Tue Oct 5 22:44:29 UTC 2021 I: starting to build sga/buster/armhf on jenkins on '2021-10-05 22:44'
Tue Oct 5 22:44:29 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_6/12068/console.log
Tue Oct 5 22:44:29 UTC 2021 I: Downloading source for buster/sga=0.10.15-4
--2021-10-05 22:44:29-- http://deb.debian.org/debian/pool/main/s/sga/sga_0.10.15-4.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2059 (2.0K)
Saving to: ‘sga_0.10.15-4.dsc’
0K .. 100% 13.7M=0s
2021-10-05 22:44:29 (13.7 MB/s) - ‘sga_0.10.15-4.dsc’ saved [2059/2059]
Tue Oct 5 22:44:29 UTC 2021 I: sga_0.10.15-4.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: sga
Binary: sga
Architecture: any
Version: 0.10.15-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>, Andreas Tille <tille@debian.org>
Homepage: https://github.com/jts/sga
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/sga
Vcs-Git: https://salsa.debian.org/med-team/sga.git
Build-Depends: debhelper (>= 11~), libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, gawk, help2man, samtools, python, python-ruffus, python-pysam
Package-List:
sga deb science optional arch=any
Checksums-Sha1:
55b540d2f1cae3a44de8da6db8f413826bdb5f14 6569986 sga_0.10.15.orig.tar.gz
919255d5b39cbb275018e332fd81763a3e2b95d2 211108 sga_0.10.15-4.debian.tar.xz
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11d5904c2e2d964ea436121f57ae451b1eabbe2b5b23f16a60f21a01a5c4e35d 211108 sga_0.10.15-4.debian.tar.xz
Files:
990aed1593f8072650c6366e5cf32519 6569986 sga_0.10.15.orig.tar.gz
33c32c000f048b1ce1677f52a900b541 211108 sga_0.10.15-4.debian.tar.xz
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Tue Oct 5 22:44:29 UTC 2021 I: Checking whether the package is not for us
Tue Oct 5 22:44:29 UTC 2021 I: Starting 1st build on remote node virt64b-armhf-rb.debian.net.
Tue Oct 5 22:44:29 UTC 2021 I: Preparing to do remote build '1' on virt64b-armhf-rb.debian.net.
Tue Oct 5 22:45:21 UTC 2021 I: Deleting $TMPDIR on virt64b-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Oct 5 10:44:35 -12 2021
I: pbuilder-time-stamp: 1633473875
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz]
I: copying local configuration
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 [sga_0.10.15-4.dsc]
I: copying [./sga_0.10.15.orig.tar.gz]
I: copying [./sga_0.10.15-4.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Sep 23 09:30:35 2018 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./sga_0.10.15-4.dsc
dpkg-source: info: extracting sga in sga-0.10.15
dpkg-source: info: unpacking sga_0.10.15.orig.tar.gz
dpkg-source: info: unpacking sga_0.10.15-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 0002-no-rpath.patch
dpkg-source: info: applying 0003-do-not-dist-unsup-script.patch
dpkg-source: info: applying 0004-Add-help-to-sga-bam2de.pl.patch
dpkg-source: info: applying 0005-Remove-extensions-on-scripts-we-ship.patch
dpkg-source: info: applying 0006-remove-google-addsense.patch
dpkg-source: info: applying gcc-7.patch
dpkg-source: info: applying no_privacy_breach_url.patch
I: using fakeroot in build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/28517/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
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=''
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='5e5b93c21178418fa79af2a2bcd3f187'
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='28517'
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/tmp.7UbTkxHJSB/pbuilderrc_a85s --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7UbTkxHJSB/b1 --logfile b1/build.log sga_0.10.15-4.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://10.0.0.15:8000/'
I: uname -a
Linux virt64b 5.10.0-8-arm64 #1 SMP Debian 5.10.46-5 (2021-09-23) aarch64 GNU/Linux
I: ls -l /bin
total 3328
-rwxr-xr-x 1 root root 767656 Apr 17 2019 bash
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2
-rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore
-rwxr-xr-x 1 root root 22432 Feb 28 2019 cat
-rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp
-rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod
-rwxr-xr-x 1 root root 42972 Feb 28 2019 chown
-rwxr-xr-x 1 root root 88376 Feb 28 2019 cp
-rwxr-xr-x 1 root root 75516 Jan 17 2019 dash
-rwxr-xr-x 1 root root 71648 Feb 28 2019 date
-rwxr-xr-x 1 root root 51212 Feb 28 2019 dd
-rwxr-xr-x 1 root root 55672 Feb 28 2019 df
-rwxr-xr-x 1 root root 88444 Feb 28 2019 dir
-rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg
lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname
-rwxr-xr-x 1 root root 22364 Feb 28 2019 echo
-rwxr-xr-x 1 root root 28 Jan 7 2019 egrep
-rwxr-xr-x 1 root root 18260 Feb 28 2019 false
-rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep
-rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt
-rwsr-xr-x 1 root root 21980 Apr 22 2020 fusermount
-rwxr-xr-x 1 root root 124508 Jan 7 2019 grep
-rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip
-rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe
-rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip
-rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname
-rwxr-xr-x 1 root root 43044 Feb 28 2019 ln
-rwxr-xr-x 1 root root 34932 Jul 26 2018 login
-rwxr-xr-x 1 root root 88444 Feb 28 2019 ls
-rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk
-rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir
-rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod
-rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp
-rwxr-xr-x 1 root root 26024 Jan 9 2019 more
-rwsr-xr-x 1 root root 34268 Jan 9 2019 mount
-rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint
-rwxr-xr-x 1 root root 84284 Feb 28 2019 mv
lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd
lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash
-rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink
-rwxr-xr-x 1 root root 42968 Feb 28 2019 rm
-rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir
-rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts
-rwxr-xr-x 1 root root 76012 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Sep 6 20:25 sh -> dash
-rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep
-rwxr-xr-x 1 root root 51124 Feb 28 2019 stty
-rwsr-xr-x 1 root root 42472 Jan 9 2019 su
-rwxr-xr-x 1 root root 22392 Feb 28 2019 sync
-rwxr-xr-x 1 root root 283324 Apr 23 2019 tar
-rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile
-rwxr-xr-x 1 root root 63464 Feb 28 2019 touch
-rwxr-xr-x 1 root root 18260 Feb 28 2019 true
-rwxr-xr-x 1 root root 9636 Apr 22 2020 ulockmgr_server
-rwsr-xr-x 1 root root 21976 Jan 9 2019 umount
-rwxr-xr-x 1 root root 22380 Feb 28 2019 uname
-rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress
-rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir
-rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl
-rwxr-xr-x 1 root root 946 Jan 21 2019 which
lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat
-rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp
-rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff
-rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep
-rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep
-rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce
-rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep
-rwxr-xr-x 1 root root 2205 Jan 5 2019 zless
-rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore
-rwxr-xr-x 1 root root 4552 Jan 5 2019 znew
I: user script /srv/workspace/pbuilder/28517/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 (>= 11~), libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, gawk, help2man, samtools, python, python-ruffus, python-pysam
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 18932 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 (>= 11~); however:
Package debhelper is not installed.
pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however:
Package libsparsehash-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev | libz-dev; however:
Package zlib1g-dev is not installed.
Package libz-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbamtools-dev; however:
Package libbamtools-dev is not installed.
pbuilder-satisfydepends-dummy depends on gawk; however:
Package gawk is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on python; however:
Package python is not installed.
pbuilder-satisfydepends-dummy depends on python-ruffus; however:
Package python-ruffus is not installed.
pbuilder-satisfydepends-dummy depends on python-pysam; however:
Package python-pysam 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gawk{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcroco3{a} libcurl3-gnutls{a} libdatrie1{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgd3{a} libglib2.0-0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libhts2{a} libice6{a} libicu63{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libsparsehash-dev{a} libssh2-1{a} libssl1.1{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxdot4{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} lsb-base{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python-ruffus{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} samtools{a} sensible-utils{a} ucf{a} x11-common{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl cwltool fonts-liberation krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libgts-bin libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs
0 packages upgraded, 123 newly installed, 0 to remove and 0 not upgraded.
Need to get 38.4 MB of archives. After unpacking 116 MB will be used.
The following packages have unmet dependencies:
pbuilder-satisfydepends-dummy : Depends: python-pysam 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gawk{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcroco3{a} libcurl3-gnutls{a} libdatrie1{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgd3{a} libglib2.0-0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libhts2{a} libice6{a} libicu63{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libsparsehash-dev{a} libssh2-1{a} libssl1.1{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxdot4{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} lsb-base{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python-ruffus{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} samtools{a} sensible-utils{a} ucf{a} x11-common{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl cwltool fonts-liberation krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libgts-bin libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs
0 packages upgraded, 123 newly installed, 0 to remove and 0 not upgraded.
Need to get 38.4 MB of archives. After unpacking 116 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/28517 and its subdirectories
Tue Oct 5 22:45:24 UTC 2021 W: No second build log, what happened?
Tue Oct 5 22:45:24 UTC 2021 W: Downloading the build dependencies failed
Tue Oct 5 22:45:24 UTC 2021 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case.
Tue Oct 5 22:45:24 UTC 2021 W: Network problems are automatically rescheduled after some hours.