Your message dated Thu, 25 Jul 2019 01:34:48 +0000 with message-id <[email protected]> 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 [email protected] immediately.) -- 932912: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=932912 Debian Bug Tracking System Contact [email protected] 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Andreas Tille <[email protected]> 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 Checksums-Sha1: dbd36bca9e94354c599f9c37231123ad32ad780f 2147 hhsuite_3.2.0-2.dsc d199328bf21c1b6f21807f3626b6f75176d36a6f 9944 hhsuite_3.2.0-2.debian.tar.xz Checksums-Sha256: 4293626d8573c71a18a880192e268a8ab2ee2ea9caf03a802ded74a77154ffdb 2147 hhsuite_3.2.0-2.dsc 9358f73551310b4b718e04321e5b4b6c05998d979f69ef55d7f6270929fdc922 9944 hhsuite_3.2.0-2.debian.tar.xz Files: 50677ad6b91138f74c433dda53f41281 2147 science optional hhsuite_3.2.0-2.dsc 9284b2efd110545f7f9929ae7c23e637 9944 science optional hhsuite_3.2.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl05A2MRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFfrw//bG4tXCZlZAIb65GWIJVNvhzS2S+Tfb8A suPDLTWnVSgNm48iGyXFLiwz7aDBJRNeipgHYSVC9xvMB0bLr6Z7ONpH6yPjhm/M Sy5H0K1XwanjoN6zjkN9TmSQ/stvahOD2At9bOL9cIl/brhocX+VWAuj5c74TuOz kQHNYlTvdgcRURkuBLdjSeJoxRvBF7Jyye2Wq+oSyicGH4kw/cYxee9JkQeB0jY2 UGDRm071UT3AMsvqFrUwSM7eTy+QkbTMTPzQxRh06eCLclkpcPZEiRDULVsScVZ0 A+vqPJ3Ruq9N1oSEkIHmq9lBFz9vCUi6lH3I5wF7xzzFb+CiSxKox5TgFwsWItY1 31XddfIAU4ZgMnnsC9DsjXqmNwOe/IerqzbhXCqLcNzL7E9UHUeBkR8vK6wUckJn f7c03U9Tw8UEz/MPocyvnV6TBmliM4uLnSb5BwKVz/QKlBS4UTsmiV6L5KiheK4x 6ETMGS+dSVtoRHnOgqQEj/xGgSXmMzTSaUoqQyPCcD3cp7EDIumrVZOk4+A/f6Ei VwGlHol6jkZXvxZ9M2Pku6K2F65nfZJQ+DaiHYAGEBORm9v/uGkH4DN0oLZQKkmb vWKoh/SqK6tfUOIwPHeLJV9mSHPXcP1d3ukiy+GnfRJa/vibdN1AI75H/dBRqtRu nROeJVLZkow= =/pBv -----END PGP SIGNATURE-----
--- End Message ---
