Mon May 6 14:29:51 UTC 2024 I: starting to build libbio-db-hts-perl/trixie/arm64 on jenkins on '2024-05-06 14:29' Mon May 6 14:29:51 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_13/16758/console.log Mon May 6 14:29:51 UTC 2024 I: Downloading source for trixie/libbio-db-hts-perl=3.01-4 --2024-05-06 14:29:51-- http://deb.debian.org/debian/pool/main/libb/libbio-db-hts-perl/libbio-db-hts-perl_3.01-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2192 (2.1K) [text/prs.lines.tag] Saving to: ‘libbio-db-hts-perl_3.01-4.dsc’ 0K .. 100% 234M=0s 2024-05-06 14:29:51 (234 MB/s) - ‘libbio-db-hts-perl_3.01-4.dsc’ saved [2192/2192] Mon May 6 14:29:51 UTC 2024 I: libbio-db-hts-perl_3.01-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-db-hts-perl Binary: libbio-db-hts-perl Architecture: any Version: 3.01-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://metacpan.org/release/Bio-DB-HTS Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/libbio-db-hts-perl Vcs-Git: https://salsa.debian.org/med-team/libbio-db-hts-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13), libbio-perl-perl, libextutils-cbuilder-perl, libextutils-pkgconfig-perl, libhts-dev, libmodule-build-perl, perl Package-List: libbio-db-hts-perl deb science optional arch=any Checksums-Sha1: 292b7464e502437666907f849b8cd91465afd042 5250834 libbio-db-hts-perl_3.01.orig.tar.gz 3044ce114f16475a8a845b6a204d9328f73b5294 3836 libbio-db-hts-perl_3.01-4.debian.tar.xz Checksums-Sha256: 12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42 5250834 libbio-db-hts-perl_3.01.orig.tar.gz f61254cb6dacbb3f8849f625e2b8a50169955b3a26ee36ff9edd2ef3ba41e243 3836 libbio-db-hts-perl_3.01-4.debian.tar.xz Files: 7b7f991deddb12084cf85e0fa3d91819 5250834 libbio-db-hts-perl_3.01.orig.tar.gz 581435791a88040638e91ab2da6e36e7 3836 libbio-db-hts-perl_3.01-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmM+n5QRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH++A/+OgAu2K3OMtOyQjh7ZvJKjTqNW0ozfAnr 5LJyzLILdpZcchdixevwClFVsi3fUD7DoYHt4R9MGNL4unfoJBdCXoQuh8EqyusX bwhfhFeizl0C4lQgETo1HuTwWa5nHWdhZYeHKjXVagFGH9GEPjqNEwwl8y/DoNM0 AKPAiZ4M2WJB+pvoSsPNwtJVlQMcHBgC9aTQm+HiiHIWY1mNYiIRCac7orr6MwTJ HqmbYSuxAd2+mb0Jzc2+3hgiouMDP+MkdMx6FC2AQ1nKBKP7e+1GYv3XEfQBHiIs mhidqIS4j0iCcs+uUFTuPpy70ZlukpghXXOPek6/7ynPPKBDT28kNKDfBj/PE1ru aCDHV3u6A4P38l1KNSA9wIm13XE8VZ7wBslIEkmVaALoCRi2gMf2PTLw1jVbBoRl jPCH9uBYOAWMwe7rT4/xAyEKMoj3wYO4Lg9ntgSqaeJlp/uH3MKbYuH5XZb02jj/ //hXFg3oBGqQVXePEAnVrn89AVNcjwBfoAaNUxvgRwkPgDo0GM1fP0SUg3ThIDnY 83GlIt2S08Ch2U/7+weXXeSBjg5iNd90kHF23v9LBD7KbcQaoA2BUf5FUnLFEJVz ZpMhp/HZl+M7tDvbNusp91Tzg1TJECo7zQfYH0XnQqQNXAAO8gZAeoOxE9zoTPXJ u/Pw1Flxj2w= =SUmk -----END PGP SIGNATURE----- Mon May 6 14:29:51 UTC 2024 I: Checking whether the package is not for us Mon May 6 14:29:51 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Mon May 6 14:29:51 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Mon May 6 14:30:31 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 8 08:52:54 -12 2025 I: pbuilder-time-stamp: 1749415974 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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-db-hts-perl_3.01-4.dsc] I: copying [./libbio-db-hts-perl_3.01.orig.tar.gz] I: copying [./libbio-db-hts-perl_3.01-4.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Oct 6 09:27:48 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libbio-db-hts-perl_3.01-4.dsc: no acceptable signature found dpkg-source: info: extracting libbio-db-hts-perl in libbio-db-hts-perl-3.01 dpkg-source: info: unpacking libbio-db-hts-perl_3.01.orig.tar.gz dpkg-source: info: unpacking libbio-db-hts-perl_3.01-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying find_htslib.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2826810/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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 parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='1e9e59e82fab47aa86b0a59acd077022' 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='2826810' 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/r-b-build.2y7MxZ7n/pbuilderrc_pUmS --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2y7MxZ7n/b1 --logfile b1/build.log libbio-db-hts-perl_3.01-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 7 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2826810/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), libbio-perl-perl, libextutils-cbuilder-perl, libextutils-pkgconfig-perl, libhts-dev, libmodule-build-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 ... 19743 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 libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libextutils-pkgconfig-perl; however: Package libextutils-pkgconfig-perl is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however: Package libmodule-build-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} libbio-perl-perl{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdata-stag-perl{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libextutils-pkgconfig-perl{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libio-string-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmodule-build-perl{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run ca-certificates curl krb5-locales 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 libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libmodule-signature-perl libpod-readme-perl libpostscript-perl libsasl2-modules 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 publicsuffix wget 0 packages upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 27.9 MB of archives. After unpacking 105 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 39 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.7.1-3 [523 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libextutils-pkgconfig-perl all 1.16-3 [9928 B] Get: 57 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.19+ds-1.1+b1 [413 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.19+ds-1.1+b1 [1604 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libmodule-build-perl all 0.423400-2 [252 kB] Fetched 27.9 MB in 0s (124 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19743 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libbio-db-hts-perl-3.01/ && 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-db-hts-perl_3.01-4_source.changes dpkg-buildpackage: info: source package libbio-db-hts-perl dpkg-buildpackage: info: source version 3.01-4 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 dh_auto_configure /usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now" Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '3.01' dh_auto_build /usr/bin/perl Build Building Bio-DB-HTS aarch64-linux-gnu-gcc -I/usr/lib/aarch64-linux-gnu/perl/5.38/CORE '-DVERSION="3.01"' '-DXS_VERSION="3.01"' -fPIC '-D_IOLIB=2' '-D_FILE_OFFSET_BITS=64' -Wno-error -Wno-unused-result -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 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' '-mbranch-protection=standard' -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' '-mbranch-protection=standard' -Wdate-time '-D_FORTIFY_SOURCE=2' -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c lib/Bio/DB/HTS.xs: In function 'XS_Bio__DB__HTS__VCF__Header_fmt_text': lib/Bio/DB/HTS.xs:1769:5: warning: 'bcf_hdr_fmt_text' is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 1769 | RETVAL = newSVpv(bcf_hdr_fmt_text(header, is_bcf, &len), 0); | ^~~~~~ In file included from lib/Bio/DB/HTS.xs:59: /usr/include/htslib/vcf.h:591:11: note: declared here 591 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) | ^~~~~~~~~~~~~~~~ lib/Bio/DB/HTS.xs: In function 'XS_Bio__DB__HTS__VCF__Row_print': lib/Bio/DB/HTS.xs:1785:13: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 1785 | printf("position:%d\t", (row->pos+1)); | ^~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | hts_pos_t {aka long int} ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs') aarch64-linux-gnu-gcc -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' '-mbranch-protection=standard' -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -lhts -lpthread -lz aarch64-linux-gnu-gcc -I/usr/lib/aarch64-linux-gnu/perl/5.38/CORE '-DVERSION="3.01"' '-DXS_VERSION="3.01"' -fPIC '-D_IOLIB=2' '-D_FILE_OFFSET_BITS=64' -Wno-error -Wno-unused-result -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 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' '-mbranch-protection=standard' -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' '-mbranch-protection=standard' -Wdate-time '-D_FORTIFY_SOURCE=2' -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs') aarch64-linux-gnu-gcc -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' '-mbranch-protection=standard' -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -lhts -lpthread -lz dh_auto_test /usr/bin/perl Build test --verbose 1 t/00load.t ....... ok 1 - use Bio::DB::HTS; ok 2 - use Bio::DB::HTS::Tabix; ok 3 - use Bio::DB::HTS::Tabix::Iterator; ok 4 - use Bio::DB::HTS::Kseq; 1..4 ok t/01bam.t ........ 1..452 # Running under perl version 5.038002 for linux # Current time local: Sun Jun 8 20:53:18 2025 # Current time GMT: Sun Jun 8 20:53:18 2025 # 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 269 ok 270 ok 271 ok 272 ok 273 ok 274 ok 275 ok 276 ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 ok 289 ok 290 ok 291 ok 292 ok 293 ok 294 ok 295 ok 296 ok 297 ok 298 ok 299 ok 300 ok 301 ok 302 ok 303 ok 304 ok 305 ok 306 ok 307 ok 308 ok 309 ok 310 ok 311 ok 312 ok 313 ok 314 ok 315 ok 316 ok 317 ok 318 ok 319 ok 320 ok 321 ok 322 ok 323 ok 324 ok 325 ok 326 ok 327 ok 328 ok 329 ok 330 ok 331 ok 332 ok 333 ok 334 ok 335 ok 336 ok 337 ok 338 ok 339 ok 340 ok 341 ok 342 ok 343 ok 344 ok 345 ok 346 ok 347 ok 348 ok 349 ok 350 ok 351 ok 352 ok 353 ok 354 ok 355 ok 356 ok 357 ok 358 ok 359 ok 360 ok 361 ok 362 ok 363 ok 364 ok 365 ok 366 ok 367 ok 368 ok 369 ok 370 ok 371 ok 372 ok 373 ok 374 ok 375 ok 376 ok 377 ok 378 ok 379 ok 380 ok 381 ok 382 ok 383 ok 384 ok 385 ok 386 ok 387 ok 388 ok 389 ok 390 ok 391 ok 392 ok 393 ok 394 ok 395 ok 396 ok 397 ok 398 ok 399 ok 400 ok 401 ok 402 ok 403 ok 404 ok 405 ok 406 ok 407 ok 408 ok 409 ok 410 ok 411 ok 412 ok 413 ok 414 ok 415 ok 416 ok 417 ok 418 ok 419 ok 420 ok 421 ok 422 ok 423 ok 424 ok 425 ok 426 ok 427 ok 428 ok 429 ok 430 ok 431 ok 432 ok 433 ok 434 ok 435 ok 436 ok 437 ok 438 ok 439 ok 440 ok 441 ok 442 ok 443 ok 444 ok 445 ok 446 ok 447 ok 448 ok 449 ok 450 ok 451 ok 452 ok t/02faidx.t ...... 1..15 ok 1 - use Bio::DB::HTS; ok 2 - use Bio::DB::HTS::Faidx; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 # 230218 ok 13 - length of I ok 14 - has sequence I ok 15 - Does not have sequence II ok t/03cram.t ....... 1..139 # Running under perl version 5.038002 for linux # Current time local: Sun Jun 8 20:53:19 2025 # Current time GMT: Sun Jun 8 20:53:19 2025 # 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 t/04tabix.t ...... 1..21 ok 1 - use Bio::DB::HTS::Tabix; ok 2 - \#CHROM FROM TO GERP ok 3 - \#CHROM FROM TO GERP ok 4 - can query a region ok 5 - can get a value from the iterator ok 6 - row value is correct ok 7 - correct number of values come back from the iterator ok 8 - A reference of type 'ARRAY' isa 'ARRAY' ok 9 - seqnames are correct ok 10 - can query a region with ':' in chr ok 11 - can get a value from the iterator ok 12 - row value is correct with ':' in chr ok 13 - can query a region with ':' in chr, no end ok 14 - can get a value from the iterator ok 15 - row value is correct with ':' in chr, no end ok 16 - can query a region with ':' in chr, no coord ok 17 - can get a value from the iterator ok 18 - row value is correct with ':' in chr, no coord ok 19 - querying non existent chrom ok 20 - \#\#fileformat=VCFv4.2 ok 21 - \#\#reference=human_b36_both.fasta ok t/05vcf.t ........ 1..177 ok 1 - use Bio::DB::HTS::VCF; ok 2 - use Bio::DB::HTS::VCF::Row; ok 3 - use Bio::DB::HTS::VCF::RowPtr; ok 4 - use Bio::DB::HTS::VCF::Header; ok 5 - use Bio::DB::HTS::VCF::HeaderPtr; ok 6 - Chromosome value read ok 7 - Chromosome value read ok 8 - Position value read ok 9 - Quality value read ok 10 - Quality value read ok 11 - ID value read ok 12 - Number of alleles value read ok 13 - A reference of type 'ARRAY' isa 'ARRAY' ok 14 - alleles are correct ok 15 - VCF file open ok 16 - correct number of variants identified in file ok 17 - Header formatted string ok 18 - VCF Header version matches ok 19 - Number of samples ok 20 - sample names correct ok 21 - Number of seqnames ok 22 ok 23 - sequence names correct ok 24 - Next row ok 25 - Chromosome value read ok 26 - Position value read ok 27 - ID value read ok 28 - Num Filters OK ok 29 - Actual Filter present ok 30 - PASS filter absent ok 31 - Variant type matches ok 32 - info read correctly ok 33 - A reference of type 'ARRAY' isa 'ARRAY' ok 34 - info flag read correctly ok 35 - info flag type correct ok 36 - A reference of type 'ARRAY' isa 'ARRAY' ok 37 - info float read correctly ok 38 - info float type correct ok 39 - A reference of type 'ARRAY' isa 'ARRAY' ok 40 - info string read correctly ok 41 - info String type correct ok 42 - A reference of type 'ARRAY' isa 'ARRAY' ok 43 - info ints read correctly ok 44 - info int type correct ok 45 - format int read ok 46 - format int read ok 47 - format id not present ok 48 - format read ok 49 - Next row ok 50 - Chromosome value read ok 51 - Position value read ok 52 - Quality value read ok 53 - Reference value read ok 54 - Num Alleles ok 55 - Is SNP ok 56 - A reference of type 'ARRAY' isa 'ARRAY' ok 57 - alleles are correct ok 58 - Num Filters OK ok 59 - PASS Filter present ok 60 - Actual Filter absent ok 61 - Made up filter not existing ok 62 - info read correctly ok 63 - format int read ok 64 - format int read ok 65 - format id not present ok 66 - format read ok 67 - Next row ok 68 - Chromosome value read ok 69 - int format type correct ok 70 - format int read ok 71 - format int read ok 72 - format int read # !!! Not sure this is correct !!! ok 73 - format int read ok 74 - format read ok 75 - A reference of type 'ARRAY' isa 'ARRAY' ok 76 - genotypes read correctly ok 77 - format id not found ok 78 - info id not found ok 79 - info read correctly ok 80 - can query a region ok 81 - can get a value from the iterator ok 82 - chr ok 83 - position ok 84 - id ok 85 - reference ok 86 - info ok 87 - info ok 88 - info ok 89 - info ok 90 - can get a value from the iterator ok 91 - chr ok 92 - position ok 93 - id ok 94 - reference ok 95 - info ok 96 - no more results ok 97 - BCF file open ok 98 - correct number of variants identified in file ok 99 - Header formatted string ok 100 - VCF Header version matches ok 101 - Number of samples ok 102 - sample names correct ok 103 - Number of seqnames ok 104 - sequence names correct ok 105 - Next row ok 106 - Chromosome value read ok 107 - Position value read ok 108 - ID value read ok 109 - Num Filters OK ok 110 - Actual Filter present ok 111 - PASS filter absent ok 112 - Variant type matches ok 113 - info read correctly ok 114 - A reference of type 'ARRAY' isa 'ARRAY' ok 115 - info flag read correctly ok 116 - info flag type correct ok 117 - A reference of type 'ARRAY' isa 'ARRAY' ok 118 - info float read correctly ok 119 - info float type correct ok 120 - A reference of type 'ARRAY' isa 'ARRAY' ok 121 - info string read correctly ok 122 - info String type correct ok 123 - A reference of type 'ARRAY' isa 'ARRAY' ok 124 - info ints read correctly ok 125 - info int type correct ok 126 - format int read ok 127 - format int read ok 128 - format ID not present ok 129 - format read ok 130 - Next row ok 131 - Chromosome value read ok 132 - Position value read ok 133 - Quality value read ok 134 - Reference value read ok 135 - Num Alleles ok 136 - Is SNP ok 137 - A reference of type 'ARRAY' isa 'ARRAY' ok 138 - alleles are correct ok 139 - Num Filters OK ok 140 - PASS Filter present ok 141 - Actual Filter absent ok 142 - Made up filter not existing ok 143 - info read correctly ok 144 - format int read ok 145 - format int read ok 146 - format ID not present ok 147 - format read ok 148 - Next row ok 149 - Chromosome value read ok 150 - int format type correct ok 151 - format int read ok 152 - format int read ok 153 - format int read # !!! Not sure this is correct !!! ok 154 - format int read ok 155 - format read ok 156 - A reference of type 'ARRAY' isa 'ARRAY' ok 157 - genotypes read correctly ok 158 - format id not found ok 159 - info id not found ok 160 - info read correctly ok 161 - can query a region ok 162 - can get a value from the iterator ok 163 - chr ok 164 - position ok 165 - id ok 166 - reference ok 167 - info ok 168 - info ok 169 - info ok 170 - info ok 171 - can get a value from the iterator ok 172 - chr ok 173 - position ok 174 - id ok 175 - reference ok 176 - info ok 177 - no more results ok t/06kseq.t ....... ok 1 - correct num. seqs in bug2335 ok 2 - sample sequence obtained ok 3 - seq matches bug2335 ok 4 - desc matches bug2335 ok 5 - name matches bug2335 ok 6 - qual matches bug2335 ok 7 - Checking qual and seq lengths are the same in bug2335 ok 8 - Checking qual and seq lengths are the same using object methods in bug2335 ok 9 - correct num. seqs in evil_wrapping ok 10 - sample sequence obtained ok 11 - seq matches evil_wrapping ok 12 - desc matches evil_wrapping ok 13 - name matches evil_wrapping ok 14 - qual matches evil_wrapping ok 15 - Checking qual and seq lengths are the same in evil_wrapping ok 16 - Checking qual and seq lengths are the same using object methods in evil_wrapping ok 17 - correct num. seqs in example ok 18 - sample sequence obtained ok 19 - seq matches example ok 20 - desc matches example ok 21 - name matches example ok 22 - qual matches example ok 23 - Checking qual and seq lengths are the same in example ok 24 - Checking qual and seq lengths are the same using object methods in example ok 25 - correct num. seqs in illumina_faked ok 26 - sample sequence obtained ok 27 - seq matches illumina_faked ok 28 - desc matches illumina_faked ok 29 - name matches illumina_faked ok 30 - qual matches illumina_faked ok 31 - Checking qual and seq lengths are the same in illumina_faked ok 32 - Checking qual and seq lengths are the same using object methods in illumina_faked ok 33 - correct num. seqs in sanger_93 ok 34 - sample sequence obtained ok 35 - seq matches sanger_93 ok 36 - desc matches sanger_93 ok 37 - name matches sanger_93 ok 38 - qual matches sanger_93 ok 39 - Checking qual and seq lengths are the same in sanger_93 ok 40 - Checking qual and seq lengths are the same using object methods in sanger_93 ok 41 - correct num. seqs in sanger_faked ok 42 - sample sequence obtained ok 43 - seq matches sanger_faked ok 44 - desc matches sanger_faked ok 45 - name matches sanger_faked ok 46 - qual matches sanger_faked ok 47 - Checking qual and seq lengths are the same in sanger_faked ok 48 - Checking qual and seq lengths are the same using object methods in sanger_faked ok 49 - correct num. seqs in solexa_example ok 50 - sample sequence obtained ok 51 - seq matches solexa_example ok 52 - desc matches solexa_example ok 53 - name matches solexa_example ok 54 - qual matches solexa_example ok 55 - Checking qual and seq lengths are the same in solexa_example ok 56 - Checking qual and seq lengths are the same using object methods in solexa_example ok 57 - correct num. seqs in solexa_faked ok 58 - sample sequence obtained ok 59 - seq matches solexa_faked ok 60 - desc matches solexa_faked ok 61 - name matches solexa_faked ok 62 - qual matches solexa_faked ok 63 - Checking qual and seq lengths are the same in solexa_faked ok 64 - Checking qual and seq lengths are the same using object methods in solexa_faked ok 65 - correct num. seqs in test1_sanger ok 66 - sample sequence obtained ok 67 - seq matches test1_sanger ok 68 - desc matches test1_sanger ok 69 - name matches test1_sanger ok 70 - qual matches test1_sanger ok 71 - Checking qual and seq lengths are the same in test1_sanger ok 72 - Checking qual and seq lengths are the same using object methods in test1_sanger ok 73 - correct num. seqs in test2_solexa ok 74 - sample sequence obtained ok 75 - seq matches test2_solexa ok 76 - desc matches test2_solexa ok 77 - name matches test2_solexa ok 78 - qual matches test2_solexa ok 79 - Checking qual and seq lengths are the same in test2_solexa ok 80 - Checking qual and seq lengths are the same using object methods in test2_solexa ok 81 - correct num. seqs in test3_illumina ok 82 - sample sequence obtained ok 83 - seq matches test3_illumina ok 84 - desc matches test3_illumina ok 85 - name matches test3_illumina ok 86 - qual matches test3_illumina ok 87 - Checking qual and seq lengths are the same in test3_illumina ok 88 - Checking qual and seq lengths are the same using object methods in test3_illumina ok 89 - correct num. seqs in tricky ok 90 - sample sequence obtained ok 91 - seq matches tricky ok 92 - desc matches tricky ok 93 - name matches tricky ok 94 - qual matches tricky ok 95 - Checking qual and seq lengths are the same in tricky ok 96 - Checking qual and seq lengths are the same using object methods in tricky ok 97 - correct num. seqs in zero_qual ok 98 - sample sequence obtained ok 99 - seq matches zero_qual ok 100 - desc matches zero_qual ok 101 - name matches zero_qual ok 102 - qual matches zero_qual ok 103 - Checking qual and seq lengths are the same in zero_qual ok 104 - Checking qual and seq lengths are the same using object methods in zero_qual 1..104 ok [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Destination address required t/07cramwrite.t .. 1..22 # Running under perl version 5.038002 for linux # Current time local: Sun Jun 8 20:53:23 2025 # Current time GMT: Sun Jun 8 20:53:23 2025 # 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 t/08bamwrite.t ... 1..22 # Running under perl version 5.038002 for linux # Current time local: Sun Jun 8 20:53:24 2025 # Current time GMT: Sun Jun 8 20:53:24 2025 # 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 t/09sam.t ........ ok 1 ok 2 # skip Cannot test header reading for htslib < 1.5 ok 3 # skip Cannot test header reading for htslib < 1.5 ok 4 # skip Cannot test header reading for htslib < 1.5 ok 5 # skip Cannot test header reading for htslib < 1.5 ok 6 # skip Cannot test header reading for htslib < 1.5 ok 7 # skip Cannot test header reading for htslib < 1.5 ok 8 # skip Cannot test header reading for htslib < 1.5 ok 9 # skip Cannot test header reading for htslib < 1.5 ok 10 # skip Cannot test header reading for htslib < 1.5 ok 11 # skip Cannot test header reading for htslib < 1.5 ok 12 ok 13 ok 14 # skip Cannot test iterating over alignments for htslib < 1.5 ok 15 # skip Cannot test iterating over alignments for htslib < 1.5 ok 16 # skip Cannot test iterating over alignments for htslib < 1.5 ok 17 # skip Cannot test iterating over alignments for htslib < 1.5 ok 18 ok 19 ok 20 ok 21 ok 22 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' ok 23 1..23 ok t/10leak.t ....... skipped: require Test::LeakTrace All tests successful. Files=11, Tests=979, 6 wallclock secs ( 0.17 usr 0.01 sys + 5.66 cusr 0.53 csys = 6.37 CPU) Result: PASS create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-db-hts-perl/ /usr/bin/perl Build install --destdir /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl --create_packlist 0 Building Bio-DB-HTS Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/auto/Bio/DB/HTS/HTS.so Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/auto/Bio/DB/HTS/HTS.bs Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/auto/Bio/DB/HTS/Faidx/Faidx.so Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/auto/Bio/DB/HTS/Faidx/Faidx.bs Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/VCF.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Target.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Tabix.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Segment.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/ReadIterator.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Query.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/PileupWrapper.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Pileup.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Kseq.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/FetchIterator.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Faidx.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Constants.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Alignment.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/AlignWrapper.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/VCF/RowPtr.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/VCF/Row.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/VCF/Iterator.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/VCF/HeaderPtr.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/VCF/Header.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Tabix/Iterator.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Kseq/Iterator.pod Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.38/Bio/DB/HTS/Kseq/Record.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::VCF::Iterator.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::VCF.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Target.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Tabix::Iterator.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Tabix.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Segment.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::ReadIterator.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Query.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::PileupWrapper.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Pileup.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq::Record.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq::Iterator.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::FetchIterator.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Faidx.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Constants.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Alignment.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::AlignWrapper.3pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS.3pm 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-db-hts-perl' in '../libbio-db-hts-perl_3.01-4_arm64.deb'. dpkg-deb: building package 'libbio-db-hts-perl-dbgsym' in '../libbio-db-hts-perl-dbgsym_3.01-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libbio-db-hts-perl_3.01-4_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-db-hts-perl_3.01-4_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/2826810 and its subdirectories I: Current time: Sun Jun 8 08:53:29 -12 2025 I: pbuilder-time-stamp: 1749416009 Mon May 6 14:30:32 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Mon May 6 14:30:32 UTC 2024 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Mon May 6 14:31:13 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Mon May 6 14:31:14 UTC 2024 I: libbio-db-hts-perl_3.01-4_arm64.changes: Format: 1.8 Date: Thu, 06 Oct 2022 11:25:46 +0200 Source: libbio-db-hts-perl Binary: libbio-db-hts-perl libbio-db-hts-perl-dbgsym Architecture: arm64 Version: 3.01-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbio-db-hts-perl - Perl interface to the HTS library Changes: libbio-db-hts-perl (3.01-4) unstable; urgency=medium . * Packaging update * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Submit. * Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright). Checksums-Sha1: a7616bfe2c0d8a2dea20d8fa84bb4c0e533bc528 184856 libbio-db-hts-perl-dbgsym_3.01-4_arm64.deb d53861f471063697167a4104ba6fa92fdf9f0b33 6400 libbio-db-hts-perl_3.01-4_arm64.buildinfo 7edfde65a213143addbc178cb558dfe30bc25964 133420 libbio-db-hts-perl_3.01-4_arm64.deb Checksums-Sha256: 74a93d62c8f8068cb98b09b52a9234d1c3d45558b2173ece5d2101fda45abc52 184856 libbio-db-hts-perl-dbgsym_3.01-4_arm64.deb 6bfad13df5e675aff94b081de28382b98b5a4c9a3678075af79fffd3a7687d8a 6400 libbio-db-hts-perl_3.01-4_arm64.buildinfo 9d7e0fee5043395d38181a039141ac9a77cb996a46cb94c30156540127f3c15c 133420 libbio-db-hts-perl_3.01-4_arm64.deb Files: 47d761e1ced2c7b662644fc9f9c4695a 184856 debug optional libbio-db-hts-perl-dbgsym_3.01-4_arm64.deb 7fe6247c05cc50ef286e73986514525d 6400 science optional libbio-db-hts-perl_3.01-4_arm64.buildinfo 36fe2b522ff8757115eb12a6271b46d5 133420 science optional libbio-db-hts-perl_3.01-4_arm64.deb Mon May 6 14:31:15 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_13-16758.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2y7MxZ7n/libbio-db-hts-perl_3.01-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2y7MxZ7n/libbio-db-hts-perl_3.01-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2y7MxZ7n/libbio-db-hts-perl_3.01-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2y7MxZ7n/b1/libbio-db-hts-perl_3.01-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2y7MxZ7n/b2/libbio-db-hts-perl_3.01-4_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: 0.433s) 0.433s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.021s) 0.021s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 810ms CPU time consumed: 808ms Mon May 6 14:31:17 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Mon May 6 14:31:17 UTC 2024 I: libbio-db-hts-perl from trixie built successfully and reproducibly on arm64. Mon May 6 14:31:18 UTC 2024 I: Submitting .buildinfo files to external archives: Mon May 6 14:31:18 UTC 2024 I: Submitting 8.0K b1/libbio-db-hts-perl_3.01-4_arm64.buildinfo.asc Mon May 6 14:31:19 UTC 2024 I: Submitting 8.0K b2/libbio-db-hts-perl_3.01-4_arm64.buildinfo.asc Mon May 6 14:31:20 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 6 14:31:20 UTC 2024 I: Done submitting .buildinfo files. Mon May 6 14:31:20 UTC 2024 I: Removing signed libbio-db-hts-perl_3.01-4_arm64.buildinfo.asc files: removed './b1/libbio-db-hts-perl_3.01-4_arm64.buildinfo.asc' removed './b2/libbio-db-hts-perl_3.01-4_arm64.buildinfo.asc'