Question: Error compiling Reapr
0
gravatar for Prakki Rama
3.4 years ago by
Prakki Rama2.3k
Singapore
Prakki Rama2.3k wrote:

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.

ADD COMMENTlink written 3.4 years ago by Prakki Rama2.3k

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!

ADD REPLYlink written 3.3 years ago by Prakki Rama2.3k
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