Running as unit: rb-build-arm64_4-45732.service ==================================================================================== Fri Nov 22 05:34:28 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_4) on jenkins, called using "codethink02-arm64 codethink01-arm64" as arguments. Fri Nov 22 05:34:28 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-I3htUtGC" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 05:34:28 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Fri Nov 22 05:34:28 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-BhlngO' Fri Nov 22 05:34:29 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Fri Nov 22 05:34:29 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-mj8a8z' ok, let's check if libbio-searchio-hmmer-perl is building anywhere yet… ok, libbio-searchio-hmmer-perl is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of libbio-searchio-hmmer-perl in unstable on arm64 on jenkins now. 1st build will be done on codethink02-arm64.debian.net. 2nd build will be done on codethink01-arm64.debian.net. ============================================================================= Fri Nov 22 05:34:37 UTC 2024 I: starting to build libbio-searchio-hmmer-perl/unstable/arm64 on jenkins on '2024-11-22 05:34' Fri Nov 22 05:34:37 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/45732/console.log 1732253677 arm64 unstable libbio-searchio-hmmer-perl Fri Nov 22 05:34:37 UTC 2024 I: Downloading source for unstable/libbio-searchio-hmmer-perl=1.7.3-2 --2024-11-22 05:34:37-- http://deb.debian.org/debian/pool/main/libb/libbio-searchio-hmmer-perl/libbio-searchio-hmmer-perl_1.7.3-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2161 (2.1K) [text/prs.lines.tag] Saving to: ‘libbio-searchio-hmmer-perl_1.7.3-2.dsc’ 0K .. 100% 209M=0s 2024-11-22 05:34:37 (209 MB/s) - ‘libbio-searchio-hmmer-perl_1.7.3-2.dsc’ saved [2161/2161] --2024-11-22 05:34:37-- http://deb.debian.org/debian/pool/main/libb/libbio-searchio-hmmer-perl/libbio-searchio-hmmer-perl_1.7.3-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2161 (2.1K) [text/prs.lines.tag] Saving to: ‘libbio-searchio-hmmer-perl_1.7.3-2.dsc’ 0K .. 100% 209M=0s 2024-11-22 05:34:37 (209 MB/s) - ‘libbio-searchio-hmmer-perl_1.7.3-2.dsc’ saved [2161/2161] Fri Nov 22 05:34:37 UTC 2024 I: libbio-searchio-hmmer-perl_1.7.3-2.dsc -----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----- Fri Nov 22 05:34:37 UTC 2024 I: Checking whether the package is not for us Fri Nov 22 05:34:37 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Fri Nov 22 05:34:37 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Fri Nov 22 05:34:37 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Fri Nov 22 05:34:37 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-LAJYAQ' ==================================================================================== Fri Nov 22 05:34:38 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "1 libbio-searchio-hmmer-perl unstable /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w 1.7.3-2" as arguments. Fri Nov 22 05:34:38 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-SVtqeT4i" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 05:34:38 UTC 2024 I: Downloading source for unstable/libbio-searchio-hmmer-perl=1.7.3-2 Reading package lists... NOTICE: 'libbio-searchio-hmmer-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl.git Please use: git clone https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 153 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (dsc) [2161 B] Get:2 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (tar) [149 kB] Get:3 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (diff) [1876 B] Fetched 153 kB in 0s (2091 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libbio-searchio-hmmer-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl.git Please use: git clone https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 153 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (dsc) [2161 B] Get:2 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (tar) [149 kB] Get:3 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (diff) [1876 B] Fetched 153 kB in 0s (2091 kB/s) Download complete and in download only mode ============================================================================= Building libbio-searchio-hmmer-perl in unstable on arm64 on codethink02-arm64 now. Date: Fri Nov 22 05:34:39 GMT 2024 Date UTC: Fri Nov 22 05:34:39 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 17:34:39 -12 2024 I: pbuilder-time-stamp: 1732253679 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libbio-searchio-hmmer-perl_1.7.3-2.dsc] I: copying [./libbio-searchio-hmmer-perl_1.7.3.orig.tar.gz] I: copying [./libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 17 15:35:51 2019 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 libbio-searchio-hmmer-perl-1.7.3 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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1952496/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='787e7d0ec4f2426cbe548003674cdb1d' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1952496' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/pbuilderrc_PpgJ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b1 --logfile b1/build.log libbio-searchio-hmmer-perl_1.7.3-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1952496/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), libbio-perl-perl, libio-string-perl, perl, libtest-most-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbio-perl-perl{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libfile-stripnondeterminism-perl{a} libicu72{a} libio-string-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-uplevel-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 22.8 MB of archives. After unpacking 88.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 36 http://deb.debian.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtest-most-perl all 0.38-1 [25.1 kB] Fetched 22.8 MB in 0s (100 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. 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Unpacking libtest-most-perl (0.38-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... 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:arm64 (0.0.8-1+b2) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+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 (2.4.7-8) ... 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 (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbio-searchio-hmmer-perl_1.7.3-2_source.changes 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 --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_clean 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=/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -j12 make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' cp lib/Bio/SearchIO/hmmer_pull.pm blib/lib/Bio/SearchIO/hmmer_pull.pm cp lib/Bio/Search/Hit/hmmer3Hit.pm blib/lib/Bio/Search/Hit/hmmer3Hit.pm cp lib/Bio/Search/Hit/HmmpfamHit.pm blib/lib/Bio/Search/Hit/HmmpfamHit.pm cp lib/Bio/Search/HSP/HmmpfamHSP.pm blib/lib/Bio/Search/HSP/HmmpfamHSP.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/Index/Hmmer.pm blib/lib/Bio/Index/Hmmer.pm cp lib/Bio/Tools/HMMER/Set.pm blib/lib/Bio/Tools/HMMER/Set.pm cp lib/Bio/Search/Hit/HMMERHit.pm blib/lib/Bio/Search/Hit/HMMERHit.pm cp lib/Bio/Search/Result/hmmer3Result.pm blib/lib/Bio/Search/Result/hmmer3Result.pm cp lib/Bio/Search/Result/HmmpfamResult.pm blib/lib/Bio/Search/Result/HmmpfamResult.pm cp lib/Bio/SearchIO/hmmer3.pm blib/lib/Bio/SearchIO/hmmer3.pm cp lib/Bio/Search/Result/HMMERResult.pm blib/lib/Bio/Search/Result/HMMERResult.pm cp lib/Bio/Tools/HMMER/Domain.pm blib/lib/Bio/Tools/HMMER/Domain.pm cp lib/Bio/Search/HSP/HMMERHSP.pm blib/lib/Bio/Search/HSP/HMMERHSP.pm cp lib/Bio/SearchIO/hmmer2.pm blib/lib/Bio/SearchIO/hmmer2.pm cp lib/Bio/Tools/HMMER/Results.pm blib/lib/Bio/Tools/HMMER/Results.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 '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t 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, 9 wallclock secs ( 0.08 usr 0.01 sys + 2.94 cusr 0.31 csys = 3.34 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' 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 -j12 install DESTDIR=/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' Manifying 2 pod documents Manifying 17 pod documents Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Index/Hmmer.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/Hmmpfam.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Results.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Domain.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Set.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HMMERResult.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HmmpfamResult.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/hmmer3Result.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HMMERHSP.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HmmpfamHSP.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HMMERHit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HmmpfamHit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/hmmer3Hit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer2.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer3.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer_pull.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_parse_hmmsearch.pl.1p Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_hmmer_to_table.pl.1p Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::Hmmpfam.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Set.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Results.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Domain.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer_pull.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer3.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer2.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::hmmer3Result.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HmmpfamResult.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HMMERResult.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::hmmer3Hit.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HmmpfamHit.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HMMERHit.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HmmpfamHSP.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HMMERHSP.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Index::Hmmer.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/bin/bp_hmmer_to_table.pl Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/bin/bp_parse_hmmsearch.pl make[1]: Leaving directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' 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 --build=binary -O../libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1952496 and its subdirectories I: Current time: Thu Nov 21 17:35:38 -12 2024 I: pbuilder-time-stamp: 1732253738 Fri Nov 22 05:35:38 UTC 2024 I: Signing ./b1/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo as libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc Fri Nov 22 05:35:38 UTC 2024 I: Signed ./b1/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo as ./b1/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc Fri Nov 22 05:35:38 UTC 2024 - build #1 for libbio-searchio-hmmer-perl/unstable/arm64 on codethink02-arm64 done. Starting cleanup. All cleanup done. Fri Nov 22 05:35:38 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-SVtqeT4i, removing. /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 05:35 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 05:34 b2 -rw-r--r-- 1 jenkins jenkins 2161 Nov 17 2019 libbio-searchio-hmmer-perl_1.7.3-2.dsc -rw------- 1 jenkins jenkins 3406 Nov 22 05:34 rbuildlog.UIi2FlA /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b1: total 188 -rw-r--r-- 1 jenkins jenkins 61787 Nov 22 05:35 build.log -rw-r--r-- 1 jenkins jenkins 1876 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2161 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2.dsc -rw-r--r-- 1 jenkins jenkins 91204 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_all.deb -rw-r--r-- 1 jenkins jenkins 5283 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6165 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1363 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes -rw-r--r-- 1 jenkins jenkins 1525 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b2: total 0 Fri Nov 22 05:35:39 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 17:34:39 -12 2024 I: pbuilder-time-stamp: 1732253679 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libbio-searchio-hmmer-perl_1.7.3-2.dsc] I: copying [./libbio-searchio-hmmer-perl_1.7.3.orig.tar.gz] I: copying [./libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 17 15:35:51 2019 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 libbio-searchio-hmmer-perl-1.7.3 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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1952496/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='787e7d0ec4f2426cbe548003674cdb1d' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1952496' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/pbuilderrc_PpgJ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b1 --logfile b1/build.log libbio-searchio-hmmer-perl_1.7.3-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1952496/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), libbio-perl-perl, libio-string-perl, perl, libtest-most-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbio-perl-perl{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libfile-stripnondeterminism-perl{a} libicu72{a} libio-string-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-uplevel-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 22.8 MB of archives. After unpacking 88.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 36 http://deb.debian.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtest-most-perl all 0.38-1 [25.1 kB] Fetched 22.8 MB in 0s (100 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libalgorithm-diff-perl. Preparing to unpack .../29-libalgorithm-diff-perl_1.201-1_all.deb ... Unpacking libalgorithm-diff-perl (1.201-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../30-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../31-libdata-stag-perl_0.14-3_all.deb ... Unpacking libdata-stag-perl (0.14-3) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../32-libbio-perl-perl_1.7.8-1_all.deb ... Unpacking libbio-perl-perl (1.7.8-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../33-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../34-libclass-data-inheritable-perl_0.10-1_all.deb ... Unpacking libclass-data-inheritable-perl (0.10-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../35-libdevel-stacktrace-perl_2.0500-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0500-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../36-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libsub-uplevel-perl. Preparing to unpack .../37-libsub-uplevel-perl_0.2800-3_all.deb ... Unpacking libsub-uplevel-perl (0.2800-3) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../38-libtest-deep-perl_1.204-1_all.deb ... Unpacking libtest-deep-perl (1.204-1) ... Selecting previously unselected package libtext-diff-perl. Preparing to unpack .../39-libtext-diff-perl_1.45-2_all.deb ... Unpacking libtext-diff-perl (1.45-2) ... Selecting previously unselected package libtest-differences-perl. Preparing to unpack .../40-libtest-differences-perl_0.71-1_all.deb ... Unpacking libtest-differences-perl (0.71-1) ... Selecting previously unselected package libtest-exception-perl. Preparing to unpack .../41-libtest-exception-perl_0.43-3_all.deb ... Unpacking libtest-exception-perl (0.43-3) ... Selecting previously unselected package libtest-warn-perl. Preparing to unpack .../42-libtest-warn-perl_0.37-2_all.deb ... Unpacking libtest-warn-perl (0.37-2) ... Selecting previously unselected package libtest-most-perl. Preparing to unpack .../43-libtest-most-perl_0.38-1_all.deb ... Unpacking libtest-most-perl (0.38-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... 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:arm64 (0.0.8-1+b2) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+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 (2.4.7-8) ... 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 (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbio-searchio-hmmer-perl_1.7.3-2_source.changes 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 --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_clean 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=/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -j12 make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' cp lib/Bio/SearchIO/hmmer_pull.pm blib/lib/Bio/SearchIO/hmmer_pull.pm cp lib/Bio/Search/Hit/hmmer3Hit.pm blib/lib/Bio/Search/Hit/hmmer3Hit.pm cp lib/Bio/Search/Hit/HmmpfamHit.pm blib/lib/Bio/Search/Hit/HmmpfamHit.pm cp lib/Bio/Search/HSP/HmmpfamHSP.pm blib/lib/Bio/Search/HSP/HmmpfamHSP.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/Index/Hmmer.pm blib/lib/Bio/Index/Hmmer.pm cp lib/Bio/Tools/HMMER/Set.pm blib/lib/Bio/Tools/HMMER/Set.pm cp lib/Bio/Search/Hit/HMMERHit.pm blib/lib/Bio/Search/Hit/HMMERHit.pm cp lib/Bio/Search/Result/hmmer3Result.pm blib/lib/Bio/Search/Result/hmmer3Result.pm cp lib/Bio/Search/Result/HmmpfamResult.pm blib/lib/Bio/Search/Result/HmmpfamResult.pm cp lib/Bio/SearchIO/hmmer3.pm blib/lib/Bio/SearchIO/hmmer3.pm cp lib/Bio/Search/Result/HMMERResult.pm blib/lib/Bio/Search/Result/HMMERResult.pm cp lib/Bio/Tools/HMMER/Domain.pm blib/lib/Bio/Tools/HMMER/Domain.pm cp lib/Bio/Search/HSP/HMMERHSP.pm blib/lib/Bio/Search/HSP/HMMERHSP.pm cp lib/Bio/SearchIO/hmmer2.pm blib/lib/Bio/SearchIO/hmmer2.pm cp lib/Bio/Tools/HMMER/Results.pm blib/lib/Bio/Tools/HMMER/Results.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 '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t 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, 9 wallclock secs ( 0.08 usr 0.01 sys + 2.94 cusr 0.31 csys = 3.34 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' 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 -j12 install DESTDIR=/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' Manifying 2 pod documents Manifying 17 pod documents Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Index/Hmmer.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/Hmmpfam.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Results.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Domain.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Set.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HMMERResult.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HmmpfamResult.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/hmmer3Result.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HMMERHSP.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HmmpfamHSP.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HMMERHit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HmmpfamHit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/hmmer3Hit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer2.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer3.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer_pull.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_parse_hmmsearch.pl.1p Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_hmmer_to_table.pl.1p Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::Hmmpfam.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Set.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Results.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Domain.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer_pull.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer3.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer2.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::hmmer3Result.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HmmpfamResult.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HMMERResult.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::hmmer3Hit.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HmmpfamHit.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HMMERHit.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HmmpfamHSP.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HMMERHSP.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Index::Hmmer.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/bin/bp_hmmer_to_table.pl Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/bin/bp_parse_hmmsearch.pl make[1]: Leaving directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' 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 --build=binary -O../libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1952496 and its subdirectories I: Current time: Thu Nov 21 17:35:38 -12 2024 I: pbuilder-time-stamp: 1732253738 Fri Nov 22 05:35:40 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Fri Nov 22 05:35:40 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Fri Nov 22 05:35:40 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Fri Nov 22 05:35:40 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-ovgBDY' ==================================================================================== Thu Dec 25 11:58:41 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "2 libbio-searchio-hmmer-perl unstable /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w 1.7.3-2" as arguments. Thu Dec 25 11:58:41 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-u412c4de" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 25 11:58:42 UTC 2025 I: Downloading source for unstable/libbio-searchio-hmmer-perl=1.7.3-2 Reading package lists... NOTICE: 'libbio-searchio-hmmer-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl.git Please use: git clone https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 153 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (dsc) [2161 B] Get:2 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (tar) [149 kB] Get:3 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (diff) [1876 B] Fetched 153 kB in 0s (8482 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libbio-searchio-hmmer-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl.git Please use: git clone https://salsa.debian.org/med-team/libbio-searchio-hmmer-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 153 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (dsc) [2161 B] Get:2 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (tar) [149 kB] Get:3 http://deb.debian.org/debian unstable/main libbio-searchio-hmmer-perl 1.7.3-2 (diff) [1876 B] Fetched 153 kB in 0s (8482 kB/s) Download complete and in download only mode ============================================================================= Re-Building libbio-searchio-hmmer-perl in unstable on arm64 on codethink01-arm64 now. Date: Thu Dec 25 11:58:42 GMT 2025 Date UTC: Thu Dec 25 11:58:42 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/pbuilderrc_WBlC + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' libbio-searchio-hmmer-perl = debian-installer -o libbio-searchio-hmmer-perl = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' libbio-searchio-hmmer-perl = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/pbuilderrc_WBlC --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b2 --logfile b2/build.log libbio-searchio-hmmer-perl_1.7.3-2.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 26 01:58:42 +14 2025 I: pbuilder-time-stamp: 1766663922 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libbio-searchio-hmmer-perl_1.7.3-2.dsc] I: copying [./libbio-searchio-hmmer-perl_1.7.3.orig.tar.gz] I: copying [./libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 17 15:35:51 2019 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 libbio-searchio-hmmer-perl-1.7.3 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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/936891/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 25 11:58 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/936891/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/936891/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=bdadaca51b9b4b4881861ffafa75ebcc LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=936891 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/pbuilderrc_WBlC --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b2 --logfile b2/build.log libbio-searchio-hmmer-perl_1.7.3-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/936891/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), libbio-perl-perl, libio-string-perl, perl, libtest-most-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbio-perl-perl{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libfile-stripnondeterminism-perl{a} libicu72{a} libio-string-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-uplevel-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 22.8 MB of archives. After unpacking 88.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 36 http://deb.debian.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtest-most-perl all 0.38-1 [25.1 kB] Fetched 22.8 MB in 0s (116 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libalgorithm-diff-perl. Preparing to unpack .../29-libalgorithm-diff-perl_1.201-1_all.deb ... Unpacking libalgorithm-diff-perl (1.201-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../30-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../31-libdata-stag-perl_0.14-3_all.deb ... Unpacking libdata-stag-perl (0.14-3) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../32-libbio-perl-perl_1.7.8-1_all.deb ... Unpacking libbio-perl-perl (1.7.8-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../33-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../34-libclass-data-inheritable-perl_0.10-1_all.deb ... Unpacking libclass-data-inheritable-perl (0.10-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../35-libdevel-stacktrace-perl_2.0500-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0500-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../36-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libsub-uplevel-perl. Preparing to unpack .../37-libsub-uplevel-perl_0.2800-3_all.deb ... Unpacking libsub-uplevel-perl (0.2800-3) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../38-libtest-deep-perl_1.204-1_all.deb ... Unpacking libtest-deep-perl (1.204-1) ... Selecting previously unselected package libtext-diff-perl. Preparing to unpack .../39-libtext-diff-perl_1.45-2_all.deb ... Unpacking libtext-diff-perl (1.45-2) ... Selecting previously unselected package libtest-differences-perl. Preparing to unpack .../40-libtest-differences-perl_0.71-1_all.deb ... Unpacking libtest-differences-perl (0.71-1) ... Selecting previously unselected package libtest-exception-perl. Preparing to unpack .../41-libtest-exception-perl_0.43-3_all.deb ... Unpacking libtest-exception-perl (0.43-3) ... Selecting previously unselected package libtest-warn-perl. Preparing to unpack .../42-libtest-warn-perl_0.37-2_all.deb ... Unpacking libtest-warn-perl (0.37-2) ... Selecting previously unselected package libtest-most-perl. Preparing to unpack .../43-libtest-most-perl_0.38-1_all.deb ... Unpacking libtest-most-perl (0.38-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... 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:arm64 (0.0.8-1+b2) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+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 (2.4.7-8) ... 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 (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/936891/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/936891/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbio-searchio-hmmer-perl_1.7.3-2_source.changes 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 --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_clean 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=/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -j12 make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' cp lib/Bio/Search/Hit/hmmer3Hit.pm blib/lib/Bio/Search/Hit/hmmer3Hit.pm cp lib/Bio/SearchIO/hmmer.pm blib/lib/Bio/SearchIO/hmmer.pm cp lib/Bio/Search/Hit/HmmpfamHit.pm blib/lib/Bio/Search/Hit/HmmpfamHit.pm cp lib/Bio/Search/HSP/HmmpfamHSP.pm blib/lib/Bio/Search/HSP/HmmpfamHSP.pm cp lib/Bio/Search/Hit/HMMERHit.pm blib/lib/Bio/Search/Hit/HMMERHit.pm cp lib/Bio/Tools/HMMER/Set.pm blib/lib/Bio/Tools/HMMER/Set.pm cp lib/Bio/Tools/Hmmpfam.pm blib/lib/Bio/Tools/Hmmpfam.pm cp lib/Bio/Tools/HMMER/Domain.pm blib/lib/Bio/Tools/HMMER/Domain.pm cp lib/Bio/SearchIO/hmmer3.pm blib/lib/Bio/SearchIO/hmmer3.pm cp lib/Bio/Search/Result/HmmpfamResult.pm blib/lib/Bio/Search/Result/HmmpfamResult.pm cp lib/Bio/SearchIO/hmmer2.pm blib/lib/Bio/SearchIO/hmmer2.pm cp lib/Bio/Tools/HMMER/Results.pm blib/lib/Bio/Tools/HMMER/Results.pm cp lib/Bio/Search/HSP/HMMERHSP.pm blib/lib/Bio/Search/HSP/HMMERHSP.pm cp lib/Bio/Search/Result/HMMERResult.pm blib/lib/Bio/Search/Result/HMMERResult.pm cp lib/Bio/Search/Result/hmmer3Result.pm blib/lib/Bio/Search/Result/hmmer3Result.pm cp lib/Bio/Index/Hmmer.pm blib/lib/Bio/Index/Hmmer.pm cp lib/Bio/SearchIO/hmmer_pull.pm blib/lib/Bio/SearchIO/hmmer_pull.pm cp bin/bp_hmmer_to_table.pl 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_hmmer_to_table.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 '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t 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, 4 wallclock secs ( 0.15 usr 0.03 sys + 3.72 cusr 0.42 csys = 4.32 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' 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 -j12 install DESTDIR=/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' Manifying 2 pod documents Manifying 17 pod documents Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Index/Hmmer.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/Hmmpfam.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Results.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Domain.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Set.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/hmmer3Result.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HMMERResult.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HmmpfamResult.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HMMERHSP.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HmmpfamHSP.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HMMERHit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HmmpfamHit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/hmmer3Hit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer_pull.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer2.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer3.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_parse_hmmsearch.pl.1p Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_hmmer_to_table.pl.1p Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::Hmmpfam.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Set.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Results.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Domain.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer_pull.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer3.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer2.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::hmmer3Result.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HmmpfamResult.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HMMERResult.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::hmmer3Hit.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HmmpfamHit.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HMMERHit.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HmmpfamHSP.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HMMERHSP.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Index::Hmmer.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/bin/bp_parse_hmmsearch.pl Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/bin/bp_hmmer_to_table.pl make[1]: Leaving directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' 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 --build=binary -O../libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/936891/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/936891/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/936891 and its subdirectories I: Current time: Fri Dec 26 01:59:16 +14 2025 I: pbuilder-time-stamp: 1766663956 + false + set +x Thu Dec 25 11:59:16 UTC 2025 I: Signing ./b2/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo as libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc Thu Dec 25 11:59:16 UTC 2025 I: Signed ./b2/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo as ./b2/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc Thu Dec 25 11:59:16 UTC 2025 - build #2 for libbio-searchio-hmmer-perl/unstable/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Thu Dec 25 11:59:16 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-u412c4de, removing. /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w: total 80 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 05:35 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 05:36 b2 -rw-r--r-- 1 jenkins jenkins 2161 Nov 17 2019 libbio-searchio-hmmer-perl_1.7.3-2.dsc -rw------- 1 jenkins jenkins 65494 Nov 22 05:35 rbuildlog.UIi2FlA /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b1: total 196 -rw-r--r-- 1 jenkins jenkins 61787 Nov 22 05:35 build.log -rw-r--r-- 1 jenkins jenkins 1876 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2161 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2.dsc -rw-r--r-- 1 jenkins jenkins 91204 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_all.deb -rw-r--r-- 1 jenkins jenkins 5283 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6165 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1363 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes -rw-r--r-- 1 jenkins jenkins 1525 Nov 22 05:35 libbio-searchio-hmmer-perl_1.7.3-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b2: total 188 -rw-r--r-- 1 jenkins jenkins 63722 Nov 22 05:36 build.log -rw-r--r-- 1 jenkins jenkins 1876 Nov 22 05:36 libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2161 Nov 22 05:36 libbio-searchio-hmmer-perl_1.7.3-2.dsc -rw-r--r-- 1 jenkins jenkins 91204 Nov 22 05:36 libbio-searchio-hmmer-perl_1.7.3-2_all.deb -rw-r--r-- 1 jenkins jenkins 5283 Nov 22 05:36 libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6165 Nov 22 05:36 libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1363 Nov 22 05:36 libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes -rw-r--r-- 1 jenkins jenkins 1525 Nov 22 05:36 libbio-searchio-hmmer-perl_1.7.3-2_source.changes Fri Nov 22 05:36:17 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Fri Nov 22 05:36:18 UTC 2024 I: libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes: Format: 1.8 Date: Tue, 29 Oct 2019 13:23:15 +0100 Source: libbio-searchio-hmmer-perl Binary: libbio-searchio-hmmer-perl Architecture: all Version: 1.7.3-2 Distribution: unstable 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: 04ab11707f2891296dd33073942556646a38b48f 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb 3d2a436f840b7a025788bfab1455ea8a6908d4a8 5283 libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo Checksums-Sha256: 9d819fc84267bb66cb062941f182db3dd90d9cc3a447056d7e7b8fbc13b54ae0 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb fdbc6b1356ded4188473d8a03ff87b06baa4555208b45663b2b5f270e148d08d 5283 libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo Files: 9bc7c69b6ba2db1798764a2605a5c9d6 91204 perl optional libbio-searchio-hmmer-perl_1.7.3-2_all.deb b824f37833be9ca740369e6ac3987ff0 5283 perl optional libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-22 05:35:39.764560696 +0000 +++ b2/build.log 2024-11-22 05:36:17.694848343 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Nov 21 17:34:39 -12 2024 -I: pbuilder-time-stamp: 1732253679 +I: Current time: Fri Dec 26 01:58:42 +14 2025 +I: pbuilder-time-stamp: 1766663922 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: unpacking libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1952496/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/936891/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 25 11:58 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/936891/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/936891/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='787e7d0ec4f2426cbe548003674cdb1d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1952496' - PS1='# ' - PS2='> ' + INVOCATION_ID=bdadaca51b9b4b4881861ffafa75ebcc + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=936891 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/pbuilderrc_PpgJ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b1 --logfile b1/build.log libbio-searchio-hmmer-perl_1.7.3-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/pbuilderrc_WBlC --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b2 --logfile b2/build.log libbio-searchio-hmmer-perl_1.7.3-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1952496/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/936891/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -156,7 +188,7 @@ Get: 42 http://deb.debian.org/debian unstable/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtest-most-perl all 0.38-1 [25.1 kB] -Fetched 22.8 MB in 0s (100 MB/s) +Fetched 22.8 MB in 0s (116 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) @@ -352,7 +384,11 @@ fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbio-searchio-hmmer-perl_1.7.3-2_source.changes +I: user script /srv/workspace/pbuilder/936891/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/936891/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbio-searchio-hmmer-perl_1.7.3-2_source.changes dpkg-buildpackage: info: source package libbio-searchio-hmmer-perl dpkg-buildpackage: info: source version 1.7.3-2 dpkg-buildpackage: info: source distribution unstable @@ -376,26 +412,26 @@ dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' -cp lib/Bio/SearchIO/hmmer_pull.pm blib/lib/Bio/SearchIO/hmmer_pull.pm cp lib/Bio/Search/Hit/hmmer3Hit.pm blib/lib/Bio/Search/Hit/hmmer3Hit.pm +cp lib/Bio/SearchIO/hmmer.pm blib/lib/Bio/SearchIO/hmmer.pm cp lib/Bio/Search/Hit/HmmpfamHit.pm blib/lib/Bio/Search/Hit/HmmpfamHit.pm cp lib/Bio/Search/HSP/HmmpfamHSP.pm blib/lib/Bio/Search/HSP/HmmpfamHSP.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/Index/Hmmer.pm blib/lib/Bio/Index/Hmmer.pm -cp lib/Bio/Tools/HMMER/Set.pm blib/lib/Bio/Tools/HMMER/Set.pm cp lib/Bio/Search/Hit/HMMERHit.pm blib/lib/Bio/Search/Hit/HMMERHit.pm -cp lib/Bio/Search/Result/hmmer3Result.pm blib/lib/Bio/Search/Result/hmmer3Result.pm -cp lib/Bio/Search/Result/HmmpfamResult.pm blib/lib/Bio/Search/Result/HmmpfamResult.pm -cp lib/Bio/SearchIO/hmmer3.pm blib/lib/Bio/SearchIO/hmmer3.pm -cp lib/Bio/Search/Result/HMMERResult.pm blib/lib/Bio/Search/Result/HMMERResult.pm +cp lib/Bio/Tools/HMMER/Set.pm blib/lib/Bio/Tools/HMMER/Set.pm +cp lib/Bio/Tools/Hmmpfam.pm blib/lib/Bio/Tools/Hmmpfam.pm cp lib/Bio/Tools/HMMER/Domain.pm blib/lib/Bio/Tools/HMMER/Domain.pm -cp lib/Bio/Search/HSP/HMMERHSP.pm blib/lib/Bio/Search/HSP/HMMERHSP.pm +cp lib/Bio/SearchIO/hmmer3.pm blib/lib/Bio/SearchIO/hmmer3.pm +cp lib/Bio/Search/Result/HmmpfamResult.pm blib/lib/Bio/Search/Result/HmmpfamResult.pm cp lib/Bio/SearchIO/hmmer2.pm blib/lib/Bio/SearchIO/hmmer2.pm cp lib/Bio/Tools/HMMER/Results.pm blib/lib/Bio/Tools/HMMER/Results.pm +cp lib/Bio/Search/HSP/HMMERHSP.pm blib/lib/Bio/Search/HSP/HMMERHSP.pm +cp lib/Bio/Search/Result/HMMERResult.pm blib/lib/Bio/Search/Result/HMMERResult.pm +cp lib/Bio/Search/Result/hmmer3Result.pm blib/lib/Bio/Search/Result/hmmer3Result.pm +cp lib/Bio/Index/Hmmer.pm blib/lib/Bio/Index/Hmmer.pm +cp lib/Bio/SearchIO/hmmer_pull.pm blib/lib/Bio/SearchIO/hmmer_pull.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_hmmer_to_table.pl "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_parse_hmmsearch.pl Manifying 2 pod documents Manifying 17 pod documents @@ -1588,7 +1624,7 @@ ok 29 ok All tests successful. -Files=7, Tests=1166, 9 wallclock secs ( 0.08 usr 0.01 sys + 2.94 cusr 0.31 csys = 3.34 CPU) +Files=7, Tests=1166, 4 wallclock secs ( 0.15 usr 0.03 sys + 3.72 cusr 0.42 csys = 4.32 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' create-stamp debian/debhelper-build-stamp @@ -1606,18 +1642,18 @@ Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Results.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Domain.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Set.pm +Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/hmmer3Result.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HMMERResult.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HmmpfamResult.pm -Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/hmmer3Result.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HMMERHSP.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HmmpfamHSP.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HMMERHit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HmmpfamHit.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/hmmer3Hit.pm +Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer_pull.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer2.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer3.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer.pm -Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer_pull.pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_parse_hmmsearch.pl.1p Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_hmmer_to_table.pl.1p Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::Hmmpfam.3pm @@ -1637,8 +1673,8 @@ Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HmmpfamHSP.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HMMERHSP.3pm Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Index::Hmmer.3pm -Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/bin/bp_hmmer_to_table.pl Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/bin/bp_parse_hmmsearch.pl +Installing /build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3/debian/libbio-searchio-hmmer-perl/usr/bin/bp_hmmer_to_table.pl make[1]: Leaving directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3' dh_installdocs dh_installchangelogs @@ -1662,12 +1698,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/936891/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/936891/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1952496 and its subdirectories -I: Current time: Thu Nov 21 17:35:38 -12 2024 -I: pbuilder-time-stamp: 1732253738 +I: removing directory /srv/workspace/pbuilder/936891 and its subdirectories +I: Current time: Fri Dec 26 01:59:16 +14 2025 +I: pbuilder-time-stamp: 1766663956 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2.diff: 76.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2.diff.gz b2/build.log: 80.5% -- replaced with stdout Compressing the 1st log... b1/build.log: 81.0% -- replaced with stdout Fri Nov 22 05:36:19 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_libbio-searchio-hmmer-perl_unstable_arm64_1732253779 + touch /var/log/reproducible-builds/diffoscope_stamp_libbio-searchio-hmmer-perl_unstable_arm64_1732253779 + RESULT=0 + systemd-run '--description=diffoscope on libbio-searchio-hmmer-perl/1.7.3-2 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_4-45732 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w --run-session -c jenkins-reproducible-unstable-diffoscope-056fbae2-6c8b-4c7c-90d4-d85af63edc23 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/dbd-tmp-rcizELf ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/libbio-searchio-hmmer-perl_1.7.3-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/libbio-searchio-hmmer-perl_1.7.3-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/libbio-searchio-hmmer-perl_1.7.3-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b1/libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b2/libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_4-45732.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/libbio-searchio-hmmer-perl_1.7.3-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/libbio-searchio-hmmer-perl_1.7.3-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/libbio-searchio-hmmer-perl_1.7.3-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b1/libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.4fRF4k8w/b2/libbio-searchio-hmmer-perl_1.7.3-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.420s) 0.419s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.017s) 0.017s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 819ms CPU time consumed: 809ms _ _ _ _ _ _ _ | (_) |__ | |__ (_) ___ ___ ___ __ _ _ __ ___| |__ (_) ___ | | | '_ \| '_ \| |/ _ \ _____/ __|/ _ \/ _` | '__/ __| '_ \| |/ _ \ _____ | | | |_) | |_) | | (_) |_____\__ \ __/ (_| | | | (__| | | | | (_) |_____| |_|_|_.__/|_.__/|_|\___/ |___/\___|\__,_|_| \___|_| |_|_|\___/ _ _ | |__ _ __ ___ _ __ ___ ___ _ __ _ __ ___ _ __| | | '_ \| '_ ` _ \| '_ ` _ \ / _ \ '__|____| '_ \ / _ \ '__| | | | | | | | | | | | | | | | __/ | |_____| |_) | __/ | | | |_| |_|_| |_| |_|_| |_| |_|\___|_| | .__/ \___|_| |_| |_| Fri Nov 22 05:36:20 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Fri Nov 22 05:36:20 UTC 2024 I: libbio-searchio-hmmer-perl from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-22 05:36:21] INFO: Starting at 2024-11-22 05:36:21.629036 [2024-11-22 05:36:21] INFO: Generating the pages of 1 package(s) [2024-11-22 05:36:21] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/libbio-searchio-hmmer-perl didn't produce a buildlog, even though it has been built. [2024-11-22 05:36:22] INFO: Finished at 2024-11-22 05:36:22.055493, took: 0:00:00.426466 Fri Nov 22 05:36:22 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/libbio-searchio-hmmer-perl.html Fri Nov 22 05:36:22 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 22 05:36:22 UTC 2024 I: Submitting 8.0K b1/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc https://buildinfo.debian.net/3d2a436f840b7a025788bfab1455ea8a6908d4a8/libbio-searchio-hmmer-perl_1.7.3-2_all Fri Nov 22 05:36:22 UTC 2024 I: Submitting 8.0K b2/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc https://buildinfo.debian.net/bd0ff4ecfe7ef98eb18412dd1ddaaf5aad13d5c7/libbio-searchio-hmmer-perl_1.7.3-2_all Fri Nov 22 05:36:24 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 22 05:36:24 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 22 05:36:24 UTC 2024 I: Removing signed libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc files: removed './b1/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc' removed './b2/libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo.asc' 1732253784 arm64 unstable libbio-searchio-hmmer-perl Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2.rbuild.log: 78.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libbio-searchio-hmmer-perl_1.7.3-2.rbuild.log.gz [2024-11-22 05:36:24] INFO: Starting at 2024-11-22 05:36:24.499395 [2024-11-22 05:36:24] INFO: Generating the pages of 1 package(s) [2024-11-22 05:36:24] INFO: Finished at 2024-11-22 05:36:24.879599, took: 0:00:00.380211 All cleanup done. Fri Nov 22 05:36:24 UTC 2024 - total duration: 0h 1m 52s. Fri Nov 22 05:36:24 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-I3htUtGC, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1min 56.239s CPU time consumed: 7.555s