Question: CNVnator Compile issue
0
gravatar for gessthomsxavier7
2.4 years ago by
gessthomsxavier720 wrote:

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 cnvnator ngs sv • 1.4k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by gessthomsxavier720
1

Have you seen this issue on CNVnator site?

ADD REPLYlink written 2.4 years ago by h.mon28k

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
ADD REPLYlink written 2.4 years ago by gessthomsxavier720

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

ADD REPLYlink written 2.4 years ago by gessthomsxavier720
1

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

ADD REPLYlink written 2.4 years ago by WouterDeCoster42k

noted and I have updated the tag. thanks

ADD REPLYlink written 2.4 years ago by gessthomsxavier720
3
gravatar for gessthomsxavier7
2.4 years ago by
gessthomsxavier720 wrote:

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
ADD COMMENTlink written 2.4 years ago by gessthomsxavier720
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