sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-10.freexian.com
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| libbio-searchio-hmmer-perl 1.7.3-2 (arm64) Sat, 16 Nov 2024 21:54:26 +0000 |
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Package: libbio-searchio-hmmer-perl
Version: 1.7.3-2
Source Version: 1.7.3-2
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: binary
I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/957781/system.tar.xz to /tmp/tmp.sbuild.fbMmy4qI7x...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
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| Chroot Setup Commands |
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Copying /tmp/debusine-fetch-exec-upload-_tq8hfaq/dpkg-dbgsym_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_tq8hfaq/dpkg_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_tq8hfaq/dselect-dbgsym_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_tq8hfaq/dselect_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_tq8hfaq/libdpkg-dev_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_tq8hfaq/dpkg-dev_1.22.12~1.gbp82cafd_all.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_tq8hfaq/libdpkg-perl_1.22.12~1.gbp82cafd_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/libbio-searchio-hmmer-perl-6qE5cT/resolver-Qm8gCB' with '<<RESOLVERDIR>>'
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Get:1 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ InRelease
Ign:1 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ InRelease
Get:2 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ Release [606 B]
Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
Get:2 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ Release [606 B]
Get:4 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ Release.gpg
Ign:4 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ Release.gpg
Get:5 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ Packages [9246 B]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9952 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 Components [4909 kB]
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The following packages will be upgraded:
apt bsdextrautils bsdutils debianutils dpkg dpkg-dev libapt-pkg6.0t64
libaudit-common libaudit1 libblkid1 libbrotli1 libcap-ng0 libdpkg-perl
libglib2.0-0t64 libmarkdown2 libmount1 libpcre2-8-0 libseccomp2 libselinux1
libsemanage2 libsmartcols1 libsystemd0 libudev1 libuuid1 libxml2 login
login.defs mount passwd util-linux
30 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 9274 kB/12.8 MB of archives.
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Get:1 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ dpkg 1.22.12~1.gbp82cafd [1513 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 bsdutils arm64 1:2.40.2-11 [104 kB]
Get:3 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ dpkg-dev 1.22.12~1.gbp82cafd [1337 kB]
Get:4 file:/build/libbio-searchio-hmmer-perl-6qE5cT/resolver-xs2T6u/apt_archive ./ libdpkg-perl 1.22.12~1.gbp82cafd [647 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 debianutils arm64 5.21 [92.1 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 libsystemd0 arm64 257~rc2-3 [416 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 libudev1 arm64 257~rc2-3 [139 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.11 [921 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 libblkid1 arm64 2.40.2-11 [162 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libmount1 arm64 2.40.2-11 [190 kB]
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Get:15 http://deb.debian.org/debian sid/main arm64 util-linux arm64 2.40.2-11 [1170 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libpcre2-8-0 arm64 10.44-4 [243 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libselinux1 arm64 3.7-3+b1 [72.1 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libseccomp2 arm64 2.5.5-1+b3 [46.8 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.11 [1287 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libaudit-common all 1:4.0.2-2 [12.7 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libcap-ng0 arm64 0.8.5-3+b1 [17.0 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libaudit1 arm64 1:4.0.2-2 [54.2 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 login arm64 1:4.16.0-2+really2.40.2-11 [80.0 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 login.defs all 1:4.16.0-5 [185 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libsemanage2 arm64 3.7-2+b1 [84.5 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 passwd arm64 1:4.16.0-5 [1210 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 libmarkdown2 arm64 2.2.7-2.1 [33.1 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
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Setting up libmarkdown2:arm64 (2.2.7-2.1) ...
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Setting up passwd (1:4.16.0-5) ...
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+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Local sources
-------------
/tmp/debusine-fetch-exec-upload-_tq8hfaq/libbio-searchio-hmmer-perl_1.7.3-2.dsc exists in /tmp/debusine-fetch-exec-upload-_tq8hfaq; copying to chroot
I: NOTICE: Log filtering will replace 'build/libbio-searchio-hmmer-perl-6qE5cT/libbio-searchio-hmmer-perl-1.7.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libbio-searchio-hmmer-perl-6qE5cT' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), build-essential, fakeroot, libbio-perl-perl, libio-string-perl, perl, libtest-most-perl
Filtered Build-Depends: debhelper-compat (= 12), build-essential, fakeroot, libbio-perl-perl, libio-string-perl, perl, libtest-most-perl
dpkg-deb: warning: root directory has unusual owner or group 998:999.
Hint: either pass --root-owner-group, see dpkg-build-api(7) or add an explicit 'Rules-Requires-Root: no' in debian/control.
dpkg-deb: warning: ignoring 1 warning about the control file(s)
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
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Reading package lists...
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Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev build-essential cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper dh-autoreconf
dh-strip-nondeterminism dwz fakeroot g++ g++-14 g++-14-aarch64-linux-gnu
g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu
gcc-aarch64-linux-gnu libalgorithm-diff-perl libasan8 libbio-perl-perl
libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdata-stag-perl
libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl
libgcc-14-dev libhwasan0 libisl23 libitm1 liblsan0 libmpc3 libmpfr6
libstdc++-14-dev libsub-uplevel-perl libtest-deep-perl
libtest-differences-perl libtest-exception-perl libtest-most-perl
libtest-warn-perl libtext-diff-perl libtool libtsan2 libubsan1
linux-libc-dev m4 po-debconf rpcsvc-proto
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales
cpp-14-doc dh-make gcc-14-doc gcc-multilib manpages-dev flex bison gdb
gcc-doc gdb-aarch64-linux-gnu bioperl libxml-sax-expatxs-perl libc-devtools
glibc-doc libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc libmail-box-perl
Recommended packages:
libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libace-perl
libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl
libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl
libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl
libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl
libset-scalar-perl libsoap-lite-perl libsort-naturally-perl
libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl
libsvg-graph-perl libxml-dom-xpath-perl libxml-parser-perl
libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl
libxml-writer-perl manpages manpages-dev perl-tk libgd-gd2-perl
| libgd-gd2-noxpm-perl libxml-libxslt-perl libxml-perl libarchive-cpio-perl
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev build-essential cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper dh-autoreconf
dh-strip-nondeterminism dwz fakeroot g++ g++-14 g++-14-aarch64-linux-gnu
g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu
gcc-aarch64-linux-gnu libalgorithm-diff-perl libasan8 libbio-perl-perl
libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdata-stag-perl
libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl
libgcc-14-dev libhwasan0 libisl23 libitm1 liblsan0 libmpc3 libmpfr6
libstdc++-14-dev libsub-uplevel-perl libtest-deep-perl
libtest-differences-perl libtest-exception-perl libtest-most-perl
libtest-warn-perl libtext-diff-perl libtool libtsan2 libubsan1
linux-libc-dev m4 po-debconf rpcsvc-proto sbuild-build-depends-main-dummy
0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded.
Need to get 64.2 MB of archives.
After this operation, 248 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B]
Get:2 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
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Get:5 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.7-1 [2454 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
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Get:20 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-8 [24.2 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-8 [2579 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-8 [1161 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-8 [2386 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-8 [1039 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-8 [1442 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-8 [2365 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8 [17.7 MB]
Get:28 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-8 [519 kB]
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Get:31 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-8 [2267 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8 [10.1 MB]
Get:33 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-8 [20.2 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:35 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:36 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:37 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-8 [517 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:42 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 libdata-stag-perl all 0.14-3 [448 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 libtest-deep-perl all 1.204-1 [52.9 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 libtext-diff-perl all 1.45-2 [27.2 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 libtest-differences-perl all 0.71-1 [17.9 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 libtest-warn-perl all 0.37-2 [14.5 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 libtest-most-perl all 0.38-1 [25.1 kB]
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) arm64 (aarch64)
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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: libbio-searchio-hmmer-perl
Binary: libbio-searchio-hmmer-perl
Architecture: all
Version: 1.7.3-2
Maintainer: Michael R. Crusoe <michael.crusoe@gmail.com>
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
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gpgv: Signature made Sun Nov 17 15:35:51 2019 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libbio-searchio-hmmer-perl_1.7.3-2.dsc: no acceptable signature found
dpkg-source: info: extracting libbio-searchio-hmmer-perl in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking libbio-searchio-hmmer-perl_1.7.3.orig.tar.gz
dpkg-source: info: unpacking libbio-searchio-hmmer-perl_1.7.3-2.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=debusine-worker
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -b -rfakeroot
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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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/HmmpfamHit.pm blib/lib/Bio/Search/Hit/HmmpfamHit.pm
cp lib/Bio/SearchIO/hmmer3.pm blib/lib/Bio/SearchIO/hmmer3.pm
cp lib/Bio/Search/HSP/HMMERHSP.pm blib/lib/Bio/Search/HSP/HMMERHSP.pm
cp lib/Bio/Search/Result/hmmer3Result.pm blib/lib/Bio/Search/Result/hmmer3Result.pm
cp lib/Bio/Search/HSP/HmmpfamHSP.pm blib/lib/Bio/Search/HSP/HmmpfamHSP.pm
cp lib/Bio/Tools/HMMER/Results.pm blib/lib/Bio/Tools/HMMER/Results.pm
cp lib/Bio/SearchIO/hmmer.pm blib/lib/Bio/SearchIO/hmmer.pm
cp lib/Bio/SearchIO/hmmer2.pm blib/lib/Bio/SearchIO/hmmer2.pm
cp lib/Bio/Search/Hit/hmmer3Hit.pm blib/lib/Bio/Search/Hit/hmmer3Hit.pm
cp lib/Bio/Index/Hmmer.pm blib/lib/Bio/Index/Hmmer.pm
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/SearchIO/hmmer_pull.pm blib/lib/Bio/SearchIO/hmmer_pull.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 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 '/<<PKGBUILDDIR>>'
dh_auto_test
make -j4 test TEST_VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 25
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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 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
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ok 73 - Check hit total conserved residues
ok 74 - Check hit total identical residues
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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
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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
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
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ok 202 - Check hit total conserved residues
ok 203 - Check hit total identical 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
ok 228
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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
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ok 266 - Check hit total conserved residues
ok 267 - Check hit total identical residues
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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
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ok 301
ok 302 - Check for hiy string
ok 303 - Check for homology string
ok 304 - Check for query string
ok 305
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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
ok 312
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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 471
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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 0.02 sys + 3.55 cusr 0.43 csys = 4.15 CPU)
Result: PASS
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/libbio-searchio-hmmer-perl/
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Manifying 2 pod documents
Manifying 17 pod documents
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Index/Hmmer.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/Hmmpfam.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Results.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Domain.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Tools/HMMER/Set.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HmmpfamResult.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/hmmer3Result.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Result/HMMERResult.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HmmpfamHSP.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/HSP/HMMERHSP.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HMMERHit.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/HmmpfamHit.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/Search/Hit/hmmer3Hit.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer_pull.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer2.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/perl5/Bio/SearchIO/hmmer3.pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_parse_hmmsearch.pl.1p
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man1/bp_hmmer_to_table.pl.1p
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer2.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::hmmer3Hit.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Domain.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HmmpfamResult.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer_pull.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HmmpfamHSP.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HmmpfamHit.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::Hmmpfam.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::hmmer3Result.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Index::Hmmer.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Hit::HMMERHit.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::Result::HMMERResult.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Search::HSP::HMMERHSP.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Set.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::Tools::HMMER::Results.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/share/man/man3/Bio::SearchIO::hmmer3.3pm
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/bin/bp_hmmer_to_table.pl
Installing /<<PKGBUILDDIR>>/debian/libbio-searchio-hmmer-perl/usr/bin/bp_parse_hmmsearch.pl
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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)
--------------------------------------------------------------------------------
Build finished at 2024-11-16T21:55:31Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
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: sid
Urgency: medium
Maintainer: Michael R. Crusoe <michael.crusoe@gmail.com>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
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:
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fa1117c990a15b8f6b9f1bc9f39c18ea9c99c382 5213 libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo
Checksums-Sha256:
9d819fc84267bb66cb062941f182db3dd90d9cc3a447056d7e7b8fbc13b54ae0 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb
69f8f7ed5fc6a11a862e35ddb94b7b4175794964e88aa53d17f7026352f1a405 5213 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
cf3715350a1140c19ebee938466cbefe 5213 perl optional libbio-searchio-hmmer-perl_1.7.3-2_arm64.buildinfo
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: libbio-searchio-hmmer-perl
Binary: libbio-searchio-hmmer-perl
Architecture: all
Version: 1.7.3-2
Checksums-Md5:
9bc7c69b6ba2db1798764a2605a5c9d6 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb
Checksums-Sha1:
04ab11707f2891296dd33073942556646a38b48f 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb
Checksums-Sha256:
9d819fc84267bb66cb062941f182db3dd90d9cc3a447056d7e7b8fbc13b54ae0 91204 libbio-searchio-hmmer-perl_1.7.3-2_all.deb
Build-Origin: Debian
Build-Architecture: arm64
Build-Date: Sat, 16 Nov 2024 21:55:31 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
autoconf (= 2.72-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.22.5-2),
autotools-dev (= 20220109.1),
base-files (= 13.5),
base-passwd (= 3.6.5),
bash (= 5.2.32-1+b2),
binutils (= 2.43.1-5),
binutils-aarch64-linux-gnu (= 2.43.1-5),
binutils-common (= 2.43.1-5),
bsdextrautils (= 2.40.2-11),
bsdutils (= 1:2.40.2-11),
build-essential (= 12.12),
bzip2 (= 1.0.8-6),
coreutils (= 9.5-1+b1),
cpp (= 4:14.2.0-1),
cpp-14 (= 14.2.0-8),
cpp-14-aarch64-linux-gnu (= 14.2.0-8),
cpp-aarch64-linux-gnu (= 4:14.2.0-1),
dash (= 0.5.12-9+b1),
debconf (= 1.5.87),
debhelper (= 13.20),
debianutils (= 5.21),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.14.0-1),
diffutils (= 1:3.10-1+b1),
dpkg (= 1.22.12~1.gbp82cafd),
dpkg-dev (= 1.22.12~1.gbp82cafd),
dwz (= 0.15-1+b1),
file (= 1:5.45-3+b1),
findutils (= 4.10.0-3),
g++ (= 4:14.2.0-1),
g++-14 (= 14.2.0-8),
g++-14-aarch64-linux-gnu (= 14.2.0-8),
g++-aarch64-linux-gnu (= 4:14.2.0-1),
gcc (= 4:14.2.0-1),
gcc-14 (= 14.2.0-8),
gcc-14-aarch64-linux-gnu (= 14.2.0-8),
gcc-14-base (= 14.2.0-8),
gcc-aarch64-linux-gnu (= 4:14.2.0-1),
gettext (= 0.22.5-2),
gettext-base (= 0.22.5-2),
grep (= 3.11-4+b1),
groff-base (= 1.23.0-5),
gzip (= 1.12-1.1+b1),
hostname (= 3.25),
init-system-helpers (= 1.67),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.2-2+b1),
libalgorithm-diff-perl (= 1.201-1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 14.2.0-8),
libatomic1 (= 14.2.0-8),
libattr1 (= 1:2.5.2-2),
libaudit-common (= 1:4.0.2-2),
libaudit1 (= 1:4.0.2-2),
libbinutils (= 2.43.1-5),
libbio-perl-perl (= 1.7.8-1),
libblkid1 (= 2.40.2-11),
libbz2-1.0 (= 1.0.8-6),
libc-bin (= 2.40-3),
libc-dev-bin (= 2.40-3),
libc6 (= 2.40-3),
libc6-dev (= 2.40-3),
libcap-ng0 (= 0.8.5-3+b1),
libcap2 (= 1:2.66-5+b1),
libcapture-tiny-perl (= 0.48-2),
libcc1-0 (= 14.2.0-8),
libclass-data-inheritable-perl (= 0.10-1),
libcrypt-dev (= 1:4.4.36-5),
libcrypt1 (= 1:4.4.36-5),
libctf-nobfd0 (= 2.43.1-5),
libctf0 (= 2.43.1-5),
libdata-stag-perl (= 0.14-3),
libdb5.3t64 (= 5.3.28+dfsg2-9),
libdebconfclient0 (= 0.273),
libdebhelper-perl (= 13.20),
libdevel-stacktrace-perl (= 2.0500-1),
libdpkg-perl (= 1.22.12~1.gbp82cafd),
libelf1t64 (= 0.192-4),
libexception-class-perl (= 1.45-1),
libfile-stripnondeterminism-perl (= 1.14.0-1),
libgcc-14-dev (= 14.2.0-8),
libgcc-s1 (= 14.2.0-8),
libgdbm-compat4t64 (= 1.24-2),
libgdbm6t64 (= 1.24-2),
libgmp10 (= 2:6.3.0+dfsg-2+b2),
libgomp1 (= 14.2.0-8),
libgprofng0 (= 2.43.1-5),
libhwasan0 (= 14.2.0-8),
libicu72 (= 72.1-5+b1),
libio-string-perl (= 1.08-4),
libisl23 (= 0.27-1),
libitm1 (= 14.2.0-8),
libjansson4 (= 2.14-2+b3),
liblsan0 (= 14.2.0-8),
liblzma5 (= 5.6.3-1+b1),
libmagic-mgc (= 1:5.45-3+b1),
libmagic1t64 (= 1:5.45-3+b1),
libmd0 (= 1.1.0-2+b1),
libmount1 (= 2.40.2-11),
libmpc3 (= 1.3.1-1+b3),
libmpfr6 (= 4.2.1-1+b2),
libpam-modules (= 1.5.3-7+b1),
libpam-modules-bin (= 1.5.3-7+b1),
libpam-runtime (= 1.5.3-7),
libpam0g (= 1.5.3-7+b1),
libpcre2-8-0 (= 10.44-4),
libperl5.40 (= 5.40.0-7),
libpipeline1 (= 1.5.8-1),
libseccomp2 (= 2.5.5-1+b3),
libselinux1 (= 3.7-3+b1),
libsframe1 (= 2.43.1-5),
libsmartcols1 (= 2.40.2-11),
libssl3t64 (= 3.3.2-2),
libstdc++-14-dev (= 14.2.0-8),
libstdc++6 (= 14.2.0-8),
libsub-uplevel-perl (= 0.2800-3),
libsystemd0 (= 257~rc2-3),
libtest-deep-perl (= 1.204-1),
libtest-differences-perl (= 0.71-1),
libtest-exception-perl (= 0.43-3),
libtest-most-perl (= 0.38-1),
libtest-warn-perl (= 0.37-2),
libtext-diff-perl (= 1.45-2),
libtinfo6 (= 6.5-2+b1),
libtool (= 2.4.7-8),
libtsan2 (= 14.2.0-8),
libubsan1 (= 14.2.0-8),
libuchardet0 (= 0.0.8-1+b2),
libudev1 (= 257~rc2-3),
libunistring5 (= 1.2-1+b1),
libuuid1 (= 2.40.2-11),
libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1),
libzstd1 (= 1.5.6+dfsg-1+b1),
linux-libc-dev (= 6.11.7-1),
m4 (= 1.4.19-4),
make (= 4.3-4.1+b1),
man-db (= 2.13.0-1),
mawk (= 1.3.4.20240905-1),
ncurses-base (= 6.5-2),
ncurses-bin (= 6.5-2+b1),
openssl-provider-legacy (= 3.3.2-2),
patch (= 2.7.6-7+b1),
perl (= 5.40.0-7),
perl-base (= 5.40.0-7),
perl-modules-5.40 (= 5.40.0-7),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.3-1+b1),
sed (= 4.9-2+b1),
sensible-utils (= 0.0.24),
sysvinit-utils (= 3.11-1),
tar (= 1.35+dfsg-3+b1),
util-linux (= 2.40.2-11),
xz-utils (= 5.6.3-1+b1),
zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_US.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1572351795"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libbio-searchio-hmmer-perl_1.7.3-2_all.deb
------------------------------------------
new Debian package, version 2.0.
size 91204 bytes: control archive=1776 bytes.
588 bytes, 16 lines control
3415 bytes, 42 lines md5sums
Package: libbio-searchio-hmmer-perl
Version: 1.7.3-2
Architecture: all
Maintainer: Michael R. Crusoe <michael.crusoe@gmail.com>
Installed-Size: 329
Depends: perl:any, libbio-perl-perl, libio-string-perl
Breaks: libbio-perl-perl (<< 1.7.3)
Replaces: libbio-perl-perl (<< 1.7.3)
Section: perl
Priority: optional
Homepage: https://metacpan.org/release/Bio-SearchIO-hmmer
Description: perl parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
This object implements a parser for hmmpfam hsp output, a program in the
HMMER package.
.
It is part of the libbio-perl collection.
drwxr-xr-x root/root 0 2019-10-29 12:23 ./
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/bin/
-rwxr-xr-x root/root 2684 2019-10-29 12:23 ./usr/bin/bp_hmmer_to_table.pl
-rwxr-xr-x root/root 6524 2019-10-29 12:23 ./usr/bin/bp_parse_hmmsearch.pl
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/doc/libbio-searchio-hmmer-perl/
-rw-r--r-- root/root 321 2019-10-29 12:23 ./usr/share/doc/libbio-searchio-hmmer-perl/changelog.Debian.gz
-rw-r--r-- root/root 165 2018-09-25 00:25 ./usr/share/doc/libbio-searchio-hmmer-perl/changelog.gz
-rw-r--r-- root/root 1658 2019-10-29 12:23 ./usr/share/doc/libbio-searchio-hmmer-perl/copyright
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/lintian/
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 135 2019-10-29 12:22 ./usr/share/lintian/overrides/libbio-searchio-hmmer-perl
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/man/
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/man/man1/
-rw-r--r-- root/root 1332 2019-10-29 12:23 ./usr/share/man/man1/bp_hmmer_to_table.pl.1p.gz
-rw-r--r-- root/root 1482 2019-10-29 12:23 ./usr/share/man/man1/bp_parse_hmmsearch.pl.1p.gz
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/man/man3/
-rw-r--r-- root/root 4674 2019-10-29 12:23 ./usr/share/man/man3/Bio::Index::Hmmer.3pm.gz
-rw-r--r-- root/root 4274 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::HSP::HMMERHSP.3pm.gz
-rw-r--r-- root/root 2456 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::HSP::HmmpfamHSP.3pm.gz
-rw-r--r-- root/root 3315 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Hit::HMMERHit.3pm.gz
-rw-r--r-- root/root 3108 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Hit::HmmpfamHit.3pm.gz
-rw-r--r-- root/root 2164 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Hit::hmmer3Hit.3pm.gz
-rw-r--r-- root/root 3722 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Result::HMMERResult.3pm.gz
-rw-r--r-- root/root 2916 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Result::HmmpfamResult.3pm.gz
-rw-r--r-- root/root 2026 2019-10-29 12:23 ./usr/share/man/man3/Bio::Search::Result::hmmer3Result.3pm.gz
-rw-r--r-- root/root 1831 2019-10-29 12:23 ./usr/share/man/man3/Bio::SearchIO::hmmer.3pm.gz
-rw-r--r-- root/root 2385 2019-10-29 12:23 ./usr/share/man/man3/Bio::SearchIO::hmmer2.3pm.gz
-rw-r--r-- root/root 2510 2019-10-29 12:23 ./usr/share/man/man3/Bio::SearchIO::hmmer3.3pm.gz
-rw-r--r-- root/root 2483 2019-10-29 12:23 ./usr/share/man/man3/Bio::SearchIO::hmmer_pull.3pm.gz
-rw-r--r-- root/root 1941 2019-10-29 12:23 ./usr/share/man/man3/Bio::Tools::HMMER::Domain.3pm.gz
-rw-r--r-- root/root 3321 2019-10-29 12:23 ./usr/share/man/man3/Bio::Tools::HMMER::Results.3pm.gz
-rw-r--r-- root/root 2081 2019-10-29 12:23 ./usr/share/man/man3/Bio::Tools::HMMER::Set.3pm.gz
-rw-r--r-- root/root 1916 2019-10-29 12:23 ./usr/share/man/man3/Bio::Tools::Hmmpfam.3pm.gz
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Index/
-rw-r--r-- root/root 12642 2018-09-25 00:25 ./usr/share/perl5/Bio/Index/Hmmer.pm
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Search/
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Search/HSP/
-rw-r--r-- root/root 12049 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/HSP/HMMERHSP.pm
-rw-r--r-- root/root 11724 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/HSP/HmmpfamHSP.pm
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Search/Hit/
-rw-r--r-- root/root 7674 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Hit/HMMERHit.pm
-rw-r--r-- root/root 10063 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Hit/HmmpfamHit.pm
-rw-r--r-- root/root 3708 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Hit/hmmer3Hit.pm
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Search/Result/
-rw-r--r-- root/root 11021 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Result/HMMERResult.pm
-rw-r--r-- root/root 11725 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Result/HmmpfamResult.pm
-rw-r--r-- root/root 4127 2018-09-25 00:25 ./usr/share/perl5/Bio/Search/Result/hmmer3Result.pm
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/SearchIO/
-rw-r--r-- root/root 4160 2018-09-25 00:25 ./usr/share/perl5/Bio/SearchIO/hmmer.pm
-rw-r--r-- root/root 41124 2018-09-25 00:25 ./usr/share/perl5/Bio/SearchIO/hmmer2.pm
-rw-r--r-- root/root 49495 2018-09-25 00:25 ./usr/share/perl5/Bio/SearchIO/hmmer3.pm
-rw-r--r-- root/root 9306 2018-09-25 00:25 ./usr/share/perl5/Bio/SearchIO/hmmer_pull.pm
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Tools/
drwxr-xr-x root/root 0 2019-10-29 12:23 ./usr/share/perl5/Bio/Tools/HMMER/
-rw-r--r-- root/root 6475 2018-09-25 00:25 ./usr/share/perl5/Bio/Tools/HMMER/Domain.pm
-rw-r--r-- root/root 21554 2018-09-25 00:25 ./usr/share/perl5/Bio/Tools/HMMER/Results.pm
-rw-r--r-- root/root 5330 2018-09-25 00:25 ./usr/share/perl5/Bio/Tools/HMMER/Set.pm
-rw-r--r-- root/root 5710 2018-09-25 00:25 ./usr/share/perl5/Bio/Tools/Hmmpfam.pm
lintian
-------
Setup apt archive
-----------------
Merged Build-Depends: lintian
Filtered Build-Depends: lintian
dpkg-deb: warning: root directory has unusual owner or group 998:999.
Hint: either pass --root-owner-group, see dpkg-build-api(7) or add an explicit 'Rules-Requires-Root: no' in debian/control.
dpkg-deb: warning: ignoring 1 warning about the control file(s)
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
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Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
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Fetched 3219 B in 0s (278 kB/s)
Reading package lists...
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Reading package lists...
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Install lintian build dependencies (apt-based resolver)
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Installing build dependencies
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Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-lintian-dummy
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Unpacking sbuild-build-depends-lintian-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-lintian-dummy (0.invalid.0) ...
Running lintian...
W: libbio-searchio-hmmer-perl: bad-whatis-entry [usr/share/man/man3/Bio::SearchIO::hmmer3.3pm.gz]
W: libbio-searchio-hmmer-perl changes: distribution-and-changes-mismatch sid unstable
W: libbio-searchio-hmmer-perl: mismatched-override script-with-language-extension usr/bin/*.* [usr/share/lintian/overrides/libbio-searchio-hmmer-perl:2]
W: libbio-searchio-hmmer-perl: script-with-language-extension [usr/bin/bp_hmmer_to_table.pl]
W: libbio-searchio-hmmer-perl: script-with-language-extension [usr/bin/bp_parse_hmmsearch.pl]
W: libbio-searchio-hmmer-perl source: upstream-metadata-field-unknown Homepage [debian/upstream/metadata]
N: 0 hints overridden; 1 unused override
I: Lintian run was successful.
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: arm64
Build Type: binary
Build-Space: 2064
Build-Time: 10
Distribution: sid
Host Architecture: arm64
Install-Time: 19
Job: /tmp/debusine-fetch-exec-upload-_tq8hfaq/libbio-searchio-hmmer-perl_1.7.3-2.dsc
Lintian: warn
Machine Architecture: arm64
Package: libbio-searchio-hmmer-perl
Package-Time: 65
Source-Version: 1.7.3-2
Space: 2064
Status: successful
Version: 1.7.3-2
--------------------------------------------------------------------------------
Finished at 2024-11-16T21:55:31Z
Build needed 00:01:05, 2064k disk space