Wed Oct 13 12:17:53 UTC 2021 I: starting to build libbio-samtools-perl/bullseye/amd64 on jenkins on '2021-10-13 12:17' Wed Oct 13 12:17:53 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_5/39731/console.log Wed Oct 13 12:17:53 UTC 2021 I: Downloading source for bullseye/libbio-samtools-perl=1.43-3 --2021-10-13 12:17:53-- http://cdn-fastly.deb.debian.org/debian/pool/main/libb/libbio-samtools-perl/libbio-samtools-perl_1.43-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2217 (2.2K) Saving to: ‘libbio-samtools-perl_1.43-3.dsc’ 0K .. 100% 239M=0s 2021-10-13 12:17:53 (239 MB/s) - ‘libbio-samtools-perl_1.43-3.dsc’ saved [2217/2217] Wed Oct 13 12:17:53 UTC 2021 I: libbio-samtools-perl_1.43-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libbio-samtools-perl Binary: libbio-samtools-perl Architecture: any Version: 1.43-3 Maintainer: Debian Perl Group Uploaders: Charles Plessy Homepage: https://metacpan.org/release/Bio-SamTools Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/perl-team/modules/packages/libbio-samtools-perl Vcs-Git: https://salsa.debian.org/perl-team/modules/packages/libbio-samtools-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13), perl-xs-dev, perl:native, libmodule-build-perl, zlib1g-dev, libbam-dev, libbio-perl-perl Package-List: libbio-samtools-perl deb perl optional arch=any Checksums-Sha1: 140779726f17ef29f1a6028b34ed836d0a85f24c 340833 libbio-samtools-perl_1.43.orig.tar.gz 095b25e7f160766ab96bf961d496e35b62846131 8324 libbio-samtools-perl_1.43-3.debian.tar.xz Checksums-Sha256: 7085ee5e97ad75dbbebd8583072d67b2b06d29e7a9f9741c9ac58dabe300d3fd 340833 libbio-samtools-perl_1.43.orig.tar.gz d4c4b834dc2e8b0e157b26c9f4f4651d5217b7dca571dab2995daeabf39960e9 8324 libbio-samtools-perl_1.43-3.debian.tar.xz Files: d36d7bfe91d6eaa8d220a2cb08d04a94 340833 libbio-samtools-perl_1.43.orig.tar.gz 3e66041e8484ac202de3b21e389c0a12 8324 libbio-samtools-perl_1.43-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl7clwwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGuaA//U7iZuY+CzYKJqBV4tPeM5Uy7aUqrurEd 6yvHystWv4L5wHur1NWOSGkO7FceA/tlGkFtpgWSWLjdUuwEh3TS33QboZNjPTjS namAJAFfwxd0cbxSuB3YlxgnlbKapKFReozNJ4X8jjm5k1LVyd2zTMn3qXLT6QCN IuuY9W7tzpEYCdkoZu0ujzQA6/+CNrhm02gn4a3hq3KJSLFkJ2G8dxl4hmBnkJFY HrNLccvC+oaIIzfE6aCFQohx3bnjo1TiqdgROnnFc/lgW/2Y95/hLZ+lU2N44WFE q26A5kR0Iz4c48UzDLXcOhGcrpjac8Rtrw9aLpoy41evgdY3nqHs1+a9vqtGZAr7 cnQzve8+zBibjlfWU3D1P9cnmy0xVoSPZkVS87FL59mc9Afmk0dhtToXYN5ulOz2 QMNLA7aT5JxABp5bk5wE/KR15sQNvfebv1gFDaK8iYjCFh5U6QVgWtu2iUeP5R+S ATR7h+7KBwbURU9aGoSQ1UmsHn8anhcoXBO24AflLxDi0IQWEPeb0SkCgWMebSJZ TZnLyWkiTxRG7LmElktG0qbvyLNFH5P2CPUCE/UphP4uyEW9W6V82A2zNkn3XEIF 0ySrN10hh14LGZIQ424jlAul2yUlTUY+MZfUyFd0fSwzSvB+UGnXExLBnsG4FjCM 2Xic7Z+oDH4= =uMkX -----END PGP SIGNATURE----- Wed Oct 13 12:17:53 UTC 2021 I: Checking whether the package is not for us Wed Oct 13 12:17:53 UTC 2021 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed Oct 13 12:17:53 UTC 2021 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed Oct 13 12:19:07 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 13 00:17:56 -12 2021 I: pbuilder-time-stamp: 1634127476 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [libbio-samtools-perl_1.43-3.dsc] I: copying [./libbio-samtools-perl_1.43.orig.tar.gz] I: copying [./libbio-samtools-perl_1.43-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.CIdRzCWk/trustedkeys.kbx': General error gpgv: Signature made Sat Jun 6 19:28:12 2020 -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 ./libbio-samtools-perl_1.43-3.dsc dpkg-source: info: extracting libbio-samtools-perl in libbio-samtools-perl-1.43 dpkg-source: info: unpacking libbio-samtools-perl_1.43.orig.tar.gz dpkg-source: info: unpacking libbio-samtools-perl_1.43-3.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/233715/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5dab1b54654647abb56b79fdff1ed824' 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='233715' 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.NwRYlLDN8G/pbuilderrc_B4KD --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.NwRYlLDN8G/b1 --logfile b1/build.log libbio-samtools-perl_1.43-3.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Oct 6 21:25 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/233715/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: amd64 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-compat (= 13), perl-xs-dev, perl:native, libmodule-build-perl, zlib1g-dev, libbam-dev, libbio-perl-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 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 perl-xs-dev; however: Package perl-xs-dev is not installed. pbuilder-satisfydepends-dummy depends on perl:native. pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however: Package libmodule-build-perl is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl 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} 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} libarchive-zip-perl{a} libbam-dev{a} libbio-perl-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libio-string-perl{a} libmagic-mgc{a} libmagic1{a} libmodule-build-perl{a} libperl-dev{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl 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 libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libmodule-signature-perl libpod-readme-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsoftware-license-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 lynx perl-tk wget 0 packages upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 23.0 MB of archives. After unpacking 84.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libbam-dev amd64 0.1.19+dfsg-2 [118 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libmodule-build-perl all 0.423100-1 [258 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libperl-dev amd64 5.32.1-4+deb11u2 [1075 kB] Fetched 23.0 MB in 1s (43.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. 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Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up libperl-dev:amd64 (5.32.1-4+deb11u2) ... Setting up file (1:5.39-3) ... Setting up libmodule-build-perl (0.423100-1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up libelf1:amd64 (0.183-1) ... 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Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/libbio-samtools-perl-1.43/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbio-samtools-perl_1.43-3_source.changes dpkg-buildpackage: info: source package libbio-samtools-perl dpkg-buildpackage: info: source version 1.43-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/libbio-samtools-perl-1.43' SAMTOOLS=/usr/include/samtools dh_auto_configure perl Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/build/libbio-samtools-perl-1.43=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/libbio-samtools-perl-1.43=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" Found /usr/include/samtools/bam.h and /usr/lib/libbam.a. Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-SamTools' version '1.43' make[1]: Leaving directory '/build/libbio-samtools-perl-1.43' dh_auto_build perl Build Building Bio-SamTools x86_64-linux-gnu-gcc -I/usr/include/samtools -Ic_bin -I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/libbio-samtools-perl-1.43=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/libbio-samtools-perl-1.43=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o c_bin/bam2bedgraph.o c_bin/bam2bedgraph.c x86_64-linux-gnu-gcc -I/usr/include/samtools -Ic_bin -I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE -DVERSION="1.43" -DXS_VERSION="1.43" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/libbio-samtools-perl-1.43=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/libbio-samtools-perl-1.43=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c lib/Bio/DB/Sam.xs: In function 'XS_Bio__DB__Bam_sort_core': lib/Bio/DB/Sam.xs:324:4: warning: implicit declaration of function 'bam_sort_core'; did you mean 'bam_format1_core'? [-Wimplicit-function-declaration] 324 | bam_sort_core(is_by_qname,filename,prefix,max_mem); | ^~~~~~~~~~~~~ | bam_format1_core lib/Bio/DB/Sam.xs: In function 'XS_Bio__DB__Bam__Header_view1': lib/Bio/DB/Sam.xs:916:8: warning: implicit declaration of function 'bam_view1' [-Wimplicit-function-declaration] 916 | bam_view1(bamh,alignment); | ^~~~~~~~~ ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs') x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/libbio-samtools-perl-1.43=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o -L/usr/lib -lbam -lpthread -lz make[1]: Entering directory '/build/libbio-samtools-perl-1.43/c_bin' gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o -Wl,-z,relro -L/usr/lib -lbam -lpthread -lm -lz make[1]: Leaving directory '/build/libbio-samtools-perl-1.43/c_bin' dh_auto_test perl Build test --verbose 1 make[1]: Entering directory '/build/libbio-samtools-perl-1.43/c_bin' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/libbio-samtools-perl-1.43/c_bin' [fai_load] build FASTA index. [bam_parse_region] fail to determine the sequence name. t/01sam.t .. 1..268 # Running under perl version 5.032001 for linux # Current time local: Wed Oct 13 00:18:52 2021 # Current time GMT: Wed Oct 13 12:18:52 2021 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok All tests successful. Files=1, Tests=268, 3 wallclock secs ( 0.06 usr 0.00 sys + 1.43 cusr 0.14 csys = 1.63 CPU) Result: PASS create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install perl Build install --destdir /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl --create_packlist 0 Building Bio-SamTools make[1]: Entering directory '/build/libbio-samtools-perl-1.43/c_bin' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/libbio-samtools-perl-1.43/c_bin' Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/DB/Sam/Sam.so Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/DB/Sam/Sam.bs Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/bin/bam2bedgraph Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Sam.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Sam/Segment.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Sam/SamToGBrowse.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Sam/Constants.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Bam/Target.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Bam/ReadIterator.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Bam/Query.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Bam/PileupWrapper.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Bam/Pileup.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Bam/FetchIterator.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Bam/Alignment.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/DB/Bam/AlignWrapper.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Sam::Constants.3pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Sam.3pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Target.3pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Query.3pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Pileup.3pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Alignment.3pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/bin/genomeCoverageBed.pl Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/bin/chrom_sizes.pl Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/bin/bamToGBrowse.pl dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbio-samtools-perl' in '../libbio-samtools-perl_1.43-3_amd64.deb'. dpkg-deb: building package 'libbio-samtools-perl-dbgsym' in '../libbio-samtools-perl-dbgsym_1.43-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libbio-samtools-perl_1.43-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/233715 and its subdirectories I: Current time: Wed Oct 13 00:19:06 -12 2021 I: pbuilder-time-stamp: 1634127546 Wed Oct 13 12:19:07 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Wed Oct 13 12:19:07 UTC 2021 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Wed Oct 13 12:20:00 UTC 2021 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Wed Oct 13 12:20:00 UTC 2021 I: libbio-samtools-perl_1.43-3_amd64.changes: Format: 1.8 Date: Sun, 07 Jun 2020 09:23:40 +0200 Source: libbio-samtools-perl Binary: libbio-samtools-perl libbio-samtools-perl-dbgsym Architecture: amd64 Version: 1.43-3 Distribution: unstable Urgency: medium Maintainer: Debian Perl Group Changed-By: Andreas Tille Description: libbio-samtools-perl - Perl interface to SamTools library for DNA sequencing Changes: libbio-samtools-perl (1.43-3) unstable; urgency=medium . * Team upload . [ gregor herrmann ] * debian/control: update Build-Depends for cross builds. * debian/watch: use uscan version 4. . [ Andreas Tille ] * Remove deprecated fields from upstream metadata * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) Checksums-Sha1: 5bf3ecaa3d6e8e9bcc20d59d65a97b0ec0e78542 95476 libbio-samtools-perl-dbgsym_1.43-3_amd64.deb 7826c4bcabbcc3813efd4c0a9bb11c2ac788b165 5338 libbio-samtools-perl_1.43-3_amd64.buildinfo 5f00da7798ec91b695e40937d4caceda6671441a 192144 libbio-samtools-perl_1.43-3_amd64.deb Checksums-Sha256: 5b060cdfd6c3bb7c248fa411234d3d10b23019dd875cf9903a9bf108052af477 95476 libbio-samtools-perl-dbgsym_1.43-3_amd64.deb 803e0800085f3ed4dd8633c1a8802e56d9ef7f3e18f6eb333b921f28e6f09c23 5338 libbio-samtools-perl_1.43-3_amd64.buildinfo b61b2ebb4dbde34a5e1eb322ecefa392df5fbb1e3060cb1cc46b6d853ccc454f 192144 libbio-samtools-perl_1.43-3_amd64.deb Files: e5ed138540c9db1fe7d6395e156eb925 95476 debug optional libbio-samtools-perl-dbgsym_1.43-3_amd64.deb 1ff1e98fe488439894b2a68ada381c3b 5338 perl optional libbio-samtools-perl_1.43-3_amd64.buildinfo 739856d79f013aae73fd90dd064a91ae 192144 perl optional libbio-samtools-perl_1.43-3_amd64.deb Wed Oct 13 12:20:01 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.NwRYlLDN8G/libbio-samtools-perl_1.43-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.NwRYlLDN8G/libbio-samtools-perl_1.43-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.NwRYlLDN8G/libbio-samtools-perl_1.43-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.NwRYlLDN8G/b1/libbio-samtools-perl_1.43-3_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.NwRYlLDN8G/b2/libbio-samtools-perl_1.43-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.286s) 0.286s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.024s) 0.023s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Oct 13 12:20:02 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Wed Oct 13 12:20:02 UTC 2021 I: libbio-samtools-perl from bullseye built successfully and reproducibly on amd64. Wed Oct 13 12:20:04 UTC 2021 I: Submitting .buildinfo files to external archives: Wed Oct 13 12:20:04 UTC 2021 I: Submitting 8.0K b1/libbio-samtools-perl_1.43-3_amd64.buildinfo.asc Wed Oct 13 12:20:06 UTC 2021 I: Submitting 8.0K b2/libbio-samtools-perl_1.43-3_amd64.buildinfo.asc Wed Oct 13 12:20:06 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Oct 13 12:20:06 UTC 2021 I: Done submitting .buildinfo files. Wed Oct 13 12:20:06 UTC 2021 I: Removing signed libbio-samtools-perl_1.43-3_amd64.buildinfo.asc files: removed './b1/libbio-samtools-perl_1.43-3_amd64.buildinfo.asc' removed './b2/libbio-samtools-perl_1.43-3_amd64.buildinfo.asc'