[Debian-med-packaging] Bug#1125659: sibelia: FTBFS: /<<PKGBUILDDIR>>/src/postprocessor.cpp:259:33: error: 'seqan' is not a namespace-name
Santiago Vila
sanvila at debian.org
Thu Jan 15 16:54:40 GMT 2026
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: ‘#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.’
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: ‘#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.’
36 | BOOST_PRAGMA_MESSAGE(
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ 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: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ 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: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ 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 ‘void 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>&)’:
/<<PKGBUILDDIR>>/src/postprocessor.cpp:259:33: error: ‘seqan’ is not a namespace-name
259 | using namespace seqan;
| ^~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:260:25: error: ‘String’ does not name a type
260 | typedef String<char> TSequence; // sequence type
| ^~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:261:25: error: ‘Align’ does not name a type
261 | typedef Align<TSequence, ArrayGaps> TAlign; // align type
| ^~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
104 | struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:262:25: error: ‘Row’ 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: ‘Iterator’ does not name a type; did you mean ‘BLCIterator’?
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: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ 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: ‘Position’ does not name a type
264 | typedef Position<TAlign>::Type TPosition;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ 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: ‘TSequence’ was not declared in this scope; did you mean ‘sequence1’?
266 | TSequence seq1 = sequence1;
| ^~~~~~~~~
| sequence1
/<<PKGBUILDDIR>>/src/postprocessor.cpp:267:26: error: expected ‘;’ before ‘seq2’
267 | TSequence seq2 = sequence2;
| ^~~~~
| ;
/<<PKGBUILDDIR>>/src/postprocessor.cpp:268:17: error: ‘TAlign’ was not declared in this scope
268 | TAlign align;
| ^~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:269:29: error: ‘align’ was not declared in this scope; did you mean ‘std::align’?
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: ‘std::align’ declared here
60 | align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept
| ^~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:269:24: error: ‘rows’ was not declared in this scope; did you mean ‘seqan2::rows’?
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: ‘seqan2::rows’ declared here
341 | rows(Align<TSource, TSpec> const & me)
| ^~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:269:17: error: ‘resize’ was not declared in this scope; did you mean ‘seqan2::resize’?
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: ‘seqan2::resize’ declared here
95 | resize(DPMatrix_<TValue, SparseDPMatrix, THost> & dpMatrix,
| ^~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:270:30: error: ‘row’ was not declared in this scope; did you mean ‘seqan2::row’?
270 | assignSource(row(align, 0), seq1);
| ^~~
| seqan2::row
/usr/include/seqan/align/align_base.h:372:1: note: ‘seqan2::row’ 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: ‘template<class> class std::auto_ptr’ 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: ‘template<class> class std::auto_ptr’ 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: ‘seq1’ was not declared in this scope
270 | assignSource(row(align, 0), seq1);
| ^~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:270:17: error: ‘assignSource’ was not declared in this scope; did you mean ‘seqan2::assignSource’?
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: ‘seqan2::assignSource’ declared here
672 | assignSource(Gaps<TSequence, AnchorGaps<TGapAnchor> > & gaps, TSequence2 const & source)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:271:45: error: ‘seq2’ was not declared in this scope; did you mean ‘seqan2’?
271 | assignSource(row(align, 1), seq2);
| ^~~~
| seqan2
/<<PKGBUILDDIR>>/src/postprocessor.cpp:272:39: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’?
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: ‘seqan2::Score’ declared here
68 | class Score;
| ^~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:272:45: error: expected primary-expression before ‘int’
272 | localAlignment(align, Score<int>(25, -75, -75));
| ^~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:272:17: error: ‘localAlignment’ was not declared in this scope; did you mean ‘seqan2::localAlignment’?
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: ‘seqan2::localAlignment’ declared here
306 | String<TScoreValue> localAlignment(StringSet<Align<TSequence, TAlignSpec> > & align,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:273:32: error: ‘clippedBeginPosition’ was not declared in this scope; did you mean ‘seqan2::clippedBeginPosition’?
273 | coord1.first = clippedBeginPosition(row(align, 0));
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::clippedBeginPosition
/usr/include/seqan/align/gaps_anchor.h:920:1: note: ‘seqan2::clippedBeginPosition’ declared here
920 | clippedBeginPosition(Gaps<TSequence, AnchorGaps<TGapAnchors> > const & gaps)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:274:33: error: ‘clippedEndPosition’ was not declared in this scope; did you mean ‘seqan2::clippedEndPosition’?
274 | coord1.second = clippedEndPosition(row(align, 0));
| ^~~~~~~~~~~~~~~~~~
| seqan2::clippedEndPosition
/usr/include/seqan/align/gaps_anchor.h:931:1: note: ‘seqan2::clippedEndPosition’ declared here
931 | clippedEndPosition(Gaps<TSequence, AnchorGaps<TGapAnchors> > const & gaps)
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/sibelia.cpp: In function ‘int main(int, char**)’:
/<<PKGBUILDDIR>>/src/sibelia.cpp:239:22: warning: ‘template<class> class std::auto_ptr’ 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
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