sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +===============================================================================+ | libbio-alignio-stockholm-perl 1.7.3-2 (amd64) Mon, 18 Aug 2025 00:29:25 +0000 | +===============================================================================+ Package: libbio-alignio-stockholm-perl Version: 1.7.3-2 Source Version: 1.7.3-2 Distribution: perl-5.42-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Mon, 18 Aug 2025 00:29:26 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup libbio-alignio-stockholm-perl_1.7.3-2 perl-5.42-throwaway amd64 -------------------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup libbio-alignio-stockholm-perl_1.7.3-2 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 18 Aug 2025 00:29:26 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:2 http://deb.debian.org/debian unstable InRelease [216 kB] Get:3 http://deb.debian.org/debian sid InRelease [216 kB] Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 file:/srv/reprepro perl-5.42/main amd64 Packages [547 kB] Get:6 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-17-1413.37-F-2025-08-16-2015.43.pdiff [102 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-17-1413.37-F-2025-08-16-2015.43.pdiff [102 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-17-1413.37-F-2025-08-16-2015.43.pdiff [73.0 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-17-1413.37-F-2025-08-16-2015.43.pdiff [73.0 kB] Fetched 734 kB in 3s (239 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu init-system-helpers libbinutils libctf-nobfd0 libctf0 libgprofng0 libidn2-0 libldap2 libsframe2 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5687 kB/5881 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [194 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.45-4 [810 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.45-4 [89.7 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.45-4 [157 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.45-4 [1042 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.45-4 [266 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.45-4 [539 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.45-4 [2556 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libsframe2 amd64 2.45-4 [79.5 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-3 [109 kB] Fetched 5687 kB in 0s (86.4 MB/s) (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 ... 14970 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.69_all.deb ... Unpacking init-system-helpers (1.69) over (1.68) ... Setting up init-system-helpers (1.69) ... (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 ... 14971 files and directories currently installed.) Preparing to unpack .../0-libgprofng0_2.45-4_amd64.deb ... Unpacking libgprofng0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../1-libctf0_2.45-4_amd64.deb ... Unpacking libctf0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../2-libctf-nobfd0_2.45-4_amd64.deb ... Unpacking libctf-nobfd0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../3-binutils-x86-64-linux-gnu_2.45-4_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.45-4) over (2.45-3) ... Preparing to unpack .../4-binutils_2.45-4_amd64.deb ... Unpacking binutils (2.45-4) over (2.45-3) ... Preparing to unpack .../5-libbinutils_2.45-4_amd64.deb ... Unpacking libbinutils:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../6-binutils-common_2.45-4_amd64.deb ... Unpacking binutils-common:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../7-libsframe2_2.45-4_amd64.deb ... Unpacking libsframe2:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../8-libidn2-0_2.3.8-3_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-3) over (2.3.8-2) ... Preparing to unpack .../9-libldap2_2.6.10+dfsg-1+b1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1+b1) over (2.6.10+dfsg-1) ... Setting up libsframe2:amd64 (2.45-4) ... Setting up binutils-common:amd64 (2.45-4) ... Setting up libctf-nobfd0:amd64 (2.45-4) ... Setting up libidn2-0:amd64 (2.3.8-3) ... Setting up libbinutils:amd64 (2.45-4) ... Setting up libldap2:amd64 (2.6.10+dfsg-1+b1) ... Setting up libctf0:amd64 (2.45-4) ... Setting up libgprofng0:amd64 (2.45-4) ... Setting up binutils-x86-64-linux-gnu (2.45-4) ... Setting up binutils (2.45-4) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Fetch source files Mon, 18 Aug 2025 00:29:33 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/libbio-alignio-stockholm-perl_1.7.3-2.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 18 Aug 2025 00:29:33 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libbio-perl-perl, libtest-most-perl, build-essential, perl Filtered Build-Depends: debhelper-compat (= 12), libbio-perl-perl, libtest-most-perl, build-essential, perl dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/libbio-alignio-stockholm-perl-wVV8eP/resolver-137moG/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/libbio-alignio-stockholm-perl-wVV8eP/resolver-137moG/apt_archive ./ InRelease Get:2 copy:/build/libbio-alignio-stockholm-perl-wVV8eP/resolver-137moG/apt_archive ./ Release [609 B] Ign:3 copy:/build/libbio-alignio-stockholm-perl-wVV8eP/resolver-137moG/apt_archive ./ Release.gpg Get:4 copy:/build/libbio-alignio-stockholm-perl-wVV8eP/resolver-137moG/apt_archive ./ Sources [663 B] Get:5 copy:/build/libbio-alignio-stockholm-perl-wVV8eP/resolver-137moG/apt_archive ./ Packages [682 B] Fetched 1954 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libalgorithm-diff-perl libarchive-zip-perl libbio-perl-perl libcapture-tiny-perl libclass-data-inheritable-perl libdata-stag-perl libdebhelper-perl libdevel-stacktrace-perl libelf1t64 libexception-class-perl libfile-stripnondeterminism-perl libio-string-perl libmagic-mgc libmagic1t64 libpipeline1 libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libxml2-16 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff bioperl libxml-sax-expatxs-perl libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-libxml-perl libwww-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libalgorithm-diff-perl libarchive-zip-perl libbio-perl-perl libcapture-tiny-perl libclass-data-inheritable-perl libdata-stag-perl libdebhelper-perl libdevel-stacktrace-perl libelf1t64 libexception-class-perl libfile-stripnondeterminism-perl libio-string-perl libmagic-mgc libmagic1t64 libpipeline1 libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libxml2-16 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 14.1 MB of archives. After this operation, 50.7 MB of additional disk space will be used. Get:1 copy:/build/libbio-alignio-stockholm-perl-wVV8eP/resolver-137moG/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [876 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-1 [94.7 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.25 [91.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.1 [640 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.25 [937 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libcapture-tiny-perl all 0.50-1 [24.6 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get:36 http://deb.debian.org/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.205-1 [52.3 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Preconfiguring packages ... Fetched 14.1 MB in 0s (68.4 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 14972 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-1_amd64.deb ... Unpacking bsdextrautils (2.41.1-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.25_all.deb ... Unpacking libdebhelper-perl (13.25) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../23-libxml2-16_2.14.5+dfsg-0.1_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../24-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../25-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../26-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../27-debhelper_13.25_all.deb ... Unpacking debhelper (13.25) ... Selecting previously unselected package libalgorithm-diff-perl. Preparing to unpack .../28-libalgorithm-diff-perl_1.201-1_all.deb ... Unpacking libalgorithm-diff-perl (1.201-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../29-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../30-libdata-stag-perl_0.14-3_all.deb ... Unpacking libdata-stag-perl (0.14-3) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../31-libbio-perl-perl_1.7.8-1_all.deb ... Unpacking libbio-perl-perl (1.7.8-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../32-libcapture-tiny-perl_0.50-1_all.deb ... Unpacking libcapture-tiny-perl (0.50-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../33-libclass-data-inheritable-perl_0.10-1_all.deb ... Unpacking libclass-data-inheritable-perl (0.10-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../34-libdevel-stacktrace-perl_2.0500-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0500-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../35-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libsub-uplevel-perl. Preparing to unpack .../36-libsub-uplevel-perl_0.2800-3_all.deb ... Unpacking libsub-uplevel-perl (0.2800-3) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../37-libtest-deep-perl_1.205-1_all.deb ... Unpacking libtest-deep-perl (1.205-1) ... Selecting previously unselected package libtext-diff-perl. Preparing to unpack .../38-libtext-diff-perl_1.45-2_all.deb ... Unpacking libtext-diff-perl (1.45-2) ... Selecting previously unselected package libtest-differences-perl. Preparing to unpack .../39-libtest-differences-perl_0.71-1_all.deb ... Unpacking libtest-differences-perl (0.71-1) ... Selecting previously unselected package libtest-exception-perl. Preparing to unpack .../40-libtest-exception-perl_0.43-3_all.deb ... Unpacking libtest-exception-perl (0.43-3) ... Selecting previously unselected package libtest-warn-perl. Preparing to unpack .../41-libtest-warn-perl_0.37-2_all.deb ... Unpacking libtest-warn-perl (0.37-2) ... Selecting previously unselected package libtest-most-perl. Preparing to unpack .../42-libtest-most-perl_0.38-1_all.deb ... Unpacking libtest-most-perl (0.38-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../43-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-1) ... Setting up libtest-deep-perl (1.205-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.1) ... Setting up libdebhelper-perl (13.25) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20240727.1) ... Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up libcapture-tiny-perl (0.50-1) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-4) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtest-exception-perl (0.43-3) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.25) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 18 Aug 2025 00:29:38 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment Mon, 18 Aug 2025 00:29:38 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.45-4 dpkg-dev_1.22.21 g++-14_14.3.0-5 gcc-14_14.3.0-5 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 linux-libc-dev_6.12.38-1 Package versions: adduser_3.152 apt_3.1.4 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.2.37-2+b5 binutils_2.45-4 binutils-common_2.45-4 binutils-gold_2.44-2 binutils-gold-x86-64-linux-gnu_2.44-2 binutils-x86-64-linux-gnu_2.45-4 bsdextrautils_2.41.1-1 bsdutils_1:2.41.1-1 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-14_14.3.0-5 cpp-14-x86-64-linux-gnu_14.3.0-5 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.25 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.8-2 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.3.0-5 g++-14-x86-64-linux-gnu_14.3.0-5 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.3.0-5 gcc-14-base_14.3.0-5 gcc-14-x86-64-linux-gnu_14.3.0-5 gcc-15-base_15.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gnupg_2.4.8-2 gnupg-l10n_2.4.8-2 gpg_2.4.8-2 gpg-agent_2.4.8-2 gpgconf_2.4.8-2 gpgsm_2.4.8-2 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libalgorithm-diff-perl_1.201-1 libapt-pkg7.0_3.1.4 libarchive-zip-perl_1.68-1 libasan8_15.2.0-1 libassuan9_3.0.2-2 libatomic1_15.2.0-1 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.45-4 libbio-perl-perl_1.7.8-1 libblkid1_2.41.1-1 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcapture-tiny-perl_0.50-1 libcc1-0_15.2.0-1 libclass-data-inheritable-perl_0.10-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-4 libctf0_2.45-4 libdata-stag-perl_0.14-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.280 libdebhelper-perl_13.25 libdevel-stacktrace-perl_2.0500-1 libdpkg-perl_1.22.21 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libexception-class-perl_1.45-1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-14-dev_14.3.0-5 libgcc-s1_15.2.0-1 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.10-2 libgomp1_15.2.0-1 libgpg-error0_1.55-2 libgprofng0_2.45-4 libhogweed6t64_3.10.1-1 libhwasan0_15.2.0-1 libidn2-0_2.3.8-3 libio-string-perl_1.08-4 libisl23_0.27-1 libitm1_15.2.0-1 libjansson4_2.14-2+b3 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.1-1 libldap2_2.6.10+dfsg-1+b1 liblsan0_15.2.0-1 liblz4-1_1.10.0-4 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.1-1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnpth0t64_1.8-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.40_5.40.1-6 libperl5.42_5.42.0-1 libpipeline1_1.5.8-1 libquadmath0_15.2.0-1 libreadline8t64_8.2-6 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe2_2.45-4 libsmartcols1_2.41.1-1 libsqlite3-0_3.46.1-7 libssl3t64_3.5.2-1 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 libsub-uplevel-perl_0.2800-3 libsystemd0_258~rc2-2 libtasn1-6_4.20.0-2 libtest-deep-perl_1.205-1 libtest-differences-perl_0.71-1 libtest-exception-perl_0.43-3 libtest-most-perl_0.38-1 libtest-warn-perl_0.37-2 libtext-diff-perl_1.45-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_15.2.0-1 libubsan1_15.2.0-1 libuchardet0_0.0.8-1+b2 libudev1_258~rc2-2 libunistring5_1.3-2 libuuid1_2.41.1-1 libxml2-16_2.14.5+dfsg-0.1 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.38-1 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 openssl-provider-legacy_3.5.2-1 passwd_1:4.17.4-2 patch_2.8-2 perl_5.42.0-1 perl-base_5.42.0-1 perl-modules-5.40_5.40.1-6 perl-modules-5.42_5.42.0-1 pinentry-curses_1.3.2-3 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 util-linux_2.41.1-1 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 18 Aug 2025 00:29:38 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libbio-alignio-stockholm-perl Binary: libbio-alignio-stockholm-perl Architecture: all Version: 1.7.3-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://metacpan.org/release/Bio-AlignIO-stockholm Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/libbio-alignio-stockholm-perl Vcs-Git: https://salsa.debian.org/med-team/libbio-alignio-stockholm-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 12), libbio-perl-perl, libtest-most-perl Build-Depends-Indep: perl Package-List: libbio-alignio-stockholm-perl deb perl optional arch=all Checksums-Sha1: 89ca9fbb76d58140f42d80776efbdce958454baa 37596 libbio-alignio-stockholm-perl_1.7.3.orig.tar.gz 9b80b333ca155afb28773df1dab39eec5da38f0d 1780 libbio-alignio-stockholm-perl_1.7.3-2.debian.tar.xz Checksums-Sha256: c2699f42341902bb1db2407708141d589d7b40cac4531879d7744147c35500e2 37596 libbio-alignio-stockholm-perl_1.7.3.orig.tar.gz f6f3683dc8b27bda0ecfe5cd4ce65bc01911798ed54e29a167fa7928d43cafe8 1780 libbio-alignio-stockholm-perl_1.7.3-2.debian.tar.xz Files: 47361a5c56b1efc8be723c76c342ea0d 37596 libbio-alignio-stockholm-perl_1.7.3.orig.tar.gz 6b5bada7af9da7f04f9c73591dcef594 1780 libbio-alignio-stockholm-perl_1.7.3-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl5eD04RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGN4xAAmF4QkmTG8izvJqmRL5YXJJTSQxuaR+IS 7NwjtQxTiDOj/Jf5nQ4hAMU5+dI55TNGvRd+Cf3j5JbQRBW7i1tvRzTLMOD/PlfD CUhboORX1kcOdQUdVuNeVxLKFBTvPps0ic0ABjhbGPQFyhdoe3yPmVIkNgOpxOZw Lb5GNtmUIl1EZdRUAum3gaScWacoflW1NjNnrMi8d2Uq3c1lDjG25pdvS1BVKsmD E7rcXzz/3p8SjcpX5kEOPHZKTfE23/QmqGmOvg3tZt2DJ40ig/JHOVipCOG1c914 q4e8piis10pS+n9gW3cXoOqdRsYuXXUjHiMml94EO9jOnQh+DunBoHp+bwuFfeIN Xcv98Qmqx/10U/WXJ04mJFT4zkAV4s7WIqRBu6xUGEEAcVL4+WX4hLvkgs1xOs1n je6IP3o7B90sbhd84v3nSlnliMoNfJP3ANDgWmIwpLTBQvWRjJ50o/QZyxoGW3Rt 1qynAQXdQ6oGC6o+vQKChZM0LS4rGhwbwoLFabfoDAQdN5AjOL8Yqps7DZJIFkMz RttwU5fANbUKWXO9sJ8LKMhwHfta0+6LYveGR4BfKJKkSKiyfu14CPLLU8EUhL/b vwzoFLSN3OIkLW6XWyWPYdyPpziwWRMPmw6iKUTXq3NqEgCM7wMJjJBNvb+UI5jC kj0G9yUG5jE= =VF0H -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./libbio-alignio-stockholm-perl_1.7.3-2.dsc: no acceptable signature found dpkg-source: info: extracting libbio-alignio-stockholm-perl in /build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3 dpkg-source: info: unpacking libbio-alignio-stockholm-perl_1.7.3.orig.tar.gz dpkg-source: info: unpacking libbio-alignio-stockholm-perl_1.7.3-2.debian.tar.xz Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 18 Aug 2025 00:29:39 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network libbio-alignio-stockholm-perl_1.7.3-2 perl-5.42-throwaway amd64 -------------------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network libbio-alignio-stockholm-perl_1.7.3-2 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3 SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-d73942ff-2a18-421e-a1ee-7fe9414bcf3e SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package libbio-alignio-stockholm-perl dpkg-buildpackage: info: source version 1.7.3-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building libbio-alignio-stockholm-perl using existing ./libbio-alignio-stockholm-perl_1.7.3.orig.tar.gz dpkg-source: info: building libbio-alignio-stockholm-perl in libbio-alignio-stockholm-perl_1.7.3-2.debian.tar.xz dpkg-source: info: building libbio-alignio-stockholm-perl in libbio-alignio-stockholm-perl_1.7.3-2.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::AlignIO::stockholm Writing MYMETA.yml and MYMETA.json dh_auto_build make -j2 make[1]: Entering directory '/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3' cp lib/Bio/Index/Stockholm.pm blib/lib/Bio/Index/Stockholm.pm cp lib/Bio/AlignIO/stockholm.pm blib/lib/Bio/AlignIO/stockholm.pm Manifying 2 pod documents make[1]: Leaving directory '/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3' dh_auto_test make -j2 test TEST_VERBOSE=1 make[1]: Entering directory '/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t Possible precedence problem between ! and numeric eq (==) at /usr/share/perl5/Bio/AlignIO/Handler/GenericAlignHandler.pm line 98. t/00-compile.t ........... 1..2 ok 1 - Bio/AlignIO/stockholm.pm loaded ok ok 2 - Bio/Index/Stockholm.pm loaded ok ok Possible precedence problem between ! and numeric eq (==) at /usr/share/perl5/Bio/AlignIO/Handler/GenericAlignHandler.pm line 98. t/AlignIO.t .............. 1..87 ok 1 - use Bio::AlignIO::stockholm; ok 2 - An object of class 'Bio::AlignIO::stockholm' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' ok 10 - Stockholm annotation ok 11 - Stockholm annotation ok 12 - stockholm output test ok 13 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 - 'Stockholm annotation' isa 'Bio::Annotation::Reference' ok 21 - Stockholm annotation ok 22 - Stockholm annotation ok 23 - Stockholm annotation ok 24 - Stockholm annotation ok 25 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI' ok 26 - Rfam meta data ok 27 - Rfam meta data ok 28 ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI' ok 36 - Rfam meta data ok 37 - Rfam meta data ok 38 - An object of class 'Bio::AlignIO::stockholm' isa 'Bio::AlignIO' ok 39 ok 40 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 41 ok 42 ok 43 ok 44 ok 45 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' ok 46 - Pfam annotation ok 47 ok 48 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 49 ok 50 ok 51 ok 52 ok 53 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI' ok 60 - Pfam aln meta data ok 61 - Pfam aln meta data ok 62 - Pfam aln meta data ok 63 - Pfam aln meta data ok 64 - Pfam aln meta data ok 65 - Pfam aln meta data ok 66 - Pfam seq meta data ok 67 - Pfam seq meta data ok 68 - Pfam seq meta data ok 69 - Pfam seq meta data ok 70 ok 71 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeatureI' ok 72 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::Meta' ok 73 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI' ok 74 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::DBLink' 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 t/author-eol.t ........... skipped: these tests are for testing by the author t/author-mojibake.t ...... skipped: these tests are for testing by the author t/author-pod-coverage.t .. skipped: these tests are for testing by the author t/author-pod-syntax.t .... skipped: these tests are for testing by the author Possible precedence problem between ! and numeric eq (==) at /usr/share/perl5/Bio/AlignIO/Handler/GenericAlignHandler.pm line 98. t/Index.t ................ 1..4 ok 1 - use Bio::Index::Stockholm; ok 2 - An object of class 'Bio::Index::Stockholm' isa 'Bio::Index::Stockholm' ok 3 ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok All tests successful. Files=7, Tests=93, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.41 cusr 0.10 csys = 0.54 CPU) Result: PASS make[1]: Leaving directory '/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-alignio-stockholm-perl/ make -j2 install DESTDIR=/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3/debian/libbio-alignio-stockholm-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3' Manifying 2 pod documents Installing /build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3/debian/libbio-alignio-stockholm-perl/usr/share/perl5/Bio/Index/Stockholm.pm Installing /build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3/debian/libbio-alignio-stockholm-perl/usr/share/perl5/Bio/AlignIO/stockholm.pm Installing /build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3/debian/libbio-alignio-stockholm-perl/usr/share/man/man3/Bio::AlignIO::stockholm.3pm Installing /build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3/debian/libbio-alignio-stockholm-perl/usr/share/man/man3/Bio::Index::Stockholm.3pm make[1]: Leaving directory '/build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbio-alignio-stockholm-perl' in '../libbio-alignio-stockholm-perl_1.7.3-2_all.deb'. dpkg-genbuildinfo -O../libbio-alignio-stockholm-perl_1.7.3-2_amd64.buildinfo dpkg-genchanges -O../libbio-alignio-stockholm-perl_1.7.3-2_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-08-18T00:29:42Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 18 Aug 2025 00:29:42 +0000 | +------------------------------------------------------------------------------+ libbio-alignio-stockholm-perl_1.7.3-2_amd64.changes: ---------------------------------------------------- Format: 1.8 Date: Tue, 03 Mar 2020 09:00:01 +0100 Source: libbio-alignio-stockholm-perl Binary: libbio-alignio-stockholm-perl Architecture: source all Version: 1.7.3-2 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbio-alignio-stockholm-perl - stockholm sequence input/output stream Closes: 952747 Changes: libbio-alignio-stockholm-perl (1.7.3-2) unstable; urgency=medium . * Team upload. * Add missing Breaks+Replaces: libbio-perl-perl (<< 1.7.3) Closes: #952747 * Add salsa-ci file (routine-update) Checksums-Sha1: 94b0bc10a10314053f2267775515556b20d31692 1376 libbio-alignio-stockholm-perl_1.7.3-2.dsc a1ba6cf1afeb8d2220ed728f7498197f2fc88af0 1788 libbio-alignio-stockholm-perl_1.7.3-2.debian.tar.xz 7ade77099cbe8082e479d6d056f6e26412cb47dc 22596 libbio-alignio-stockholm-perl_1.7.3-2_all.deb 263817edb511999d51e21111ea302e3d4f38d224 5548 libbio-alignio-stockholm-perl_1.7.3-2_amd64.buildinfo Checksums-Sha256: f57e93117188637f5383f4c688e3c22f106ec25c43a441f2b229fd858c59ba70 1376 libbio-alignio-stockholm-perl_1.7.3-2.dsc 924582a7aba9644153def4bf3e497f232652335c49a92da42bed360ad1e0fc04 1788 libbio-alignio-stockholm-perl_1.7.3-2.debian.tar.xz 5ab92e71c5fd9d3689049ed4ba3d7eecabd8edd2708f6136de0a92645c1bed23 22596 libbio-alignio-stockholm-perl_1.7.3-2_all.deb 994091466857da275811eee796a854b7322e5df364e4d35082e5141cc3e83d05 5548 libbio-alignio-stockholm-perl_1.7.3-2_amd64.buildinfo Files: 79b18f9e0f0dcfe57d84197e708ae054 1376 perl optional libbio-alignio-stockholm-perl_1.7.3-2.dsc 3dfcb843d880a79e8557ac3aeeec0681 1788 perl optional libbio-alignio-stockholm-perl_1.7.3-2.debian.tar.xz 98443efac6ecd394eaa91c5c86a26421 22596 perl optional libbio-alignio-stockholm-perl_1.7.3-2_all.deb 3e673fbf3916e2f09123047baa1a5dc5 5548 perl optional libbio-alignio-stockholm-perl_1.7.3-2_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo Mon, 18 Aug 2025 00:29:42 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: libbio-alignio-stockholm-perl Binary: libbio-alignio-stockholm-perl Architecture: all source Version: 1.7.3-2 Checksums-Md5: 79b18f9e0f0dcfe57d84197e708ae054 1376 libbio-alignio-stockholm-perl_1.7.3-2.dsc 98443efac6ecd394eaa91c5c86a26421 22596 libbio-alignio-stockholm-perl_1.7.3-2_all.deb Checksums-Sha1: 94b0bc10a10314053f2267775515556b20d31692 1376 libbio-alignio-stockholm-perl_1.7.3-2.dsc 7ade77099cbe8082e479d6d056f6e26412cb47dc 22596 libbio-alignio-stockholm-perl_1.7.3-2_all.deb Checksums-Sha256: f57e93117188637f5383f4c688e3c22f106ec25c43a441f2b229fd858c59ba70 1376 libbio-alignio-stockholm-perl_1.7.3-2.dsc 5ab92e71c5fd9d3689049ed4ba3d7eecabd8edd2708f6136de0a92645c1bed23 22596 libbio-alignio-stockholm-perl_1.7.3-2_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 18 Aug 2025 00:29:42 +0000 Build-Path: /build/libbio-alignio-stockholm-perl-wVV8eP/libbio-alignio-stockholm-perl-1.7.3 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.2.37-2+b5), binutils (= 2.45-4), binutils-common (= 2.45-4), binutils-x86-64-linux-gnu (= 2.45-4), bsdextrautils (= 2.41.1-1), bsdutils (= 1:2.41.1-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-14 (= 14.3.0-5), cpp-14-x86-64-linux-gnu (= 14.3.0-5), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.25), debianutils (= 5.23.2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.3.0-5), g++-14-x86-64-linux-gnu (= 14.3.0-5), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.3.0-5), gcc-14-base (= 14.3.0-5), gcc-14-x86-64-linux-gnu (= 14.3.0-5), gcc-15-base (= 15.2.0-1), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libalgorithm-diff-perl (= 1.201-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-1), libatomic1 (= 15.2.0-1), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.45-4), libbio-perl-perl (= 1.7.8-1), libblkid1 (= 2.41.1-1), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcapture-tiny-perl (= 0.50-1), libcc1-0 (= 15.2.0-1), libclass-data-inheritable-perl (= 0.10-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-4), libctf0 (= 2.45-4), libdata-stag-perl (= 0.14-3), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.25), libdevel-stacktrace-perl (= 2.0500-1), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.192-4), libexception-class-perl (= 1.45-1), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-14-dev (= 14.3.0-5), libgcc-s1 (= 15.2.0-1), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-3), libgomp1 (= 15.2.0-1), libgprofng0 (= 2.45-4), libhwasan0 (= 15.2.0-1), libio-string-perl (= 1.08-4), libisl23 (= 0.27-1), libitm1 (= 15.2.0-1), libjansson4 (= 2.14-2+b3), liblastlog2-2 (= 2.41.1-1), liblsan0 (= 15.2.0-1), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.1-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.42 (= 5.42.0-1), libpipeline1 (= 1.5.8-1), libquadmath0 (= 15.2.0-1), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe2 (= 2.45-4), libsmartcols1 (= 2.41.1-1), libsqlite3-0 (= 3.46.1-7), libssl3t64 (= 3.5.2-1), libstdc++-14-dev (= 14.3.0-5), libstdc++6 (= 15.2.0-1), libsub-uplevel-perl (= 0.2800-3), libsystemd0 (= 258~rc2-2), libtest-deep-perl (= 1.205-1), libtest-differences-perl (= 0.71-1), libtest-exception-perl (= 0.43-3), libtest-most-perl (= 0.38-1), libtest-warn-perl (= 0.37-2), libtext-diff-perl (= 1.45-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 15.2.0-1), libubsan1 (= 15.2.0-1), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 258~rc2-2), libunistring5 (= 1.3-2), libuuid1 (= 2.41.1-1), libxml2-16 (= 2.14.5+dfsg-0.1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.38-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), openssl-provider-legacy (= 3.5.2-1), patch (= 2.8-2), perl (= 5.42.0-1), perl-base (= 5.42.0-1), perl-modules-5.42 (= 5.42.0-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.1-1), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1583222401" +------------------------------------------------------------------------------+ | Package contents Mon, 18 Aug 2025 00:29:42 +0000 | +------------------------------------------------------------------------------+ libbio-alignio-stockholm-perl_1.7.3-2_all.deb --------------------------------------------- new Debian package, version 2.0. size 22596 bytes: control archive=888 bytes. 665 bytes, 16 lines control 591 bytes, 7 lines md5sums Package: libbio-alignio-stockholm-perl Version: 1.7.3-2 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 66 Depends: perl:any, libbio-perl-perl Breaks: libbio-perl-perl (<< 1.7.3) Replaces: libbio-perl-perl (<< 1.7.3) Section: perl Priority: optional Homepage: https://metacpan.org/release/Bio-AlignIO-stockholm Description: stockholm sequence input/output stream Indexes Stockholm format alignments such as those from Pfam and Rfam. Returns raw stream data using the ID or a Bio::SimpleAlign object (via Bio::AlignIO). . Bio::AlignIO::stockholm also allows for ID parsing using a callback: drwxr-xr-x root/root 0 2020-03-03 08:00 ./ drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/ drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/share/ drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/share/doc/libbio-alignio-stockholm-perl/ -rw-r--r-- root/root 305 2020-03-03 08:00 ./usr/share/doc/libbio-alignio-stockholm-perl/changelog.Debian.gz -rw-r--r-- root/root 166 2018-09-25 00:13 ./usr/share/doc/libbio-alignio-stockholm-perl/changelog.gz -rw-r--r-- root/root 1160 2020-03-03 08:00 ./usr/share/doc/libbio-alignio-stockholm-perl/copyright drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/share/man/ drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/share/man/man3/ -rw-r--r-- root/root 4270 2020-03-03 08:00 ./usr/share/man/man3/Bio::AlignIO::stockholm.3pm.gz -rw-r--r-- root/root 4662 2020-03-03 08:00 ./usr/share/man/man3/Bio::Index::Stockholm.3pm.gz drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/share/perl5/ drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/share/perl5/Bio/ drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/share/perl5/Bio/AlignIO/ -rw-r--r-- root/root 26826 2018-09-25 00:13 ./usr/share/perl5/Bio/AlignIO/stockholm.pm drwxr-xr-x root/root 0 2020-03-03 08:00 ./usr/share/perl5/Bio/Index/ -rw-r--r-- root/root 12966 2018-09-25 00:13 ./usr/share/perl5/Bio/Index/Stockholm.pm +------------------------------------------------------------------------------+ | Post Build Mon, 18 Aug 2025 00:29:42 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 18 Aug 2025 00:29:42 +0000 | +------------------------------------------------------------------------------+ Purging /build/libbio-alignio-stockholm-perl-wVV8eP Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 18 Aug 2025 00:29:43 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 684 Build-Time: 3 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 5 Job: /srv/debomatic/incoming/libbio-alignio-stockholm-perl_1.7.3-2.dsc Machine Architecture: amd64 Package: libbio-alignio-stockholm-perl Package-Time: 17 Source-Version: 1.7.3-2 Space: 684 Status: successful Version: 1.7.3-2 -------------------------------------------------------------------------------- Finished at 2025-08-18T00:29:42Z Build needed 00:00:17, 684k disk space