Premo fails to build in Debian Wheezy

[CarlosBorroto]

This probably should go into premo repository. I'm opening it here cause I found it while building gkno.

$ cat logs/build_premo.err 
/home/cborroto/src/gkno_launcher/tools/premo/src/libs/bamtools/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/home/cborroto/src/gkno_launcher/tools/premo/src/libs/bamtools/internal/index/BamStandardIndex_p.cpp:958:89: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/cborroto/src/gkno_launcher/tools/premo/src/libs/bamtools/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendRequest(size_t)’:
/home/cborroto/src/gkno_launcher/tools/premo/src/libs/bamtools/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/cborroto/src/gkno_launcher/tools/premo/src/libs/bamtools/internal/io/TcpSocket_p.cpp: In member function ‘std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)’:
/home/cborroto/src/gkno_launcher/tools/premo/src/libs/bamtools/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/cborroto/src/gkno_launcher/tools/premo/src/app/fastqreader.cpp: In member function ‘void FastqReader::close()’:
/home/cborroto/src/gkno_launcher/tools/premo/src/app/fastqreader.cpp:69:9: error: conditional expression between distinct pointer types ‘gzFile’ and ‘FILE* {aka _IO_FILE*}’ lacks a cast
/home/cborroto/src/gkno_launcher/tools/premo/src/app/fastqreader.cpp: In member function ‘bool FastqReader::isOpen() const’:
/home/cborroto/src/gkno_launcher/tools/premo/src/app/fastqreader.cpp:100:14: error: conditional expression between distinct pointer types ‘gzFile’ and ‘FILE* {aka _IO_FILE*}’ lacks a cast
/home/cborroto/src/gkno_launcher/tools/premo/src/app/fastqreader.cpp: In member function ‘bool FastqReader::open(const string&)’:
/home/cborroto/src/gkno_launcher/tools/premo/src/app/fastqreader.cpp:137:5: error: conditional expression between distinct pointer types ‘gzFile’ and ‘FILE* {aka _IO_FILE*}’ lacks a cast
/home/cborroto/src/gkno_launcher/tools/premo/src/app/fastqreader.cpp: In member function ‘bool FastqReader::isOpen() const’:
/home/cborroto/src/gkno_launcher/tools/premo/src/app/fastqreader.cpp:101:1: warning: control reaches end of non-void function [-Wreturn-type]
make[2]: *** [src/app/CMakeFiles/PremoApp.dir/fastqreader.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/app/CMakeFiles/PremoApp.dir/all] Error 2
make: *** [all] Error 2

This is in a Debian Wheezy(recently released stable version) system with cmake 2.8.9 and gcc 4.7.2.

Thanks for all your help, Carlos PS: Could you share what system you use? I really want to get gkno to build and work. I know how hard is to support every possible combination of development tools and libraries.

[pezmaster31]

I wrote premo pretty much just for this project anyway, so no worries reporting here. Sounds like this one is purely just a g++ version issue (4.5.x on our dev servers, 4.6.3 on my machine), where your newer version is more strict about the pointer comparison taking place. I'll look into cleaning that up and get back to you.

To your other question: gkno itself has been running on a few Linux distros: mostly Fedora 14 or 16 on our dev servers & cluster. I'm running Linux Mint 13 (based on Ubuntu 12.04) on my personal machine. There are probably others as well, but I'm not sure or don't have access to them at the moment. The cmake versions involved are mostly 2.8.4 on our servers, 2.8.7 on my laptop.

• Derek

[pezmaster31]

Pushed a fix. Should be good to go. Feel free to re-open if the problem persists.

Thanks again for the feedback.

• Derek