Dear Group,
I am trying to install SpeedSeq with cnvnator. A make cnvnator produces a linker error when trying to link in ROOT.
I have tested the link command with a simple ROOT program and it is correct. The problem is weird as the missing constructor listed below TString(...) ,is not called by the code as far as I can see (the code calls a constructor witha different parameter list ).
I am using gcc/5.4.0 and root/5.34.32 on Centos 7. 7
We have managed to compile a newer version of cnvnator separately. Can we avoid this failure by editing speedseq.config to point to a separate version?
thanks
Simon
Dear Group, I am trying to install SpeedSeq with cnvnator. A
make cnvnatorproduces a linker error when trying to link in ROOT. I have tested the link command with a simple ROOT program and it is correct. The problem is weird as the missing constructor listed below TString(...) ,is not called by the code as far as I can see (the code calls a constructor witha different parameter list ).g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.3.3\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.3.1/libhts.a -lz -L/usr/local/root/5.34.32/lib/root -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore obj/HisMaker.o: In function, std::allocator > const&)'**
etc
HisMaker::HisMaker(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, Genome*)': HisMaker.cpp:(.text+0x4380): undefined reference to **TString::TString(std::__cxx11::basic_string<char, std::char_traitsI am using gcc/5.4.0 and root/5.34.32 on Centos 7. 7
We have managed to compile a newer version of cnvnator separately. Can we avoid this failure by editing speedseq.config to point to a separate version? thanks Simon