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CNVnator Compile issue

Hi all, Im trying to install CNVnator. make gives the following error. Any help will be appreciated. The os is centos 7.2

make

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 /home/biouser/bin/CNVnator/src/samtools/libbam.a /home/biouser/bin/CNVnator/src/samtools/htslib-1.4/libhts.a -lz -L/home/biouser/bin/CNVnator/yeppp-1.0.0/binaries/linux/x86_64/ -lyeppp -L/home/biouser/bin/root/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
/bin/ld: /home/biouser/bin/CNVnator/src/samtools/htslib-1.4/libhts.a(plugin.o): undefined reference to symbol 'dlclose@@GLIBC_2.2.5'
/usr/lib64/libdl.so.2: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1
cnv sv ngs cnvnator
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written by gessthomsxavier7 • gessthomsxavier7

Have you seen this issue on CNVnator site?

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written by h.mon h.mon

according to that link I tried to compile using samtools-1.2. now it gives 

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 /home/biouser/bin/CNVnator/src/samtools/libbam.a /home/biouser/bin/CNVnator/src/samtools/htslib-1.2.1/libhts.a -lz -L/home/biouser/bin/CNVnator/yeppp-1.0.0/binaries/linux/x86_64/ -lyeppp -L/home/biouser/bin/root/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
/bin/ld: warning: libtbb.so.2, needed by /home/biouser/bin/root/lib/libTree.so, not found (try using -rpath or -rpath-link)
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::task_group_context::cancel_group_execution()'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::interface5::internal::task_base::destroy(tbb::task&)'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::task::note_affinity(unsigned short)'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::task_group_context::is_group_execution_cancelled() const'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::internal::throw_exception_v4(tbb::internal::exception_id)'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `typeinfo for tbb::task'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::task_group_context::reset()'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `vtable for tbb::task'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::task_group_context::init()'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::internal::allocate_additional_child_of_proxy::allocate(unsigned long) const'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `ROOT::TThreadExecutor::ParallelFor(unsigned int, unsigned int, unsigned int, std::function<void (unsigned int)> const&)'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::task_group_context::~task_group_context()'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `tbb::internal::allocate_root_with_context_proxy::allocate(unsigned long) const'
/home/biouser/bin/root/lib/libTree.so: undefined reference to `ROOT::TThreadExecutor::TThreadExecutor()'
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1
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written by gessthomsxavier7 • gessthomsxavier7

The issue is solved. I was executing sudo make, instead I tried make and it compiled successfully

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written by gessthomsxavier7 • gessthomsxavier7

cnvnator would be a very logical tag for this question - as such the developer(s) can easily find your thread.

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written by WouterDeCoster WouterDeCoster

1 answer

This issue is solved. Thanks to h.mon . I copied samtools-1.2 files to src/samtools dir and executed make. It executed without any errors. While running cnvnator I faced this error

cnvnator: error while loading shared libraries: libyeppp.so: cannot open shared object file: No such file or directory

It was solved by exporting 

export YEPPPLIBDIR=/home/biouser/bin/CNVnator/yeppp-1.0.0/binaries/linux/x86_64
export LD_LIBRARY_PATH=$YEPPPLIBDIR:$LD_LIBRARY_PATH
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written by gessthomsxavier7 • gessthomsxavier7

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