Error compiling Reapr

Question

[Prakki Rama]

Hi all,

I get this error when I compile Reapr tool. May I know if anyone experienced this before and suggest me some solution.

------------------------------------------------------------------------------
                               Compiling Reapr
------------------------------------------------------------------------------

g++ -Wl,-rpath,/gpfshome/prakkisr/sw/Reapr_1.0.18/src/bamtools/lib  -Wall -O3  -I /gpfshome/prakkisr/sw/Reapr_1.0.18/src/bamtools/include -L /gpfshome/prakkisr/sw/Reapr_1.0.18/src/bamtools/lib -c errorWindow.cpp

g++ -Wl,-rpath,/gpfshome/prakkisr/sw/Reapr_1.0.18/src/bamtools/lib  -Wall -O3  -I /gpfshome/prakkisr/sw/Reapr_1.0.18/src/bamtools/include -L /gpfshome/prakkisr/sw/Reapr_1.0.18/src/bamtools/lib -lbamtools -c utils.cpp

utils.cpp: In function ‘void loadGaps(std::string, std::map<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::list<std::pair<long unsigned int, long unsigned int>, std::allocator<std::pair<long unsigned int, long unsigned int> > >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::list<std::pair<long unsigned int, long unsigned int>, std::allocator<std::pair<long unsigned int, long unsigned int> > > > > >&)’:

utils.cpp:37: error: ‘Tabix’ was not declared in this scope

utils.cpp:37: error: expected ‘;’ before ‘ti’

utils.cpp:40: error: ‘ti’ was not declared in this scope

make: *** [utils.o] Error 1

I checked the part of code in utils.cpp. It looks like this:

void loadGaps(string fname, map<string, list<pair<unsigned long, unsigned long > > >& gaps)
{
    Tabix ti(fname); ## 37th line
    string line;

    while (ti.getNextLine(line))
    {
        vector<string> data;
        split(line, '\t', data);
        gaps[data[0]].push_back( make_pair(atoi(data[1].c_str()) - 1, atoi(data[2].c_str()) - 1) );
    }
}

I would really appreciate your valuable suggestions. Thanks.

[Prakki Rama]

I installed a newer version in other OS and it ran fine. Seems like my system has some problems with dependencies, which was generating this error!