{"action":"created","issue":{"url":"https://api.github.com/repos/abyzovlab/CNVnator/issues/31","repository_url":"https://api.github.com/repos/abyzovlab/CNVnator","labels_url":"https://api.github.com/repos/abyzovlab/CNVnator/issues/31/labels{/name}","comments_url":"https://api.github.com/repos/abyzovlab/CNVnator/issues/31/comments","events_url":"https://api.github.com/repos/abyzovlab/CNVnator/issues/31/events","html_url":"https://github.com/abyzovlab/CNVnator/issues/31","id":168590560,"number":31,"title":"Compiling CNVnator 0.3.2. Error when linking: undefined reference to `TString::TString","user":{"login":"lindenb","id":33838,"avatar_url":"https://avatars.githubusercontent.com/u/33838?v=3","gravatar_id":"","url":"https://api.github.com/users/lindenb","html_url":"https://github.com/lindenb","followers_url":"https://api.github.com/users/lindenb/followers","following_url":"https://api.github.com/users/lindenb/following{/other_user}","gists_url":"https://api.github.com/users/lindenb/gists{/gist_id}","starred_url":"https://api.github.com/users/lindenb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lindenb/subscriptions","organizations_url":"https://api.github.com/users/lindenb/orgs","repos_url":"https://api.github.com/users/lindenb/repos","events_url":"https://api.github.com/users/lindenb/events{/privacy}","received_events_url":"https://api.github.com/users/lindenb/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-08-01T08:13:20Z","updated_at":"2016-08-03T16:52:52Z","closed_at":"2016-08-03T07:33:32Z","body":"Hi,\r\nI'm trying to compile CNVnator with root-6.06 but there is a problem when linking. Here is the makefile trace:\r\n\r\n```\r\n$ g++ --version\r\ng++ (GCC) 5.2.0\r\n\r\n$ echo ${ROOTSYS}\r\n/ccc/products/root-6.06.06/default\r\n```\r\n\r\n\r\n```\r\n$ make SAMDIR=/ccc/work/cont007/fg0019/lindenbp/packages/samtools HTSDIR=/ccc/work/cont007/fg0019/lindenbp/packages/htslib  -B\r\nCompiling with parallel (OpenMP) support\r\ng++ -O3 -std=c++11 -DCNVNATOR_VERSION=\\\"v0.3.2\\\" -fopenmp -I/ccc/products/root-6.06.06/default/include      -I/ccc/work/cont007/fg0019/lindenbp/packages/samtools -I/ccc/work/cont007/fg0019/lindenbp/packages/htslib -c cnvnator.cpp -o obj/cnvnator.o\r\ng++ -O3 -std=c++11 -DCNVNATOR_VERSION=\\\"v0.3.2\\\" -fopenmp -I/ccc/products/root-6.06.06/default/include      -I/ccc/work/cont007/fg0019/lindenbp/packages/samtools -I/ccc/work/cont007/fg0019/lindenbp/packages/htslib -c EXOnator.cpp -o obj/EXOnator.o\r\ng++ -O3 -std=c++11 -DCNVNATOR_VERSION=\\\"v0.3.2\\\" -fopenmp -I/ccc/products/root-6.06.06/default/include      -I/ccc/work/cont007/fg0019/lindenbp/packages/samtools -I/ccc/work/cont007/fg0019/lindenbp/packages/htslib -c HisMaker.cpp -o obj/HisMaker.o\r\ng++ -O3 -std=c++11 -DCNVNATOR_VERSION=\\\"v0.3.2\\\" -fopenmp -I/ccc/products/root-6.06.06/default/include      -I/ccc/work/cont007/fg0019/lindenbp/packages/samtools -I/ccc/work/cont007/fg0019/lindenbp/packages/htslib -c AliParser.cpp -o obj/AliParser.o\r\ng++ -O3 -std=c++11 -DCNVNATOR_VERSION=\\\"v0.3.2\\\" -fopenmp -I/ccc/products/root-6.06.06/default/include      -I/ccc/work/cont007/fg0019/lindenbp/packages/samtools -I/ccc/work/cont007/fg0019/lindenbp/packages/htslib -c Genotyper.cpp -o obj/Genotyper.o\r\ng++ -O3 -std=c++11 -DCNVNATOR_VERSION=\\\"v0.3.2\\\" -fopenmp -I/ccc/products/root-6.06.06/default/include      -I/ccc/work/cont007/fg0019/lindenbp/packages/samtools -I/ccc/work/cont007/fg0019/lindenbp/packages/htslib -c Interval.cpp -o obj/Interval.o\r\ng++ -O3 -std=c++11 -DCNVNATOR_VERSION=\\\"v0.3.2\\\" -fopenmp -I/ccc/products/root-6.06.06/default/include      -I/ccc/work/cont007/fg0019/lindenbp/packages/samtools -I/ccc/work/cont007/fg0019/lindenbp/packages/htslib -c Genome.cpp -o obj/Genome.o\r\ng++ -O3 -std=c++11 -DCNVNATOR_VERSION=\\\"v0.3.2\\\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o /ccc/work/cont007/fg0019/lindenbp/packages/samtools/libbam.a /ccc/work/cont007/fg0019/lindenbp/packages/htslib/libhts.a -lz -L/ccc/products/root-6.06.06/default/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore\r\nobj/HisMaker.o: In function `HisMaker::HisMaker(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, Genome*)':\r\nHisMaker.cpp:(.text+0x4280): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/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)':\r\nHisMaker.cpp:(.text+0x810a): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/HisMaker.o: In function `HisMaker::HisMaker(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, bool, Genome*)':\r\nHisMaker.cpp:(.text+0xa86a): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/HisMaker.o: In function `HisMaker::generateView(TString, int, int, bool, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)':\r\nHisMaker.cpp:(.text+0xb903): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nHisMaker.cpp:(.text+0xbd5e): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nHisMaker.cpp:(.text+0xc723): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/HisMaker.o: In function `HisMaker::view(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool)':\r\nHisMaker.cpp:(.text+0xd4b2): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/HisMaker.o: In function `HisMaker::genotype(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool)':\r\nHisMaker.cpp:(.text+0xda50): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/HisMaker.o: In function `HisMaker::eval(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool)':\r\nHisMaker.cpp:(.text+0x11da1): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/HisMaker.o: In function `HisMaker::produceHistogramsNew(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)':\r\nHisMaker.cpp:(.text+0x1334b): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/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)':\r\nHisMaker.cpp:(.text+0x15c71): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/HisMaker.o: In function `HisMaker::callSVs(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool, bool)':\r\nHisMaker.cpp:(.text+0x168e7): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nHisMaker.cpp:(.text+0x1696f): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nHisMaker.cpp:(.text+0x16a06): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'\r\nobj/HisMaker.o:HisMaker.cpp:(.text+0x16a94): more undefined references to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' follow\r\ncollect2: error: ld returned 1 exit status\r\nMakefile:59: recipe for target 'cnvnator' failed\r\n```\r\n\r\ncan you please help me ?\r\nthanks.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/abyzovlab/CNVnator/issues/comments/237296426","html_url":"https://github.com/abyzovlab/CNVnator/issues/31#issuecomment-237296426","issue_url":"https://api.github.com/repos/abyzovlab/CNVnator/issues/31","id":237296426,"user":{"login":"abyzov","id":9872185,"avatar_url":"https://avatars.githubusercontent.com/u/9872185?v=3","gravatar_id":"","url":"https://api.github.com/users/abyzov","html_url":"https://github.com/abyzov","followers_url":"https://api.github.com/users/abyzov/followers","following_url":"https://api.github.com/users/abyzov/following{/other_user}","gists_url":"https://api.github.com/users/abyzov/gists{/gist_id}","starred_url":"https://api.github.com/users/abyzov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/abyzov/subscriptions","organizations_url":"https://api.github.com/users/abyzov/orgs","repos_url":"https://api.github.com/users/abyzov/repos","events_url":"https://api.github.com/users/abyzov/events{/privacy}","received_events_url":"https://api.github.com/users/abyzov/received_events","type":"User","site_admin":false},"created_at":"2016-08-03T16:52:52Z","updated_at":"2016-08-03T16:52:52Z","body":"Glad to hear this!\n\nAlexej Abyzov, Ph.D.\nSenior Associate Consultant,\nAssistant Professor of Biomedical Informatics,\nDepartment of Health Sciences Research,\nCenter for Individualized Medicine, Mayo Clinic\n-----------------------------\nMayo Clinic, Harwick 3-12\n200 1st street SW, Rochester, MN 55905\ntel: +1-(507)-538-0978\nfax: +1-(507)-284-0745\n\n"}}
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