Thu Mar 20 02:20:04 UTC 2025 I: starting to build snippy/trixie/armhf on jenkins on '2025-03-20 02:19'
Thu Mar 20 02:20:04 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_27/14189/console.log
Thu Mar 20 02:20:04 UTC 2025 I: Downloading source for trixie/snippy=4.6.0+dfsg-5
--2025-03-20 02:20:04-- http://deb.debian.org/debian/pool/main/s/snippy/snippy_4.6.0%2bdfsg-5.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2353 (2.3K) [text/prs.lines.tag]
Saving to: ‘snippy_4.6.0+dfsg-5.dsc’
0K .. 100% 363M=0s
2025-03-20 02:20:04 (363 MB/s) - ‘snippy_4.6.0+dfsg-5.dsc’ saved [2353/2353]
Thu Mar 20 02:20:04 UTC 2025 I: snippy_4.6.0+dfsg-5.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: snippy
Binary: snippy, snippy-examples
Architecture: all
Version: 4.6.0+dfsg-5
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/tseemann/snippy/
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/snippy
Vcs-Git: https://salsa.debian.org/med-team/snippy.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), any2fasta <!nocheck>, bcftools <!nocheck>, bedtools <!nocheck>, bwa <!nocheck>, freebayes <!nocheck>, libbio-perl-perl <!nocheck>, libvcflib-tools <!nocheck>, minimap2 <!nocheck>, parallel <!nocheck>, samtools <!nocheck>, samclip <!nocheck>, seqtk <!nocheck>, snp-sites <!nocheck>, snpeff <!nocheck>, vt <!nocheck>
Package-List:
snippy deb science optional arch=all
snippy-examples deb science optional arch=all
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Files:
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Thu Mar 20 02:20:04 UTC 2025 I: Checking whether the package is not for us
Thu Mar 20 02:20:04 UTC 2025 I: Starting 1st build on remote node virt64z-armhf-rb.debian.net.
Thu Mar 20 02:20:04 UTC 2025 I: Preparing to do remote build '1' on virt64z-armhf-rb.debian.net.
Thu Mar 20 02:20:39 UTC 2025 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Wed Mar 19 14:20:10 -12 2025
I: pbuilder-time-stamp: 1742437210
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 [snippy_4.6.0+dfsg-5.dsc]
I: copying [./snippy_4.6.0+dfsg.orig.tar.xz]
I: copying [./snippy_4.6.0+dfsg-5.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./snippy_4.6.0+dfsg-5.dsc: unsupported subcommand
dpkg-source: info: extracting snippy in snippy-4.6.0+dfsg
dpkg-source: info: unpacking snippy_4.6.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking snippy_4.6.0+dfsg-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying debian_packaged_libs.patch
dpkg-source: info: applying snpeff.config.patch
dpkg-source: info: applying snpeff_v5.1+.patch
dpkg-source: info: applying make-4.4.1.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/22895/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='bb5b084bd00e4f2ea4f81bbd2bcbf187'
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='22895'
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.ehZYQiT0/pbuilderrc_0uKq --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.ehZYQiT0/b1 --logfile b1/build.log snippy_4.6.0+dfsg-5.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 virt64z 6.1.0-32-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/22895/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 <pbuilder-maint@lists.alioth.debian.org>
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), any2fasta, bcftools, bedtools, bwa, freebayes, libbio-perl-perl, libvcflib-tools, minimap2, parallel, samtools, samclip, seqtk, snp-sites, snpeff, vt
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19510 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 any2fasta; however:
Package any2fasta is not installed.
pbuilder-satisfydepends-dummy depends on bcftools; however:
Package bcftools is not installed.
pbuilder-satisfydepends-dummy depends on bedtools; however:
Package bedtools is not installed.
pbuilder-satisfydepends-dummy depends on bwa; however:
Package bwa is not installed.
pbuilder-satisfydepends-dummy depends on freebayes; however:
Package freebayes is not installed.
pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however:
Package libbio-perl-perl is not installed.
pbuilder-satisfydepends-dummy depends on libvcflib-tools; however:
Package libvcflib-tools is not installed.
pbuilder-satisfydepends-dummy depends on minimap2; however:
Package minimap2 is not installed.
pbuilder-satisfydepends-dummy depends on parallel; however:
Package parallel is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on samclip; however:
Package samclip is not installed.
pbuilder-satisfydepends-dummy depends on seqtk; however:
Package seqtk is not installed.
pbuilder-satisfydepends-dummy depends on snp-sites; however:
Package snp-sites is not installed.
pbuilder-satisfydepends-dummy depends on snpeff; however:
Package snpeff is not installed.
pbuilder-satisfydepends-dummy depends on vt; however:
Package vt 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:
any2fasta{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bedtools{a} bsdextrautils{a} bwa{a} ca-certificates{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} debhelper{a} dh-autoreconf{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} groff-base{a} intltool-debian{a} libapparmor1{a} libarchive-zip-perl{a} libbio-perl-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-stag-perl{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libidn2-0{a} libio-string-perl{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv0{a} libsm6{a} libsnp-sites1{a} libssh2-1t64{a} libsystemd-shared{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{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} libxrender1{a} libxss1{a} libxt6t64{a} m4{a} man-db{a} minimap2{a} openssl{a} parallel{a} po-debconf{a} procps{a} r-base-core{a} readline-common{a} samclip{a} samtools{a} sensible-utils{a} seqtk{a} shared-mime-info{a} snp-sites{a} sysstat{a} systemd{a} systemd-sysv{a} tzdata{a} ucf{a} unzip{a} vt{a} x11-common{a} xdg-utils{a} zip{a}
The following packages are RECOMMENDED but will NOT be installed:
bioperl-run chrony curl krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libfile-mimeinfo-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libkmod2 libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libnet-dbus-perl libnss-systemd libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl linux-sysctl-defaults lynx ntpsec openntpd perl-tk psmisc publicsuffix python3-gffutils python3-matplotlib r-base-dev r-doc-html r-recommended systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs
0 packages upgraded, 153 newly installed, 0 to remove and 0 not upgraded.
Need to get 85.2 MB of archives. After unpacking 223 MB will be used.
The following packages have unmet dependencies:
pbuilder-satisfydepends-dummy : Depends: freebayes which is a virtual package and is not provided by any available package
Depends: libvcflib-tools which is a virtual package and is not provided by any available package
Depends: snpeff but it is not installable
Unable to resolve dependencies! Giving up...
The following NEW packages will be installed:
any2fasta{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bedtools{a} bsdextrautils{a} bwa{a} ca-certificates{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} debhelper{a} dh-autoreconf{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} groff-base{a} intltool-debian{a} libapparmor1{a} libarchive-zip-perl{a} libbio-perl-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-stag-perl{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libidn2-0{a} libio-string-perl{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv0{a} libsm6{a} libsnp-sites1{a} libssh2-1t64{a} libsystemd-shared{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{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} libxrender1{a} libxss1{a} libxt6t64{a} m4{a} man-db{a} minimap2{a} openssl{a} parallel{a} po-debconf{a} procps{a} r-base-core{a} readline-common{a} samclip{a} samtools{a} sensible-utils{a} seqtk{a} shared-mime-info{a} snp-sites{a} sysstat{a} systemd{a} systemd-sysv{a} tzdata{a} ucf{a} unzip{a} vt{a} x11-common{a} xdg-utils{a} zip{a}
The following packages are RECOMMENDED but will NOT be installed:
bioperl-run chrony curl krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libfile-mimeinfo-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libkmod2 libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libnet-dbus-perl libnss-systemd libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl linux-sysctl-defaults lynx ntpsec openntpd perl-tk psmisc publicsuffix python3-gffutils python3-matplotlib r-base-dev r-doc-html r-recommended systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs
0 packages upgraded, 153 newly installed, 0 to remove and 0 not upgraded.
Need to get 85.2 MB of archives. After unpacking 223 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/22895 and its subdirectories
Thu Mar 20 02:20:42 UTC 2025 W: No second build log, what happened?
Thu Mar 20 02:20:42 UTC 2025 W: Downloading the build dependencies failed
Thu Mar 20 02:20:42 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 Mar 20 02:20:42 UTC 2025 W: Network problems are automatically rescheduled after some hours.