Package: src:sibelia Version: 3.0.7+dfsg-5 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202601/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:sibelia, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src debian/rules override_dh_auto_configure make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_configure -- -DCMAKE_POLICY_VERSION_MINIMUM=3.5 cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ../src CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument <min> value. Or, use the <min>...<max> syntax to tell CMake that the project requires at least <min> but has been updated to work with policies introduced by <max> or earlier. -- The CXX compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (0.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build -O--sourcedirectory=src cd obj-x86_64-linux-gnu && make -j2 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<<PKGBUILDDIR>>/src -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake "--color=" Sibelia make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 10%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o [ 10%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o /usr/bin/c++ -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/sibelia.cpp.o -MF CMakeFiles/Sibelia.dir/sibelia.cpp.o.d -o CMakeFiles/Sibelia.dir/sibelia.cpp.o -c /<<PKGBUILDDIR>>/src/sibelia.cpp /usr/bin/c++ -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/postprocessor.cpp.o -MF CMakeFiles/Sibelia.dir/postprocessor.cpp.o.d -o CMakeFiles/Sibelia.dir/postprocessor.cpp.o -c /<<PKGBUILDDIR>>/src/postprocessor.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /<<PKGBUILDDIR>>/src/common.h:31, from /<<PKGBUILDDIR>>/src/fasta.h:10, from /<<PKGBUILDDIR>>/src/postprocessor.h:13, from /<<PKGBUILDDIR>>/src/postprocessor.cpp:9: /usr/include/boost/bind.hpp:36:1: note: â#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.â 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /<<PKGBUILDDIR>>/src/common.h:31, from /<<PKGBUILDDIR>>/src/fasta.h:10, from /<<PKGBUILDDIR>>/src/postprocessor.h:13, from /<<PKGBUILDDIR>>/src/sibelia.cpp:8: /usr/include/boost/bind.hpp:36:1: note: â#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.â 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/common.h:104:51: warning: âtemplate<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iteratorâ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType> | ^~~~~~~~ In file included from /usr/include/c++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/algorithm:62, from /usr/include/seqan/align.h:53, from /<<PKGBUILDDIR>>/src/postprocessor.h:10: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12, from /<<PKGBUILDDIR>>/src/blockinstance.h:11, from /<<PKGBUILDDIR>>/src/postprocessor.h:14: /<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: âtemplate<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iteratorâ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator<std::bidirectional_iterator_tag, T> | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: âtemplate<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iteratorâ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t> | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp: In member function âvoid SyntenyFinder::Postprocessor::LocalAlignment(const std::string&, const std::string&, std::pair<long unsigned int, long unsigned int>&, std::pair<long unsigned int, long unsigned int>&)â: /<<PKGBUILDDIR>>/src/postprocessor.cpp:259:33: error: âseqanâ is not a namespace-name 259 | using namespace seqan; | ^~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:260:25: error: âStringâ does not name a type 260 | typedef String<char> TSequence; // sequence type | ^~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:261:25: error: âAlignâ does not name a type 261 | typedef Align<TSequence, ArrayGaps> TAlign; // align type | ^~~~~ /<<PKGBUILDDIR>>/src/common.h:104:51: warning: âtemplate<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iteratorâ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType> | ^~~~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:262:25: error: âRowâ does not name a type 262 | typedef Row<TAlign>::Type TRow; | ^~~ In file included from /usr/include/c++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/tclap/SwitchArg.h:29, from /usr/include/tclap/CmdLine.h:27, from /<<PKGBUILDDIR>>/src/sibelia.cpp:7: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:263:25: error: âIteratorâ does not name a type; did you mean âBLCIteratorâ? 263 | typedef Iterator<TRow>::Type TIterator; | ^~~~~~~~ | BLCIterator In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12, from /<<PKGBUILDDIR>>/src/blockinstance.h:11, from /<<PKGBUILDDIR>>/src/postprocessor.h:14: /<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: âtemplate<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iteratorâ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator<std::bidirectional_iterator_tag, T> | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:264:25: error: âPositionâ does not name a type 264 | typedef Position<TAlign>::Type TPosition; | ^~~~~~~~ /<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: âtemplate<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iteratorâ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t> | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:266:17: error: âTSequenceâ was not declared in this scope; did you mean âsequence1â? 266 | TSequence seq1 = sequence1; | ^~~~~~~~~ | sequence1 /<<PKGBUILDDIR>>/src/postprocessor.cpp:267:26: error: expected â;â before âseq2â 267 | TSequence seq2 = sequence2; | ^~~~~ | ; /<<PKGBUILDDIR>>/src/postprocessor.cpp:268:17: error: âTAlignâ was not declared in this scope 268 | TAlign align; | ^~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:269:29: error: âalignâ was not declared in this scope; did you mean âstd::alignâ? 269 | resize(rows(align), 2); | ^~~~~ | std::align In file included from /usr/include/c++/15/memory:76, from /usr/include/seqan/basic/test_system.h:53, from /usr/include/seqan/basic.h:65, from /usr/include/seqan/align.h:55: /usr/include/c++/15/bits/align.h:60:1: note: âstd::alignâ declared here 60 | align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept | ^~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:269:24: error: ârowsâ was not declared in this scope; did you mean âseqan2::rowsâ? 269 | resize(rows(align), 2); | ^~~~ | seqan2::rows In file included from /usr/include/seqan/align.h:97: /usr/include/seqan/align/align_base.h:341:1: note: âseqan2::rowsâ declared here 341 | rows(Align<TSource, TSpec> const & me) | ^~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:269:17: error: âresizeâ was not declared in this scope; did you mean âseqan2::resizeâ? 269 | resize(rows(align), 2); | ^~~~~~ | seqan2::resize In file included from /usr/include/seqan/align.h:146: /usr/include/seqan/align/dp_matrix_sparse.h:95:1: note: âseqan2::resizeâ declared here 95 | resize(DPMatrix_<TValue, SparseDPMatrix, THost> & dpMatrix, | ^~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:270:30: error: ârowâ was not declared in this scope; did you mean âseqan2::rowâ? 270 | assignSource(row(align, 0), seq1); | ^~~ | seqan2::row /usr/include/seqan/align/align_base.h:372:1: note: âseqan2::rowâ declared here 372 | row(Align<TSource, TSpec> const & me, | ^~~ In file included from /<<PKGBUILDDIR>>/src/blockfinder.h:11, from /<<PKGBUILDDIR>>/src/util.h:10, from /<<PKGBUILDDIR>>/src/sibelia.cpp:9: /<<PKGBUILDDIR>>/src/indexedsequence.h:37:22: warning: âtemplate<class> class std::auto_ptrâ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr<DNASequence> sequence_; | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /usr/include/seqan/basic/test_system.h:53, from /usr/include/seqan/basic.h:65, from /usr/include/seqan/align.h:55, from /<<PKGBUILDDIR>>/src/postprocessor.h:10: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template<typename> class auto_ptr; | ^~~~~~~~ /<<PKGBUILDDIR>>/src/indexedsequence.h:38:22: warning: âtemplate<class> class std::auto_ptrâ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr<BifurcationStorage> bifStorage_; | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template<typename> class auto_ptr; | ^~~~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:270:45: error: âseq1â was not declared in this scope 270 | assignSource(row(align, 0), seq1); | ^~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:270:17: error: âassignSourceâ was not declared in this scope; did you mean âseqan2::assignSourceâ? 270 | assignSource(row(align, 0), seq1); | ^~~~~~~~~~~~ | seqan2::assignSource In file included from /usr/include/seqan/align.h:89: /usr/include/seqan/align/gaps_anchor.h:672:1: note: âseqan2::assignSourceâ declared here 672 | assignSource(Gaps<TSequence, AnchorGaps<TGapAnchor> > & gaps, TSequence2 const & source) | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:271:45: error: âseq2â was not declared in this scope; did you mean âseqan2â? 271 | assignSource(row(align, 1), seq2); | ^~~~ | seqan2 /<<PKGBUILDDIR>>/src/postprocessor.cpp:272:39: error: âScoreâ was not declared in this scope; did you mean âseqan2::Scoreâ? 272 | localAlignment(align, Score<int>(25, -75, -75)); | ^~~~~ | seqan2::Score In file included from /usr/include/seqan/score.h:45, from /usr/include/seqan/graph_align.h:45, from /usr/include/seqan/align.h:59: /usr/include/seqan/score/score_base.h:68:7: note: âseqan2::Scoreâ declared here 68 | class Score; | ^~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:272:45: error: expected primary-expression before âintâ 272 | localAlignment(align, Score<int>(25, -75, -75)); | ^~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:272:17: error: âlocalAlignmentâ was not declared in this scope; did you mean âseqan2::localAlignmentâ? 272 | localAlignment(align, Score<int>(25, -75, -75)); | ^~~~~~~~~~~~~~ | seqan2::localAlignment In file included from /usr/include/seqan/align.h:209: /usr/include/seqan/align/local_alignment_banded.h:306:21: note: âseqan2::localAlignmentâ declared here 306 | String<TScoreValue> localAlignment(StringSet<Align<TSequence, TAlignSpec> > & align, | ^~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:273:32: error: âclippedBeginPositionâ was not declared in this scope; did you mean âseqan2::clippedBeginPositionâ? 273 | coord1.first = clippedBeginPosition(row(align, 0)); | ^~~~~~~~~~~~~~~~~~~~ | seqan2::clippedBeginPosition /usr/include/seqan/align/gaps_anchor.h:920:1: note: âseqan2::clippedBeginPositionâ declared here 920 | clippedBeginPosition(Gaps<TSequence, AnchorGaps<TGapAnchors> > const & gaps) | ^~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/postprocessor.cpp:274:33: error: âclippedEndPositionâ was not declared in this scope; did you mean âseqan2::clippedEndPositionâ? 274 | coord1.second = clippedEndPosition(row(align, 0)); | ^~~~~~~~~~~~~~~~~~ | seqan2::clippedEndPosition /usr/include/seqan/align/gaps_anchor.h:931:1: note: âseqan2::clippedEndPositionâ declared here 931 | clippedEndPosition(Gaps<TSequence, AnchorGaps<TGapAnchors> > const & gaps) | ^~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/sibelia.cpp: In function âint main(int, char**)â: /<<PKGBUILDDIR>>/src/sibelia.cpp:239:22: warning: âtemplate<class> class std::auto_ptrâ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 239 | std::auto_ptr<SyntenyFinder::BlockFinder> finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template<typename> class auto_ptr; | ^~~~~~~~ make[3]: *** [CMakeFiles/Sibelia.dir/build.make:96: CMakeFiles/Sibelia.dir/postprocessor.cpp.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/Sibelia.dir/all] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[1]: *** [Makefile:159: all] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2 make: *** [debian/rules:11: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
