[Debichem-devel] Bug#982567: openms build-depends on removed package
Andreas Tille
tille at debian.org
Fri Feb 19 21:19:11 GMT 2021
Hi Filippo,
this is extremely unfortunate. However, I guess the alternative would
have been to keep some RC buggy seqan-dev which would not have helped
openms as well. I tried the same as Peter and replaced the
Build-Depends seqan-dev by libseqan2-dev.
I can confirm the observation from Peter about the missing header file.
I simply tried to comment those missing headers (next one is also
missing):
// #include <seqan/seq_io/guess_stream_format.h>
// #include <seqan/seq_io/read_fasta_fastq.h>
This leaded to:
...
cd /build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openms && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DOpenMS_EXPORTS -DQT_CORE_LIB -DQT_NETWORK_LIB -DQT_NO_DEBUG -I/build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openms -I/build/openms-2.6.0+cleaned1/src/openms -I/build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openms/OpenMS_autogen/include -I/build/openms-2.6.0+cleaned1/src/openms/include -I/build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openms/include -isystem /usr/lib -isystem /usr/lib/x86_64-linux-gnu/include -isystem /build/openms-2.6.0+cleaned1/src/openms/thirdparty/evergreen/src -isystem /usr/include/hdf5/serial -isystem /usr/include/libsvm -isystem /usr/include/eigen3 -isystem /usr/include/libwildmagic -isystem /build/openms-2.6.0+cleaned1/src/openswathalgo/include -isystem /build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openswathalgo/include -isystem /build/openms-2.6.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include -isystem /build/openms-2.6.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtNetwork -isystem /build/openms-2.6.0+cleaned1/src/openms/thirdparty/eol-bspline -isystem /build/openms-2.6.0+cleaned1/src/openms/thirdparty/IsoSpec -isystem /build/openms-2.6.0+cleaned1/src/openms/thirdparty/json -g -O2 -ffile-prefix-map=/build/openms-2.6.0+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -Wall -Wextra -Wno-non-virtual-dtor -Wno-unknown-pragmas -Wno-long-long -Wno-unused-function -Wno-variadic-macros -fPIC -fopenmp -o CMakeFiles/OpenMS.dir/source/FORMAT/FASTAFile.cpp.o -c /build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:50:18: error: 'RecordReader' in namespace 'seqan' does not name a template type
50 | typedef seqan::RecordReader<std::fstream, seqan::SinglePass<> > FASTARecordReader;
| ^~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In member function 'void OpenMS::FASTAFile::readStart(const OpenMS::String&)':
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:93:66: error: expected primary-expression before '(' token
93 | reader_ = std::unique_ptr<void, std::function<void(void*) > >(new FASTARecordReader(infile_),
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:93:71: error: expected type-specifier before 'FASTARecordReader'
93 | reader_ = std::unique_ptr<void, std::function<void(void*) > >(new FASTARecordReader(infile_),
| ^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In lambda function:
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:26: error: 'FASTARecordReader' does not name a type
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:43: error: expected '>' before '*' token
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:43: error: expected '(' before '*' token
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^
| (
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:44: error: expected primary-expression before '>' token
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:50: error: expected ')' before ';' token
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^
| )
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In member function 'bool OpenMS::FASTAFile::readNext(OpenMS::FASTAFile::FASTAEntry&)':
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:35: error: 'FASTARecordReader' does not name a type
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:52: error: expected '>' before '*' token
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:52: error: expected '(' before '*' token
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ^
| (
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:53: error: expected primary-expression before '>' token
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:71: error: expected ')' before '{' token
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ~ ^
| )
105 | {
| ~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:109:17: warning: suggest braces around empty body in an 'if' statement [-Wempty-body]
109 | String id, s;
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:20: error: 'id' was not declared in this scope
110 | if (readRecord(id, s, *static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:24: error: 's' was not declared in this scope
110 | if (readRecord(id, s, *static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:40: error: 'FASTARecordReader' does not name a type
110 | if (readRecord(id, s, *static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:57: error: expected '>' before '*' token
110 | if (readRecord(id, s, *static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:57: error: expected '(' before '*' token
110 | if (readRecord(id, s, *static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^
| (
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:58: error: expected primary-expression before '>' token
110 | if (readRecord(id, s, *static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:83: error: 'Fasta' is not a member of 'seqan'
110 | if (readRecord(id, s, *static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:9: error: 'readRecord' was not declared in this scope; did you mean 'reader_'?
110 | if (readRecord(id, s, *static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^~~~~~~~~~
| reader_
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:97: error: expected ')' before '{' token
110 | if (readRecord(id, s, *static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ~ ^
| )
111 | {
| ~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:116:20: warning: suggest braces around empty body in an 'if' statement [-Wempty-body]
116 | ++entries_read_;
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:117:5: error: 's' was not declared in this scope
117 | s.removeWhitespaces();
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:121:5: error: 'id' was not declared in this scope
121 | id.trim();
| ^~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In member function 'std::streampos OpenMS::FASTAFile::position() const':
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:139:41: error: 'FASTARecordReader' does not name a type
139 | return seqan::position(*static_cast<FASTARecordReader*>(reader_.get()));
| ^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:139:58: error: expected '>' before '*' token
139 | return seqan::position(*static_cast<FASTARecordReader*>(reader_.get()));
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:139:58: error: expected '(' before '*' token
139 | return seqan::position(*static_cast<FASTARecordReader*>(reader_.get()));
| ^
| (
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:139:59: error: expected primary-expression before '>' token
139 | return seqan::position(*static_cast<FASTARecordReader*>(reader_.get()));
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In member function 'bool OpenMS::FASTAFile::setPosition(const streampos&)':
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:144:45: error: 'FASTARecordReader' does not name a type
144 | return (seqan::setPosition(*static_cast<FASTARecordReader*>(reader_.get()), pos) == 0);
| ^~~~~~~~~~~~~~~~~
So it seems we need to seek for that missing function inside
libseqan2-dev and replace the include by a new one. Hopefully
it is that simple and we can save the case.
Kind regards
Andreas.
--
http://fam-tille.de
More information about the Debichem-devel
mailing list