[Debian-med-packaging] Bug#932912: hhsuite: FTBFS when built with dpkg-buildpackage -A

Santiago Vila sanvila at debian.org
Wed Jul 24 17:28:36 BST 2019 

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.

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