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  • #16
    a problem while compling samtools

    When I complie samtools, there is a problem:

    make[1]: Entering directory '/database/yuhao/CNV/CNVnator_v0.2.5/src/samtools-0.1.6'
    gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bgzf.c -c bgzf.c
    /ngs/self-software/gcc4.6.2/libexec/gcc/x86_64-unknown-linux-gnu/4.6.2/cc1:error while loading shared libraries: libmpc.so.2: cannot open shared object file:No such file or directory
    make[1]: ***[bgzf.o] Error 1
    make[1]: Leaving directory '/database/yuhao/CNV/CNVnator_v0.2.5/src/samtools-0.1.6'
    make: *** [all-recur] Error 1

    Can anyone tell me how to solve this problem?

    Comment


    • #17
      Hi,what is the command to run CNVnator that just installed? THx!

      Comment


      • #18
        install libmpc.so.2 first

        Comment


        • #19
          Hi everyone,

          Does someone know if it's possible to install CNVnator on 32-bit system?
          here is the error that "make" generate

          /usr/local/src/cnvnator/CNVnator_v0.2.5/src# make
          g++ -pthread -m64 -DCNVNATOR_VERSION=\"v0.2.5\" -o cnvnator obj/cnvnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o /usr/local/src/samtools/samtools-0.1.18/libbam.a -lz -L/usr/local/src/cnvnator/ROOT_package/root/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lMatrix -lPhysics -lMathCore -lThread -lGui -pthread
          /usr/bin/ld: skipping incompatible /usr/local/lib/libz.a when searching for -lz
          /usr/bin/ld: cannot find -lz
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libCore.so when searching for -lCore
          /usr/bin/ld: cannot find -lCore
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libCint.so when searching for -lCint
          /usr/bin/ld: cannot find -lCint
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libRIO.so when searching for -lRIO
          /usr/bin/ld: cannot find -lRIO
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libNet.so when searching for -lNet
          /usr/bin/ld: cannot find -lNet
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libHist.so when searching for -lHist
          /usr/bin/ld: cannot find -lHist
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libGraf.so when searching for -lGraf
          /usr/bin/ld: cannot find -lGraf
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libGraf3d.so when searching for -lGraf3d
          /usr/bin/ld: cannot find -lGraf3d
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libGpad.so when searching for -lGpad
          /usr/bin/ld: cannot find -lGpad
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libTree.so when searching for -lTree
          /usr/bin/ld: cannot find -lTree
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libRint.so when searching for -lRint
          /usr/bin/ld: cannot find -lRint
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libMatrix.so when searching for -lMatrix
          /usr/bin/ld: cannot find -lMatrix
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libPhysics.so when searching for -lPhysics
          /usr/bin/ld: cannot find -lPhysics
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libMathCore.so when searching for -lMathCore
          /usr/bin/ld: cannot find -lMathCore
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libThread.so when searching for -lThread
          /usr/bin/ld: cannot find -lThread
          /usr/bin/ld: skipping incompatible /usr/local/src/cnvnator/ROOT_package/root/lib/libGui.so when searching for -lGui
          /usr/bin/ld: cannot find -lGui
          collect2: ld a retourné 1 code d'état d'exécution
          make: *** [cnvnator] Erreur 1


          I try without -m64 option of ROOTFLAGS, but in this case I have :
          make
          g++ -pthread -DCNVNATOR_VERSION=\"v0.2.5\" -o cnvnator obj/cnvnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o /usr/local/src/samtools/samtools-0.1.18/libbam.a -lz -L/usr/local/src/cnvnator/ROOT_package/root/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lMatrix -lPhysics -lMathCore -lThread -lGui -pthread
          /usr/bin/ld: i386:x86-64 architecture of input file `obj/cnvnator.o' is incompatible with i386 output
          /usr/bin/ld: i386:x86-64 architecture of input file `obj/HisMaker.o' is incompatible with i386 output
          /usr/bin/ld: i386:x86-64 architecture of input file `obj/AliParser.o' is incompatible with i386 output
          /usr/bin/ld: i386:x86-64 architecture of input file `obj/Genotyper.o' is incompatible with i386 output
          /usr/bin/ld: i386:x86-64 architecture of input file `obj/Interval.o' is incompatible with i386 output
          /usr/bin/ld: i386:x86-64 architecture of input file `obj/Genome.o' is incompatible with i386 output
          ......

          So, what I'm understanding is that I'm trying to install a program that use 64-bit libraries while I am on a 32-bit system. Is that correct? Is there any solution to solve this problem?

          Maria

          Comment


          • #20
            Hello Shriram,

            I got the same error like "In file included from cnvnator.cpp:8:
            HisMaker.hh:11:20: error: TFrame.h: No such file or directory"

            I have give following path:
            export ROOTSYS=/opt/installers/root
            export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib

            Is i m giving wrong path??

            Give me your input, how you had resolved this error??
            Thanks

            Originally posted by shriram View Post
            Unable to install the CNVnator, I get following errors

            g++ -pthread -m64 -DCNVNATOR_VERSION=\"v0.2.5\" -I:/nexsan/sbhosle/software/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
            In file included from cnvnator.cpp:8:
            HisMaker.hh:11:20: error: TFrame.h: No such file or directory
            HisMaker.hh:12:18: error: TKey.h: No such file or directory
            HisMaker.hh:13:26: error: TApplication.h: No such file or directory
            HisMaker.hh:14:19: error: TROOT.h: No such file or directory
            HisMaker.hh:15:20: error: TTimer.h: No such file or directory
            HisMaker.hh:16:21: error: Getline.h: No such file or directory
            HisMaker.hh:17:19: error: TFile.h: No such file or directory
            HisMaker.hh:18:19: error: TTree.h: No such file or directory
            HisMaker.hh:19:18: error: TH1D.h: No such file or directory
            HisMaker.hh:20:18: error: TH2D.h: No such file or directory
            HisMaker.hh:21:18: error: TH3D.h: No such file or directory
            HisMaker.hh:22:19: error: TMath.h: No such file or directory
            HisMaker.hh:23:17: error: TF1.h: No such file or directory
            HisMaker.hh:24:19: error: TLine.h: No such file or directory
            HisMaker.hh:25:21: error: TCanvas.h: No such file or directory
            HisMaker.hh:26:20: error: TStyle.h: No such file or directory
            HisMaker.hh:27:27: error: Math/DistFunc.h: No such file or directory
            HisMaker.hh:28:22: error: TPRegexp.h: No such file or directory
            HisMaker.hh:29:24: error: THashTable.h: No such file or directory
            HisMaker.hh:30:20: error: TGraph.h: No such file or directory
            In file included from cnvnator.cpp:8:
            HisMaker.hh:37: error: 'TString' does not name a type
            HisMaker.hh:38: error: 'TString' does not name a type
            HisMaker.hh:39: error: 'TString' does not name a type
            HisMaker.hh:57: error: 'TString' does not name a type
            HisMaker.hh:58: error: 'TString' does not name a type
            HisMaker.hh:59: error: 'TString' does not name a type
            HisMaker.hh:60: error: ISO C++ forbids declaration of 'TH1' with no type
            HisMaker.hh:60: error: expected ';' before '*' token
            HisMaker.hh:61: error: ISO C++ forbids declaration of 'TH1' with no type
            HisMaker.hh:61: error: expected ';' before '*' token
            HisMaker.hh:62: error: ISO C++ forbids declaration of 'TH2' with no type
            HisMaker.hh:62: error: expected ';' before '*' token
            HisMaker.hh:63: error: ISO C++ forbids declaration of 'TH1' with no type
            HisMaker.hh:63: error: expected ';' before '*' token
            HisMaker.hh:67: error: ISO C++ forbids declaration of 'TF1' with no type
            HisMaker.hh:67: error: expected ';' before '*' token
            HisMaker.hh:68: error: ISO C++ forbids declaration of 'TH1' with no type
            HisMaker.hh:68: error: expected ';' before '*' token
            HisMaker.hh:71: error: ISO C++ forbids declaration of 'TCanvas' with no type
            HisMaker.hh:71: error: expected ';' before '*' token
            HisMaker.hh:84: error: 'TString' has not been declared
            HisMaker.hh:87: error: 'TH1' has not been declared
            HisMaker.hh:87: error: 'TH1' has not been declared
            HisMaker.hh:88: error: 'TH1' has not been declared
            HisMaker.hh:88: error: 'TH1' has not been declared
            HisMaker.hh:89: error: 'TH1' has not been declared
            HisMaker.hh:89: error: 'TH1' has not been declared
            HisMaker.hh:93: error: 'TH1' has not been declared
            HisMaker.hh:93: error: 'TH1' has not been declared
            HisMaker.hh:94: error: 'TH1' has not been declared
            HisMaker.hh:94: error: 'TH1' has not been declared
            HisMaker.hh:95: error: 'TH1' has not been declared
            HisMaker.hh:95: error: 'TH1' has not been declared
            HisMaker.hh:100: error: 'TH1' has not been declared
            HisMaker.hh:100: error: 'TH1' has not been declared
            HisMaker.hh:100: error: 'TH1' has not been declared
            HisMaker.hh:101: error: 'TH1' has not been declared
            HisMaker.hh:101: error: 'TH1' has not been declared
            HisMaker.hh:101: error: 'TH1' has not been declared
            HisMaker.hh:104: error: ISO C++ forbids declaration of 'TH1' with no type
            HisMaker.hh:104: error: expected ';' before '*' token
            HisMaker.hh:105: error: ISO C++ forbids declaration of 'TH1' with no type
            HisMaker.hh:105: error: expected ';' before '*' token
            HisMaker.hh:109: error: 'TString' does not name a type
            HisMaker.hh:110: error: 'TString' does not name a type
            HisMaker.hh:111: error: 'TString' does not name a type
            HisMaker.hh:112: error: 'TString' does not name a type
            HisMaker.hh:113: error: 'TString' does not name a type
            HisMaker.hh:117: error: 'TString' does not name a type
            HisMaker.hh:118: error: 'TString' does not name a type
            HisMaker.hh:119: error: 'TString' does not name a type
            HisMaker.hh:120: error: 'TString' does not name a type
            HisMaker.hh:121: error: 'TString' does not name a type
            HisMaker.hh:122: error: 'TString' does not name a type
            HisMaker.hh:123: error: 'TString' does not name a type
            HisMaker.hh:124: error: 'TString' does not name a type
            HisMaker.hh:126: error: 'TH1' has not been declared
            HisMaker.hh:139: error: ISO C++ forbids declaration of 'TTree' with no type
            HisMaker.hh:139: error: expected ';' before '*' token
            HisMaker.hh:150: error: 'TH1' has not been declared
            HisMaker.hh:150: error: 'TH1' has not been declared
            HisMaker.hh:150: error: 'TH2' has not been declared
            HisMaker.hh:150: error: 'TH1' has not been declared
            HisMaker.hh:151: error: 'TH1' has not been declared
            HisMaker.hh:151: error: 'TH1' has not been declared
            HisMaker.hh:151: error: 'TH2' has not been declared
            HisMaker.hh:151: error: 'TH1' has not been declared
            HisMaker.hh:165: error: 'TString' has not been declared
            HisMaker.hh:168: error: 'TString' has not been declared
            HisMaker.hh:168: error: 'TString' has not been declared
            HisMaker.hh:169: error: 'TVirtualPad' has not been declared
            HisMaker.hh:169: error: 'TH1' has not been declared
            HisMaker.hh:169: error: 'TH1' has not been declared
            HisMaker.hh:169: error: 'TH1' has not been declared
            HisMaker.hh:170: error: 'TH1' has not been declared
            HisMaker.hh:170: error: 'TH1' has not been declared
            HisMaker.hh:171: error: 'TString' has not been declared
            HisMaker.hh:172: error: 'TString' has not been declared
            HisMaker.hh:172: error: 'TString' has not been declared
            HisMaker.hh:172: error: 'TString' has not been declared
            HisMaker.hh:172: error: 'TString' has not been declared
            HisMaker.hh:178: error: ISO C++ forbids declaration of 'TF1' with no type
            HisMaker.hh:178: error: expected ';' before '*' token
            HisMaker.hh:188: error: 'TH1' has not been declared
            HisMaker.hh:198: error: 'TH1' has not been declared
            cnvnator.cpp: In function 'int main(int, char**)':
            cnvnator.cpp:86: error: 'TString' was not declared in this scope
            cnvnator.cpp:86: error: expected `;' before 'tmp'
            cnvnator.cpp:87: error: 'tmp' was not declared in this scope
            cnvnator.cpp:92: error: 'tmp' was not declared in this scope
            cnvnator.cpp:186: error: 'TApplication' was not declared in this scope
            cnvnator.cpp:186: error: expected `;' before 'theApp'
            cnvnator.cpp:188: error: 'theApp' was not declared in this scope
            cnvnator.cpp:192: error: 'TApplication' was not declared in this scope
            cnvnator.cpp:192: error: expected `;' before 'theApp'
            cnvnator.cpp:194: error: 'theApp' was not declared in this scope
            cnvnator.cpp:212: error: 'TApplication' was not declared in this scope
            cnvnator.cpp:212: error: expected `;' before 'theApp'
            cnvnator.cpp:214: error: 'theApp' was not declared in this scope
            make: *** [obj/cnvnator.o] Error 1

            Thanks,
            Shriram


            Issue has been solved, it was problem with LD_LIBRAY_PATH and ROOTSYS

            Comment


            • #21
              CNVnator installation

              This is what I have in my LD_LIBRARY_PATH
              LD_LIBRARY_PATH=/compilers/gcc/4.3.5//lib:/compilers/gcc/4.3.5/lib64:${ROOTSYS}/lib

              Comment


              • #22
                Thank you dmacmillan ! your post was very helpful .. I have installed CNVnator successfully

                Comment


                • #23
                  thank you shriram..issue resolved

                  export PATH=/home/ionadmin/root/bin/:$PATH
                  export ROOTSYS=/home/ionadmin/root/
                  export LD_LIBRARY_PATH=/home/ionadmin/root/lib/

                  Comment


                  • #24
                    I my case I hade to add "-lpthread" to the make file:

                    ROOTLIBS = -L$(ROOTSYS)/lib -ldl -lpthread -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d \
                    -lGpad -lTree -lRint -lMatrix -lPhysics \
                    -lMathCore -lThread -lGui

                    Comment


                    • #25
                      Hi,
                      I would like to install CNVnator. I installed root and setted environmental variable.
                      In detail, the directory where i decompressed root is /root/source-codes/root and to set environmental variable I used this code
                      export ROOTSYS=$HOME/root
                      export PATH=$PATH:$ROOTSYS/bin
                      export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROOTSYS/lib
                      Then I entered into the src directory of CNVnator and typed the make command.
                      This is the error
                      g++ -m64 -DCNVNATOR_VERSION="v0.3" -I/root/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
                      In file included from cnvnator.cpp:8:0:
                      HisMaker.hh:11:20: fatal error: TFrame.h: No such file or directory
                      #include <TFrame.h>
                      ^
                      compilation terminated.
                      make: *** [obj/cnvnator.o] Error 1

                      How don't know what is the error.
                      Could anyone help me?

                      Comment


                      • #26
                        A Docker container for human CNV calling with CNVnator was recently developed. All you need to do is download the container and and make sure you have a WGS .bam. Calling then starts automatically, so no need to compile and run the software yourself. More info is available in this blogpost goo.gl/uodlUO.

                        Comment

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