[Debian-med-packaging] Bug#1125658: shasta: FTBFS: /<<PKGBUILDDIR>>/src/Align4.cpp:1002:21: error: 'seqan' is not a namespace-name
Santiago Vila
sanvila at debian.org
Thu Jan 15 16:54:38 GMT 2026
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
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make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DBUILD_ID=0.12.0 \
-DBUILD_STATIC_EXECUTABLE=OFF \
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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
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-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
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-- BUILD_ID is: 0.12.0
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cd obj-x86_64-linux-gnu && make -j2 INSTALL="install --strip-program=true" VERBOSE=1
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/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
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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
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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
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[ 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
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