compile errors

[xiekunwhy]

Hi,

I got following errors when compiling Look4LTRs, is there some bug in chromosometest?

Best, Kun

[ 88%] Linking CXX executable look4ltrs
[ 88%] Built target look4ltrs
Scanning dependencies of target chromtest
[ 88%] Building CXX object CMakeFiles/chromtest.dir/src/test/chromosometest.cpp.o
In file included from /Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/../nonltr/EnrichmentMarkovView.h:75,
                 from /Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/../nonltr/TableBuilder.h:12,
                 from /Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/chromosometest.cpp:2:
/Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/../nonltr/EnrichmentMarkovView.cpp: In member function 'void nonltr::EnrichmentMarkovView<I, V>::processTable()':
/Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/../nonltr/EnrichmentMarkovView.cpp:136:34: warning: there are no arguments to 'getSegmentLengthAndCount' that depend on a template parameter, so a declaration of 'getSegmentLengthAndCount' must be available [-fpermissive]
  136 |         std::pair<I,I> segInfo = getSegmentLengthAndCount();
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~
/Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/chromosometest.cpp: In function 'int main()':
/Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/chromosometest.cpp:9:82: error: no matching function for call to 'nonltr::TableBuilder::TableBuilder(const char [40])'
    9 |     TableBuilder *tb = new TableBuilder("/home/transposons/Genomes/TAIR10/Fasta/");
      |                                                                                  ^
/Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/../nonltr/TableBuilder.h:59:9: note: candidate: 'nonltr::TableBuilder::TableBuilder(std::string, int, int, int)'
   59 |         TableBuilder(string, int, int, int);
      |         ^~~~~~~~~~~~
/Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/../nonltr/TableBuilder.h:59:9: note:   candidate expects 4 arguments, 1 provided
/Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/../nonltr/TableBuilder.h:28:7: note: candidate: 'nonltr::TableBuilder::TableBuilder(const nonltr::TableBuilder&)'
   28 | class TableBuilder {
      |       ^~~~~~~~~~~~
/Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/../nonltr/TableBuilder.h:28:7: note:   no known conversion for argument 1 from 'const char [40]' to 'const nonltr::TableBuilder&'
/Bio/User/kxie/pipeline/genome/compareGenomics/v2.0/apps/Look4LTRs/src/test/chromosometest.cpp:11:12: error: 'c' was not declared in this scope
   11 |     delete c;
      |            ^
make[2]: *** [CMakeFiles/chromtest.dir/src/test/chromosometest.cpp.o] Error 1
make[1]: *** [CMakeFiles/chromtest.dir/all] Error 2
make: *** [all] Error 2

[AnthonyGarza124]

Hello,

Apologies for getting back to you so late. In the README.md file, can you follow the instructions in the Requirements section for creating a conda environment? Compile using the conda environment and hopefully the error should resolve itself. If it does not work, please keep me updated and I will work to resolve this issue with you.

Best Regards, Anthony Garza

[hyphaltip]

These errors are due to uncompilable code in that test script. See pull request #5 to fix.