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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 at the time of compilation. #143

Closed as7a5 closed 3 years ago

as7a5 commented 5 years ago

I get an error as the following:

[root@bigpurple-hn1 CNVnator]# make Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c cnvnator.cpp -o obj/cnvnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c EXOnator.cpp -o obj/EXOnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c HisMaker.cpp -o obj/HisMaker.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c AliParser.cpp -o obj/AliParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c FastaParser.cpp -o obj/FastaParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c VcfParser.cpp -o obj/VcfParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Genotyper.cpp -o obj/Genotyper.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Interval.cpp -o obj/Interval.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Genome.cpp -o obj/Genome.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.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-1.9/libhts.a -lz -lbz2 -lcurl -llzma -L/gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore /bin/ld: samtools/htslib-1.9/libhts.a(hfile_s3.o): undefined reference to symbol 'HMAC@@libcrypto.so.10' //usr/lib64/libcrypto.so.10: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make: *** [cnvnator] Error 1

I apreciate any help.

thanks

abyzov commented 5 years ago

Hi, not sure but the problem may be related to a compile. Which version are you using?

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

as7a5 commented 5 years ago

It is the latest. From github. I am trying to compile it on redhat 7.4. gcc 6.1.0 (I tries other versions too).

as7a5 commented 5 years ago

I should add that the compilation of the previous version was quite smooth.

suvakov commented 5 years ago

Hi, You probably did not compile samtools with htslib. If so, following file is missing: samtools/htslib-1.9/libhts.a In new version CNVnator is using some additional samtools/htslib functions and that require libhts. I suggest you to download latest samtools release from: https://github.com/samtools/samtools/releases After extracting files and compiling with ./configure make replace "samtools" symbolic link in your CNVnator folder with new samtools folder.

as7a5 commented 5 years ago

Actually that file very much exists. And I did do a new installation of sam tools to just make sure. The problem presses. Thanks

On Mar 4, 2019, at 8:53 PM, Milovan Šuvakov notifications@github.com wrote:

Hi, You probably did not compile samtools with htslib. If so, following file is missing: samtools/htslib-1.9/libhts.a In new version CNVnator is using some additional samtools/htslib functions and that require libhts. I suggest you to download latest samtools release from: https://github.com/samtools/samtools/releases https://github.com/samtools/samtools/releases After extracting files and compiling with ./configure make replace "samtools" symbolic link in your CNVnator folder with new samtools folder.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/abyzovlab/CNVnator/issues/143#issuecomment-469502497, or mute the thread https://github.com/notifications/unsubscribe-auth/AMlvelYjtnYH7-FJdiAkzPllhN57pImhks5vTc4BgaJpZM4bVJnM.

suvakov commented 5 years ago

Can you please try to compile with: make LIBS="-lcrypto"

as7a5 commented 5 years ago

[root@bigpurple-hn1 CNVnator]# make clean Compiling with parallel (OpenMP) support rm -fr obj cnvnator [root@bigpurple-hn1 CNVnator]# make LIBS="-lcrypto" Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c cnvnator.cpp -o obj/cnvnator.o In file included from cnvnator.cpp:14:0: HisMaker.hh:11:20: fatal error: TFrame.h: No such file or directory

include 

                ^

compilation terminated. make: *** [obj/cnvnator.o] Error 1

On Mar 5, 2019, at 4:42 PM, Milovan Šuvakov notifications@github.com wrote:

Can you please try to compile with: make clean make LIBS="-lcrypto"

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/abyzovlab/CNVnator/issues/143#issuecomment-469869078, or mute the thread https://github.com/notifications/unsubscribe-auth/AMlvesdnR-17-9KhdUwDmveMB6qdI1Nxks5vTuTLgaJpZM4bVJnM.

suvakov commented 5 years ago

This is different error. Root is missing now. Try before make: . /gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/bin/thisroot.sh

as7a5 commented 5 years ago

Thank you very much it went through.

On Mar 5, 2019, at 4:53 PM, Milovan Šuvakov notifications@github.com wrote:

This is different error. Root is missing now. Try before make: . /gpfs/share/apps/root/6.14.6/raw/source/root-6.14.06/mybuild/bin/thisroot.sh

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/abyzovlab/CNVnator/issues/143#issuecomment-469872678, or mute the thread https://github.com/notifications/unsubscribe-auth/AMlveiCyz69nINP_qlf7E05MGyNHBfoMks5vTudIgaJpZM4bVJnM.

angelcymak commented 5 years ago

Hi, I encountered the same problem. The samtools libhts.a file exists but I reinstalled samtools anyway.

I also followed the make LIBS="-lcrypto" suggestion but got the following errors:

What should I try next?

[CNVnator]$ make LIBS="-lcrypto" Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c cnvnator.cpp -o obj/cnvnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c EXOnator.cpp -o obj/EXOnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c HisMaker.cpp -o obj/HisMaker.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c AliParser.cpp -o obj/AliParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c FastaParser.cpp -o obj/FastaParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c VcfParser.cpp -o obj/VcfParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c Genotyper.cpp -o obj/Genotyper.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labshare/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c Interval.cpp -o obj/Interval.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labshare/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c Genome.cpp -o obj/Genome.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.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-1.9/libhts.a -lcrypto -lz -lbz2 -lcurl -llzma -L/media/eburchardraid01/labshare/data/opt/yeppp-1.0.0/binaries/linux/x86_64 -lyeppp -L/media/eburchardraid01/labshare/data/opt/root/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+0x5331): undefined reference toTString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function `HisMaker::pe_for_file(std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >*, int, double, double)': HisMaker.cpp:(.text+0x9df1): undefined reference to `TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > 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+0xc98a): undefined reference toTString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function `HisMaker::generateView(TString, int, int, bool, bool, std::cxx11::basic_string<char, std::char_traits, std::allocator >, int)': HisMaker.cpp:(.text+0x13c02): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' HisMaker.cpp:(.text+0x13f3f): undefined reference toTString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x149d6): undefined reference to `TString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function `HisMaker::genotype(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int, bool, bool)': HisMaker.cpp:(.text+0x15040): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' obj/HisMaker.o: In functionHisMaker::printRegion(TString, int, int, bool, bool)': HisMaker.cpp:(.text+0x156e4): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' HisMaker.cpp:(.text+0x16152): undefined reference toTString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function `HisMaker::estimateDepthMaximum(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int)': HisMaker.cpp:(.text+0x167a5): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' obj/HisMaker.o: In functionHisMaker::produceHistogramsNew(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int)': HisMaker.cpp:(.text+0x18ec6): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' obj/HisMaker.o: In functionHisMaker::mergeTrees(std::cxx11::basic_string<char, std::char_traits, std::allocator >*, int, std::cxx11::basic_string<char, std::char_traits, std::allocator >, int)': HisMaker.cpp:(.text+0x1b87a): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' obj/HisMaker.o: In functionHisMaker::generateView(bool, bool)': HisMaker.cpp:(.text+0x1cbc4): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' HisMaker.cpp:(.text+0x1d760): undefined reference toTString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::generateViewBAF(TString, int, int, bool, bool)': HisMaker.cpp:(.text+0x1e25d): undefined reference toTString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x1ee64): undefined reference to TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' obj/HisMaker.o: In functionHisMaker::view(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int, bool, bool)': HisMaker.cpp:(.text+0x1fcbf): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' obj/HisMaker.o: In functionHisMaker::callSVs(std::cxx11::basic_string<char, std::char_traits, std::allocator >*, int, bool, bool, double)': HisMaker.cpp:(.text+0x203e8): undefined reference to `TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x20465): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' HisMaker.cpp:(.text+0x204f6): undefined reference toTString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x20579): undefined reference to `TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o:HisMaker.cpp:(.text+0x22a61): more undefined references to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' follow obj/HisMaker.o: In functionHisMaker::eval(std::cxx11::basic_string<char, std::char_traits, std::allocator >*, int, bool, bool)': HisMaker.cpp:(.text+0x2519a): undefined reference to `TString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::produceHistograms(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, bool)': HisMaker.cpp:(.text+0x28238): undefined reference toTString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x28276): undefined reference to `TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x282be): undefined reference to TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' HisMaker.cpp:(.text+0x28337): undefined reference toTString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x28471): undefined reference to `TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o:HisMaker.cpp:(.text+0x29b84): more undefined references to `TString::TString(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)' follow collect2: error: ld returned 1 exit status make: *** [cnvnator] Error 1

abyzov commented 5 years ago

Hi, please try to use root-config script in the ‘bin’ dir of your ROOT installation. The script will tell which libraries you need to link. Then modify Makefile accordingly. Currently it links the following libraries (from your output) -L/media/eburchardraid01/labshare/data/opt/root/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore

root-config --libs

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 Apr 5, 2019, at 1:06 PM, Angel Mak notifications@github.com<mailto:notifications@github.com> wrote:

Hi, I encountered the same problem. I samtools libhts.a file exists but I reinstalled samtools anyway.

I also followed the make LIBS="-lcrypto" suggestion but got the following errors:

What should I try next?

[cmak@eburchardlab CNVnator]$ make LIBS="-lcrypto" Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c cnvnator.cpp -o obj/cnvnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c EXOnator.cpp -o obj/EXOnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c HisMaker.cpp -o obj/HisMaker.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c AliParser.cpp -o obj/AliParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c FastaParser.cpp -o obj/FastaParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c VcfParser.cpp -o obj/VcfParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labsha re/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c Genotyper.cpp -o obj/Genotyper.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labshare/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c Interval.cpp -o obj/Interval.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -I/media/eburchardraid01/labshare/data/opt/root/include -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -I/media/eburchardraid01/labshare/data/opt/yeppp-1.0.0/library/headers -DUSE_YEPPP -c Genome.cpp -o obj/Genome.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION="v0.4" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.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-1.9/libhts.a -lcrypto -lz -lbz2 -lcurl -llzma -L/media/eburchardraid01/labshare/data/opt/yeppp-1.0.0/binaries/linux/x86_64 -lyeppp -L/media/eburchardraid01/labshare/data/opt/root/lib -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore obj/HisMaker.o: In function HisMaker::HisMaker(std::cxx11::basic_string<char, std::char_traits, std::allocator >, Genome*)': HisMaker.cpp:(.text+0x5331): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::pe_for_file(std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, double, double)': HisMaker.cpp:(.text+0x9df1): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::HisMaker(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, bool, Genome)': HisMaker.cpp:(.text+0xc98a): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::generateView(TString, int, int, bool, bool, std::cxx11::basic_string<char, std::char_traits, std::allocator >, int)': HisMaker.cpp:(.text+0x13c02): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x13f3f): undefined reference to TString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x149d6): undefined reference to TString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::genotype(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, bool, bool)': HisMaker.cpp:(.text+0x15040): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::printRegion(TString, int, int, bool, bool)': HisMaker.cpp:(.text+0x156e4): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x16152): undefined reference to TString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::estimateDepthMaximum(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int)': HisMaker.cpp:(.text+0x167a5): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::produceHistogramsNew(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int)': HisMaker.cpp:(.text+0x18ec6): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::mergeTrees(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, std::cxx11::basic_string<char, std::char_traits, std::allocator >, int)': HisMaker.cpp:(.text+0x1b87a): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::generateView(bool, bool)': HisMaker.cpp:(.text+0x1cbc4): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x1d760): undefined reference to TString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::generateViewBAF(TString, int, int, bool, bool)': HisMaker.cpp:(.text+0x1e25d): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x1ee64): undefined reference to TString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::view(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, bool, bool)': HisMaker.cpp:(.text+0x1fcbf): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::callSVs(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, bool, bool, double)': HisMaker.cpp:(.text+0x203e8): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x20465): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x204f6): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x20579): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o:HisMaker.cpp:(.text+0x22a61): more undefined references to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' follow obj/HisMaker.o: In function HisMaker::eval(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, bool, bool)': HisMaker.cpp:(.text+0x2519a): undefined reference to TString::operator=(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o: In function HisMaker::produceHistograms(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, std::cxx11::basic_string<char, std::char_traits, std::allocator >*, int, bool)': HisMaker.cpp:(.text+0x28238): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x28276): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x282be): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x28337): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' HisMaker.cpp:(.text+0x28471): undefined reference to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' obj/HisMaker.o:HisMaker.cpp:(.text+0x29b84): more undefined references to TString::TString(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' follow collect2: error: ld returned 1 exit status make: *** [cnvnator] Error 1

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