stevemussmann
commented
6 years ago Hello Milaja,
The error that caused compilation to fail seems to be related to the boost program_options library which I used for handling command line input. I have seen a similar error previously when there was a problem with the C++ Boost libraries installation.
What version of the Boost libraries do you have installed? I think the oldest version I have tested is 1.54 and the most recent is 1.60. Also, I once encountered a problem where the program_options library did not install alongside the rest of the Boost installation. I fixed this by either downloading the source for Boost and compiling, or specifically installing the library from my system's package manager. For example, under Ubuntu this would be:
sudo apt-get install libboost-program-options-dev
I hope that helps. Let me know if you encounter any more issues,
-Steve
milaja
iosefward
chenqing-1996
Hi Steve,
Thank you for putting this program out there!
However, we have a problem trying to compile the program on a university computer cluster (Linux). The cluster manager forwarded me the error, he was using gcc 4.9.3 when compiling. I hope you can help.
The error: g++ -O3 -Wall -c main.cpp main.cpp: In function ‘int main(int, char)’: main.cpp:1153:19: warning: narrowing conversion of ‘l’ from ‘unsigned int’ to ‘char’ inside { } is ill-formed in C++11 [-Wnarrowing] char targ[]={l}, targ2[]={j}; ^ main.cpp:1153:32: warning: narrowing conversion of ‘j’ from ‘unsigned int’ to ‘char’ inside { } is ill-formed in C++11 [-Wnarrowing] char targ[]={l}, targ2[]={j}; ^ main.cpp:1174:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(iterAllele->second == sampleIndiv[l]->getAllele(j,m)) ^ main.cpp: In function ‘void readInputFile(Indiv, unsigned int&, unsigned int&, unsigned int&, unsigned int*, std::string&, int)’: main.cpp:1257:7: warning: unused variable ‘lastChar’ [-Wunused-variable] char lastChar='a', nextChar; ^ main.cpp:1257:21: warning: variable ‘nextChar’ set but not used [-Wunused-but-set-variable] char lastChar='a', nextChar; ^ main.cpp: In function ‘void getEmpiricalAlleleFreqs(double*, Indiv*, unsigned int, unsigned int, unsigned int, unsigned int, bool)’: main.cpp:1505:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (sampleIndiv[m]->getAllele(j,0) == k) ^ main.cpp:1508:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (sampleIndiv[m]->getAllele(j,1) == k) ^ main.cpp: In function ‘void parseComLine(int, char, std::string&, int&, unsigned int&, unsigned int&, unsigned int&, std::string&, double&, double&, double&, bool&, bool&, bool&, bool&, bool&, bool&, int&)’: main.cpp:1735:47: error: ‘class boost::program_options::typed_value<std::basic_string, char>’ has no member named ‘required’
("file,F", opt::value(&infileName)->required(), "Specify input file")
^
main.cpp:1736:41: error: ‘class boost::program_options::typed_value<int, char>’ has no member named ‘required’
("loci,l", opt::value(&MAXLOCI)->required(), "Specify number of loci in input file")
^
main.cpp:1768:13: error: ‘required_option’ in namespace ‘opt’ does not name a type
catch(opt::required_option& e) //catch errors resulting from required options
^
main.cpp:1770:42: error: ‘e’ was not declared in this scope
std::cerr << std::endl << "ERROR: " << e.what() << std::endl << std::endl;
^
make: *** [main.o] Error 1
Many thanks, Milaja