Thu Oct 7 04:40:18 UTC 2021 I: starting to build tophat/buster/i386 on jenkins on '2021-10-07 04:40' Thu Oct 7 04:40:18 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_6/26150/console.log Thu Oct 7 04:40:18 UTC 2021 I: Downloading source for buster/tophat=2.1.1+dfsg1-2 --2021-10-07 04:40:18-- http://deb.debian.org/debian/pool/main/t/tophat/tophat_2.1.1%2bdfsg1-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2184 (2.1K) Saving to: ‘tophat_2.1.1+dfsg1-2.dsc’ 0K .. 100% 117M=0s 2021-10-07 04:40:18 (117 MB/s) - ‘tophat_2.1.1+dfsg1-2.dsc’ saved [2184/2184] Thu Oct 7 04:40:18 UTC 2021 I: tophat_2.1.1+dfsg1-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tophat Binary: tophat Architecture: any Version: 2.1.1+dfsg1-2 Maintainer: Debian Med Packaging Team Uploaders: Carlos Borroto , Alexandre Mestiashvili , Andreas Tille Homepage: http://ccb.jhu.edu/software/tophat Standards-Version: 4.2.0 Vcs-Browser: https://salsa.debian.org/med-team/tophat Vcs-Git: https://salsa.debian.org/med-team/tophat.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), libbam-dev, zlib1g-dev, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man, bowtie Package-List: tophat deb science optional arch=any Checksums-Sha1: 3069f6eb5159064a49d0a1f41b570e7ff56be9bd 349996 tophat_2.1.1+dfsg1.orig.tar.xz 26f4696a5f2c785711e2b61ec51e9dfc04c183b5 18636 tophat_2.1.1+dfsg1-2.debian.tar.xz Checksums-Sha256: 16c1b414e8dcb6bb241cc7560d1e7495f00b39fd0ef5b2c3d09e19c1685219c3 349996 tophat_2.1.1+dfsg1.orig.tar.xz 34b340161a2340e6acb44968bf4adaaf43b02e74412441b11f0dc20dde2283ce 18636 tophat_2.1.1+dfsg1-2.debian.tar.xz Files: 9e350c80adba6b6fdc8045ef4e085800 349996 tophat_2.1.1+dfsg1.orig.tar.xz 5072d66e095477f87ce398ccfd02098f 18636 tophat_2.1.1+dfsg1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlt3y6wRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHrYw//bxAuZXH2PYThUeeT9evLGxgJtc+GfxoJ da6D3XLsyhyF2O3BwaN9FJfvo3hakzaQRYf4DDXzLsfYKFnmQvrpgpZ09NTLCN5x yhwds1ZprEfSFm9xqH9XGC5Zrhv9/Yv1q8EtiGuEUr6CQvh9UKcmZA/Q3edlumDb oE3LhzMG/iWiUXZwRn0YS0qj85yTQKB9K+be9Z7vjqVqU3kEwqDvBs3GSBWfd03W +/+4OQC6toZ37AgocFzJtWAfVQl6pfWTLfHtX7W2aeWJEHj7AzVbemYndzStAklg +erwoEBgMBfN/JMxGvSn9g+FhJTfFXKcMtNcH4mt4g+6zv90ovde3BxGDCLEh1HK IFjIx9jqEgdS6CoJZANkC5wdbdTD2oCALT3Qcu2QdsDKL1x4icrDyqoUN5OQKrEo myvH4TGknLWFtfMKUEekNvvVTdAGrocFmSPXhaviFQ+zF7BntJOKBcI7Yq+z4Xlm aIfd1yC6pNJ7RNkrE2xQ1CcrzrZzkwoCrIr03k7y4CcuURMC56Rk0qxNQDB6dMX6 1eLxoBhRYrOxTqZrpf4+Ule3A52V61ZSwDSvSvWJRnFAZrh8RIehukJi3lGT3ip2 4NPp04aAznjvwk/e2LYnjPrXK91mn+srmCG3rfwHkCxVJoP4A4QLAwQq7FXlTRq3 8twRndXKRyU= =6hDw -----END PGP SIGNATURE----- Thu Oct 7 04:40:18 UTC 2021 I: Checking whether the package is not for us Thu Oct 7 04:40:18 UTC 2021 I: Starting 1st build on remote node ionos6-i386.debian.net. Thu Oct 7 04:40:18 UTC 2021 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Thu Oct 7 04:40:30 UTC 2021 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Nov 8 23:03:19 -12 2022 I: pbuilder-time-stamp: 1667991799 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: using eatmydata during job I: Copying source file I: copying [tophat_2.1.1+dfsg1-2.dsc] I: copying [./tophat_2.1.1+dfsg1.orig.tar.xz] I: copying [./tophat_2.1.1+dfsg1-2.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 Fri Aug 17 19:33:00 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 ./tophat_2.1.1+dfsg1-2.dsc dpkg-source: info: extracting tophat in tophat-2.1.1+dfsg1 dpkg-source: info: unpacking tophat_2.1.1+dfsg1.orig.tar.xz dpkg-source: info: unpacking tophat_2.1.1+dfsg1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying remove_3rd_party_code.patch dpkg-source: info: applying fix_includes_path.patch dpkg-source: info: applying fix-gcc6.patch dpkg-source: info: applying remove-convenience-copy-of-samtools.patch dpkg-source: info: applying fix-compatibility-with-recent-samtools.patch dpkg-source: info: applying fix_makefile.am.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/54083/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='7caea1c950f44961a2563bfbe60eb072' 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='54083' 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.n0XtWY9IZu/pbuilderrc_sZIC --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.n0XtWY9IZu/b1 --logfile b1/build.log tophat_2.1.1+dfsg1-2.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://85.184.249.68:3128' I: uname -a Linux ionos6-i386 5.10.0-8-amd64 #1 SMP Debian 5.10.46-5 (2021-09-23) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 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 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 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 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 206392 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 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 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 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Oct 10 02:48 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 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/54083/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 (>= 11~), libbam-dev, zlib1g-dev, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man, bowtie dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19234 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 libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on seqan-dev (>= 1.4); however: Package seqan-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on bowtie; however: Package bowtie 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} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libboost-atomic1.67-dev{a} libboost-atomic1.67.0{a} libboost-chrono1.67-dev{a} libboost-chrono1.67.0{a} libboost-date-time1.67-dev{a} libboost-date-time1.67.0{a} libboost-serialization1.67-dev{a} libboost-serialization1.67.0{a} libboost-system-dev{a} libboost-system1.67-dev{a} libboost-thread-dev{a} libboost-thread1.67-dev{a} libboost-thread1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} seqan-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 38.4 MB of archives. After unpacking 261 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: bowtie 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} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libboost-atomic1.67-dev{a} libboost-atomic1.67.0{a} libboost-chrono1.67-dev{a} libboost-chrono1.67.0{a} libboost-date-time1.67-dev{a} libboost-date-time1.67.0{a} libboost-serialization1.67-dev{a} libboost-serialization1.67.0{a} libboost-system-dev{a} libboost-system1.67-dev{a} libboost-thread-dev{a} libboost-thread1.67-dev{a} libboost-thread1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} seqan-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 38.4 MB of archives. After unpacking 261 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/54083 and its subdirectories Thu Oct 7 04:40:31 UTC 2021 W: No second build log, what happened? Thu Oct 7 04:40:31 UTC 2021 W: Downloading the build dependencies failed Thu Oct 7 04:40:31 UTC 2021 W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case. Thu Oct 7 04:40:31 UTC 2021 W: Network problems are automatically rescheduled after some hours.