sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +=========================================================================================+ | libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (amd64) Mon, 03 Jun 2024 18:40:37 +0000 | +=========================================================================================+ Package: libbio-tools-run-alignment-tcoffee-perl Version: 1.7.4-3 Source Version: 1.7.4-3 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-923c9d31-5f63-4165-ae89-39d3ab6bef1b' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup libbio-tools-run-alignment-tcoffee-perl_1.7.4-3 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup libbio-tools-run-alignment-tcoffee-perl_1.7.4-3 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/libbio-tools-run-alignment-tcoffee-perl-7xk2vn/resolver-PY8sxU' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:2 http://localhost:3142/debian unstable InRelease [198 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:3 http://localhost:3142/debian sid InRelease [198 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-03-1404.32-F-2024-06-03-0205.12.pdiff [25.4 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-03-1404.32-F-2024-06-03-0205.12.pdiff [25.4 kB] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-03-1404.32-F-2024-06-03-0205.12.pdiff [22.0 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-03-1404.32-F-2024-06-03-0205.12.pdiff [22.0 kB] Fetched 571 kB in 2s (258 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: login passwd 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1564 kB of archives. After this operation, 57.3 kB disk space will be freed. Get:1 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.13+dfsg1-5 [590 kB] Get:2 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.13+dfsg1-5 [974 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1564 kB in 0s (81.8 MB/s) (Reading database ... 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Setting up passwd (1:4.13+dfsg1-5) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/libbio-tools-run-alignment-tcoffee-perl-7xk2vn/libbio-tools-run-alignment-tcoffee-perl-1.7.4' with '<>' I: NOTICE: Log filtering will replace 'build/libbio-tools-run-alignment-tcoffee-perl-7xk2vn' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot, clustalw, libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libtest-exception-perl, perl, t-coffee Filtered Build-Depends: debhelper-compat (= 13), build-essential, fakeroot, clustalw, libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libtest-exception-perl, perl, t-coffee dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [795 B] Get:5 copy:/<>/apt_archive ./ Packages [763 B] Fetched 2167 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 clustalw debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbio-perl-perl libbio-perl-run-perl libdata-stag-perl libdebhelper-perl libdevel-checkbin-perl libelf1t64 libfakeroot libfile-sort-perl libfile-stripnondeterminism-perl libicu72 libio-pty-perl libio-string-perl libipc-run-perl libmagic-mgc libmagic1t64 libpipeline1 libsub-uplevel-perl libtest-exception-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils t-coffee Suggested packages: autoconf-archive gnu-standards autoconf-doc clustalx seaview dh-make gettext-doc libasprintf-dev libgettextpo-dev groff bioperl libxml-sax-expatxs-perl libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl boxshade t-coffee-examples Recommended packages: curl | wget | lynx 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 libalgorithm-diff-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 amap-align clustalo dialign-tx fsa kalign mafft muscle mustang ncbi-blast+ poa prank probcons proda tm-align The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils clustalw debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbio-perl-perl libbio-perl-run-perl libdata-stag-perl libdebhelper-perl libdevel-checkbin-perl libelf1t64 libfakeroot libfile-sort-perl libfile-stripnondeterminism-perl libicu72 libio-pty-perl libio-string-perl libipc-run-perl libmagic-mgc libmagic1t64 libpipeline1 libsub-uplevel-perl libtest-exception-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils t-coffee 0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 24.2 MB/24.2 MB of archives. After this operation, 89.3 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.40/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB] Get:2 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [932 B] Get:3 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:6 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:7 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:9 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get:10 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-7 [95.9 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:12 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get:13 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:14 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:15 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:16 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:17 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get:18 http://localhost:3142/debian unstable/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:21 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:24 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:25 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:26 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB] Get:29 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get:30 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:31 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:32 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB] Get:34 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libfile-sort-perl all 1.01-3 [21.3 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libbio-perl-run-perl all 1.7.3-11 [528 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libdevel-checkbin-perl all 0.04-3 [5228 B] Get:42 http://localhost:3142/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:44 http://localhost:3142/debian unstable/main amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [1032 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.2 MB in 0s (118 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 21765 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... 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Setting up fakeroot (1.34-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3) ... Setting up libfile-sort-perl (1.01-3) ... 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 libbio-perl-run-perl (1.7.3-11) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... 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 (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64) Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40.1-7 bsdutils_1:2.40.1-7 build-essential_12.10 bzip2_1.0.8-5.1 clustalw_2.1+lgpl-7 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libasan8_14.1.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libbio-perl-perl_1.7.8-1 libbio-perl-run-perl_1.7.3-11 libblkid1_2.40.1-7 libbz2-1.0_1.0.8-5.1 libc-bin_2.38-12 libc-dev-bin_2.38-12 libc-l10n_2.38-12 libc6_2.38-12 libc6-dev_2.38-12 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14.1.0-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-4 libctf0_2.42-4 libdata-stag-perl_0.14-3 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.15.3 libdevel-checkbin-perl_0.04-3 libdpkg-perl_1.22.6 libeatmydata1_131-2 libelf1t64_0.191-1+b1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-sort-perl_1.01-3 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.2.0-25 libgcc-s1_14.1.0-1 libgcrypt20_1.10.3-3 libgdbm-compat4t64_1.23-5.1+b1 libgdbm6t64_1.23-5.1+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-4 libgomp1_14.1.0-1 libgpg-error0_1.49-2 libgprofng0_2.42-4 libhogweed6t64_3.9.1-2.2 libhwasan0_14.1.0-1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libio-pty-perl_1:1.20-1+b2 libio-string-perl_1.08-4 libipc-run-perl_20231003.0-2 libisl23_0.26-3+b2 libitm1_14.1.0-1 libjansson4_2.14-2+b2 libksba8_1.6.6-1 libldap-2.5-0_2.5.17+dfsg-1+b1 liblsan0_14.1.0-1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.1-7 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.9.1-2.2 libnpth0t64_1.6-3.1 libp11-kit0_0.25.3-5 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0~rc1-1 libpipeline1_1.5.7-2 libquadmath0_14.1.0-1 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1 libselinux1_3.5-2+b2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b3 libsepol2_3.5-2+b1 libsframe1_2.42-4 libsmartcols1_2.40.1-7 libsqlite3-0_3.46.0-1 libssl3t64_3.2.1-3 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 libsub-uplevel-perl_0.2800-3 libsystemd0_256~rc3-7 libtasn1-6_4.19.0-3+b2 libtest-exception-perl_0.43-3 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.1.0-1 libubsan1_14.1.0-1 libuchardet0_0.0.8-1+b1 libudev1_256~rc3-7 libunistring5_1.2-1 libuuid1_2.40.1-7 libxml2_2.12.7+dfsg-3 libxxhash0_0.8.2-2+b1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.12-1 locales-all_2.38-12 login_1:4.13+dfsg1-5 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.13+dfsg1-5 patch_2.7.6-7 perl_5.40.0~rc1-1 perl-base_5.40.0~rc1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0~rc1-1 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.09-1 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.1-7 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-tools-run-alignment-tcoffee-perl Binary: libbio-tools-run-alignment-tcoffee-perl Architecture: all Version: 1.7.4-3 Maintainer: Debian Perl Group Uploaders: David Miguel Susano Pinto Homepage: https://metacpan.org/release/Bio-Tools-Run-Alignment-TCoffee Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl Vcs-Git: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13) Build-Depends-Indep: clustalw , libbio-perl-perl , libbio-perl-run-perl , libdevel-checkbin-perl, libtest-exception-perl , perl, t-coffee Package-List: libbio-tools-run-alignment-tcoffee-perl deb science optional arch=all Checksums-Sha1: dda94eb00899c2865e61c7feb6205971c317a26a 29373 libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz 9cfe1c2bfcc88a86fff487599a91d70fd296550f 2536 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz Checksums-Sha256: 3d8b41b9701933249cde26dd0e8a919958b218f1f585183a7a225e6a254d6523 29373 libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz 4935d6d288109914fd62dab352c8607fdb6f98c6d1d86051bcb3aee6a4fd391a 2536 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz Files: 49c2a232f3c64b8a4add2560f1c0322b 29373 libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz 9166dd5e7ea488e1517195b5b459cd14 2536 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz -----BEGIN PGP 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verify inline signature for ./libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc: no acceptable signature found dpkg-source: info: extracting libbio-tools-run-alignment-tcoffee-perl in /<> dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying doc-typos.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network libbio-tools-run-alignment-tcoffee-perl_1.7.4-3 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network libbio-tools-run-alignment-tcoffee-perl_1.7.4-3 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en 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=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-923c9d31-5f63-4165-ae89-39d3ab6bef1b SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package libbio-tools-run-alignment-tcoffee-perl dpkg-buildpackage: info: source version 1.7.4-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Jelmer Vernooij 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-tools-run-alignment-tcoffee-perl using existing ./libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building libbio-tools-run-alignment-tcoffee-perl in libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz dpkg-source: info: building libbio-tools-run-alignment-tcoffee-perl in libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.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=/<>=. -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=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Locating bin:t_coffee... found at /usr/bin/t_coffee. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Tools::Run::Alignment::TCoffee Writing MYMETA.yml and MYMETA.json dh_auto_build make -j2 make[1]: Entering directory '/<>' cp lib/Bio/Tools/Run/Alignment/TCoffee.pm blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm Manifying 1 pod document make[1]: Leaving directory '/<>' dh_auto_test make -j2 test TEST_VERBOSE=1 make[1]: Entering directory '/<>' 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 t/00-compile.t ........... 1..1 ok 1 - Bio/Tools/Run/Alignment/TCoffee.pm loaded ok 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-no-tabs.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 ! 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[Final Evaluation][TOT= 396][100 %] t/TCoffee.t .............. ok 1 - An object of class 'Bio::Tools::Run::Alignment::TCoffee' isa 'Bio::Tools::Run::Alignment::TCoffee' ok 2 - set factory parameter ok 3 - get factory parameter ok 4 - Code tested only on t_coffee versions > 1.22 #Single Thread ok 5 ok 6 #Single Thread ok 7 #Single Thread #Single Thread #Single Thread #Single Thread #Single Thread ok 8 ok 9 - no T-COFFEE errors ok 10 ok 11 ok 12 #Single Thread #Single Thread ok 13 ok 14 ok 15 #Single Thread #Single Thread ok 16 ok 17 - expect 21 >= val >= 23 ok 18 - expect 47 or 48 #Single Thread ok 19 - simple generic run ok 20 #Single Thread #Single Thread #Single Thread #Single Thread #Single Thread ok 21 ok 22 - no T-COFFEE errors ok 23 ok 24 - expect 13 or 14 ok 25 - expect 41 or 42 1..25 rmdir /tmp/Dpqwu3iBzz ok All tests successful. Files=7, Tests=26, 8 wallclock secs ( 0.02 usr 0.01 sys + 4.00 cusr 4.15 csys = 8.18 CPU) Result: PASS make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-tools-run-alignment-tcoffee-perl/ make -j2 install DESTDIR=/<>/debian/libbio-tools-run-alignment-tcoffee-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/<>' Manifying 1 pod document Installing /<>/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm Installing /<>/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/man/man3/Bio::Tools::Run::Alignment::TCoffee.3pm make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs dh_installman dh_lintian 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-tools-run-alignment-tcoffee-perl' in '../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb'. dpkg-genbuildinfo -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_amd64.buildinfo dpkg-genchanges -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_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 2024-06-03T18:40:59Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_amd64.changes: -------------------------------------------------------------- Format: 1.8 Date: Fri, 14 Oct 2022 16:06:32 +0100 Source: libbio-tools-run-alignment-tcoffee-perl Binary: libbio-tools-run-alignment-tcoffee-perl Architecture: source all Version: 1.7.4-3 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Perl Group Changed-By: Jelmer Vernooij Description: libbio-tools-run-alignment-tcoffee-perl - Bioperl interface to T-Coffee Changes: libbio-tools-run-alignment-tcoffee-perl (1.7.4-3) unstable; urgency=medium . [ Debian Janitor ] * Remove constraints unnecessary since buster * Update standards version to 4.6.0, no changes needed. 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12.10), bzip2 (= 1.0.8-5.1), clustalw (= 2.1+lgpl-7), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-25), cpp-13-x86-64-linux-gnu (= 13.2.0-25), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-8), debconf (= 1.5.86), debhelper (= 13.15.3), debianutils (= 5.17), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.9.0-6), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-25), g++-13-x86-64-linux-gnu (= 13.2.0-25), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-25), gcc-13-base (= 13.2.0-25), gcc-13-x86-64-linux-gnu (= 13.2.0-25), gcc-14-base (= 14.1.0-1), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+b1), grep (= 3.11-4), groff-base (= 1.23.0-4), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.1.0-1), libatomic1 (= 14.1.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-4), libbio-perl-perl (= 1.7.8-1), libbio-perl-run-perl (= 1.7.3-11), libblkid1 (= 2.40.1-7), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.38-12), libc-dev-bin (= 2.38-12), libc6 (= 2.38-12), libc6-dev (= 2.38-12), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.1.0-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4), libctf0 (= 2.42-4), libdata-stag-perl (= 0.14-3), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.15.3), libdevel-checkbin-perl (= 0.04-3), libdpkg-perl (= 1.22.6), libelf1t64 (= 0.191-1+b1), libfile-sort-perl (= 1.01-3), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.2.0-25), libgcc-s1 (= 14.1.0-1), libgdbm-compat4t64 (= 1.23-5.1+b1), libgdbm6t64 (= 1.23-5.1+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.1.0-1), libgprofng0 (= 2.42-4), libhwasan0 (= 14.1.0-1), libicu72 (= 72.1-4+b1), libio-pty-perl (= 1:1.20-1+b2), libio-string-perl (= 1.08-4), libipc-run-perl (= 20231003.0-2), libisl23 (= 0.26-3+b2), libitm1 (= 14.1.0-1), libjansson4 (= 2.14-2+b2), liblsan0 (= 14.1.0-1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.1-7), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0~rc1-1), libpipeline1 (= 1.5.7-2), libquadmath0 (= 14.1.0-1), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-2+b2), libsframe1 (= 2.42-4), libsmartcols1 (= 2.40.1-7), libssl3t64 (= 3.2.1-3), libstdc++-13-dev (= 13.2.0-25), libstdc++6 (= 14.1.0-1), libsub-uplevel-perl (= 0.2800-3), libsystemd0 (= 256~rc3-7), libtest-exception-perl (= 0.43-3), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.1.0-1), libubsan1 (= 14.1.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256~rc3-7), libunistring5 (= 1.2-1), libuuid1 (= 2.40.1-7), libxml2 (= 2.12.7+dfsg-3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.12-1), login (= 1:4.13+dfsg1-5), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), patch (= 2.7.6-7), perl (= 5.40.0~rc1-1), perl-base (= 5.40.0~rc1-1), perl-modules-5.40 (= 5.40.0~rc1-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.09-1), t-coffee (= 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.1-7), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1665759992" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb ------------------------------------------------------- new Debian package, version 2.0. size 23064 bytes: control archive=856 bytes. 622 bytes, 15 lines control 590 bytes, 6 lines md5sums Package: libbio-tools-run-alignment-tcoffee-perl Version: 1.7.4-3 Architecture: all Maintainer: Debian Perl Group Installed-Size: 68 Depends: perl:any, libbio-perl-perl, libbio-perl-run-perl, t-coffee Section: science Priority: optional Homepage: https://metacpan.org/release/Bio-Tools-Run-Alignment-TCoffee Description: Bioperl interface to T-Coffee Bio::Tools::Run::Alignment::TCoffee provides a Perl interface to T-Coffee, a program for multiple alignments of DNA, RNA, and protein sequences and structures. . This module distribution is part of the Bioperl project. drwxr-xr-x root/root 0 2022-10-14 15:06 ./ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/doc/libbio-tools-run-alignment-tcoffee-perl/ -rw-r--r-- root/root 602 2022-10-14 15:06 ./usr/share/doc/libbio-tools-run-alignment-tcoffee-perl/changelog.Debian.gz -rw-r--r-- root/root 582 2018-07-09 18:30 ./usr/share/doc/libbio-tools-run-alignment-tcoffee-perl/changelog.gz -rw-r--r-- root/root 1135 2022-10-14 15:06 ./usr/share/doc/libbio-tools-run-alignment-tcoffee-perl/copyright drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 231 2022-10-14 15:06 ./usr/share/lintian/overrides/libbio-tools-run-alignment-tcoffee-perl drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/man/ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/man/man3/ -rw-r--r-- root/root 8665 2022-10-14 15:06 ./usr/share/man/man3/Bio::Tools::Run::Alignment::TCoffee.3pm.gz drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/perl5/ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/perl5/Bio/ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/perl5/Bio/Tools/ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/perl5/Bio/Tools/Run/ drwxr-xr-x root/root 0 2022-10-14 15:06 ./usr/share/perl5/Bio/Tools/Run/Alignment/ -rw-r--r-- root/root 39380 2022-10-14 15:06 ./usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 800 Build-Time: 11 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 5 Job: /srv/debomatic/incoming/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc Machine Architecture: amd64 Package: libbio-tools-run-alignment-tcoffee-perl Package-Time: 22 Source-Version: 1.7.4-3 Space: 800 Status: successful Version: 1.7.4-3 -------------------------------------------------------------------------------- Finished at 2024-06-03T18:40:59Z Build needed 00:00:22, 800k disk space