Your message dated Thu, 25 Jul 2019 01:34:48 +0000
with message-id <e1hqsee-0007xt...@fasolo.debian.org>
and subject line Bug#932912: fixed in hhsuite 3.2.0-2
has caused the Debian Bug report #932912,
regarding hhsuite: FTBFS when built with dpkg-buildpackage -A
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
932912: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=932912
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:hhsuite
Version: 3.2.0-1
Severity: serious
Tags: ftbfs
Dear maintainer:
I tried to build this package in sid but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-indep
dh build-indep --builddirectory=mybuild
dh_update_autotools_config -i -O--builddirectory=mybuild
dh_autoreconf -i -O--builddirectory=mybuild
dh_auto_configure -i -O--builddirectory=mybuild
cd mybuild && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None
-DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var
-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run
"-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON
-DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ..
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
[... snipped ...]
make -f src/CMakeFiles/a3m_database_extract.dir/build.make
src/CMakeFiles/a3m_database_extract.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild
/<<PKGBUILDDIR>>/mybuild/src
/<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake
--color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/a3m_database_extract.dir/build.make
src/CMakeFiles/a3m_database_extract.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'src/CMakeFiles/a3m_database_extract.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 80%] Built target a3m_database_extract
make -f src/CMakeFiles/a3m_reduce.dir/build.make
src/CMakeFiles/a3m_reduce.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild
/<<PKGBUILDDIR>>/mybuild/src
/<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/a3m_reduce.dir/build.make
src/CMakeFiles/a3m_reduce.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'src/CMakeFiles/a3m_reduce.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 82%] Built target a3m_reduce
make -f src/CMakeFiles/a3m_database_filter.dir/build.make
src/CMakeFiles/a3m_database_filter.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild
/<<PKGBUILDDIR>>/mybuild/src
/<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake
--color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/a3m_database_filter.dir/build.make
src/CMakeFiles/a3m_database_filter.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'src/CMakeFiles/a3m_database_filter.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 85%] Built target a3m_database_filter
make -f src/CMakeFiles/hhblits_omp.dir/build.make
src/CMakeFiles/hhblits_omp.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild
/<<PKGBUILDDIR>>/mybuild/src
/<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhblits_omp.dir/DependInfo.cmake
--color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/hhblits_omp.dir/build.make
src/CMakeFiles/hhblits_omp.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'src/CMakeFiles/hhblits_omp.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 87%] Built target hhblits_omp
make -f src/CMakeFiles/a3m_database_reduce.dir/build.make
src/CMakeFiles/a3m_database_reduce.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild
/<<PKGBUILDDIR>>/mybuild/src
/<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake
--color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/a3m_database_reduce.dir/build.make
src/CMakeFiles/a3m_database_reduce.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'src/CMakeFiles/a3m_database_reduce.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 90%] Built target a3m_database_reduce
make -f src/CMakeFiles/cstranslate.dir/build.make
src/CMakeFiles/cstranslate.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild
/<<PKGBUILDDIR>>/mybuild/src
/<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/cstranslate.dir/DependInfo.cmake
--color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/cstranslate.dir/build.make
src/CMakeFiles/cstranslate.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'src/CMakeFiles/cstranslate.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 92%] Built target cstranslate
make -f src/CMakeFiles/hhconsensus.dir/build.make
src/CMakeFiles/hhconsensus.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild
/<<PKGBUILDDIR>>/mybuild/src
/<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhconsensus.dir/DependInfo.cmake
--color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/hhconsensus.dir/build.make
src/CMakeFiles/hhconsensus.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'src/CMakeFiles/hhconsensus.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 95%] Built target hhconsensus
make -f src/CMakeFiles/hhblits_ca3m.dir/build.make
src/CMakeFiles/hhblits_ca3m.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild
/<<PKGBUILDDIR>>/mybuild/src
/<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake
--color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/hhblits_ca3m.dir/build.make
src/CMakeFiles/hhblits_ca3m.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'src/CMakeFiles/hhblits_ca3m.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 97%] Built target hhblits_ca3m
make -f src/CMakeFiles/hhalign_omp.dir/build.make
src/CMakeFiles/hhalign_omp.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild
/<<PKGBUILDDIR>>/mybuild/src
/<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake
--color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/hhalign_omp.dir/build.make
src/CMakeFiles/hhalign_omp.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'src/CMakeFiles/hhalign_omp.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[100%] Built target hhalign_omp
make[2]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/mybuild/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/context_data.crf
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/context_data.lib
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/cs219.lib
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/do_not_delete
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/do_not_delete.phr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/do_not_delete.pin
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/do_not_delete.psq
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhblits
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhfilter
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhsearch
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhalign
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhconsensus
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_extract
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_reduce
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_database_reduce
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_database_extract
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_database_filter
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/cstranslate
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhblits_omp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhsearch_omp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhalign_omp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhblits_ca3m
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/a3m.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/addss.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/Align.pm
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/check_a3m.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/cif2fasta.py
-- Installing:
/<<PKGBUILDDIR>>/debian/tmp/usr/scripts/create_profile_from_hhm.pl
-- Installing:
/<<PKGBUILDDIR>>/debian/tmp/usr/scripts/create_profile_from_hmmer.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/ffindex.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/get_a3m_size.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/hh_reader.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/hhmakemodel.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/hhmakemodel.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/HHPaths.pm
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/hhsuitedb.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/mergeali.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/multithread.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/pdb2fasta.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/pdbfilter.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/pdbfilter.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/reformat.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/renumberpdb.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/splitfasta.pl
make[1]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm
chmod: cannot access 'debian/hhsuite/usr/share/hhsuite/scripts/*.pm': No such
file or directory
make[1]: *** [debian/rules:42: override_dh_install] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:45: binary-indep] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-indep subprocess
returned exit status 2
--------------------------------------------------------------------------------
The build was made in my autobuilder with "dpkg-buildpackage -A"
and it also fails here:
https://buildd.debian.org/status/package.php?p=hhsuite
where you can get a full build log if you need it.
Thanks.
--- End Message ---
--- Begin Message ---
Source: hhsuite
Source-Version: 3.2.0-2
We believe that the bug you reported is fixed in the latest version of
hhsuite, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 932...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated hhsuite package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 25 Jul 2019 03:06:04 +0200
Source: hhsuite
Binary: hhsuite hhsuite-data
Architecture: source
Version: 3.2.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
hhsuite - sensitive protein sequence searching based on HMM-HMM alignment
hhsuite-data - sensitive protein sequence searching based on HMM-HMM alignment
(
Closes: 932912
Changes:
hhsuite (3.2.0-2) unstable; urgency=medium
.
[ Santiago Vila ]
* Fix FTBFS when built with dpkg-buildpackage -A
Closes: #932912
.
[ Andreas Tille ]
* debhelper-compat 12
* Standards-Version: 4.4.0
* Fix autopkgtest
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Files:
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--- End Message ---
