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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
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cnvnator-multi error #79

Closed mswierniak closed 8 years ago

mswierniak commented 8 years ago

Hi, I have a problem with CNVnator compilation. Root (v.5.34.36) is installed and sourced (also added to the speedseq.cinfig). I'm using Ubuntu 14.04.4 LTS. When I've tried to 'make cnvnator-multi' I've got: :~/speedseq$ make cnvnator-multi make -C src/cnvnator ...

g++ -m64 -O3 -DCNVNATOR_VERSION=\"v0.3\" -o bin/cnvnator-multi src/obj/cnvnator.o src/obj/HisMaker.o src/obj/AliParser.o src/obj/Genotyper.o src/obj/Interval.o src/obj/Genome.o src/obj/TreeBuilder.o src/samtools/libbam.a -lz -L/home/mswierniak/root/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lMatrix -lPhysics -lMathCore -lThread -lGui /usr/bin/ld: src/obj/TreeBuilder.o: undefined reference to symbol 'pthread_create@@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 make[1]: * [cnvnator-multi] Error 1 make[1]: Leaving directory `/home/mswierniak/speedseq/src/cnvnator' make: * [cnvnator-multi] Error 2

mswierniak commented 8 years ago

It seems I solved it by myself by adding -lpthread to ROOTLIBS in the /speedseq/src/cnvnator/Makefile.