Public bug reported: Imported from Debian bug http://bugs.debian.org/1125658:
Package: src:shasta Version: 0.12.0-1 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:shasta, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --with python3,sphinxdoc dh_clean debian/rules binary dh binary --with python3,sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_configure -- -DBUILD_ID=0.12.0 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON 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 -DBUILD_ID=0.12.0 -DBUILD_STATIC_EXECUTABLE=OFF -DBUILD_DYNAMIC_EXECUTABLE=ON .. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- 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 -- Processor architecture is x86_64 -- CMAKE_SYSTEM_NAME is Linux -- BUILD_STATIC_LIBRARY is ON -- BUILD_STATIC_EXECUTABLE is OFF -- BUILD_DYNAMIC_LIBRARY is ON -- BUILD_DYNAMIC_EXECUTABLE is ON -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.12.0 -- Configuring done (0.3s) -- 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>>' debian/rules override_dh_auto_build make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_build cd obj-x86_64-linux-gnu && make -j2 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<<PKGBUILDDIR>> -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[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/staticLibrary /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/staticLibrary /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" shastaStaticLibrary make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/dynamicLibrary /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/dynamicLibrary /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake "--color=" shastaDynamicLibrary make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o [ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/<<PKGBUILDDIR>>/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -c /<<PKGBUILDDIR>>/src/Align4.cpp cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/<<PKGBUILDDIR>>/staticLibrary/../src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /<<PKGBUILDDIR>>/src/Align4.cpp /<<PKGBUILDDIR>>/src/Align4.cpp: In member function ���bool shasta::Align4::Aligner::computeBandedAlignment(const std::array<std::span<long unsigned int>, 2>&, int32_t, int32_t, shasta::Alignment&, shasta::AlignmentInfo&, bool) const���: /<<PKGBUILDDIR>>/src/Align4.cpp:1002:21: error: ���seqan��� is not a namespace-name 1002 | using namespace seqan; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp: In member function ���bool shasta::Align4::Aligner::computeBandedAlignment(const std::array<std::span<long unsigned int>, 2>&, int32_t, int32_t, shasta::Alignment&, shasta::AlignmentInfo&, bool) const���: /<<PKGBUILDDIR>>/src/Align4.cpp:1002:21: error: ���seqan��� is not a namespace-name 1002 | using namespace seqan; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1003:23: error: ���String��� does not name a type 1003 | using TSequence = String<KmerId>; | ^~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1003:23: error: ���String��� does not name a type 1003 | using TSequence = String<KmerId>; | ^~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1004:34: error: ���TSequence��� was not declared in this scope 1004 | using TStringSet = StringSet<TSequence>; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1004:24: error: ���StringSet��� does not name a type 1004 | using TStringSet = StringSet<TSequence>; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1005:49: error: ���Dependent��� was not declared in this scope; did you mean ���seqan2::Dependent���? 1005 | using TDepStringSet = StringSet< TSequence, Dependent<> >; | ^~~~~~~~~ | seqan2::Dependent In file included from /usr/include/seqan/sequence.h:137, from /usr/include/seqan/modifier.h:47, from /usr/include/seqan/align.h:57, from /<<PKGBUILDDIR>>/src/Align4.cpp:15: /usr/include/seqan/sequence/string_set_dependent_tight.h:137:8: note: ���seqan2::Dependent��� declared here 137 | struct Dependent; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1004:34: error: ���TSequence��� was not declared in this scope 1004 | using TStringSet = StringSet<TSequence>; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1005:27: error: ���StringSet��� does not name a type 1005 | using TDepStringSet = StringSet< TSequence, Dependent<> >; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1004:24: error: ���StringSet��� does not name a type 1004 | using TStringSet = StringSet<TSequence>; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1005:49: error: ���Dependent��� was not declared in this scope; did you mean ���seqan2::Dependent���? 1005 | using TDepStringSet = StringSet< TSequence, Dependent<> >; | ^~~~~~~~~ | seqan2::Dependent In file included from /usr/include/seqan/sequence.h:137, from /usr/include/seqan/modifier.h:47, from /usr/include/seqan/align.h:57, from /<<PKGBUILDDIR>>/src/Align4.cpp:15: /usr/include/seqan/sequence/string_set_dependent_tight.h:137:8: note: ���seqan2::Dependent��� declared here 137 | struct Dependent; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1005:27: error: ���StringSet��� does not name a type 1005 | using TDepStringSet = StringSet< TSequence, Dependent<> >; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1006:32: error: ���seqan��� was not declared in this scope; did you mean ���seqan2���? 1006 | using TAlignGraph = Graph< seqan::Alignment<TDepStringSet> >; | ^~~~~ | seqan2 /<<PKGBUILDDIR>>/src/Align4.cpp:1006:25: error: ���Graph��� does not name a type 1006 | using TAlignGraph = Graph< seqan::Alignment<TDepStringSet> >; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1018:34: error: invalid types ���int[uint64_t {aka long unsigned int}]��� for array subscript 1018 | appendValue(sequences[i], kmerId + 100); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1006:32: error: ���seqan��� was not declared in this scope; did you mean ���seqan2���? 1006 | using TAlignGraph = Graph< seqan::Alignment<TDepStringSet> >; | ^~~~~ | seqan2 /<<PKGBUILDDIR>>/src/Align4.cpp:1018:13: error: ���appendValue��� was not declared in this scope; did you mean ���seqan2::appendValue���? 1018 | appendValue(sequences[i], kmerId + 100); | ^~~~~~~~~~~ | seqan2::appendValue In file included from /usr/include/seqan/file.h:92, from /usr/include/seqan/stream.h:62, from /usr/include/seqan/score.h:43, from /usr/include/seqan/graph_align.h:45, from /usr/include/seqan/align.h:59: /usr/include/seqan/file/string_external.h:2069:5: note: ���seqan2::appendValue��� declared here 2069 | appendValue(String<TTargetValue, External<TConfig> > &me, | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1006:25: error: ���Graph��� does not name a type 1006 | using TAlignGraph = Graph< seqan::Alignment<TDepStringSet> >; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1018:34: error: invalid types ���int[uint64_t {aka long unsigned int}]��� for array subscript 1018 | appendValue(sequences[i], kmerId + 100); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1018:13: error: ���appendValue��� was not declared in this scope; did you mean ���seqan2::appendValue���? 1018 | appendValue(sequences[i], kmerId + 100); | ^~~~~~~~~~~ | seqan2::appendValue In file included from /usr/include/seqan/file.h:92, from /usr/include/seqan/stream.h:62, from /usr/include/seqan/score.h:43, from /usr/include/seqan/graph_align.h:45, from /usr/include/seqan/align.h:59: /usr/include/seqan/file/string_external.h:2069:5: note: ���seqan2::appendValue��� declared here 2069 | appendValue(String<TTargetValue, External<TConfig> > &me, | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1022:5: error: ���TStringSet��� was not declared in this scope 1022 | TStringSet sequencesSet; | ^~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1022:5: error: ���TStringSet��� was not declared in this scope 1022 | TStringSet sequencesSet; | ^~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1023:17: error: ���sequencesSet��� was not declared in this scope; did you mean ���sequences���? 1023 | appendValue(sequencesSet, sequences[0]); | ^~~~~~~~~~~~ | sequences /<<PKGBUILDDIR>>/src/Align4.cpp:1023:40: error: invalid types ���int[int]��� for array subscript 1023 | appendValue(sequencesSet, sequences[0]); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1023:5: error: ���appendValue��� was not declared in this scope; did you mean ���seqan2::appendValue���? 1023 | appendValue(sequencesSet, sequences[0]); | ^~~~~~~~~~~ | seqan2::appendValue /usr/include/seqan/file/string_external.h:2069:5: note: ���seqan2::appendValue��� declared here 2069 | appendValue(String<TTargetValue, External<TConfig> > &me, | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1024:40: error: invalid types ���int[int]��� for array subscript 1024 | appendValue(sequencesSet, sequences[1]); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1023:17: error: ���sequencesSet��� was not declared in this scope; did you mean ���sequences���? 1023 | appendValue(sequencesSet, sequences[0]); | ^~~~~~~~~~~~ | sequences /<<PKGBUILDDIR>>/src/Align4.cpp:1023:40: error: invalid types ���int[int]��� for array subscript 1023 | appendValue(sequencesSet, sequences[0]); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1023:5: error: ���appendValue��� was not declared in this scope; did you mean ���seqan2::appendValue���? 1023 | appendValue(sequencesSet, sequences[0]); | ^~~~~~~~~~~ | seqan2::appendValue /usr/include/seqan/file/string_external.h:2069:5: note: ���seqan2::appendValue��� declared here 2069 | appendValue(String<TTargetValue, External<TConfig> > &me, | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1024:40: error: invalid types ���int[int]��� for array subscript 1024 | appendValue(sequencesSet, sequences[1]); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1027:5: error: ���TAlignGraph��� was not declared in this scope 1027 | TAlignGraph graph(sequencesSet); | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1029:9: error: ���graph��� was not declared in this scope; did you mean ���boost::graph���? 1029 | graph, | ^~~~~ | boost::graph In file included from /usr/include/boost/graph/properties.hpp:23, from /usr/include/boost/pending/disjoint_sets.hpp:15, from /<<PKGBUILDDIR>>/src/Align4.cpp:18: /usr/include/boost/graph/graph_traits.hpp:336:11: note: ���boost::graph��� declared here 336 | namespace graph | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1030:20: error: ���Simple��� was not declared in this scope; did you mean ���seqan2::Simple���? 1030 | Score<int, Simple>(matchScore, mismatchScore, gapScore), | ^~~~~~ | seqan2::Simple In file included from /usr/include/seqan/basic/basic_smart_pointer.h:53, from /usr/include/seqan/basic/basic_allocator.h:46, from /usr/include/seqan/basic.h:74, from /usr/include/seqan/align.h:55: /usr/include/seqan/basic/holder_base.h:106:22: note: ���seqan2::Simple��� declared here 106 | typedef Tag<Simple_> Simple; | ^~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1030:9: error: ���Score��� was not declared in this scope; did you mean ���seqan2::Score���? 1030 | Score<int, Simple>(matchScore, mismatchScore, gapScore), | ^~~~~~~~~~~~~~~~~~ | seqan2::Score /<<PKGBUILDDIR>>/src/Align4.cpp:1027:5: error: ���TAlignGraph��� was not declared in this scope 1027 | TAlignGraph graph(sequencesSet); | ^~~~~~~~~~~ In file included from /usr/include/seqan/score.h:45: /usr/include/seqan/score/score_base.h:68:7: note: ���seqan2::Score��� declared here 68 | class Score; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1031:9: error: ���AlignConfig��� was not declared in this scope; did you mean ���seqan2::AlignConfig���? 1031 | AlignConfig<true, true, true, true>(), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::AlignConfig In file included from /usr/include/seqan/align.h:70: /usr/include/seqan/align/align_config.h:93:7: note: ���seqan2::AlignConfig��� declared here 93 | class AlignConfig | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1029:9: error: ���graph��� was not declared in this scope; did you mean ���boost::graph���? 1029 | graph, | ^~~~~ | boost::graph In file included from /usr/include/boost/graph/properties.hpp:23, from /usr/include/boost/pending/disjoint_sets.hpp:15, from /<<PKGBUILDDIR>>/src/Align4.cpp:18: /usr/include/boost/graph/graph_traits.hpp:336:11: note: ���boost::graph��� declared here 336 | namespace graph | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1033:9: error: ���LinearGaps��� was not declared in this scope; did you mean ���seqan2::LinearGaps���? 1033 | LinearGaps()); | ^~~~~~~~~~ | seqan2::LinearGaps In file included from /usr/include/seqan/align.h:111: /usr/include/seqan/align/dp_profile.h:300:26: note: ���seqan2::LinearGaps��� declared here 300 | typedef Tag<LinearGaps_> LinearGaps; | ^~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1030:20: error: ���Simple��� was not declared in this scope; did you mean ���seqan2::Simple���? 1030 | Score<int, Simple>(matchScore, mismatchScore, gapScore), | ^~~~~~ | seqan2::Simple /<<PKGBUILDDIR>>/src/Align4.cpp:1028:23: error: ���globalAlignment��� was not declared in this scope; did you mean ���seqan2::globalAlignment���? 1028 | const int score = globalAlignment( | ^~~~~~~~~~~~~~~ | seqan2::globalAlignment In file included from /usr/include/seqan/basic/basic_smart_pointer.h:53, from /usr/include/seqan/basic/basic_allocator.h:46, from /usr/include/seqan/basic.h:74, from /usr/include/seqan/align.h:55: /usr/include/seqan/basic/holder_base.h:106:22: note: ���seqan2::Simple��� declared here 106 | typedef Tag<Simple_> Simple; | ^~~~~~ In file included from /usr/include/seqan/align.h:218: /usr/include/seqan/align/global_alignment_specialized.h:121:5: note: ���seqan2::globalAlignment��� declared here 121 | int globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH, | ^~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:17: error: ���seqan��� is not a class, namespace, or enumeration 1034 | if(score == seqan::MinValue<int>::VALUE) { | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:33: error: expected primary-expression before ���int��� 1034 | if(score == seqan::MinValue<int>::VALUE) { | ^~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:33: error: expected ���)��� before ���int��� 1034 | if(score == seqan::MinValue<int>::VALUE) { | ~ ^~~ | ) /<<PKGBUILDDIR>>/src/Align4.cpp:1030:9: error: ���Score��� was not declared in this scope; did you mean ���seqan2::Score���? 1030 | Score<int, Simple>(matchScore, mismatchScore, gapScore), | ^~~~~~~~~~~~~~~~~~ | seqan2::Score In file included from /usr/include/seqan/score.h:45: /usr/include/seqan/score/score_base.h:68:7: note: ���seqan2::Score��� declared here 68 | class Score; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1041:14: error: expected ���;��� before ���align��� 1041 | TSequence align; | ^~~~~~ | ; /<<PKGBUILDDIR>>/src/Align4.cpp:1031:9: error: ���AlignConfig��� was not declared in this scope; did you mean ���seqan2::AlignConfig���? 1031 | AlignConfig<true, true, true, true>(), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::AlignConfig In file included from /usr/include/seqan/align.h:70: /usr/include/seqan/align/align_config.h:93:7: note: ���seqan2::AlignConfig��� declared here 93 | class AlignConfig | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1042:5: error: ���convertAlignment��� was not declared in this scope; did you mean ���seqan2::convertAlignment���? 1042 | convertAlignment(graph, align); | ^~~~~~~~~~~~~~~~ | seqan2::convertAlignment In file included from /usr/include/seqan/graph_align.h:52: /usr/include/seqan/graph_align/graph_impl_align.h:1666:1: note: ���seqan2::convertAlignment��� declared here 1666 | convertAlignment(String<TValue, TSpec1> const& mat, | ^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1043:38: error: expected primary-expression before ���int��� 1043 | const int totalAlignmentLength = int(seqan::length(align)); | ^~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1033:9: error: ���LinearGaps��� was not declared in this scope; did you mean ���seqan2::LinearGaps���? 1033 | LinearGaps()); | ^~~~~~~~~~ | seqan2::LinearGaps In file included from /usr/include/seqan/align.h:111: /usr/include/seqan/align/dp_profile.h:300:26: note: ���seqan2::LinearGaps��� declared here 300 | typedef Tag<LinearGaps_> LinearGaps; | ^~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1057:20: warning: pointer to a function used in arithmetic [-Wpointer-arith] 1057 | if( align[i] != seqanGapValue and | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1028:23: error: ���globalAlignment��� was not declared in this scope; did you mean ���seqan2::globalAlignment���? 1028 | const int score = globalAlignment( | ^~~~~~~~~~~~~~~ | seqan2::globalAlignment In file included from /usr/include/seqan/align.h:218: /usr/include/seqan/align/global_alignment_specialized.h:121:5: note: ���seqan2::globalAlignment��� declared here 121 | int globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH, | ^~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:17: error: ���seqan��� is not a class, namespace, or enumeration 1034 | if(score == seqan::MinValue<int>::VALUE) { | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:33: error: expected primary-expression before ���int��� 1034 | if(score == seqan::MinValue<int>::VALUE) { | ^~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:33: error: expected ���)��� before ���int��� 1034 | if(score == seqan::MinValue<int>::VALUE) { | ~ ^~~ | ) /<<PKGBUILDDIR>>/src/Align4.cpp:1057:22: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] 1057 | if( align[i] != seqanGapValue and | ~~~~~~~~~^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1058:38: warning: pointer to a function used in arithmetic [-Wpointer-arith] 1058 | align[i + alignmentLength] != seqanGapValue and | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1058:40: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] 1058 | align[i + alignmentLength] != seqanGapValue and | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1062:19: warning: pointer to a function used in arithmetic [-Wpointer-arith] 1062 | if(align[i] != seqanGapValue) { | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1062:21: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] 1062 | if(align[i] != seqanGapValue) { | ~~~~~~~~~^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1065:37: warning: pointer to a function used in arithmetic [-Wpointer-arith] 1065 | if(align[i + alignmentLength] != seqanGapValue) { | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1065:39: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] 1065 | if(align[i + alignmentLength] != seqanGapValue) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1041:14: error: expected ���;��� before ���align��� 1041 | TSequence align; | ^~~~~~ | ; /<<PKGBUILDDIR>>/src/Align4.cpp:1042:5: error: ���convertAlignment��� was not declared in this scope; did you mean ���seqan2::convertAlignment���? 1042 | convertAlignment(graph, align); | ^~~~~~~~~~~~~~~~ | seqan2::convertAlignment In file included from /usr/include/seqan/graph_align.h:52: /usr/include/seqan/graph_align/graph_impl_align.h:1666:1: note: ���seqan2::convertAlignment��� declared here 1666 | convertAlignment(String<TValue, TSpec1> const& mat, | ^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1043:38: error: expected primary-expression before ���int��� 1043 | const int totalAlignmentLength = int(seqan::length(align)); | ^~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1057:20: warning: pointer to a function used in arithmetic [-Wpointer-arith] 1057 | if( align[i] != seqanGapValue and | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1057:22: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] 1057 | if( align[i] != seqanGapValue and | ~~~~~~~~~^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1058:38: warning: pointer to a function used in arithmetic [-Wpointer-arith] 1058 | align[i + alignmentLength] != seqanGapValue and | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1058:40: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] 1058 | align[i + alignmentLength] != seqanGapValue and | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1062:19: warning: pointer to a function used in arithmetic [-Wpointer-arith] 1062 | if(align[i] != seqanGapValue) { | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1062:21: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] 1062 | if(align[i] != seqanGapValue) { | ~~~~~~~~~^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1065:37: warning: pointer to a function used in arithmetic [-Wpointer-arith] 1065 | if(align[i + alignmentLength] != seqanGapValue) { | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1065:39: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] 1065 | if(align[i + alignmentLength] != seqanGapValue) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ make[4]: *** [staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make:82: staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o] Error 1 make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:155: staticLibrary/CMakeFiles/shastaStaticLibrary.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/<<PKGBUILDDIR>>/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /<<PKGBUILDDIR>>/src/Alignment.cpp make[4]: *** [dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make:82: dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o] Error 1 make[4]: *** Waiting for unfinished jobs.... make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:187: dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/all] Error 2 make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[2]: *** [Makefile:139: all] Error 2 make[2]: 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[1]: *** [debian/rules:25: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:15: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 -------------------------------------------------------------------------------- ** Affects: shasta (Ubuntu) Importance: Undecided Status: New ** Affects: shasta (Debian) Importance: Undecided Status: New ** Tags: ftbfs update-excuse ** Bug watch added: Debian Bug tracker #1125658 https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1125658 ** Changed in: shasta (Debian) Remote watch: None => Debian Bug tracker #1125658 ** Tags added: ftbfs update-excuse -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/2138955 Title: shasta: FTBFS: /<<PKGBUILDDIR>>/src/Align4.cpp:1002:21: error: 'seqan' is not a namespace-name To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/shasta/+bug/2138955/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
