Thu Nov 7 14:44:50 UTC 2024 I: starting to build libbio-db-hts-perl/trixie/arm64 on jenkins on '2024-11-07 14:44' Thu Nov 7 14:44:50 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_9/44617/console.log Thu Nov 7 14:44:50 UTC 2024 I: Downloading source for trixie/libbio-db-hts-perl=3.01-5 --2024-11-07 14:44:50-- http://deb.debian.org/debian/pool/main/libb/libbio-db-hts-perl/libbio-db-hts-perl_3.01-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2359 (2.3K) [text/prs.lines.tag] Saving to: ‘libbio-db-hts-perl_3.01-5.dsc’ 0K .. 100% 282M=0s 2024-11-07 14:44:50 (282 MB/s) - ‘libbio-db-hts-perl_3.01-5.dsc’ saved [2359/2359] Thu Nov 7 14:44:50 UTC 2024 I: libbio-db-hts-perl_3.01-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-db-hts-perl Binary: libbio-db-hts-perl Architecture: any Version: 3.01-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://metacpan.org/release/Bio-DB-HTS Standards-Version: 4.7.0 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 d7bdd735f08c9aea21c5f359e7a01c07d722f0ca 4096 libbio-db-hts-perl_3.01-5.debian.tar.xz Checksums-Sha256: 12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42 5250834 libbio-db-hts-perl_3.01.orig.tar.gz d009dc57129ec9a2a4ba62d70811490db0aeb2acfdc6cb794fa3071b8cebc4fb 4096 libbio-db-hts-perl_3.01-5.debian.tar.xz Files: 7b7f991deddb12084cf85e0fa3d91819 5250834 libbio-db-hts-perl_3.01.orig.tar.gz d0d56c1490e0cdd62bdeb2c994b1514b 4096 libbio-db-hts-perl_3.01-5.debian.tar.xz Dgit: 066421607e4883c179f44720397f941c8efd751c debian archive/debian/3.01-5 https://git.dgit.debian.org/libbio-db-hts-perl -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcj+yIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdq54xAAhta6QAwaac6CAuVYFwB8EHkq4OHo 08DvOIeFOH6fBdltLQ6UHBIKs90GMW5lFlhhFoaWsLs+7Eu1J3uczU0d4YDO/UOH mC/7tV0hMdTl2xXH9PbBVeBRNLV47XDarI/K/zJdDOgyj5Mazc9XWkn5CQEw55rL 9NpRGDJi7gLLp7+mCUX0fQ26P1Zw4wcFoIY7F5rOLz5/eLIpq8+8aLz18ZeqEBG4 ma69MVCsz8edcVMa+/X+yFAcnSE2GtxzUnce8WsVG1RaSiAxDH8pczECSM0m3Sw+ MEmFMf/qV4YpDXIG4e47RbV5/g/DBlmr2RJBCG9sUSEvk6qQN3p9TR2Qdu79Grm4 Ts25KPT8qxUz2QEpJYM9zg7Fr/5eorF3gvmPWdWwsGWGWkdb5NjsyZw6odNY0OHZ jAUZZzDKgbpmzCDnKimY8nmx+drv0S9AV66lXy7n27eu0Lyo7z23ADwCVEjnVgVu TFUS2kc0za2ntIOlhEMPwzlgjWMs4i/96diuASkToHp3Tk11WHoUUBsw5IsoD9hT UHrQJVKmkxroEgXxTuFpK9F3IR3iS2V1/h9lAE5hEZ4yyFAYWwE77UxiiZLLJOsM xJEg0C0K4R3lMsBSjqooI1ri3wPTlhEWpYq66wi24DqQQXcEimukdQbJH+/E43Mw JGIGp285WiFbjf4= =ZoVb -----END PGP SIGNATURE----- Thu Nov 7 14:44:50 UTC 2024 I: Checking whether the package is not for us Thu Nov 7 14:44:50 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Thu Nov 7 14:44:50 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Thu Nov 7 14:45:36 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 10 09:07:53 -12 2025 I: pbuilder-time-stamp: 1765400873 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_3.01-5.dsc] I: copying [./libbio-db-hts-perl_3.01.orig.tar.gz] I: copying [./libbio-db-hts-perl_3.01-5.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Oct 31 21:48:18 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libbio-db-hts-perl_3.01-5.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_3.01-5.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/2448773/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='d3bd328fd5ce454e9d67ebdd719b32df' 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='2448773' 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.x5IbPuJx/pbuilderrc_BM5Z --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.x5IbPuJx/b1 --logfile b1/build.log libbio-db-hts-perl_3.01-5.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 codethink03-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2448773/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 ... 20089 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} libbrotli-dev{a} libbrotli1{a} libbz2-dev{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} libevent-2.1-7t64{a} libextutils-pkgconfig-perl{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{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} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{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: bzip2-doc ca-certificates curl krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-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 libtasn1-doc 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, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 39.3 MB of archives. After unpacking 146 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-9 [96.6 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 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 2.72-3 [493 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 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 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 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b5 [296 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libbrotli-dev arm64 1.1.0-2+b5 [308 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 40 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.10.1-2 [328 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libgnutls-dane0t64 arm64 3.8.6-2+b1 [437 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libgnutls-openssl27t64 arm64 3.8.6-2+b1 [437 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libgnutls28-dev arm64 3.8.6-2+b1 [1398 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libnghttp3-dev arm64 1.4.0-1+b1 [85.2 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.6.0-1 [23.7 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libngtcp2-dev arm64 1.6.0-1 [165 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.10.1-2 [456 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libextutils-pkgconfig-perl all 1.16-3 [9928 B] Get: 82 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libmodule-build-perl all 0.423400-2 [252 kB] Fetched 39.3 MB in 0s (82.9 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 ... 20089 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. 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Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../77-libdeflate0_1.22-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.22-1) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../78-libdeflate-dev_1.22-1_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.22-1) ... Selecting previously unselected package pkg-config:arm64. Preparing to unpack .../79-pkg-config_1.8.1-4_arm64.deb ... Unpacking pkg-config:arm64 (1.8.1-4) ... Selecting previously unselected package libextutils-pkgconfig-perl. Preparing to unpack .../80-libextutils-pkgconfig-perl_1.16-3_all.deb ... Unpacking libextutils-pkgconfig-perl (1.16-3) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../81-libhtscodecs2_1.6.1-1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.1-1) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../82-libhts3t64_1.20+ds-2_arm64.deb ... Unpacking libhts3t64:arm64 (1.20+ds-2) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../83-liblzma-dev_5.6.3-1+b1_arm64.deb ... Unpacking liblzma-dev:arm64 (5.6.3-1+b1) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../84-libhts-dev_1.20+ds-2_arm64.deb ... Unpacking libhts-dev:arm64 (1.20+ds-2) ... Selecting previously unselected package libmodule-build-perl. Preparing to unpack .../85-libmodule-build-perl_0.423400-2_all.deb ... Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.423400-2) ... Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgnutls-openssl27t64:arm64 (3.8.6-2+b1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up libzstd-dev:arm64 (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b5) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:arm64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libmodule-build-perl (0.423400-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:arm64 (1.22.0-1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-2+b2) ... Setting up libgnutls-dane0t64:arm64 (3.8.6-2+b1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libssl-dev:arm64 (3.3.2-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libidn2-dev:arm64 (2.3.7-2+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.4.0-1+b1) ... Setting up libnghttp3-dev:arm64 (1.4.0-1+b1) ... Setting up liblzma-dev:arm64 (5.6.3-1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libngtcp2-16:arm64 (1.6.0-1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libtasn1-6-dev:arm64 (4.19.0-3+b3) ... Setting up libdeflate-dev:arm64 (1.22-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b5) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Setting up libp11-kit-dev:arm64 (0.25.5-2+b1) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:arm64 (3.10-1+b1) ... Setting up libtool (2.4.7-7) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.6.0-1) ... Setting up libngtcp2-dev:arm64 (1.6.0-1) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up pkg-config:arm64 (1.8.1-4) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:arm64 (3.8.6-2+b1) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up libextutils-pkgconfig-perl (1.16-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.10.1-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:arm64 (1.20+ds-2) ... Setting up debhelper (13.20) ... Setting up libcurl4-gnutls-dev:arm64 (8.10.1-2) ... Setting up libhts-dev:arm64 (1.20+ds-2) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... 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_3.01-5_source.changes dpkg-buildpackage: info: source package libbio-db-hts-perl dpkg-buildpackage: info: source version 3.01-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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/reproducible-path/libbio-db-hts-perl-3.01' # Nudge configure steps to locate htslib, as for some reason it # fails to find the htslb on its own with the logic provided in # Build.PL. dh_auto_configure -- \ --htslib-includedir \ /usr/include \ --htslib-libdir \ /usr/lib/aarch64-linux-gnu /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" --htslib-includedir /usr/include --htslib-libdir /usr/lib/aarch64-linux-gnu Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '3.01' make[1]: Leaving directory '/build/reproducible-path/libbio-db-hts-perl-3.01' dh_auto_build /usr/bin/perl Build Building Bio-DB-HTS aarch64-linux-gnu-gcc -I/usr/include -I/usr/lib/aarch64-linux-gnu/perl/5.40/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 -L/usr/lib/aarch64-linux-gnu -lhts -lpthread -lz aarch64-linux-gnu-gcc -I/usr/include -I/usr/lib/aarch64-linux-gnu/perl/5.40/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 -L/usr/lib/aarch64-linux-gnu -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 5.040000 for linux # Current time local: Wed Dec 10 21:08:23 2025 # Current time GMT: Wed Dec 10 21:08:23 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 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 5.040000 for linux # Current time local: Wed Dec 10 21:08:24 2025 # Current time GMT: Wed Dec 10 21:08:24 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 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 5.040000 for linux # Current time local: Wed Dec 10 21:08:28 2025 # Current time GMT: Wed Dec 10 21:08:28 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 5.040000 for linux # Current time local: Wed Dec 10 21:08:29 2025 # Current time GMT: Wed Dec 10 21:08:29 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 ( 0.14 usr 0.03 sys + 5.83 cusr 0.62 csys = 6.62 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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/Bio/DB/HTS.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/ConfigData.pm Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/aarch64-linux-gnu/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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/perl5/5.40/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::ConfigData.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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbio-db-hts-perl-dbgsym' in '../libbio-db-hts-perl-dbgsym_3.01-5_arm64.deb'. dpkg-deb: building package 'libbio-db-hts-perl' in '../libbio-db-hts-perl_3.01-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libbio-db-hts-perl_3.01-5_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-db-hts-perl_3.01-5_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/2448773 and its subdirectories I: Current time: Wed Dec 10 09:08:35 -12 2025 I: pbuilder-time-stamp: 1765400915 Thu Nov 7 14:45:37 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Thu Nov 7 14:45:37 UTC 2024 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Thu Nov 7 14:47:03 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Thu Nov 7 14:47:04 UTC 2024 I: libbio-db-hts-perl_3.01-5_arm64.changes: Format: 1.8 Date: Thu, 31 Oct 2024 22:38:00 +0100 Source: libbio-db-hts-perl Binary: libbio-db-hts-perl libbio-db-hts-perl-dbgsym Architecture: arm64 Version: 3.01-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: libbio-db-hts-perl - Perl interface to the HTS library Closes: 1086359 Changes: libbio-db-hts-perl (3.01-5) unstable; urgency=medium . * d/rules: nudge configure steps to find htslib. (Closes: #1086359) * find_htslib.patch: remove DT_RUNPATH injection. * d/control: declare myself as uploader. * d/control: declare compliance to standards version 4.7.0. * d/*lintian-overrides: freshen section override. Checksums-Sha1: 47109a4bfa56c35b35651b42286242c952ee5aa7 183244 libbio-db-hts-perl-dbgsym_3.01-5_arm64.deb 44cda80d86b82eb1011938ff5ce1c9c60d64c7da 7053 libbio-db-hts-perl_3.01-5_arm64.buildinfo 8ba5d7e257c81660bf36a01eea840c7c301da67e 136948 libbio-db-hts-perl_3.01-5_arm64.deb Checksums-Sha256: fb9ae9d2a6755c9cac515c8577a236156e038d1d84725912accc33f318ac9e8b 183244 libbio-db-hts-perl-dbgsym_3.01-5_arm64.deb 977eaa239996f1a74628f42b4520d3c6fe90f42279de7f12fcfa3cb3982e366b 7053 libbio-db-hts-perl_3.01-5_arm64.buildinfo 6bb376f71b2cff4517cb427cc26886644a1288166c0a9fa20baf49f49fef65e1 136948 libbio-db-hts-perl_3.01-5_arm64.deb Files: 52ebe3484f1918f006c5a89c283f0c27 183244 debug optional libbio-db-hts-perl-dbgsym_3.01-5_arm64.deb e9151481f928412849a910b7042b2938 7053 science optional libbio-db-hts-perl_3.01-5_arm64.buildinfo dd91a3a206e797c9fa1eaf0f53cbfc32 136948 science optional libbio-db-hts-perl_3.01-5_arm64.deb Thu Nov 7 14:47:07 UTC 2024 I: diffoscope 282 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_9-44617.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.x5IbPuJx/libbio-db-hts-perl_3.01-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.x5IbPuJx/libbio-db-hts-perl_3.01-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.x5IbPuJx/libbio-db-hts-perl_3.01-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.x5IbPuJx/b1/libbio-db-hts-perl_3.01-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.x5IbPuJx/b2/libbio-db-hts-perl_3.01-5_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: 2.635s) 2.635s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.114s) 0.114s 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: 2.996s CPU time consumed: 1.737s Thu Nov 7 14:47:10 UTC 2024 I: diffoscope 282 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 7 14:47:10 UTC 2024 I: libbio-db-hts-perl from trixie built successfully and reproducibly on arm64. Thu Nov 7 14:47:12 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 7 14:47:12 UTC 2024 I: Submitting 8.0K b1/libbio-db-hts-perl_3.01-5_arm64.buildinfo.asc Thu Nov 7 14:47:13 UTC 2024 I: Submitting 8.0K b2/libbio-db-hts-perl_3.01-5_arm64.buildinfo.asc Thu Nov 7 14:47:14 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 7 14:47:14 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 7 14:47:14 UTC 2024 I: Removing signed libbio-db-hts-perl_3.01-5_arm64.buildinfo.asc files: removed './b1/libbio-db-hts-perl_3.01-5_arm64.buildinfo.asc' removed './b2/libbio-db-hts-perl_3.01-5_arm64.buildinfo.asc'