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 âbool shasta::Align4::Aligner::computeBandedAlignment(const std::array<std::span<long unsigned int>, 2>&, int32_t, int32_t, shasta::Alignment&, shasta::AlignmentInfo&, bool) constâ: /<<PKGBUILDDIR>>/src/Align4.cpp:1002:21: error: âseqanâ is not a namespace-name 1002 | using namespace seqan; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp: In member function âbool shasta::Align4::Aligner::computeBandedAlignment(const std::array<std::span<long unsigned int>, 2>&, int32_t, int32_t, shasta::Alignment&, shasta::AlignmentInfo&, bool) constâ: /<<PKGBUILDDIR>>/src/Align4.cpp:1002:21: error: âseqanâ is not a namespace-name 1002 | using namespace seqan; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1003:23: error: âStringâ does not name a type 1003 | using TSequence = String<KmerId>; | ^~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1003:23: error: âStringâ does not name a type 1003 | using TSequence = String<KmerId>; | ^~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1004:34: error: âTSequenceâ was not declared in this scope 1004 | using TStringSet = StringSet<TSequence>; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1004:24: error: âStringSetâ does not name a type 1004 | using TStringSet = StringSet<TSequence>; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1005:49: error: âDependentâ was not declared in this scope; did you mean âseqan2::Dependentâ? 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: âseqan2::Dependentâ declared here 137 | struct Dependent; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1004:34: error: âTSequenceâ was not declared in this scope 1004 | using TStringSet = StringSet<TSequence>; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1005:27: error: âStringSetâ does not name a type 1005 | using TDepStringSet = StringSet< TSequence, Dependent<> >; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1004:24: error: âStringSetâ does not name a type 1004 | using TStringSet = StringSet<TSequence>; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1005:49: error: âDependentâ was not declared in this scope; did you mean âseqan2::Dependentâ? 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: âseqan2::Dependentâ declared here 137 | struct Dependent; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1005:27: error: âStringSetâ does not name a type 1005 | using TDepStringSet = StringSet< TSequence, Dependent<> >; | ^~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1006:32: error: âseqanâ was not declared in this scope; did you mean âseqan2â? 1006 | using TAlignGraph = Graph< seqan::Alignment<TDepStringSet> >; | ^~~~~ | seqan2 /<<PKGBUILDDIR>>/src/Align4.cpp:1006:25: error: âGraphâ does not name a type 1006 | using TAlignGraph = Graph< seqan::Alignment<TDepStringSet> >; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1018:34: error: invalid types âint[uint64_t {aka long unsigned int}]â for array subscript 1018 | appendValue(sequences[i], kmerId + 100); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1006:32: error: âseqanâ was not declared in this scope; did you mean âseqan2â? 1006 | using TAlignGraph = Graph< seqan::Alignment<TDepStringSet> >; | ^~~~~ | seqan2 /<<PKGBUILDDIR>>/src/Align4.cpp:1018:13: error: âappendValueâ was not declared in this scope; did you mean âseqan2::appendValueâ? 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: âseqan2::appendValueâ declared here 2069 | appendValue(String<TTargetValue, External<TConfig> > &me, | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1006:25: error: âGraphâ does not name a type 1006 | using TAlignGraph = Graph< seqan::Alignment<TDepStringSet> >; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1018:34: error: invalid types âint[uint64_t {aka long unsigned int}]â for array subscript 1018 | appendValue(sequences[i], kmerId + 100); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1018:13: error: âappendValueâ was not declared in this scope; did you mean âseqan2::appendValueâ? 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: âseqan2::appendValueâ declared here 2069 | appendValue(String<TTargetValue, External<TConfig> > &me, | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1022:5: error: âTStringSetâ was not declared in this scope 1022 | TStringSet sequencesSet; | ^~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1022:5: error: âTStringSetâ was not declared in this scope 1022 | TStringSet sequencesSet; | ^~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1023:17: error: âsequencesSetâ was not declared in this scope; did you mean âsequencesâ? 1023 | appendValue(sequencesSet, sequences[0]); | ^~~~~~~~~~~~ | sequences /<<PKGBUILDDIR>>/src/Align4.cpp:1023:40: error: invalid types âint[int]â for array subscript 1023 | appendValue(sequencesSet, sequences[0]); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1023:5: error: âappendValueâ was not declared in this scope; did you mean âseqan2::appendValueâ? 1023 | appendValue(sequencesSet, sequences[0]); | ^~~~~~~~~~~ | seqan2::appendValue /usr/include/seqan/file/string_external.h:2069:5: note: âseqan2::appendValueâ declared here 2069 | appendValue(String<TTargetValue, External<TConfig> > &me, | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1024:40: error: invalid types âint[int]â for array subscript 1024 | appendValue(sequencesSet, sequences[1]); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1023:17: error: âsequencesSetâ was not declared in this scope; did you mean âsequencesâ? 1023 | appendValue(sequencesSet, sequences[0]); | ^~~~~~~~~~~~ | sequences /<<PKGBUILDDIR>>/src/Align4.cpp:1023:40: error: invalid types âint[int]â for array subscript 1023 | appendValue(sequencesSet, sequences[0]); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1023:5: error: âappendValueâ was not declared in this scope; did you mean âseqan2::appendValueâ? 1023 | appendValue(sequencesSet, sequences[0]); | ^~~~~~~~~~~ | seqan2::appendValue /usr/include/seqan/file/string_external.h:2069:5: note: âseqan2::appendValueâ declared here 2069 | appendValue(String<TTargetValue, External<TConfig> > &me, | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1024:40: error: invalid types âint[int]â for array subscript 1024 | appendValue(sequencesSet, sequences[1]); | ^ /<<PKGBUILDDIR>>/src/Align4.cpp:1027:5: error: âTAlignGraphâ was not declared in this scope 1027 | TAlignGraph graph(sequencesSet); | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1029:9: error: âgraphâ was not declared in this scope; did you mean âboost::graphâ? 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: âboost::graphâ declared here 336 | namespace graph | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1030:20: error: âSimpleâ was not declared in this scope; did you mean âseqan2::Simpleâ? 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: âseqan2::Simpleâ declared here 106 | typedef Tag<Simple_> Simple; | ^~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1030:9: error: âScoreâ was not declared in this scope; did you mean âseqan2::Scoreâ? 1030 | Score<int, Simple>(matchScore, mismatchScore, gapScore), | ^~~~~~~~~~~~~~~~~~ | seqan2::Score /<<PKGBUILDDIR>>/src/Align4.cpp:1027:5: error: âTAlignGraphâ 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: âseqan2::Scoreâ declared here 68 | class Score; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1031:9: error: âAlignConfigâ was not declared in this scope; did you mean âseqan2::AlignConfigâ? 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: âseqan2::AlignConfigâ declared here 93 | class AlignConfig | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1029:9: error: âgraphâ was not declared in this scope; did you mean âboost::graphâ? 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: âboost::graphâ declared here 336 | namespace graph | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1033:9: error: âLinearGapsâ was not declared in this scope; did you mean âseqan2::LinearGapsâ? 1033 | LinearGaps()); | ^~~~~~~~~~ | seqan2::LinearGaps In file included from /usr/include/seqan/align.h:111: /usr/include/seqan/align/dp_profile.h:300:26: note: âseqan2::LinearGapsâ declared here 300 | typedef Tag<LinearGaps_> LinearGaps; | ^~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1030:20: error: âSimpleâ was not declared in this scope; did you mean âseqan2::Simpleâ? 1030 | Score<int, Simple>(matchScore, mismatchScore, gapScore), | ^~~~~~ | seqan2::Simple /<<PKGBUILDDIR>>/src/Align4.cpp:1028:23: error: âglobalAlignmentâ was not declared in this scope; did you mean âseqan2::globalAlignmentâ? 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: âseqan2::Simpleâ 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: âseqan2::globalAlignmentâ declared here 121 | int globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH, | ^~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:17: error: âseqanâ 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 âintâ 1034 | if(score == seqan::MinValue<int>::VALUE) { | ^~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:33: error: expected â)â before âintâ 1034 | if(score == seqan::MinValue<int>::VALUE) { | ~ ^~~ | ) /<<PKGBUILDDIR>>/src/Align4.cpp:1030:9: error: âScoreâ was not declared in this scope; did you mean âseqan2::Scoreâ? 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: âseqan2::Scoreâ declared here 68 | class Score; | ^~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1041:14: error: expected â;â before âalignâ 1041 | TSequence align; | ^~~~~~ | ; /<<PKGBUILDDIR>>/src/Align4.cpp:1031:9: error: âAlignConfigâ was not declared in this scope; did you mean âseqan2::AlignConfigâ? 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: âseqan2::AlignConfigâ declared here 93 | class AlignConfig | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1042:5: error: âconvertAlignmentâ was not declared in this scope; did you mean âseqan2::convertAlignmentâ? 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: âseqan2::convertAlignmentâ declared here 1666 | convertAlignment(String<TValue, TSpec1> const& mat, | ^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1043:38: error: expected primary-expression before âintâ 1043 | const int totalAlignmentLength = int(seqan::length(align)); | ^~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1033:9: error: âLinearGapsâ was not declared in this scope; did you mean âseqan2::LinearGapsâ? 1033 | LinearGaps()); | ^~~~~~~~~~ | seqan2::LinearGaps In file included from /usr/include/seqan/align.h:111: /usr/include/seqan/align/dp_profile.h:300:26: note: âseqan2::LinearGapsâ 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: âglobalAlignmentâ was not declared in this scope; did you mean âseqan2::globalAlignmentâ? 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: âseqan2::globalAlignmentâ declared here 121 | int globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH, | ^~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:17: error: âseqanâ 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 âintâ 1034 | if(score == seqan::MinValue<int>::VALUE) { | ^~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1034:33: error: expected â)â before âintâ 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 â;â before âalignâ 1041 | TSequence align; | ^~~~~~ | ; /<<PKGBUILDDIR>>/src/Align4.cpp:1042:5: error: âconvertAlignmentâ was not declared in this scope; did you mean âseqan2::convertAlignmentâ? 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: âseqan2::convertAlignmentâ declared here 1666 | convertAlignment(String<TValue, TSpec1> const& mat, | ^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/Align4.cpp:1043:38: error: expected primary-expression before âintâ 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 --------------------------------------------------------------------------------
