Wed Nov 27 21:52:03 UTC 2024 I: starting to build psortb/trixie/armhf on jenkins on '2024-11-27 21:51'
Wed Nov 27 21:52:03 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_31/9124/console.log
Wed Nov 27 21:52:03 UTC 2024 I: Downloading source for trixie/psortb=3.0.6+dfsg-4
--2024-11-27 21:52:03-- http://deb.debian.org/debian/pool/main/p/psortb/psortb_3.0.6%2bdfsg-4.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2254 (2.2K) [text/prs.lines.tag]
Saving to: ‘psortb_3.0.6+dfsg-4.dsc’
0K .. 100% 244M=0s
2024-11-27 21:52:03 (244 MB/s) - ‘psortb_3.0.6+dfsg-4.dsc’ saved [2254/2254]
Wed Nov 27 21:52:03 UTC 2024 I: psortb_3.0.6+dfsg-4.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: psortb
Binary: psortb
Architecture: any
Version: 3.0.6+dfsg-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://www.psort.org/
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/psortb
Vcs-Git: https://salsa.debian.org/med-team/psortb.git
Testsuite: autopkgtest-pkg-perl
Build-Depends: debhelper-compat (= 13), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkgconf, pftools
Package-List:
psortb deb science optional arch=any
Checksums-Sha1:
c47d0ec328df75f2151dd6d5b5840768006519f8 17036876 psortb_3.0.6+dfsg.orig.tar.xz
c10819ffb3b3d31ca99a66f9768493ed46e5a541 7480 psortb_3.0.6+dfsg-4.debian.tar.xz
Checksums-Sha256:
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fc09ccbf18a26cefd75e8c6030e192878b94b251a6a3206614931820ef6344d0 7480 psortb_3.0.6+dfsg-4.debian.tar.xz
Files:
c4feab06d3031fecac1ab90258550209 17036876 psortb_3.0.6+dfsg.orig.tar.xz
dbe47096a741a5132191480aa07bb7d4 7480 psortb_3.0.6+dfsg-4.debian.tar.xz
Dgit: 4806a2aae47b085aac7d4851a89b803020876c96 debian archive/debian/3.0.6+dfsg-4 https://git.dgit.debian.org/psortb
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Wed Nov 27 21:52:03 UTC 2024 I: Checking whether the package is not for us
Wed Nov 27 21:52:03 UTC 2024 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net.
Wed Nov 27 21:52:03 UTC 2024 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net.
Wed Nov 27 21:53:13 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Wed Nov 27 09:52:17 -12 2024
I: pbuilder-time-stamp: 1732744337
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 [psortb_3.0.6+dfsg-4.dsc]
I: copying [./psortb_3.0.6+dfsg.orig.tar.xz]
I: copying [./psortb_3.0.6+dfsg-4.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun May 26 07:54:47 2024
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./psortb_3.0.6+dfsg-4.dsc: no acceptable signature found
dpkg-source: info: extracting psortb in psortb-3.0.6+dfsg
dpkg-source: info: unpacking psortb_3.0.6+dfsg.orig.tar.xz
dpkg-source: info: unpacking psortb_3.0.6+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying biosquid_includes.patch
dpkg-source: info: applying fix_hmmer_interface.patch
dpkg-source: info: applying fix_build_Algorithm-SVM.patch
dpkg-source: info: applying remove-bundled-party-libsvm.patch
dpkg-source: info: applying path_to_conf.patch
dpkg-source: info: applying fix_module_path.patch
dpkg-source: info: applying add_missing_header.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/19778/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='39be1322daf24b7ba8b623aed04cdaa9'
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='19778'
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.Jl5o3nfy/pbuilderrc_sf39 --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.Jl5o3nfy/b1 --logfile b1/build.log psortb_3.0.6+dfsg-4.dsc'
SUDO_GID='113'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux virt64c 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/19778/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), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkgconf, pftools
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19689 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 libsvm-dev; however:
Package libsvm-dev is not installed.
pbuilder-satisfydepends-dummy depends on bioperl; however:
Package bioperl is not installed.
pbuilder-satisfydepends-dummy depends on ncbi-blast+-legacy; however:
Package ncbi-blast+-legacy is not installed.
pbuilder-satisfydepends-dummy depends on libsquid-dev; however:
Package libsquid-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhmmer2-dev; however:
Package libhmmer2-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsvmloc-dev; however:
Package libsvmloc-dev is not installed.
pbuilder-satisfydepends-dummy depends on libmodhmm-dev; however:
Package libmodhmm-dev is not installed.
pbuilder-satisfydepends-dummy depends on pkgconf; however:
Package pkgconf is not installed.
pbuilder-satisfydepends-dummy depends on pftools; however:
Package pftools 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} bioperl{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} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbio-perl-perl{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libcom-err2{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodhmm-dev{a} libmodhmm0{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libsquid-dev{a} libsquid1t64{a} libsub-uplevel-perl{a} libsvm-dev{a} libsvm3{a} libsvmloc-dev{a} libsvmloc0{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} netbase{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a}
The following packages are RECOMMENDED but will NOT be installed:
bioperl-run ca-certificates curl krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libhttp-message-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-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 libyaml-perl lynx perl-doc perl-tk wget
0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded.
Need to get 47.6 MB of archives. After unpacking 182 MB will be used.
The following packages have unmet dependencies:
pbuilder-satisfydepends-dummy : Depends: pftools 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} bioperl{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} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbio-perl-perl{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libcom-err2{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodhmm-dev{a} libmodhmm0{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libsquid-dev{a} libsquid1t64{a} libsub-uplevel-perl{a} libsvm-dev{a} libsvm3{a} libsvmloc-dev{a} libsvmloc0{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} netbase{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a}
The following packages are RECOMMENDED but will NOT be installed:
bioperl-run ca-certificates curl krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libhttp-message-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-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 libyaml-perl lynx perl-doc perl-tk wget
0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded.
Need to get 47.6 MB of archives. After unpacking 182 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/19778 and its subdirectories
Wed Nov 27 21:53:15 UTC 2024 W: No second build log, what happened?
Wed Nov 27 21:53:16 UTC 2024 W: Downloading the build dependencies failed
Wed Nov 27 21:53:16 UTC 2024 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case.
Wed Nov 27 21:53:16 UTC 2024 W: Network problems are automatically rescheduled after some hours.