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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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error trying to install CNVnator #138

Closed cacat93 closed 3 years ago

cacat93 commented 5 years ago

when trying to 'make' CNVnator I get the following error:

Please help with any suggestions

Compiling with NO parallel support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.3.3\" -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lz -lbz2 -lcurl -llzma -L/home/t/tb275/Documents/rootbuild/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore /usr/bin/ld: samtools/htslib-1.9/libhts.a(thread_pool.o): undefined reference to symbol 'pthread_mutexattr_settype@@GLIBC_2.2.5' //usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make: *** [cnvnator] Error 1

abyzov commented 5 years ago

Hi, not sure but looks like it could be related to a compiler or using different compiler to compile samtools and CNVnator.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

On Feb 5, 2019, at 6:31 PM, cacat93 notifications@github.com<mailto:notifications@github.com> wrote:

when trying to 'make' CNVnator I get the following error:

Please help with any suggestions

Compiling with NO parallel support g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.3.3" -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lz -lbz2 -lcurl -llzma -L/home/t/tb275/Documents/rootbuild/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore /usr/bin/ld: samtools/htslib-1.9/libhts.a(thread_pool.o): undefined reference to symbol 'pthread_mutexattr_settype@@GLIBC_2.2.5' //usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make: *** [cnvnator] Error 1

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anthonypalacios commented 4 years ago

I have this same issue....was there a solution or possible cause?

Thank you

abyzov commented 4 years ago

Hi, I haven’t heard back from the other user. Not sure whether ensuring using the same compiler help.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

anthonypalacios commented 4 years ago

Thank you Alexej....I am having a similar issue when compiling.

root variable exported root library in path gcc version = 7.4 g++ version = 4.9.4 samtools 1.10 Using htslib 1.10

make LIBS="-lcrypto" OMP-no

/usr/bin/ld: samtools/htslib-1.10/libhts.a(thread_pool.o): undefined reference to symbol 'pthread_mutexattr_settype@@GLIBC_2.2.5' //lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line

(make verbose output)

obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.10/libhts.a -lcrypto -lz -lbz2 -lcurl -llzma -lreadline -L/software/root/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore Makefile:66: recipe for target 'cnvnator' failed

Miajss commented 4 years ago

I am using the same compiler version (gcc-7.4.0) for samtools and CNVnator, and still getting a similar error.

Compiling with NO parallel support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.10/libhts.a -lz -lbz2 -lcurl -llzma -lreadline -L/home/mia/software/yeppp-1.0.0/binaries/linux/x86_64/ -lyeppp -L/home/mia/software/root_v6.18.04.Linux-ubuntu18-x86_64-gcc7.4/root/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore /usr/bin/ld: samtools/htslib-1.10/libhts.a(thread_pool.o): undefined reference to symbol 'pthread_mutexattr_settype@@GLIBC_2.2.5' //lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status Makefile:66: recipe for target 'cnvnator' failed make: *** [cnvnator] Error 1

Has any solution been found?

abyzov commented 4 years ago

Hi, some people were eventually able to compile it but I don’t know exactly how they did it.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

On Feb 10, 2020, at 5:24 PM, miajss notifications@github.com<mailto:notifications@github.com> wrote:

I am using the same compiler version (7.4.0) for samtools and CNVnator, and still getting a similar error.

Compiling with NO parallel support g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4.1" -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.10/libhts.a -lz -lbz2 -lcurl -llzma -lreadline -L/home/mia/software/yeppp-1.0.0/binaries/linux/x86_64/ -lyeppp -L/home/mia/software/root_v6.18.04.Linux-ubuntu18-x86_64-gcc7.4/root/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore /usr/bin/ld: samtools/htslib-1.10/libhts.a(thread_pool.o): undefined reference to symbol 'pthread_mutexattr_settype@@GLIBC_2.2.5' //lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status Makefile:66: recipe for target 'cnvnator' failed make: *** [cnvnator] Error 1

Has any solution been found?

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suvakov commented 4 years ago

We have similar issue before on some platforms but with different library (crypto instead pthread). Solution can be to compile with -lpthread:

make LIBS="-lcrypto -lpthread " or without OMP: make LIBS="-lcrypto -lpthread " OMP=no