[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



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