObV/b1 --logfile b1/build.log r-bioc-structuralvariantannotation_1.20.0+ds-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-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/9080/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-genomicranges (>= 1.56.1), r-bioc-rtracklayer (>= 1.64.0), r-bioc-variantannotation (>= 1.50.0), r-bioc-biocgenerics (>= 0.50.0), r-cran-assertthat, r-bioc-biostrings (>= 2.72.1), r-bioc-pwalign (>= 1.0.0-2~0exp1), r-cran-stringr, r-cran-dplyr, r-cran-rlang, r-bioc-genomicfeatures (>= 1.56.0), r-bioc-iranges (>= 2.38.1), r-bioc-s4vectors (>= 0.42.1), r-bioc-summarizedexperiment (>= 1.34.0), r-bioc-genomeinfodb (>= 1.40.1) 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-genomicranges (>= 1.56.1); however: Package r-bioc-genomicranges 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-variantannotation (>= 1.50.0); however: Package r-bioc-variantannotation is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biocgenerics (>= 0.50.0); however: Package r-bioc-biocgenerics is not installed. pbuilder-satisfydepends-dummy depends on r-cran-assertthat; however: Package r-cran-assertthat is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-biostrings (>= 2.72.1); however: Package r-bioc-biostrings is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-pwalign (>= 1.0.0-2~0exp1); however: Package r-bioc-pwalign is not installed. pbuilder-satisfydepends-dummy depends on r-cran-stringr; however: Package r-cran-stringr is not installed. pbuilder-satisfydepends-dummy depends on r-cran-dplyr; however: Package r-cran-dplyr is not installed. pbuilder-satisfydepends-dummy depends on r-cran-rlang; however: Package r-cran-rlang 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-iranges (>= 2.38.1); however: Package r-bioc-iranges is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-s4vectors (>= 0.42.1); however: Package r-bioc-s4vectors is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-summarizedexperiment (>= 1.34.0); however: Package r-bioc-summarizedexperiment is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-genomeinfodb (>= 1.40.1); however: Package r-bioc-genomeinfodb 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} r-bioc-biocgenerics{a} r-bioc-s4vectors{a} r-cran-assertthat{a} r-cran-cli{a} r-cran-dplyr{a} r-cran-fansi{a} r-cran-generics{a} r-cran-glue{a} r-cran-lifecycle{a} r-cran-magrittr{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-r6{a} r-cran-rlang{a} r-cran-stringi{a} r-cran-stringr{a} r-cran-tibble{a} r-cran-tidyselect{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-withr{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-cran-bench r-cran-bit64 r-cran-broom r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-formattable r-cran-fs r-cran-ggplot2 r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-lintr r-cran-lobstr r-cran-lubridate r-cran-mockery r-cran-pkgdown r-cran-pkgload r-cran-processx r-cran-ps r-cran-purrr r-cran-rmarkdown r-cran-rmysql r-cran-rpostgresql r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-testthat r-cran-tidyr r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 206 newly installed, 0 to remove and 0 not upgraded. Need to get 117 MB of archives. After unpacking 341 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: r-bioc-genomicranges (>= 1.56.1) which is a virtual package and is not provided by any available package Depends: r-bioc-rtracklayer (>= 1.64.0) which is a virtual package and is not provided by any available package Depends: r-bioc-variantannotation (>= 1.50.0) which is a virtual package and is not provided by any available package Depends: r-bioc-biostrings (>= 2.72.1) which is a virtual package and is not provided by any available package Depends: r-bioc-pwalign (>= 1.0.0-2~0exp1) 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-iranges (>= 2.38.1) which is a virtual package and is not provided by any available package Depends: r-bioc-summarizedexperiment (>= 1.34.0) but it is not installable Depends: r-bioc-genomeinfodb (>= 1.40.1) 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} r-bioc-biocgenerics{a} r-bioc-s4vectors{a} r-cran-assertthat{a} r-cran-cli{a} r-cran-dplyr{a} r-cran-fansi{a} r-cran-generics{a} r-cran-glue{a} r-cran-lifecycle{a} r-cran-magrittr{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-r6{a} r-cran-rlang{a} r-cran-stringi{a} r-cran-stringr{a} r-cran-tibble{a} r-cran-tidyselect{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-withr{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-cran-bench r-cran-bit64 r-cran-broom r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-formattable r-cran-fs r-cran-ggplot2 r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-lintr r-cran-lobstr r-cran-lubridate r-cran-mockery r-cran-pkgdown r-cran-pkgload r-cran-processx r-cran-ps r-cran-purrr r-cran-rmarkdown r-cran-rmysql r-cran-rpostgresql r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-testthat r-cran-tidyr r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 206 newly installed, 0 to remove and 0 not upgraded. Need to get 117 MB of archives. After unpacking 341 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/9080 and its subdirectories r-bioc-structuralvariantannotation failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.build1.log.gz' Fri Nov 22 14:32:15 UTC 2024 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 76.3% -- replaced with stdout Fri Nov 22 14:32:15 UTC 2024 W: Downloading the build dependencies failed Fri Nov 22 14:32:15 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 Nov 22 14:32:15 UTC 2024 W: Network problems are automatically rescheduled after some hours. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-22 14:32:16] INFO: Starting at 2024-11-22 14:32:16.365120 [2024-11-22 14:32:16] INFO: Generating the pages of 1 package(s) [2024-11-22 14:32:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/r-bioc-structuralvariantannotation_1.20.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/r-bioc-structuralvariantannotation_1.20.0+ds-1.diff.gz is missing [2024-11-22 14:32:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.diff.gz is missing [2024-11-22 14:32:16] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/r-bioc-structuralvariantannotation_1.20.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/r-bioc-structuralvariantannotation_1.20.0+ds-1.diff.gz is missing [2024-11-22 14:32:16] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/i386/r-bioc-structuralvariantannotation didn't produce a buildlog, even though it has been built. [2024-11-22 14:32:16] INFO: Finished at 2024-11-22 14:32:16.888499, took: 0:00:00.523386 Fri Nov 22 14:32:16 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/i386/r-bioc-structuralvariantannotation.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.rbuild.log: 73.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.rbuild.log.gz [2024-11-22 14:32:17] INFO: Starting at 2024-11-22 14:32:17.260839 [2024-11-22 14:32:17] INFO: Generating the pages of 1 package(s) [2024-11-22 14:32:17] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/r-bioc-structuralvariantannotation_1.20.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/r-bioc-structuralvariantannotation_1.20.0+ds-1.diff.gz is missing [2024-11-22 14:32:17] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.diff.gz is missing [2024-11-22 14:32:17] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/r-bioc-structuralvariantannotation_1.20.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/r-bioc-structuralvariantannotation_1.20.0+ds-1.diff.gz is missing [2024-11-22 14:32:17] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/r-bioc-structuralvariantannotation_1.20.0+ds-1.diff.gz is missing [2024-11-22 14:32:17] INFO: Finished at 2024-11-22 14:32:17.594381, took: 0:00:00.333548 All cleanup done. Fri Nov 22 14:32:17 UTC 2024 - total duration: 0h 0m 46s. Fri Nov 22 14:32:17 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-9fYqDMxC, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 48.098s CPU time consumed: 5.191s