Thu Jul 29 22:25:14 UTC 2021 I: starting to build libbio-samtools-perl/bullseye/arm64 on jenkins on '2021-07-29 22:24' Thu Jul 29 22:25:14 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_27/22134/console.log Thu Jul 29 22:25:14 UTC 2021 I: Downloading source for bullseye/libbio-samtools-perl=1.43-3 --2021-07-29 22:25:14-- 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% 132M=0s 2021-07-29 22:25:14 (132 MB/s) - ‘libbio-samtools-perl_1.43-3.dsc’ saved [2217/2217] Thu Jul 29 22:25:14 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----- Thu Jul 29 22:25:14 UTC 2021 I: Checking whether the package is not for us Thu Jul 29 22:25:14 UTC 2021 I: Starting 1st build on remote node codethink15-arm64.debian.net. Thu Jul 29 22:25:14 UTC 2021 I: Preparing to do remote build '1' on codethink15-arm64.debian.net. Thu Jul 29 22:26:03 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 31 16:48:16 -12 2022 I: pbuilder-time-stamp: 1662007696 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.TCUpMwtu/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/2495/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='2495' 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.O3ec8RG3xe/pbuilderrc_V7iO --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.O3ec8RG3xe/b1 --logfile b1/build.log libbio-samtools-perl_1.43-3.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink15-arm64 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 2021 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 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 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 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 2021 more -rwsr-xr-x 1 root root 51360 Feb 7 2021 mount -rwxr-xr-x 1 root root 14496 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 30 03:47 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 2021 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/2495/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: arm64 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 ... 19646 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 22.6 MB of archives. After unpacking 83.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libbam-dev arm64 0.1.19+dfsg-2 [113 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libdata-stag-perl all 0.14-2 [448 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libmodule-build-perl all 0.423100-1 [258 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libperl-dev arm64 5.32.1-4 [992 kB] Fetched 22.6 MB in 3s (7215 kB/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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.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_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. 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Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (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:arm64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up libperl-dev:arm64 (5.32.1-4) ... 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:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up libelf1:arm64 (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 arm64 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=aarch64-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 aarch64-linux-gnu-gcc -I/usr/include/samtools -Ic_bin -I/usr/lib/aarch64-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 aarch64-linux-gnu-gcc -I/usr/include/samtools -Ic_bin -I/usr/lib/aarch64-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') aarch64-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 Aug 31 16:48:52 2022 # Current time GMT: Thu Sep 1 04:48:52 2022 # 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, 2 wallclock secs ( 0.06 usr 0.02 sys + 1.81 cusr 0.13 csys = 2.02 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/aarch64-linux-gnu/perl5/5.32/auto/Bio/DB/Sam/Sam.so Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-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/aarch64-linux-gnu/perl5/5.32/Bio/DB/Sam.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Sam/Segment.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Sam/SamToGBrowse.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Sam/Constants.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Bam/Target.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Bam/ReadIterator.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Bam/Query.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Bam/PileupWrapper.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Bam/Pileup.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Bam/FetchIterator.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-linux-gnu/perl5/5.32/Bio/DB/Bam/Alignment.pm Installing /build/libbio-samtools-perl-1.43/debian/libbio-samtools-perl/usr/lib/aarch64-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_arm64.deb'. dpkg-deb: building package 'libbio-samtools-perl-dbgsym' in '../libbio-samtools-perl-dbgsym_1.43-3_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libbio-samtools-perl_1.43-3_arm64.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/2495 and its subdirectories I: Current time: Wed Aug 31 16:49:02 -12 2022 I: pbuilder-time-stamp: 1662007742 Thu Jul 29 22:26:03 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink14-arm64.debian.net. Thu Jul 29 22:26:03 UTC 2021 I: Preparing to do remote build '2' on codethink14-arm64.debian.net. Thu Jul 29 22:26:53 UTC 2021 I: Deleting $TMPDIR on codethink14-arm64.debian.net. Thu Jul 29 22:26:53 UTC 2021 I: libbio-samtools-perl_1.43-3_arm64.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: arm64 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: a5a1d94facfb0d62ba90e5c9776915ec840114b6 94032 libbio-samtools-perl-dbgsym_1.43-3_arm64.deb eb74c5b03faefebcc3e04a95d7081308a61b1600 5166 libbio-samtools-perl_1.43-3_arm64.buildinfo ad085cc28753294a01620ee628b956e8e5aca542 183764 libbio-samtools-perl_1.43-3_arm64.deb Checksums-Sha256: fb3ea7b10faebea5bb49c66e78e39afb0bd897bd5ed447847c0e15286d8c8eb9 94032 libbio-samtools-perl-dbgsym_1.43-3_arm64.deb 9ae4d556291608509014b5d44e30706063c1d8b39ef426b633cbffff4ed408a2 5166 libbio-samtools-perl_1.43-3_arm64.buildinfo 506eaad0b69d06cfd2c5e1f9d27fce7d3d06c26dde8bfd75be49735432efcb7d 183764 libbio-samtools-perl_1.43-3_arm64.deb Files: f80ba93e531bdd950cffdf283d3f9c71 94032 debug optional libbio-samtools-perl-dbgsym_1.43-3_arm64.deb 45fb1309a83471c4c259bdda5c798c01 5166 perl optional libbio-samtools-perl_1.43-3_arm64.buildinfo 8866d18a720d3714b62229e1b2adbbb1 183764 perl optional libbio-samtools-perl_1.43-3_arm64.deb Thu Jul 29 22:26:55 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.O3ec8RG3xe/libbio-samtools-perl_1.43-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.O3ec8RG3xe/libbio-samtools-perl_1.43-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.O3ec8RG3xe/libbio-samtools-perl_1.43-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.O3ec8RG3xe/b1/libbio-samtools-perl_1.43-3_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.O3ec8RG3xe/b2/libbio-samtools-perl_1.43-3_arm64.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: 0.249s) 0.249s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.022s) 0.022s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Jul 29 22:26:56 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Thu Jul 29 22:26:56 UTC 2021 I: libbio-samtools-perl from bullseye built successfully and reproducibly on arm64. Thu Jul 29 22:26:57 UTC 2021 I: Submitting .buildinfo files to external archives: Thu Jul 29 22:26:57 UTC 2021 I: Submitting 8.0K b1/libbio-samtools-perl_1.43-3_arm64.buildinfo.asc Thu Jul 29 22:26:59 UTC 2021 I: Submitting 8.0K b2/libbio-samtools-perl_1.43-3_arm64.buildinfo.asc Thu Jul 29 22:27:00 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jul 29 22:27:00 UTC 2021 I: Done submitting .buildinfo files. Thu Jul 29 22:27:00 UTC 2021 I: Removing signed libbio-samtools-perl_1.43-3_arm64.buildinfo.asc files: removed './b1/libbio-samtools-perl_1.43-3_arm64.buildinfo.asc' removed './b2/libbio-samtools-perl_1.43-3_arm64.buildinfo.asc'