sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | libbio-searchio-hmmer-perl 1.7.3-2 (amd64) Sun, 04 Aug 2024 04:18:04 +0000 | +==============================================================================+ Package: libbio-searchio-hmmer-perl Version: 1.7.3-2 Source Version: 1.7.3-2 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-fa514c47-15cf-48bb-8e70-38af33a680ef' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup libbio-searchio-hmmer-perl_1.7.3-2 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup libbio-searchio-hmmer-perl_1.7.3-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/libbio-searchio-hmmer-perl-677xKh/resolver-21RhZE' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://localhost:3142/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/libbio-searchio-hmmer-perl_1.7.3-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/libbio-searchio-hmmer-perl-677xKh/libbio-searchio-hmmer-perl-1.7.3' with '<>' I: NOTICE: Log filtering will replace 'build/libbio-searchio-hmmer-perl-677xKh' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), build-essential, fakeroot, libbio-perl-perl, libio-string-perl, perl, libtest-most-perl Filtered Build-Depends: debhelper-compat (= 12), build-essential, fakeroot, libbio-perl-perl, libio-string-perl, perl, libtest-most-perl 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 [699 B] Get:5 copy:/<>/apt_archive ./ Packages [711 B] Fetched 2019 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 fakeroot 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 libfakeroot libfile-stripnondeterminism-perl libicu72 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 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc 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 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 fakeroot 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 libfakeroot libfile-stripnondeterminism-perl libicu72 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 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. Need to get 23.1 MB of archives. After this operation, 85.9 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [908 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-1 [96.1 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-2 [1411 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.16 [88.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 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 1.14.0-1 [19.5 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 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 libicu72 amd64 72.1-5 [9396 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.16 [891 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.35.1-1 [28.6 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.35.1-1 [74.5 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:39 http://deb.debian.org/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.1 MB in 0s (123 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 22966 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_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_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... 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 libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.16) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.35.1-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up fakeroot (1.35.1-1) ... 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 libclass-data-inheritable-perl (0.08-3) ... Setting up libtext-diff-perl (1.45-2) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.71-3) ... Setting up libcapture-tiny-perl (0.48-2) ... 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:amd64 (0.0.8-1+b1) ... 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 libxml2:amd64 (2.12.7+dfsg-3+b1) ... 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 libtool (2.4.7-7) ... 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 (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.16) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.42.90.20240720-2 dpkg-dev_1.22.11 g++-13_13.3.0-4 g++-14_14.2.0-1 gcc-13_13.3.0-4 gcc-14_14.2.0-1 libc6-dev_2.39-6 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 linux-libc-dev_6.9.12-1 Package versions: adduser_3.137 apt_2.9.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.4 base-passwd_3.6.4 bash_5.2.21-2.1 binutils_2.42.90.20240720-2 binutils-common_2.42.90.20240720-2 binutils-x86-64-linux-gnu_2.42.90.20240720-2 bsdextrautils_2.40.2-1 bsdutils_1:2.40.2-1 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-4 cpp-13-x86-64-linux-gnu_13.3.0-4 cpp-14_14.2.0-1 cpp-14-x86-64-linux-gnu_14.2.0-1 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.16 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.35.1-1 file_1:5.45-3 findutils_4.10.0-2 g++_4:14.1.0-2 g++-13_13.3.0-4 g++-13-x86-64-linux-gnu_13.3.0-4 g++-14_14.2.0-1 g++-14-x86-64-linux-gnu_14.2.0-1 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-4 gcc-13-base_13.3.0-4 gcc-13-x86-64-linux-gnu_13.3.0-4 gcc-14_14.2.0-1 gcc-14-base_14.2.0-1 gcc-14-x86-64-linux-gnu_14.2.0-1 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8 gpg_2.2.43-8 gpg-agent_2.2.43-8 gpg-wks-client_2.2.43-8 gpgconf_2.2.43-8 gpgsm_2.2.43-8 gpgv_2.2.43-8 grep_3.11-4 groff-base_1.23.0-5 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 libalgorithm-diff-perl_1.201-1 libapt-pkg6.0t64_2.9.7 libarchive-zip-perl_1.68-1 libasan8_14.2.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.2.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-4 libaudit1_1:3.1.2-4+b1 libbinutils_2.42.90.20240720-2 libbio-perl-perl_1.7.8-1 libblkid1_2.40.2-1 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-6 libc-dev-bin_2.39-6 libc-l10n_2.39-6 libc6_2.39-6 libc6-dev_2.39-6 libcap-ng0_0.8.5-1+b1 libcap2_1:2.66-5 libcapture-tiny-perl_0.48-2 libcc1-0_14.2.0-1 libclass-data-inheritable-perl_0.08-3 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42.90.20240720-2 libctf0_2.42.90.20240720-2 libdata-stag-perl_0.14-3 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.16 libdevel-stacktrace-perl_2.0500-1 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libexception-class-perl_1.45-1 libfakeroot_1.35.1-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-4 libgcc-14-dev_14.2.0-1 libgcc-s1_14.2.0-1 libgcrypt20_1.11.0-5 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-1 libgpg-error0_1.50-2 libgprofng0_2.42.90.20240720-2 libhogweed6t64_3.10-1 libhwasan0_14.2.0-1 libicu72_72.1-5 libidn2-0_2.3.7-2 libio-string-perl_1.08-4 libisl23_0.26-3+b2 libitm1_14.2.0-1 libjansson4_2.14-2+b2 libksba8_1.6.7-2 libldap-2.5-0_2.5.18+dfsg-2+b1 liblsan0_14.2.0-1 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-1 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnpth0t64_1.6-3.1 libp11-kit0_0.25.5-2 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_5.40.0-1 libpipeline1_1.5.7-2 libquadmath0_14.2.0-1 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1+b1 libselinux1_3.5-2+b3 libsemanage-common_3.5-1 libsemanage2_3.5-1+b4 libsepol2_3.5-2+b1 libsframe1_2.42.90.20240720-2 libsmartcols1_2.40.2-1 libsqlite3-0_3.46.0-1 libssl3t64_3.3.1-2 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 libsub-uplevel-perl_0.2800-3 libsystemd0_256.4-2 libtasn1-6_4.19.0-3+b2 libtest-deep-perl_1.204-1 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_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-1 libubsan1_14.2.0-1 libuchardet0_0.0.8-1+b1 libudev1_256.4-2 libunistring5_1.2-1 libuuid1_2.40.2-1 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.9.12-1 locales-all_2.39-6 login_1:4.15.3-3 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-2 mawk_1.3.4.20240622-2 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.15.3-3 patch_2.7.6-7 perl_5.40.0-1 perl-base_5.40.0-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-1 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_0.0.24 sysvinit-utils_3.09-2 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-1 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-searchio-hmmer-perl Binary: libbio-searchio-hmmer-perl Architecture: all Version: 1.7.3-2 Maintainer: Michael R. Crusoe Homepage: https://metacpan.org/release/Bio-SearchIO-hmmer Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl Vcs-Git: https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 12) Build-Depends-Indep: libbio-perl-perl, libio-string-perl, perl, libtest-most-perl Package-List: libbio-searchio-hmmer-perl deb perl optional arch=all Checksums-Sha1: 761710daafb048ef59907a984bbc14d16115ea45 149093 libbio-searchio-hmmer-perl_1.7.3.orig.tar.gz 47b753ff5667da5ee362ed1b0c02dd37b110df02 1876 libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz Checksums-Sha256: 686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246 149093 libbio-searchio-hmmer-perl_1.7.3.orig.tar.gz e37f213f807ec9fe319ce2544f248f6ae902234491f965faf760364cc2dba016 1876 libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz Files: 3c8600a080ce60eea5d3015c99032e05 149093 libbio-searchio-hmmer-perl_1.7.3.orig.tar.gz eb7acaaa4d29481aaf9871d7af9542d4 1876 libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl3RaNcACgkQPCZ2P2xn 5uLbWg//YRzRkr4Vh7V51LERhcaUqsYOFXuOeKSpsnaOP/DgHCG3yFp9fNBbEMnJ c58I7uh45R/eKx4nQeAyX42aYMLJiQCmDZNDXiBc9OTyOQAuLyfSS0yCeqhY7kg8 5Gxuvr0Mg8n2KPwPGARIp3avqB7E6XtQMzGaY4ZzrdH/PjGLgzBKkPUsUnjXquTw TDDHI3WmyzOii/fDAjaNyi2OkR5Chf76lUvFMSL6ksK8sC+WlgFyJBeIJhEop1hp A7SenRTeCSkHk8Vmjo34nHYUgC2117F9kXC154RbCVobbMV7qJ92k0LXKn2Oep5K 2Op25BLAXNAZYbid0q6cB8CHcoczb2GLUerUg0WoYc15sVWak7BUTdirZhXALQRw NTxZF1VDu0kPbYoHykNYJPl/j0ebcDPrMxAeEcrxZ6GIywN9cmz1bGf0c/Kz17Jb /LwT7MYooUS7BDAlUz+dQMO6y4EI5dTy/VgIvKNntbZxHKB6yGyr0LGfv7oS080f m9S0lCe7gbdRj29hysoDjQ7CUzDW+GbIMjcLnUUIkXspqenBPV3G5z7VT+4wSdTl K7bWDaMa0P8BX5FAWEGhqGLMWy52BPgx2LBuYtEsqrtDaXusaIPPZZbrUg/qqUx6 2m3NXj/ItgLle6+ktiNe9EDxhSGYNQJqXJagPnNa/KejMsmg/Fk= =yCtx -----END PGP SIGNATURE----- gpgv: Signature made Sun Nov 17 15:35:51 2019 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libbio-searchio-hmmer-perl_1.7.3-2.dsc: no acceptable signature found dpkg-source: info: extracting libbio-searchio-hmmer-perl in /<> dpkg-source: info: unpacking libbio-searchio-hmmer-perl_1.7.3.orig.tar.gz dpkg-source: info: unpacking libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network libbio-searchio-hmmer-perl_1.7.3-2 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network libbio-searchio-hmmer-perl_1.7.3-2 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-fa514c47-15cf-48bb-8e70-38af33a680ef 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-searchio-hmmer-perl dpkg-buildpackage: info: source version 1.7.3-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot 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-searchio-hmmer-perl using existing ./libbio-searchio-hmmer-perl_1.7.3.orig.tar.gz dpkg-source: info: building libbio-searchio-hmmer-perl in libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz dpkg-source: info: building libbio-searchio-hmmer-perl in libbio-searchio-hmmer-perl_1.7.3-2.dsc debian/rules build dh build 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" Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::SearchIO::hmmer Writing MYMETA.yml and MYMETA.json dh_auto_build make -j2 make[1]: Entering directory '/<>' cp lib/Bio/SearchIO/hmmer_pull.pm blib/lib/Bio/SearchIO/hmmer_pull.pm cp lib/Bio/Search/HSP/HMMERHSP.pm blib/lib/Bio/Search/HSP/HMMERHSP.pm cp lib/Bio/Search/Hit/hmmer3Hit.pm blib/lib/Bio/Search/Hit/hmmer3Hit.pm cp lib/Bio/Tools/HMMER/Set.pm blib/lib/Bio/Tools/HMMER/Set.pm cp lib/Bio/Search/Result/HmmpfamResult.pm blib/lib/Bio/Search/Result/HmmpfamResult.pm cp lib/Bio/Tools/HMMER/Domain.pm blib/lib/Bio/Tools/HMMER/Domain.pm cp lib/Bio/Search/Hit/HMMERHit.pm blib/lib/Bio/Search/Hit/HMMERHit.pm cp lib/Bio/SearchIO/hmmer3.pm blib/lib/Bio/SearchIO/hmmer3.pm cp lib/Bio/SearchIO/hmmer2.pm blib/lib/Bio/SearchIO/hmmer2.pm cp lib/Bio/Search/HSP/HmmpfamHSP.pm blib/lib/Bio/Search/HSP/HmmpfamHSP.pm cp lib/Bio/Search/Hit/HmmpfamHit.pm blib/lib/Bio/Search/Hit/HmmpfamHit.pm cp lib/Bio/Search/Result/HMMERResult.pm blib/lib/Bio/Search/Result/HMMERResult.pm cp lib/Bio/Tools/HMMER/Results.pm blib/lib/Bio/Tools/HMMER/Results.pm cp lib/Bio/Index/Hmmer.pm blib/lib/Bio/Index/Hmmer.pm cp lib/Bio/SearchIO/hmmer.pm blib/lib/Bio/SearchIO/hmmer.pm cp lib/Bio/Tools/Hmmpfam.pm blib/lib/Bio/Tools/Hmmpfam.pm cp lib/Bio/Search/Result/hmmer3Result.pm blib/lib/Bio/Search/Result/hmmer3Result.pm cp bin/bp_hmmer_to_table.pl blib/script/bp_hmmer_to_table.pl "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_hmmer_to_table.pl cp bin/bp_parse_hmmsearch.pl blib/script/bp_parse_hmmsearch.pl "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_parse_hmmsearch.pl Manifying 2 pod documents Manifying 17 pod documents 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..19 ok 1 - Bio/Index/Hmmer.pm loaded ok ok 2 - Bio/Search/HSP/HMMERHSP.pm loaded ok ok 3 - Bio/Search/HSP/HmmpfamHSP.pm loaded ok ok 4 - Bio/Search/Hit/HMMERHit.pm loaded ok ok 5 - Bio/Search/Hit/HmmpfamHit.pm loaded ok ok 6 - Bio/Search/Hit/hmmer3Hit.pm loaded ok ok 7 - Bio/Search/Result/HMMERResult.pm loaded ok ok 8 - Bio/Search/Result/HmmpfamResult.pm loaded ok ok 9 - Bio/Search/Result/hmmer3Result.pm loaded ok ok 10 - Bio/SearchIO/hmmer.pm loaded ok ok 11 - Bio/SearchIO/hmmer2.pm loaded ok ok 12 - Bio/SearchIO/hmmer3.pm loaded ok ok 13 - Bio/SearchIO/hmmer_pull.pm loaded ok ok 14 - Bio/Tools/HMMER/Domain.pm loaded ok ok 15 - Bio/Tools/HMMER/Results.pm loaded ok ok 16 - Bio/Tools/HMMER/Set.pm loaded ok ok 17 - Bio/Tools/Hmmpfam.pm loaded ok ok 18 - bin/bp_hmmer_to_table.pl compiled ok ok 19 - bin/bp_parse_hmmsearch.pl compiled ok ok t/author-mojibake.t ...... skipped: these tests are for testing by the author t/author-pod-syntax.t .... skipped: these tests are for testing by the author t/LocalDB-Index.t ........ 1..4 ok 1 - use Bio::Index::Hmmer; ok 2 - An object of class 'Bio::Index::Hmmer' isa 'Bio::Index::Hmmer' ok 3 ok 4 ok t/SearchIO-hmmer_pull.t .. 1..290 ok 1 - use Bio::SearchIO; 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 t/SearchIO.t ............. 1..824 ok 1 - use Bio::SearchIO; ok 2 - Check for the correct result reference type ok 3 - Check algorithm ok 4 - Check algorithm version ok 5 - Check hmm_name ok 6 - Check sequence_file ok 7 - Check query_name ok 8 - Check query_length absence ok 9 - Check query_description ok 10 - Check num_hits ok 11 - Check for the correct hit reference type ok 12 - Check hit name ok 13 - Check for hit description ok 14 - Check hit raw_score ok 15 - Check hit bits (0) ok 16 - Check hit significance ok 17 - Check num_hsps ok 18 - Check hit length ok 19 ok 20 ok 21 - Check hit total conserved residues ok 22 - Check hit total identical residues ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 - Check for correct hsp reference type ok 30 - Check for query seq_id ok 31 - Check for hit seq_id ok 32 - Check for hit hmmfrom value ok 33 - Check for hit hmm to value ok 34 - Check for query alifrom value ok 35 - Check for query ali to value ok 36 - Check for hsp score ok 37 - Check for hsp bits (0) ok 38 - Check for hsp c-Evalue ok 39 - Check for hsp query length ok 40 - Check for hsp hit length ok 41 - Check for hsp total length ok 42 - Check for hsp query gaps ok 43 - Check for hsp hit gaps ok 44 - Check for hsp total gaps ok 45 - Check hit length consistency ok 46 - Check query length consistency ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 - Check for query string ok 57 - Check for hit string ok 58 - Check for homology string ok 59 - Check if homology string and hit string have an equal length ok 60 - Check if query string and homology string have an equal length ok 61 ok 62 ok 63 - Check for the correct hit reference type ok 64 - Check hit name ok 65 - Check for hit description ok 66 - Check hit raw_score ok 67 - Check hit bits (0) ok 68 - Check hit significance ok 69 - Check num_hsps ok 70 - Check hit length ok 71 ok 72 ok 73 - Check hit total conserved residues ok 74 - Check hit total identical residues ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 - Check for correct hsp reference type ok 82 - Check for query seq_id ok 83 - Check for hit seq_id ok 84 - Check for hit hmmfrom value ok 85 - Check for hit hmm to value ok 86 - Check for query alifrom value ok 87 - Check for query ali to value ok 88 - Check for hsp score ok 89 - Check for hsp bits (0) ok 90 - Check for hsp c-Evalue ok 91 - Check for hsp query length ok 92 - Check for hsp hit length ok 93 - Check for hsp total length ok 94 - Check for hsp query gaps ok 95 - Check for hsp hit gaps ok 96 - Check for hsp total gaps ok 97 - Check hit length consistency ok 98 - Check query length consistency ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 - Check for query string ok 109 - Check for hit string ok 110 - Check for homology string ok 111 - Check if homology string and hit string have an equal length ok 112 - Check if query string and homology string have an equal length ok 113 - Check for the correct result reference type ok 114 - Check algorithm ok 115 - Check algorithm version ok 116 - Check hmm_name ok 117 - Check sequence_file ok 118 - Check database_name ok 119 - Check query_name ok 120 - Check query_length ok 121 - Check query_description ok 122 - Check num_hits ok 123 - Check for the correct hit reference type ok 124 - Check hit name ok 125 - Check for hit description ok 126 - Check hit raw_score ok 127 - Check hit bits (0) ok 128 - Check hit significance ok 129 - Check num_hsps ok 130 - Check hit length ok 131 - Check for correct hsp reference type ok 132 - Check for query seq_id ok 133 - Check for hit seq_id ok 134 - Check for hit hmmfrom value ok 135 - Check for hit hmm to value ok 136 - Check for query alifrom value ok 137 - Check for query ali to value ok 138 - Check for hsp score ok 139 - Check for hsp bits (0) ok 140 - Check for hsp c-Evalue ok 141 - Check for hsp query length ok 142 - Check for hsp hit length ok 143 - Check for hsp total length ok 144 - Check for hsp query gaps ok 145 - Check for hsp hit gaps ok 146 - Check for hsp total gaps ok 147 - Check hit length ok 148 ok 149 ok 150 - Check for query seq_id ok 151 - Check for hit seq_id ok 152 - Check for hit hmmfrom value ok 153 - Check for hit hmm to value ok 154 - Check for query alifrom value ok 155 - Check for query ali to value ok 156 - Check for hsp score ok 157 - Check for hsp bits (0) ok 158 - Check for hsp c-Evalue ok 159 - Check for hsp query length ok 160 - Check for hsp hit length ok 161 - Check for hsp total length ok 162 - Check for hsp query gaps ok 163 - Check for hsp hit gaps ok 164 - Check for hsp total gaps ok 165 - Check hit length ok 166 ok 167 ok 168 - Check for query seq_id ok 169 - Check for hit seq_id ok 170 - Check for hit hmmfrom value ok 171 - Check for hit hmm to value ok 172 - Check for query alifrom value ok 173 - Check for query ali to value ok 174 - Check for hsp score ok 175 - Check for hsp bits (0) ok 176 - Check for hsp c-Evalue ok 177 - Check for hsp query length ok 178 - Check for hsp hit length ok 179 - Check for hsp total length ok 180 - Check for hsp query gaps ok 181 - Check for hsp hit gaps ok 182 - Check for hsp total gaps ok 183 - Check for the correct result reference type ok 184 - Check algorithm ok 185 - Check algorithm version ok 186 - Check hmm_name ok 187 - Check sequence_file ok 188 - Check query_name ok 189 - Check query_length absence ok 190 - Check query_description ok 191 - Check num_hits ok 192 - Check for the correct hit reference type ok 193 - Check hit name ok 194 - Check for hit description ok 195 - Check hit raw_score ok 196 - Check hit bits (0) ok 197 - Check hit significance ok 198 - Check num_hsps ok 199 - Check hit length ok 200 ok 201 ok 202 - Check hit total conserved residues ok 203 - Check hit total identical residues ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 - Check for correct hsp reference type ok 211 - Check for query seq_id ok 212 - Check for hit seq_id ok 213 - Check for hit hmmfrom value ok 214 - Check for hit hmm to value ok 215 - Check for query alifrom value ok 216 - Check for query ali to value ok 217 - Check for hsp score ok 218 - Check for hsp bits (0) ok 219 - Check for hsp evalue ok 220 - Check for hsp query length ok 221 - Check for hsp hit length ok 222 - Check for hsp total length ok 223 - Check for hsp query gaps ok 224 - Check for hsp hit gaps ok 225 - Check for hsp total gaps ok 226 - Check hit length consistency ok 227 - Check query length consistency ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 - Check for hiy string ok 239 - Check for query string ok 240 - Check for homology string ok 241 - Check for nomatch indices in query ok 242 - Check for nomatch indices in hit ok 243 - Check for gap indices in query ok 244 - Check for gap indices in hit ok 245 - Check for the correct result reference type ok 246 - Check algorithm ok 247 - Check algorithm version ok 248 - Check hmm_name ok 249 - Check database_name ok 250 - Check sequence_file ok 251 - Check query_name ok 252 - Check query_length ok 253 - Check query_accession ok 254 - Check query_description ok 255 - Check num_hits ok 256 - Check for the correct hit reference type ok 257 - Check hit name ok 258 - Check for hit description ok 259 - Check hit raw_score ok 260 - Check hit bits (0) ok 261 - Check hit significance ok 262 - Check num_hsps ok 263 - Check hit length absence ok 264 ok 265 ok 266 - Check hit total conserved residues ok 267 - Check hit total identical residues ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 ok 274 - Check for correct hsp reference type ok 275 - Check for query seq_id ok 276 - Check for hit seq_id ok 277 - Check for hit hmmfrom value ok 278 - Check for hit hmm to value ok 279 - Check for query alifrom value ok 280 - Check for query ali to value ok 281 - Check for hsp score ok 282 - Check for hsp bits (0) ok 283 - Check for hsp evalue ok 284 - Check for hsp query length ok 285 - Check for hsp hit length ok 286 - Check for hsp total length ok 287 - Check for hsp query gaps ok 288 - Check for hsp hit gaps ok 289 - Check for hsp total gaps ok 290 - Check hit length consistency ok 291 - Check query length consistency ok 292 ok 293 ok 294 ok 295 ok 296 ok 297 ok 298 ok 299 ok 300 ok 301 ok 302 - Check for hiy string ok 303 - Check for homology string ok 304 - Check for query string ok 305 ok 306 ok 307 - Check hit name ok 308 - Check for hit description ok 309 - Check hit raw_score ok 310 - Check hit bits (0) ok 311 - Check hit significance ok 312 ok 313 ok 314 ok 315 ok 316 - Check for consensus structure string ok 317 - Check for hsp seq_str ok 318 - Check for query string ok 319 - Check for hit string ok 320 - Check for homology string ok 321 - Check if correct searchio object is returned ok 322 - Check for the correct result reference type ok 323 - Check algorithm ok 324 - Check algorithm version ok 325 - Check hmm_name ok 326 - Check sequence_file ok 327 - Check query_name ok 328 - Check query_length ok 329 - Check query_accession ok 330 - Check query_description ok 331 - Check num_hits ok 332 - Check for the correct hit reference type ok 333 - Check hit name ok 334 - Check for hit description ok 335 - Check hit raw_score ok 336 - Check hit bits (0) ok 337 - Check hit significance ok 338 - Check num_hsps ok 339 - Check hit length absence ok 340 ok 341 ok 342 - Check for correct hsp reference type ok 343 - Check for hit seq_id ok 344 - Check for query seq_id ok 345 - Check for hit hmmfrom value ok 346 - Check for hit hmm to value ok 347 - Check for query alifrom value ok 348 - Check for query ali to value ok 349 - Check for hsp score ok 350 - Check for hsp bits (0) ok 351 - Check for hsp c-Evalue ok 352 - Check for hsp query length ok 353 - Check for hsp hit length ok 354 - Check for hsp total length ok 355 - Check for hsp query gaps ok 356 - Check for hsp hit gaps ok 357 - Check for hsp total gaps ok 358 - Check hit length consistency ok 359 - Check query length consistency ok 360 ok 361 ok 362 ok 363 ok 364 ok 365 ok 366 ok 367 ok 368 ok 369 ok 370 - Check for query string ok 371 - Check for hit string ok 372 - Check for homology string ok 373 - Check for posterior probability string ok 374 - Check algorithm ok 375 - Check algorithm version ok 376 - Check hmm_name ok 377 - Check sequence_file ok 378 - Check query_name ok 379 - Check query_length ok 380 - Check query_description ok 381 - Check num_hits ok 382 - Check for the correct hit reference type ok 383 - Check hit name ok 384 - Check for hit description ok 385 - Check num_hsps ok 386 - Check for correct hsp reference type ok 387 - Check for hit seq_id ok 388 - Check for query seq_id ok 389 - Check for hit hmmfrom value ok 390 - Check for hit hmm to value ok 391 - Check for query alifrom value ok 392 - Check for query ali to value ok 393 - Check for hsp score ok 394 - Check for hsp bits (0) ok 395 - Check for hsp c-Evalue ok 396 - Check for the correct hit reference type ok 397 - Check hit name ok 398 - Check for hit description ok 399 - Check num_hsps ok 400 - Check for correct hsp reference type ok 401 - Check for hit seq_id ok 402 - Check for query seq_id ok 403 - Check for hit hmmfrom value ok 404 - Check for hit hmm to value ok 405 - Check for query alifrom value ok 406 - Check for query ali to value ok 407 - Check for hsp score ok 408 - Check for hsp bits (0) ok 409 - Check for hsp c-Evalue ok 410 - Check for the correct result reference type ok 411 - Check algorithm ok 412 - Check algorithm version ok 413 - Check hmm_name ok 414 - Check sequence_file ok 415 - Check query_name ok 416 - Check query_length ok 417 - Check query_description ok 418 - Check num_hits ok 419 - Check if correct searchio object is returned ok 420 - Check for the correct result reference type ok 421 - Check algorithm ok 422 - Check algorithm version ok 423 - Check hmm_name ok 424 - Check sequence_file ok 425 - Check query_name ok 426 - Check query_length ok 427 - Check query_accession ok 428 - Check query_description ok 429 - Check num_hits ok 430 - Check for the correct result reference type ok 431 - Check algorithm ok 432 - Check algorithm version ok 433 - Check hmm_name ok 434 - Check sequence_file ok 435 - Check query_name ok 436 - Check query_length ok 437 - Check query_accession ok 438 - Check query_description ok 439 - Check num_hits ok 440 - Check for the correct hit reference type ok 441 - Check hit name ok 442 - Check for hit description ok 443 - Check hit raw_score ok 444 - Check hit bits (0) ok 445 - Check hit significance ok 446 - Check num_hsps ok 447 - Check for correct hsp reference type ok 448 - Check for hit seq_id ok 449 - Check for query seq_id ok 450 - Check for hit alifrom value ok 451 - Check for hit ali to value ok 452 - Check for query hmmfrom value ok 453 - Check for query hmm to value ok 454 - Check for hsp score ok 455 - Check for hsp bits (0) ok 456 - Check for hsp c-Evalue ok 457 - Check for hsp query length ok 458 - Check for hsp hit length ok 459 - Check for hsp total length ok 460 - Check for hsp query gaps ok 461 - Check for hsp hit gaps ok 462 - Check for hsp total gaps ok 463 - Check hit length consistency ok 464 - Check query length consistency ok 465 ok 466 ok 467 ok 468 ok 469 ok 470 ok 471 ok 472 ok 473 ok 474 ok 475 - Check for consensus structure string ok 476 - Check for query string ok 477 - Check for hit string ok 478 - Check for homology string ok 479 - Check for posterior probability string ok 480 - Check for the correct result reference type ok 481 - Check algorithm ok 482 - Check algorithm version ok 483 - Check hmm_name ok 484 - Check sequence_file ok 485 - Check query_name ok 486 - Check query_length ok 487 - Check query_accession ok 488 - Check query_description ok 489 - Check num_hits ok 490 - Check for the correct hit reference type ok 491 - Check hit name ok 492 - Check for hit description ok 493 - Check hit raw_score ok 494 - Check hit bits (0) ok 495 - Check hit significance ok 496 - Check num_hsps ok 497 - Check hit length absence ok 498 ok 499 ok 500 - Check for correct hsp reference type ok 501 - Check for hit seq_id ok 502 - Check for query seq_id ok 503 - Check for hit alifrom value ok 504 - Check for hit ali to value ok 505 - Check for query hmmfrom value ok 506 - Check for query hmm to value ok 507 - Check for hsp score ok 508 - Check for hsp bits (0) ok 509 - Check for hsp c-Evalue ok 510 - Check for hsp query length ok 511 - Check for hsp hit length ok 512 - Check for hsp total length ok 513 - Check for hsp query gaps ok 514 - Check for hsp hit gaps ok 515 - Check for hsp total gaps ok 516 - Check hit length consistency ok 517 - Check query length consistency ok 518 ok 519 ok 520 ok 521 ok 522 ok 523 ok 524 ok 525 ok 526 ok 527 ok 528 - Check for consensus structure string ok 529 - Check for query string ok 530 - Check for hit string ok 531 - Check for homology string ok 532 - Check for posterior probability string ok 533 - Check for the correct result reference type ok 534 - Check algorithm ok 535 - Check algorithm version ok 536 - Check hmm_name ok 537 - Check sequence_file ok 538 - Check query_name ok 539 - Check query_length ok 540 - Check query_description ok 541 - Check num_hits ok 542 - Check for the correct hit reference type ok 543 - Check hit name ok 544 - Check for hit description ok 545 - Check hit raw_score ok 546 - Check hit significance ok 547 - Check num_hsps ok 548 - Check for correct hsp reference type ok 549 - Check for hit envfrom value ok 550 - Check for hit env to value ok 551 - Check for query hmmfrom value ok 552 - Check for query hmm to value ok 553 - Check for hsp score ok 554 - Check for hsp c-Evalue ok 555 - Check for correct hsp reference type ok 556 - Check for hit envfrom value ok 557 - Check for hit env to value ok 558 - Check for query hmmfrom value ok 559 - Check for query hmm to value ok 560 - Check for hsp score ok 561 - Check for hsp c-Evalue ok 562 - Check for correct hsp reference type ok 563 - Check for hit envfrom value ok 564 - Check for hit env to value ok 565 - Check for query hmmfrom value ok 566 - Check for query hmm to value ok 567 - Check for hsp score ok 568 - Check for hsp c-Evalue ok 569 - Check for correct hsp reference type ok 570 - Check for hit envfrom value ok 571 - Check for hit env to value ok 572 - Check for query hmmfrom value ok 573 - Check for query hmm to value ok 574 - Check for hsp score ok 575 - Check for hsp c-Evalue ok 576 - Check for correct hsp reference type ok 577 - Check for hit envfrom value ok 578 - Check for hit env to value ok 579 - Check for query hmmfrom value ok 580 - Check for query hmm to value ok 581 - Check for hsp score ok 582 - Check for hsp c-Evalue ok 583 - Check for correct hsp reference type ok 584 - Check for hit envfrom value ok 585 - Check for hit env to value ok 586 - Check for query hmmfrom value ok 587 - Check for query hmm to value ok 588 - Check for hsp score ok 589 - Check for hsp c-Evalue ok 590 - Check hit length ok 591 ok 592 ok 593 - Check for the correct hit reference type ok 594 - Check hit name ok 595 - Check for hit description ok 596 - Check hit raw_score ok 597 - Check hit significance ok 598 - Check num_hsps ok 599 - Check for correct hsp reference type ok 600 - Check for hit envfrom value ok 601 - Check for hit env to value ok 602 - Check for query hmmfrom value ok 603 - Check for query hmm to value ok 604 - Check for hsp score ok 605 - Check for hsp c-Evalue ok 606 - Check for correct hsp reference type ok 607 - Check for hit envfrom value ok 608 - Check for hit env to value ok 609 - Check for query hmmfrom value ok 610 - Check for query hmm to value ok 611 - Check for hsp score ok 612 - Check for hsp c-Evalue ok 613 - Check for correct hsp reference type ok 614 - Check for hit envfrom value ok 615 - Check for hit env to value ok 616 - Check for query hmmfrom value ok 617 - Check for query hmm to value ok 618 - Check for hsp score ok 619 - Check for hsp c-Evalue ok 620 - Check for the correct result reference type ok 621 - Check algorithm ok 622 - Check algorithm version ok 623 - Check hmm_name ok 624 - Check sequence_file ok 625 - Check query_name ok 626 - Check query_length ok 627 - Check query_description ok 628 - Check num_hits ok 629 - Check for the correct hit reference type ok 630 - Check hit name ok 631 - Check for hit description ok 632 - Check hit raw_score ok 633 - Check hit significance ok 634 - Check num_hsps ok 635 - Check for correct hsp reference type ok 636 - Check hit sequence ok 637 - Check query sequence ok 638 - Check for correct hsp reference type ok 639 - Check hit sequence ok 640 - Check query sequence ok 641 - Check hit length ok 642 ok 643 ok 644 - Check for the correct hit reference type ok 645 - Check hit name ok 646 - Check for hit description ok 647 - Check hit raw_score ok 648 - Check hit significance ok 649 - Check num_hsps ok 650 - Check for correct hsp reference type ok 651 - Check hit sequence ok 652 - Check query sequence ok 653 - Check for correct hsp reference type ok 654 - Check hit sequence ok 655 - Check query sequence ok 656 - Check for the correct hit reference type ok 657 - Check hit name ok 658 - Check for hit description ok 659 - Check hit raw_score ok 660 - Check hit significance ok 661 - Check num_hsps ok 662 - Check for correct hsp reference type ok 663 - Check hit sequence ok 664 - Check query sequence ok 665 - Check for correct hsp reference type ok 666 - Check hit sequence ok 667 - Check query sequence ok 668 - Check for the correct result reference type ok 669 - Check algorithm ok 670 - Check algorithm version ok 671 - Check query_name ok 672 - Check query_length ok 673 - Check query_description ok 674 - Check num_hits ok 675 - Check for the correct hit reference type ok 676 - Check hit name ok 677 - Check for hit description ok 678 - Check hit raw_score ok 679 - Check hit significance ok 680 - Check num_hsps ok 681 - Check for correct hsp reference type ok 682 - Check for query string ok 683 - Check for hit string ok 684 - Check for homology string ok 685 - Check for posterior probability string ok 686 - Check if loading hmmpfam output via the hmm2 parser directly works ok 687 - Check for the correct result reference type ok 688 - Check if loading hmmsearch2 output via the hmm2 parser directly works ok 689 - Check for the correct result reference type ok 690 - Check if loading hmmscan output via the hmm3 parser directly works ok 691 - Check for the correct result reference type ok 692 - Check if loading hmmsearch3 output via the hmm3 parser directly works ok 693 - Check for the correct result reference type ok 694 - Check if selecting the correct hmmpfam parser using -version works ok 695 - Check for the correct result reference type ok 696 - Check if selecting the correct hmmsearch2 parser using -version works ok 697 - Check for the correct result reference type ok 698 - Check if selecting the correct hmmscan parser using -version works ok 699 - Check for the correct result reference type ok 700 - Check if selecting the correct hmmsearch3 parser using -version works ok 701 - Check for the correct result reference type ok 702 - Check if reading from a pipe works ok 703 - Check for the correct result reference type ok 704 - Check num_hits ok 705 - Check query_length ok 706 - Check hit length ok 707 - bug3376 ok 708 - bug3421 - Check if can correctly parse an HSP with line full of dashes ok 709 - bug3302 - Check if can parse multiresult hmmer ok 710 - Check algorithm ok 711 - Check nhmmer algorithm version ok 712 - Check hmm_name ok 713 - Check sequence_file ok 714 - Check query_name ok 715 - Check query_length ok 716 - Check query_accession ok 717 - Check query_description ok 718 - Check num_hits ok 719 - Check for the correct hit reference type ok 720 - Check nhmmer hit name ok 721 - Check nhmmer hit description ok 722 - Check nhmmer hit score ok 723 - Check nhmmer hit bits (0) ok 724 - Check nhmmer hit significance ok 725 - Check num_hsps ok 726 - Check nhmmer hit length ok 727 ok 728 ok 729 - Check for correct hsp reference type ok 730 - Check for nhmmer hit seq_id ok 731 - Check for nhmmer query seq_id ok 732 - Check nhmmer hsp hit start ok 733 - Check nhmmer hsp hit end ok 734 - Check nhmmer hsp query start ok 735 - Check nhmmer hsp query end ok 736 - Check nhmmer hsp hit strand ok 737 - Check nhmmer hsp query strand ok 738 - Check nhmmer hsp score ok 739 - Check nhmmer hsp bits (0) ok 740 - Check nhmmer hsp evalue ok 741 - Check for hsp query length ok 742 - Check for hsp hit length ok 743 - Check for hsp total length ok 744 - Check for hsp query gaps ok 745 - Check for hsp hit gaps ok 746 - Check for hsp total gaps ok 747 - Check hit length consistency ok 748 - Check query length consistency ok 749 ok 750 ok 751 ok 752 ok 753 ok 754 ok 755 ok 756 ok 757 ok 758 - Check for consensus structure string ok 759 - Check for nhmmer query string ok 760 - Check for nhmmer homology string ok 761 - Check for nhmmer hit string ok 762 - Check for nhmmer posterior probability string ok 763 - Check if nhmmer homology string and hit string have an equal length ok 764 - Check if nhmmer query string and homology string have an equal length ok 765 - Check nhmmer hit name ok 766 - Check nhmmer hit description ok 767 - Check nhmmer hit score ok 768 - Check nhmmer hit bits (0) ok 769 - Check nhmmer hit significance ok 770 - Check nhmmer hit length ok 771 - Check for nhmmer hit seq_id ok 772 - Check for nhmmer query seq_id ok 773 - Check nhmmer hsp query start ok 774 - Check nhmmer hsp query end ok 775 - Check nhmmer hsp hit start ok 776 - Check nhmmer hsp hit end ok 777 - Check nhmmer hsp hit strand ok 778 - Check nhmmer hsp query strand ok 779 - Check nhmmer hsp score ok 780 - Check nhmmer hsp bits (0) ok 781 - Check nhmmer hsp evalue ok 782 - Check for hsp query length ok 783 - Check for hsp hit length ok 784 - Check for hsp total length ok 785 - Check for hsp query gaps ok 786 - Check for hsp hit gaps ok 787 - Check for hsp total gaps ok 788 - Check hit length consistency ok 789 - Check query length consistency ok 790 ok 791 - Check for consensus structure string ok 792 - Check for nhmmer query string ok 793 - Check for nhmmer homology string ok 794 - Check for nhmmer hit string ok 795 - Check for nhmmer posterior probability string ok 796 - Check if nhmmer homology string and hit string have an equal length ok 797 - Check if nhmmer query string and homology string have an equal length ok 798 - Check Significance filtered num_hits ok 799 - Check Significance filtered hit ID ok 800 - Check Significance filtered hit ID ok 801 - Check Significance filtered hit ID ok 802 - Check Significance filtered hit ID ok 803 - Check Significance filtered hit ID ok 804 ok 805 - Check Score filtered num_hits ok 806 - Check Score filtered hit ID ok 807 - Check Score filtered hit ID ok 808 - Check Score filtered hit ID ok 809 - Check Score filtered hit ID ok 810 ok 811 - Check Bits filtered num_hits ok 812 - Check Bits filtered num_hits ok 813 - Check Bits filtered num_hits ok 814 - Check Hit_filter filtered num_hits ok 815 - Check Hit_filter filtered hits ID ok 816 ok 817 - Correct parsing of alignments with stops ok 818 - Check algorithm ok 819 - Check query_name ok 820 - Check query_length absence ok 821 - Check query_description ok 822 - Check num_hits ok 823 - query name okay ok 824 - Check num_hsps ok t/Tools.t ................ 1..29 ok 1 - use Bio::Tools::HMMER::Domain; ok 2 - use Bio::Tools::HMMER::Set; ok 3 - use Bio::Tools::HMMER::Results; 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 All tests successful. Files=7, Tests=1166, 3 wallclock secs ( 0.08 usr 0.00 sys + 2.43 cusr 0.34 csys = 2.85 CPU) Result: PASS make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install --destdir=debian/libbio-searchio-hmmer-perl/ make -j2 install DESTDIR=/<>/debian/libbio-searchio-hmmer-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/<>' Manifying 2 pod documents Manifying 17 pod documents Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer_pull.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer2.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer3.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HmmpfamHSP.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HMMERHSP.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HMMERHit.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HmmpfamHit.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/hmmer3Hit.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HmmpfamResult.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/hmmer3Result.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HMMERResult.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Index/Hmmer.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/Hmmpfam.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Results.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Domain.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Set.pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_parse_hmmsearch.pl.1p Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_hmmer_to_table.pl.1p Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer3.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HMMERResult.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HMMERHSP.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::hmmer3Hit.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HmmpfamHit.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HmmpfamResult.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Index::Hmmer.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Domain.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::Hmmpfam.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer_pull.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::hmmer3Result.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HMMERHit.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HmmpfamHSP.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Set.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer2.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Results.3pm Installing /<>/debian/libbio-searchio-hmmer-perl/usr/bin/bp_parse_hmmsearch.pl Installing /<>/debian/libbio-searchio-hmmer-perl/usr/bin/bp_hmmer_to_table.pl 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-searchio-hmmer-perl' in '../libbio-searchio-hmmer-perl_1.7.3-2_all.deb'. dpkg-genbuildinfo -O../libbio-searchio-hmmer-perl_1.7.3-2_amd64.buildinfo dpkg-genchanges -O../libbio-searchio-hmmer-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 2024-08-04T04:18:22Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ libbio-searchio-hmmer-perl_1.7.3-2_amd64.changes: ------------------------------------------------- Format: 1.8 Date: Tue, 29 Oct 2019 13:23:15 +0100 Source: libbio-searchio-hmmer-perl Binary: libbio-searchio-hmmer-perl Architecture: source all Version: 1.7.3-2 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Michael R. Crusoe Changed-By: Michael R. Crusoe Description: libbio-searchio-hmmer-perl - perl parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmm Closes: 942789 Changes: libbio-searchio-hmmer-perl (1.7.3-2) unstable; urgency=medium . * Remove obsolete fields Name, Contact from debian/upstream/metadata. * Turn on the autopkgtests * debian/control: Breaks+Replaces the old libbio-bio-perl. (Closes: #942789) Checksums-Sha1: af5498bc6116333692aca57b7c1954b6351dc5c5 1278 libbio-searchio-hmmer-perl_1.7.3-2.dsc 08223e252bd44e3beb75c8dbcb7b710448e0caba 1884 libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz 04ab11707f2891296dd33073942556646a38b48f 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb 51ca9e587bef34b320c415e86553e6e927927089 5719 libbio-searchio-hmmer-perl_1.7.3-2_amd64.buildinfo Checksums-Sha256: e9ab6e40d36cff662bcc19565ad77890e9be13a08aadffaf5c03482d64ef9f1f 1278 libbio-searchio-hmmer-perl_1.7.3-2.dsc 597655cd9cc36b81836be05733c2a060c9c1e44b14b2adb6fa112e33bc58fac1 1884 libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz 9d819fc84267bb66cb062941f182db3dd90d9cc3a447056d7e7b8fbc13b54ae0 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb f0726b086b543fe8315e2ead44daf4daf1daedf1427614e7c1dbffb6645654c1 5719 libbio-searchio-hmmer-perl_1.7.3-2_amd64.buildinfo Files: 5efd9f839c5d7f4aaf7170a3f80d16b7 1278 perl optional libbio-searchio-hmmer-perl_1.7.3-2.dsc 0508ebc3b1dbb26e025286af2781f41f 1884 perl optional libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz 9bc7c69b6ba2db1798764a2605a5c9d6 91204 perl optional libbio-searchio-hmmer-perl_1.7.3-2_all.deb 5bf7ec14481aaf97b3b97224328b782b 5719 perl optional libbio-searchio-hmmer-perl_1.7.3-2_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: libbio-searchio-hmmer-perl Binary: libbio-searchio-hmmer-perl Architecture: all source Version: 1.7.3-2 Checksums-Md5: 5efd9f839c5d7f4aaf7170a3f80d16b7 1278 libbio-searchio-hmmer-perl_1.7.3-2.dsc 9bc7c69b6ba2db1798764a2605a5c9d6 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb Checksums-Sha1: af5498bc6116333692aca57b7c1954b6351dc5c5 1278 libbio-searchio-hmmer-perl_1.7.3-2.dsc 04ab11707f2891296dd33073942556646a38b48f 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb Checksums-Sha256: e9ab6e40d36cff662bcc19565ad77890e9be13a08aadffaf5c03482d64ef9f1f 1278 libbio-searchio-hmmer-perl_1.7.3-2.dsc 9d819fc84267bb66cb062941f182db3dd90d9cc3a447056d7e7b8fbc13b54ae0 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 04 Aug 2024 04:18:22 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.4), base-passwd (= 3.6.4), bash (= 5.2.21-2.1), binutils (= 2.42.90.20240720-2), binutils-common (= 2.42.90.20240720-2), binutils-x86-64-linux-gnu (= 2.42.90.20240720-2), bsdextrautils (= 2.40.2-1), bsdutils (= 1:2.40.2-1), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-4), cpp-13-x86-64-linux-gnu (= 13.3.0-4), cpp-14 (= 14.2.0-1), cpp-14-x86-64-linux-gnu (= 14.2.0-1), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.16), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-2), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-1), g++-14-x86-64-linux-gnu (= 14.2.0-1), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-4), gcc-13-base (= 13.3.0-4), gcc-13-x86-64-linux-gnu (= 13.3.0-4), gcc-14 (= 14.2.0-1), gcc-14-base (= 14.2.0-1), gcc-14-x86-64-linux-gnu (= 14.2.0-1), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), 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), libalgorithm-diff-perl (= 1.201-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-1), libatomic1 (= 14.2.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-4), libaudit1 (= 1:3.1.2-4+b1), libbinutils (= 2.42.90.20240720-2), libbio-perl-perl (= 1.7.8-1), libblkid1 (= 2.40.2-1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-6), libc-dev-bin (= 2.39-6), libc6 (= 2.39-6), libc6-dev (= 2.39-6), libcap-ng0 (= 0.8.5-1+b1), libcap2 (= 1:2.66-5), libcapture-tiny-perl (= 0.48-2), libcc1-0 (= 14.2.0-1), libclass-data-inheritable-perl (= 0.08-3), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42.90.20240720-2), libctf0 (= 2.42.90.20240720-2), libdata-stag-perl (= 0.14-3), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.16), libdevel-stacktrace-perl (= 2.0500-1), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libexception-class-perl (= 1.45-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-4), libgcc-14-dev (= 14.2.0-1), libgcc-s1 (= 14.2.0-1), libgdbm-compat4t64 (= 1.23-6), libgdbm6t64 (= 1.23-6), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-1), libgprofng0 (= 2.42.90.20240720-2), libhwasan0 (= 14.2.0-1), libicu72 (= 72.1-5), libio-string-perl (= 1.08-4), libisl23 (= 0.26-3+b2), libitm1 (= 14.2.0-1), libjansson4 (= 2.14-2+b2), liblsan0 (= 14.2.0-1), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-1), 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 (= 5.40.0-1), libpipeline1 (= 1.5.7-2), libquadmath0 (= 14.2.0-1), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.5-2+b3), libsframe1 (= 2.42.90.20240720-2), libsmartcols1 (= 2.40.2-1), libssl3t64 (= 3.3.1-2), libstdc++-14-dev (= 14.2.0-1), libstdc++6 (= 14.2.0-1), libsub-uplevel-perl (= 0.2800-3), libsystemd0 (= 256.4-2), libtest-deep-perl (= 1.204-1), 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 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-1), libubsan1 (= 14.2.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.4-2), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-1), libxml2 (= 2.12.7+dfsg-3+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.9.12-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-2), mawk (= 1.3.4.20240622-2), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), patch (= 2.7.6-7), perl (= 5.40.0-1), perl-base (= 5.40.0-1), perl-modules-5.40 (= 5.40.0-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.09-2), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.2-1), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) 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="1572351795" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libbio-searchio-hmmer-perl_1.7.3-2_all.deb ------------------------------------------ new Debian package, version 2.0. size 91204 bytes: control archive=1776 bytes. 588 bytes, 16 lines control 3415 bytes, 42 lines md5sums Package: libbio-searchio-hmmer-perl Version: 1.7.3-2 Architecture: all Maintainer: Michael R. Crusoe Installed-Size: 329 Depends: perl:any, libbio-perl-perl, libio-string-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-SearchIO-hmmer Description: perl parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) This object implements a parser for hmmpfam hsp output, a program in the HMMER package. . It is part of the libbio-perl collection. drwxr-xr-x root/root 0 2019-10-29 12:23 ./ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/bin/ -rwxr-xr-x root/root 2684 2019-10-29 12:23 ./usr/bin/bp_hmmer_to_table.pl -rwxr-xr-x root/root 6524 2019-10-29 12:23 ./usr/bin/bp_parse_hmmsearch.pl drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/doc/libbio-searchio-hmmer-perl/ -rw-r--r-- root/root 321 2019-10-29 12:23 ./usr/share/doc/libbio-searchio-hmmer-perl/changelog.Debian.gz -rw-r--r-- root/root 165 2018-09-25 00:25 ./usr/share/doc/libbio-searchio-hmmer-perl/changelog.gz -rw-r--r-- root/root 1658 2019-10-29 12:23 ./usr/share/doc/libbio-searchio-hmmer-perl/copyright drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/lintian/ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 135 2019-10-29 12:22 ./usr/share/lintian/overrides/libbio-searchio-hmmer-perl drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/man/ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/man/man1/ -rw-r--r-- root/root 1332 2019-10-29 12:23 ./usr/share/man/man1/bp_hmmer_to_table.pl.1p.gz -rw-r--r-- root/root 1482 2019-10-29 12:23 ./usr/share/man/man1/bp_parse_hmmsearch.pl.1p.gz drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/man/man3/ -rw-r--r-- root/root 4674 2019-10-29 12:23 ./usr/share/man/man3/Bio::Index::Hmmer.3pm.gz -rw-r--r-- root/root 4274 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::HSP::HMMERHSP.3pm.gz -rw-r--r-- root/root 2456 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::HSP::HmmpfamHSP.3pm.gz -rw-r--r-- root/root 3315 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Hit::HMMERHit.3pm.gz -rw-r--r-- root/root 3108 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Hit::HmmpfamHit.3pm.gz -rw-r--r-- root/root 2164 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Hit::hmmer3Hit.3pm.gz -rw-r--r-- root/root 3722 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Result::HMMERResult.3pm.gz -rw-r--r-- root/root 2916 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Result::HmmpfamResult.3pm.gz -rw-r--r-- root/root 2026 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Result::hmmer3Result.3pm.gz -rw-r--r-- root/root 1831 2019-10-29 12:23 ./usr/share/man/man3/Bio::SearchIO::hmmer.3pm.gz -rw-r--r-- root/root 2385 2019-10-29 12:23 ./usr/share/man/man3/Bio::SearchIO::hmmer2.3pm.gz -rw-r--r-- root/root 2510 2019-10-29 12:23 ./usr/share/man/man3/Bio::SearchIO::hmmer3.3pm.gz -rw-r--r-- root/root 2483 2019-10-29 12:23 ./usr/share/man/man3/Bio::SearchIO::hmmer_pull.3pm.gz -rw-r--r-- root/root 1941 2019-10-29 12:23 ./usr/share/man/man3/Bio::Tools::HMMER::Domain.3pm.gz -rw-r--r-- root/root 3321 2019-10-29 12:23 ./usr/share/man/man3/Bio::Tools::HMMER::Results.3pm.gz -rw-r--r-- root/root 2081 2019-10-29 12:23 ./usr/share/man/man3/Bio::Tools::HMMER::Set.3pm.gz -rw-r--r-- root/root 1916 2019-10-29 12:23 ./usr/share/man/man3/Bio::Tools::Hmmpfam.3pm.gz drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Index/ -rw-r--r-- root/root 12642 2018-09-25 00:25 ./usr/share/perl5/Bio/Index/Hmmer.pm drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Search/ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Search/HSP/ -rw-r--r-- root/root 12049 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/HSP/HMMERHSP.pm -rw-r--r-- root/root 11724 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/HSP/HmmpfamHSP.pm drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Search/Hit/ -rw-r--r-- root/root 7674 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Hit/HMMERHit.pm -rw-r--r-- root/root 10063 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Hit/HmmpfamHit.pm -rw-r--r-- root/root 3708 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Hit/hmmer3Hit.pm drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Search/Result/ -rw-r--r-- root/root 11021 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Result/HMMERResult.pm -rw-r--r-- root/root 11725 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Result/HmmpfamResult.pm -rw-r--r-- root/root 4127 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Result/hmmer3Result.pm drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/SearchIO/ -rw-r--r-- root/root 4160 2018-09-25 00:25 ./usr/share/perl5/Bio/SearchIO/hmmer.pm -rw-r--r-- root/root 41124 2018-09-25 00:25 ./usr/share/perl5/Bio/SearchIO/hmmer2.pm -rw-r--r-- root/root 49495 2018-09-25 00:25 ./usr/share/perl5/Bio/SearchIO/hmmer3.pm -rw-r--r-- root/root 9306 2018-09-25 00:25 ./usr/share/perl5/Bio/SearchIO/hmmer_pull.pm drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Tools/ drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Tools/HMMER/ -rw-r--r-- root/root 6475 2018-09-25 00:25 ./usr/share/perl5/Bio/Tools/HMMER/Domain.pm -rw-r--r-- root/root 21554 2018-09-25 00:25 ./usr/share/perl5/Bio/Tools/HMMER/Results.pm -rw-r--r-- root/root 5330 2018-09-25 00:25 ./usr/share/perl5/Bio/Tools/HMMER/Set.pm -rw-r--r-- root/root 5710 2018-09-25 00:25 ./usr/share/perl5/Bio/Tools/Hmmpfam.pm +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 2072 Build-Time: 6 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 5 Job: /srv/debomatic/incoming/libbio-searchio-hmmer-perl_1.7.3-2.dsc Machine Architecture: amd64 Package: libbio-searchio-hmmer-perl Package-Time: 18 Source-Version: 1.7.3-2 Space: 2072 Status: successful Version: 1.7.3-2 -------------------------------------------------------------------------------- Finished at 2024-08-04T04:18:22Z Build needed 00:00:18, 2072k disk space