[Debian-med-packaging] Bug#949542: C++ help needed for pbdagcon

[Andreas Tille]

Control: tags -1 help

I have fixed Python2->Python3 migration as well as the FTBFS with
pbseqlib 5.3.3+dfsg-1 issue in Git[1].  Unfortunately there is another
build issue in the C++ code which I have no idea how to fix:


...
g++ -g -O2 -fdebug-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wall -Wuninitialized -pedantic -Wdate-    time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+ds/DAZZ_DB -I/build/pbdagcon-0.3+git20180411.c14c422+ds/DALIGNER -I/usr/include/pbseq/alignment -I/usr/include/    pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party   -c -o DazAlnProvider.o DazAlnProvider.cpp
In file included from DazAlnProvider.cpp:10:
DazAlnProvider.hpp:97:19: error: expected ')' before '&' token
   97 |     Target(DAZZ_DB& db, int tspace, int small);
      |           ~       ^
      |                   )
DazAlnProvider.hpp:122:5: error: 'DAZZ_DB' does not name a type
  122 |     DAZZ_DB db_;
      |     ^~~~~~~
DazAlnProvider.hpp:161:5: error: 'DAZZ_DB' does not name a type
  161 |     DAZZ_DB db_;
      |     ^~~~~~~
DazAlnProvider.cpp: In constructor 'DazAlnProvider::DazAlnProvider(const ProgramOpts&)':
DazAlnProvider.cpp:34:33: error: 'db_' was not declared in this scope
   34 |     int status = Open_DB(path, &db_);
      |                                 ^~~
DazAlnProvider.cpp: In destructor 'virtual DazAlnProvider::~DazAlnProvider()':
DazAlnProvider.cpp:74:15: error: 'db_' was not declared in this scope
   74 |     Close_DB(&db_);
      |               ^~~
DazAlnProvider.cpp: In member function 'virtual bool DazAlnProvider::nextTarget(std::string&, std::vector<dagcon::Alignment>&)':
DazAlnProvider.cpp:125:25: error: 'db_' was not declared in this scope
  125 |     seq = Load_Subread(&db_, trg_->id, 0, trg_->length, targSeqBuf_, 0);
      |                         ^~~
DazAlnProvider.cpp: At global scope:
DazAlnProvider.cpp:225:15: error: expected constructor, destructor, or type conversion before '(' token
  225 | Target::Target(DAZZ_DB& db, int tspace, int small) :
      |               ^
DazAlnProvider.cpp: In member function 'void Target::firstRecord(Record&, bool)':
DazAlnProvider.cpp:246:14: error: 'db_' was not declared in this scope
  246 |     length = db_.reads[id].rlen;
      |              ^~~


Any help would be welcome

       Andreas.

[1] https://salsa.debian.org/med-team/pbdagcon

-- 
http://fam-tille.de