Thu Oct 7 04:39:50 UTC 2021 I: starting to build bedtools/buster/i386 on jenkins on '2021-10-07 04:39' Thu Oct 7 04:39:50 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/2226/console.log Thu Oct 7 04:39:50 UTC 2021 I: Downloading source for buster/bedtools=2.27.1+dfsg-4 --2021-10-07 04:39:50-- http://deb.debian.org/debian/pool/main/b/bedtools/bedtools_2.27.1%2bdfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2244 (2.2K) Saving to: ‘bedtools_2.27.1+dfsg-4.dsc’ 0K .. 100% 153M=0s 2021-10-07 04:39:51 (153 MB/s) - ‘bedtools_2.27.1+dfsg-4.dsc’ saved [2244/2244] Thu Oct 7 04:39:51 UTC 2021 I: bedtools_2.27.1+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bedtools Binary: bedtools, bedtools-test Architecture: amd64 arm64 armel armhf i386 mips64el mipsel ppc64el all Version: 2.27.1+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://github.com/arq5x/bedtools2 Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/bedtools Vcs-Git: https://salsa.debian.org/med-team/bedtools.git Testsuite: autopkgtest Testsuite-Triggers: samtools, tabix Build-Depends: debhelper (>= 11~), python, zlib1g-dev, samtools Package-List: bedtools deb science optional arch=amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el bedtools-test deb science optional arch=all Checksums-Sha1: cc527e860debca686d0fe451031bce236d3c6250 13457456 bedtools_2.27.1+dfsg.orig.tar.xz 27fb51ccc6d30f2ce71d73321464119d4a27fa98 12164 bedtools_2.27.1+dfsg-4.debian.tar.xz Checksums-Sha256: f1c468c9dbd82a5c13f51c1df1fffd5ea736901cfc0ec9fb9c428d085390823d 13457456 bedtools_2.27.1+dfsg.orig.tar.xz 1d271ae0819175b24e86651a4d8edfba8adc0d46d261241d712ae07b73821087 12164 bedtools_2.27.1+dfsg-4.debian.tar.xz Files: e2fa100bf82db2b97fddc72aab5a1227 13457456 bedtools_2.27.1+dfsg.orig.tar.xz 0771088ea68eef745728eac3b41cb9e1 12164 bedtools_2.27.1+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEc0cUmcxg7Z7ugFlGxb1sjyKV1QIFAlxlaacACgkQxb1sjyKV 1QIrgQ//QjQWCJ/AuqqDZt5pLon5+UY5gKEChKD+FBYYrmLvddE1euDDd1lUQp48 zXT5c7a2uFZ5Vi4qDJKXlQIJpJFxNktv61xdv5gF0voy73fBztUF8TQr0qFD7ljg Jac+rrOXpzimTSPXZje52qEQLL6MKPqejcH0/m8bg9U4F5fsPhYP6voZOi4/gv54 yIcredbD7fnGg9lB/rTjONhQyDOOKggtyOuDrHaRSmgcLuhhoAFFptlhc1wSV1zI dXT5nBgu2kTJTem4eiLJuu6NOjYc6UvNW6QjyJuvR2p+1gWNKCtB1si17Yhj1siH +B+RsQ3H0tIAFN9Xnpq1+eWXBT0wlURK7ZlBsd9v7oaNO9S34rcUo1olk9Q9TRZf cGzlGUgVP0gM9WOEs2GmZMNPhaDowL19vI4+W2KSPTIUBKJJFUId5Y9ie3FnM//K 4wIW9BAjEBCSPfnumDtkTzSHmRNLDcDiuo4y49oxlRKqjdI8JfoUNPBgOQFbX7Ho Mj3XTx+iwTWcYF/cfDlJROWNqnlNsrp3Yyr8LnLXqSZrPbvkJtRgxEkf/yQEnGgZ XzCer8B7Oah3FK6y2wFiCbJL+rCon8qg9zr9afa3ud8NzOuUnVUQEAPAw+/YoFVC +AFMFYs5UoplZYzpDLfV4z+cZ1e4GdFeBzqYXwgLhpa8kpK/4sY= =dMXR -----END PGP SIGNATURE----- Thu Oct 7 04:39:51 UTC 2021 I: Checking whether the package is not for us Thu Oct 7 04:39:51 UTC 2021 I: Starting 1st build on remote node ionos6-i386.debian.net. Thu Oct 7 04:39:51 UTC 2021 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Thu Oct 7 04:40:05 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 23:02:52 -12 2022 I: pbuilder-time-stamp: 1667991772 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 [bedtools_2.27.1+dfsg-4.dsc] I: copying [./bedtools_2.27.1+dfsg.orig.tar.xz] I: copying [./bedtools_2.27.1+dfsg-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 Thu Feb 14 01:14:15 2019 -12 gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bedtools_2.27.1+dfsg-4.dsc dpkg-source: info: extracting bedtools in bedtools-2.27.1+dfsg dpkg-source: info: unpacking bedtools_2.27.1+dfsg.orig.tar.xz dpkg-source: info: unpacking bedtools_2.27.1+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gzstream.h.patch dpkg-source: info: applying fix_test_script.patch dpkg-source: info: applying remove_barski_binding_site.png.patch dpkg-source: info: applying reproducible_build.patch dpkg-source: info: applying louder dpkg-source: info: applying flag_no_overwrite I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/52059/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='e77e80b300eb4e5e96a0be1a335f9d8b' 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='52059' 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.JQlsiI0tna/pbuilderrc_prbV --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.JQlsiI0tna/b1 --logfile b1/build.log bedtools_2.27.1+dfsg-4.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/52059/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~), python, zlib1g-dev, samtools 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 python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{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} 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, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 25.7 MB of archives. After unpacking 92.6 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: samtools 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} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{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} 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, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 25.7 MB of archives. After unpacking 92.6 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/52059 and its subdirectories Thu Oct 7 04:40:05 UTC 2021 W: No second build log, what happened? Thu Oct 7 04:40:05 UTC 2021 W: Downloading the build dependencies failed Thu Oct 7 04:40:05 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 04:40:05 UTC 2021 W: Network problems are automatically rescheduled after some hours.