[Debian-med-packaging] C++ help needed for libsmithwaterman

[Andreas Tille]

Hi,

I need to package libsmithwaterman[1] as a pre-pre-dependency for some
Debian Med package.  The code comes with a manually crafted Makefile
that simply creates an executable while the pre-depencency of my
package[2] needs a devel package (tries to include one of the contained
headers SmithWatermanGotoh.h).

I considered it the easiest way to build the lib by adding configure.ac
and Makefile.am as quilt patch and use autoconf which does at least to
the point where some C++ error stops the build (due to stricter compile
options).  Any hint how to fix:

...
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c SWMain.cpp  -fPIC -DPIC -o .libs/libsmithwaterman_la-SWMain.o
SWMain.cpp: In function ‘int main(int, char**)’:
SWMain.cpp:92:77: error: no matching function for call to ‘CSmithWatermanGotoh::Align(unsigned int&, std::__cxx11::string&, const char*&, const unsigned int&, const char*&, const unsigned int&)’
    sw.Align(referenceSW, cigarSW, pReference, referenceLen, pQuery, queryLen);
                                                                             ^
In file included from SWMain.cpp:6:0:
SmithWatermanGotoh.h:28:10: note: candidate: void CSmithWatermanGotoh::Align(unsigned int&, std::__cxx11::string&, const string&, const string&)
     void Align(unsigned int& referenceAl, string& cigarAl, const string& s1, const string& s2);
          ^
SmithWatermanGotoh.h:28:10: note:   candidate expects 4 arguments, 6 provided
SWMain.cpp:93:84: error: no matching function for call to ‘CBandedSmithWaterman::Align(unsigned int&, std::__cxx11::string&, const char*&, const unsigned int&, const char*&, const unsigned int&, std::pair<std::pair<unsigned int, unsigned int>, std::pair<unsigned int, unsigned int> >&)’
    bsw.Align(referenceBSW, cigarBSW, pReference, referenceLen, pQuery, queryLen, hr);
                                                                                    ^
In file included from SWMain.cpp:7:0:
BandedSmithWaterman.h:35:7: note: candidate: void CBandedSmithWaterman::Align(unsigned int&, std::__cxx11::string&, const string&, const string&, std::pair<std::pair<unsigned int, unsigned int>, std::pair<unsigned int, unsigned int> >&)
  void Align(unsigned int& referenceAl, string& stringAl, const string& s1, const string& s2, pair< pair<unsigned int, unsigned int>, pair<unsigned int, unsigned int> >& hr);
       ^
BandedSmithWaterman.h:35:7: note:   candidate expects 5 arguments, 7 provided
Makefile:604: recipe for target 'libsmithwaterman_la-SWMain.lo' failed


would be welcome.  Bonus points for verifying my probably weak autoconf
stuff. :-)

Thanks for your time

     Andreas.

[1] https://anonscm.debian.org/git/debian-med/libsmithwaterman.git
[2] https://anonscm.debian.org/git/debian-med/libvcflib.git

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