I: pbuilder: network access will be disabled during build
I: Current time: Mon Mar 10 09:07:37 -12 2025
I: pbuilder-time-stamp: 1741640857
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
dpkg-source: warning: cannot verify inline signature for ./libbio-searchio-hmmer-perl_1.7.3-2.dsc: unsupported subcommand
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/1804031/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='4d7344ff82254dbca734a7e619a6807e'
  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='1804031'
  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.UP6imny8/pbuilderrc_lERk --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.UP6imny8/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 codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Mar  4 11:20 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1804031/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 <pbuilder-maint@lists.alioth.debian.org>
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 ... 19897 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} libunistring5{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, 45 newly installed, 0 to remove and 0 not upgraded.
Need to get 23.5 MB of archives. After unpacking 90.6 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 0.23.1-1 [241 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 1.23.0-7 [1129 kB]
Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 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 1.4.19-7 [285 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 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 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 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 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 libunistring5 arm64 1.3-1 [449 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB]
Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB]
Get: 31 http://deb.debian.org/debian unstable/main arm64 libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get: 32 http://deb.debian.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB]
Get: 33 http://deb.debian.org/debian unstable/main arm64 libdata-stag-perl all 0.14-3 [448 kB]
Get: 34 http://deb.debian.org/debian unstable/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 35 http://deb.debian.org/debian unstable/main arm64 libcapture-tiny-perl all 0.50-1 [24.6 kB]
Get: 36 http://deb.debian.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.10-1 [8632 B]
Get: 37 http://deb.debian.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get: 38 http://deb.debian.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB]
Get: 39 http://deb.debian.org/debian unstable/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get: 40 http://deb.debian.org/debian unstable/main arm64 libtest-deep-perl all 1.204-1 [52.9 kB]
Get: 41 http://deb.debian.org/debian unstable/main arm64 libtext-diff-perl all 1.45-2 [27.2 kB]
Get: 42 http://deb.debian.org/debian unstable/main arm64 libtest-differences-perl all 0.71-1 [17.9 kB]
Get: 43 http://deb.debian.org/debian unstable/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB]
Get: 44 http://deb.debian.org/debian unstable/main arm64 libtest-warn-perl all 0.37-2 [14.5 kB]
Get: 45 http://deb.debian.org/debian unstable/main arm64 libtest-most-perl all 0.38-1 [25.1 kB]
Fetched 23.5 MB in 0s (157 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
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(Reading database ... 19897 files and directories currently installed.)
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Setting up libtest-deep-perl (1.204-1) ...
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Setting up libmagic1t64:arm64 (1:5.45-3+b1) ...
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Setting up libio-string-perl (1.08-4) ...
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Setting up libclass-data-inheritable-perl (0.10-1) ...
Setting up libtext-diff-perl (1.45-2) ...
Setting up libunistring5:arm64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up libcapture-tiny-perl (0.50-1) ...
Setting up dwz (0.15-1+b1) ...
Setting up libdata-stag-perl (0.14-3) ...
Setting up sensible-utils (0.0.24) ...
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+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-4) ...
Setting up libtest-warn-perl (0.37-2) ...
Setting up libtest-differences-perl (0.71-1) ...
Setting up libexception-class-perl (1.45-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libtest-exception-perl (0.43-3) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
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 (13.24.1) ...
Processing triggers for libc-bin (2.41-4) ...
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 (1.37-1).
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 <michael.crusoe@gmail.com>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   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/Tools/HMMER/Domain.pm blib/lib/Bio/Tools/HMMER/Domain.pm
cp lib/Bio/Search/Result/HmmpfamResult.pm blib/lib/Bio/Search/Result/HmmpfamResult.pm
cp lib/Bio/Search/HSP/HMMERHSP.pm blib/lib/Bio/Search/HSP/HMMERHSP.pm
cp lib/Bio/Search/Hit/hmmer3Hit.pm blib/lib/Bio/Search/Hit/hmmer3Hit.pm
cp lib/Bio/SearchIO/hmmer3.pm blib/lib/Bio/SearchIO/hmmer3.pm
cp lib/Bio/Search/Hit/HmmpfamHit.pm blib/lib/Bio/Search/Hit/HmmpfamHit.pm
cp lib/Bio/Search/Result/HMMERResult.pm blib/lib/Bio/Search/Result/HMMERResult.pm
cp lib/Bio/Tools/Hmmpfam.pm blib/lib/Bio/Tools/Hmmpfam.pm
cp lib/Bio/Search/Hit/HMMERHit.pm blib/lib/Bio/Search/Hit/HMMERHit.pm
cp lib/Bio/SearchIO/hmmer2.pm blib/lib/Bio/SearchIO/hmmer2.pm
cp lib/Bio/Search/Result/hmmer3Result.pm blib/lib/Bio/Search/Result/hmmer3Result.pm
cp lib/Bio/SearchIO/hmmer.pm blib/lib/Bio/SearchIO/hmmer.pm
cp lib/Bio/Search/HSP/HmmpfamHSP.pm blib/lib/Bio/Search/HSP/HmmpfamHSP.pm
cp lib/Bio/Tools/HMMER/Set.pm blib/lib/Bio/Tools/HMMER/Set.pm
cp lib/Bio/Tools/HMMER/Results.pm blib/lib/Bio/Tools/HMMER/Results.pm
cp lib/Bio/Index/Hmmer.pm blib/lib/Bio/Index/Hmmer.pm
cp lib/Bio/SearchIO/hmmer_pull.pm blib/lib/Bio/SearchIO/hmmer_pull.pm
cp bin/bp_parse_hmmsearch.pl blib/script/bp_parse_hmmsearch.pl
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_parse_hmmsearch.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_hmmer_to_table.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;
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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
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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
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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
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ok 73 - Check hit total conserved residues
ok 74 - Check hit total identical residues
ok 75
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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
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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
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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
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ok 202 - Check hit total conserved residues
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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
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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
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ok 266 - Check hit total conserved residues
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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
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ok 302 - Check for hiy string
ok 303 - Check for homology string
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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
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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
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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
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ok 474
ok 475 - Check for consensus structure string
ok 476 - Check for query string
ok 477 - Check for hit string
ok 478 - Check for homology string
ok 479 - Check for posterior probability string
ok 480 - Check for the correct result reference type
ok 481 - Check algorithm
ok 482 - Check algorithm version
ok 483 - Check hmm_name
ok 484 - Check sequence_file
ok 485 - Check query_name
ok 486 - Check query_length
ok 487 - Check query_accession
ok 488 - Check query_description
ok 489 - Check num_hits
ok 490 - Check for the correct hit reference type
ok 491 - Check hit name
ok 492 - Check for hit description
ok 493 - Check hit raw_score
ok 494 - Check hit bits (0)
ok 495 - Check hit significance
ok 496 - Check num_hsps
ok 497 - Check hit length absence
ok 498
ok 499
ok 500 - Check for correct hsp reference type
ok 501 - Check for hit seq_id
ok 502 - Check for query seq_id
ok 503 - Check for hit alifrom value
ok 504 - Check for hit ali to value
ok 505 - Check for query hmmfrom value
ok 506 - Check for query hmm to value
ok 507 - Check for hsp score
ok 508 - Check for hsp bits (0)
ok 509 - Check for hsp c-Evalue
ok 510 - Check for hsp query length
ok 511 - Check for hsp hit length
ok 512 - Check for hsp total length
ok 513 - Check for hsp query gaps
ok 514 - Check for hsp hit gaps
ok 515 - Check for hsp total gaps
ok 516 - Check hit length consistency
ok 517 - Check query length consistency
ok 518
ok 519
ok 520
ok 521
ok 522
ok 523
ok 524
ok 525
ok 526
ok 527
ok 528 - Check for consensus structure string
ok 529 - Check for query string
ok 530 - Check for hit string
ok 531 - Check for homology string
ok 532 - Check for posterior probability string
ok 533 - Check for the correct result reference type
ok 534 - Check algorithm
ok 535 - Check algorithm version
ok 536 - Check hmm_name
ok 537 - Check sequence_file
ok 538 - Check query_name
ok 539 - Check query_length
ok 540 - Check query_description
ok 541 - Check num_hits
ok 542 - Check for the correct hit reference type
ok 543 - Check hit name
ok 544 - Check for hit description
ok 545 - Check hit raw_score
ok 546 - Check hit significance
ok 547 - Check num_hsps
ok 548 - Check for correct hsp reference type
ok 549 - Check for hit envfrom value
ok 550 - Check for hit env to value
ok 551 - Check for query hmmfrom value
ok 552 - Check for query hmm to value
ok 553 - Check for hsp score
ok 554 - Check for hsp c-Evalue
ok 555 - Check for correct hsp reference type
ok 556 - Check for hit envfrom value
ok 557 - Check for hit env to value
ok 558 - Check for query hmmfrom value
ok 559 - Check for query hmm to value
ok 560 - Check for hsp score
ok 561 - Check for hsp c-Evalue
ok 562 - Check for correct hsp reference type
ok 563 - Check for hit envfrom value
ok 564 - Check for hit env to value
ok 565 - Check for query hmmfrom value
ok 566 - Check for query hmm to value
ok 567 - Check for hsp score
ok 568 - Check for hsp c-Evalue
ok 569 - Check for correct hsp reference type
ok 570 - Check for hit envfrom value
ok 571 - Check for hit env to value
ok 572 - Check for query hmmfrom value
ok 573 - Check for query hmm to value
ok 574 - Check for hsp score
ok 575 - Check for hsp c-Evalue
ok 576 - Check for correct hsp reference type
ok 577 - Check for hit envfrom value
ok 578 - Check for hit env to value
ok 579 - Check for query hmmfrom value
ok 580 - Check for query hmm to value
ok 581 - Check for hsp score
ok 582 - Check for hsp c-Evalue
ok 583 - Check for correct hsp reference type
ok 584 - Check for hit envfrom value
ok 585 - Check for hit env to value
ok 586 - Check for query hmmfrom value
ok 587 - Check for query hmm to value
ok 588 - Check for hsp score
ok 589 - Check for hsp c-Evalue
ok 590 - Check hit length
ok 591
ok 592
ok 593 - Check for the correct hit reference type
ok 594 - Check hit name
ok 595 - Check for hit description
ok 596 - Check hit raw_score
ok 597 - Check hit significance
ok 598 - Check num_hsps
ok 599 - Check for correct hsp reference type
ok 600 - Check for hit envfrom value
ok 601 - Check for hit env to value
ok 602 - Check for query hmmfrom value
ok 603 - Check for query hmm to value
ok 604 - Check for hsp score
ok 605 - Check for hsp c-Evalue
ok 606 - Check for correct hsp reference type
ok 607 - Check for hit envfrom value
ok 608 - Check for hit env to value
ok 609 - Check for query hmmfrom value
ok 610 - Check for query hmm to value
ok 611 - Check for hsp score
ok 612 - Check for hsp c-Evalue
ok 613 - Check for correct hsp reference type
ok 614 - Check for hit envfrom value
ok 615 - Check for hit env to value
ok 616 - Check for query hmmfrom value
ok 617 - Check for query hmm to value
ok 618 - Check for hsp score
ok 619 - Check for hsp c-Evalue
ok 620 - Check for the correct result reference type
ok 621 - Check algorithm
ok 622 - Check algorithm version
ok 623 - Check hmm_name
ok 624 - Check sequence_file
ok 625 - Check query_name
ok 626 - Check query_length
ok 627 - Check query_description
ok 628 - Check num_hits
ok 629 - Check for the correct hit reference type
ok 630 - Check hit name
ok 631 - Check for hit description
ok 632 - Check hit raw_score
ok 633 - Check hit significance
ok 634 - Check num_hsps
ok 635 - Check for correct hsp reference type
ok 636 - Check hit sequence
ok 637 - Check query sequence
ok 638 - Check for correct hsp reference type
ok 639 - Check hit sequence
ok 640 - Check query sequence
ok 641 - Check hit length
ok 642
ok 643
ok 644 - Check for the correct hit reference type
ok 645 - Check hit name
ok 646 - Check for hit description
ok 647 - Check hit raw_score
ok 648 - Check hit significance
ok 649 - Check num_hsps
ok 650 - Check for correct hsp reference type
ok 651 - Check hit sequence
ok 652 - Check query sequence
ok 653 - Check for correct hsp reference type
ok 654 - Check hit sequence
ok 655 - Check query sequence
ok 656 - Check for the correct hit reference type
ok 657 - Check hit name
ok 658 - Check for hit description
ok 659 - Check hit raw_score
ok 660 - Check hit significance
ok 661 - Check num_hsps
ok 662 - Check for correct hsp reference type
ok 663 - Check hit sequence
ok 664 - Check query sequence
ok 665 - Check for correct hsp reference type
ok 666 - Check hit sequence
ok 667 - Check query sequence
ok 668 - Check for the correct result reference type
ok 669 - Check algorithm
ok 670 - Check algorithm version
ok 671 - Check query_name
ok 672 - Check query_length
ok 673 - Check query_description
ok 674 - Check num_hits
ok 675 - Check for the correct hit reference type
ok 676 - Check hit name
ok 677 - Check for hit description
ok 678 - Check hit raw_score
ok 679 - Check hit significance
ok 680 - Check num_hsps
ok 681 - Check for correct hsp reference type
ok 682 - Check for query string
ok 683 - Check for hit string
ok 684 - Check for homology string
ok 685 - Check for posterior probability string
ok 686 - Check if loading hmmpfam output via the hmm2 parser directly works
ok 687 - Check for the correct result reference type
ok 688 - Check if loading hmmsearch2 output via the hmm2 parser directly works
ok 689 - Check for the correct result reference type
ok 690 - Check if loading hmmscan output via the hmm3 parser directly works
ok 691 - Check for the correct result reference type
ok 692 - Check if loading hmmsearch3 output via the hmm3 parser directly works
ok 693 - Check for the correct result reference type
ok 694 - Check if selecting the correct hmmpfam parser using -version works
ok 695 - Check for the correct result reference type
ok 696 - Check if selecting the correct hmmsearch2 parser using -version works
ok 697 - Check for the correct result reference type
ok 698 - Check if selecting the correct hmmscan parser using -version works
ok 699 - Check for the correct result reference type
ok 700 - Check if selecting the correct hmmsearch3 parser using -version works
ok 701 - Check for the correct result reference type
ok 702 - Check if reading from a pipe works
ok 703 - Check for the correct result reference type
ok 704 - Check num_hits
ok 705 - Check query_length
ok 706 - Check hit length
ok 707 - bug3376
ok 708 - bug3421 - Check if can correctly parse an HSP with line full of dashes
ok 709 - bug3302 - Check if can parse multiresult hmmer
ok 710 - Check algorithm
ok 711 - Check nhmmer algorithm version
ok 712 - Check hmm_name
ok 713 - Check sequence_file
ok 714 - Check query_name
ok 715 - Check query_length
ok 716 - Check query_accession
ok 717 - Check query_description
ok 718 - Check num_hits
ok 719 - Check for the correct hit reference type
ok 720 - Check nhmmer hit name
ok 721 - Check nhmmer hit description
ok 722 - Check nhmmer hit score
ok 723 - Check nhmmer hit bits (0)
ok 724 - Check nhmmer hit significance
ok 725 - Check num_hsps
ok 726 - Check nhmmer hit length
ok 727
ok 728
ok 729 - Check for correct hsp reference type
ok 730 - Check for nhmmer hit seq_id
ok 731 - Check for nhmmer query seq_id
ok 732 - Check nhmmer hsp hit start
ok 733 - Check nhmmer hsp hit end
ok 734 - Check nhmmer hsp query start
ok 735 - Check nhmmer hsp query end
ok 736 - Check nhmmer hsp hit strand
ok 737 - Check nhmmer hsp query strand
ok 738 - Check nhmmer hsp score
ok 739 - Check nhmmer hsp bits (0)
ok 740 - Check nhmmer hsp evalue
ok 741 - Check for hsp query length
ok 742 - Check for hsp hit length
ok 743 - Check for hsp total length
ok 744 - Check for hsp query gaps
ok 745 - Check for hsp hit gaps
ok 746 - Check for hsp total gaps
ok 747 - Check hit length consistency
ok 748 - Check query length consistency
ok 749
ok 750
ok 751
ok 752
ok 753
ok 754
ok 755
ok 756
ok 757
ok 758 - Check for consensus structure string
ok 759 - Check for nhmmer query string
ok 760 - Check for nhmmer homology string
ok 761 - Check for nhmmer hit string
ok 762 - Check for nhmmer posterior probability string
ok 763 - Check if nhmmer homology string and hit string have an equal length
ok 764 - Check if nhmmer query string and homology string have an equal length
ok 765 - Check nhmmer hit name
ok 766 - Check nhmmer hit description
ok 767 - Check nhmmer hit score
ok 768 - Check nhmmer hit bits (0)
ok 769 - Check nhmmer hit significance
ok 770 - Check nhmmer hit length
ok 771 - Check for nhmmer hit seq_id
ok 772 - Check for nhmmer query seq_id
ok 773 - Check nhmmer hsp query start
ok 774 - Check nhmmer hsp query end
ok 775 - Check nhmmer hsp hit start
ok 776 - Check nhmmer hsp hit end
ok 777 - Check nhmmer hsp hit strand
ok 778 - Check nhmmer hsp query strand
ok 779 - Check nhmmer hsp score
ok 780 - Check nhmmer hsp bits (0)
ok 781 - Check nhmmer hsp evalue
ok 782 - Check for hsp query length
ok 783 - Check for hsp hit length
ok 784 - Check for hsp total length
ok 785 - Check for hsp query gaps
ok 786 - Check for hsp hit gaps
ok 787 - Check for hsp total gaps
ok 788 - Check hit length consistency
ok 789 - Check query length consistency
ok 790
ok 791 - Check for consensus structure string
ok 792 - Check for nhmmer query string
ok 793 - Check for nhmmer homology string
ok 794 - Check for nhmmer hit string
ok 795 - Check for nhmmer posterior probability string
ok 796 - Check if nhmmer homology string and hit string have an equal length
ok 797 - Check if nhmmer query string and homology string have an equal length
ok 798 - Check Significance filtered num_hits
ok 799 - Check Significance filtered hit ID
ok 800 - Check Significance filtered hit ID
ok 801 - Check Significance filtered hit ID
ok 802 - Check Significance filtered hit ID
ok 803 - Check Significance filtered hit ID
ok 804
ok 805 - Check Score filtered num_hits
ok 806 - Check Score filtered hit ID
ok 807 - Check Score filtered hit ID
ok 808 - Check Score filtered hit ID
ok 809 - Check Score filtered hit ID
ok 810
ok 811 - Check Bits filtered num_hits
ok 812 - Check Bits filtered num_hits
ok 813 - Check Bits filtered num_hits
ok 814 - Check Hit_filter filtered num_hits
ok 815 - Check Hit_filter filtered hits ID
ok 816
ok 817 - Correct parsing of alignments with stops
ok 818 - Check algorithm
ok 819 - Check query_name
ok 820 - Check query_length absence
ok 821 - Check query_description
ok 822 - Check num_hits
ok 823 - query name okay
ok 824 - Check num_hsps
ok
t/Tools.t ................ 
1..29
ok 1 - use Bio::Tools::HMMER::Domain;
ok 2 - use Bio::Tools::HMMER::Set;
ok 3 - use Bio::Tools::HMMER::Results;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok
All tests successful.
Files=7, Tests=1166,  3 wallclock secs ( 0.10 usr  0.03 sys +  3.16 cusr  0.43 csys =  3.72 CPU)
Result: PASS
make[1]: Leaving directory '/build/reproducible-path/libbio-searchio-hmmer-perl-1.7.3'
   create-stamp debian/debhelper-build-stamp
   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/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/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/HSP/HMMERHSP.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/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/Set.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/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/hmmer.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/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/1804031 and its subdirectories
I: Current time: Mon Mar 10 09:08:08 -12 2025
I: pbuilder-time-stamp: 1741640888