Compile Errors: *** [Makefile:59: cnvnator] Error 1

[walidabualafia]

Hi all,

I am trying to compile speedseq, and I have all the deps installed in my environment. I keep getting back this error, not sure why:

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Compiling with parallel (OpenMP) support
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/hpcf/authorized_apps/rhel7_apps/root/install/6.14.06/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
obj/HisMaker.o: In function `HisMaker::HisMaker(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, Genome*)':
HisMaker.cpp:(.text+0x40d0): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::pe_for_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, double, double)':
HisMaker.cpp:(.text+0x7aae): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::HisMaker(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, bool, Genome*)':
HisMaker.cpp:(.text+0x92bb): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::generateView(TString, int, int, bool, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)':
HisMaker.cpp:(.text+0xa5a3): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0xad42): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0xb453): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::view(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool)':
HisMaker.cpp:(.text+0xc0b9): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::genotype(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool)':
HisMaker.cpp:(.text+0xc48b): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::eval(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool)':
HisMaker.cpp:(.text+0x1031d): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::produceHistogramsNew(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)':
HisMaker.cpp:(.text+0x12468): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::mergeTrees(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)':
HisMaker.cpp:(.text+0x14b6a): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::callSVs(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool, bool)':
HisMaker.cpp:(.text+0x15dca): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x15e3d): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x15ec1): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o:HisMaker.cpp:(.text+0x15f3d): more undefined references to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' follow
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:59: cnvnator] Error 1
make[1]: Leaving directory '/research/path/to/speedseq/src/CNVnator'
make: *** [Makefile:139: cnvnator] Error 2

Does anyone know what might be causing this issue or how to get around it? Any support would be helpful.

Thanks! Walid