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  • CNVnator Install Instructions

    Hello all, I managed to install CNVnator after much hair-ripping. But now that I have figured everything out, follow the steps to this procedure and hopefully you will have no more issues with installation! Here we go:

    1. Install "root" http://root.cern.ch/drupal/content/downloading-root

    2. Once you have downloaded the package, unzip it, personally I use this code to untar things...
    Code:
    tar -zxvf [name of tar file]
    where you replace [name of tar file] with the actual name of your tar file e.g. "root_v5.32.00.source.tar.gz" (without quotations)

    3. now you have a folder called "root" containing everything inside the package you just extracted. Note the path to this "root" folder and save that path somewhere. I will refer to the "root" folder path as "rootpath" from now on

    4. Now you want to open up a terminal window and type the commands to install root, which is fairly simple.
    Code:
    cd root
    Code:
    ./configure
    wait for it to finish....
    Code:
    make
    wait again....
    done!

    5. NOW you want to download CNVnator http://sv.gersteinlab.org/cnvnator/

    6. To unzip it you can do it conventionally or use terminal
    Code:
    unzip -o [zip file name]
    7. You now have a folder called "CNVnator" or whatever you extracted it to. So just do the following commands from terminal:
    Code:
    cd CNVnator
    now if you type "ls" and hi enter you should see the src, license, and readme
    Code:
    cd src/samtools
    Code:
    make
    now wait for it to finish...
    Code:
    cd ..
    now your back in the "src" directory

    EVERYTHING up until this point should just work. BUT the next code you type will not unless you do the following first, so just follow...
    Code:
    export ROOTSYS=[rootpath]
    *recall that "rootpath" is the file path to your ".../root" folder where root is installed
    Now type
    Code:
    export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib
    and hit enter. No errors should come up.

    8. Now for the final step... cd back into your CNVnator/src folder and type "make" and hit enter. You should get no errors and now will be able to use CNVnator! Happy analyzing!

  • #2
    What platform are you using? I'm having a real hard time getting it to compile on OSX 10.7 with root 5.32.

    Comment


    • #3
      CentOS 2.16.0, fairly old, but still capable. What part exactly are you stuck on?

      Comment


      • #4
        I can get root to compile and the ROOTSYS and LD_LIBRARY_PATH are pointing to the right places. The problem (I think) is getting CNVator to link to libbam.a. I'v tried the included samtools and also the latest version but each time I get an error like this:

        g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
        g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c HisMaker.cpp -o obj/HisMaker.o
        g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c AliParser.cpp -o obj/AliParser.o
        g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c Genotyper.cpp -o obj/Genotyper.o
        g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c Genome.cpp -o obj/Genome.o
        g++ -pthread -m64 -o cnvnator obj/cnvnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Genome.o samtools/libbam.a -L/Users/aaron/bin/root/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lfreetype -pthread -lm -ldl
        Undefined symbols for architecture x86_64:
        "_deflateInit2_", referenced from:
        _deflate_block in libbam.a(bgzf.o)
        ....
        "_deflateSetHeader", referenced from:
        _razf_open_w in libbam.a(razf.o)
        ld: symbol(s) not found for architecture x86_64

        Any ideas?

        Comment


        • #5
          Can you type "set" without quotations into your command line and paste the results of ROOTSYS and LD_LIBRARY_PATH? I had a similar error and it turned out my LD_LIBRARY_PATH was not set correctly, each time you open a new terminal it will reset so you must do it all in one go to compile CNVnator.

          Comment


          • #6
            $ set
            Apple_PubSub_Socket_Render=/tmp/launch-PdMC3B/Render
            BASH=/bin/bash
            BASH_ARGC=()
            BASH_ARGV=()
            BASH_LINENO=()
            BASH_SOURCE=()
            BASH_VERSINFO=([0]="3" [1]="2" [2]="48" [3]="1" [4]="release" [5]="x86_64-apple-darwin11")
            BASH_VERSION='3.2.48(1)-release'
            CLASSPATH=.:/Users/aaron/Library/Java
            COLUMNS=169
            COMMAND_MODE=unix2003
            DIRSTACK=()
            DISPLAY=/tmp/launch-dwl7XD/org.x:0
            DYLD_LIBRARY_PATH=/Users/aaron/programs/root-5.32/lib
            EDITOR=emacs
            EUID=503
            GROUPS=()
            HISTFILE=/Users/aaron/.bash_history
            HISTFILESIZE=10000
            HISTSIZE=500
            HISTTIMEFORMAT='%Y-%m-%d %H:%M '
            HOME=/Users/aaron
            HOSTNAME=agamemnon.local
            HOSTTYPE=x86_64
            IFS=$' \t\n'
            LANG=en_US.UTF-8
            LD_LIBRARY_PATH=/Users/aaron/programs/root-5.32/lib:/usr/local/mysql/lib
            LIBPATH=/Users/aaron/programs/root-5.32/lib
            LINES=50
            LOGNAME=aaron
            MACHTYPE=x86_64-apple-darwin11
            MAILCHECK=60
            MANPATH=/Users/aaron/programs/root-5.32/man:/Library/Frameworks/EPD64.framework/Versions/Current/share/man:/Library/Frameworks/Python.framework/Versions/Current/share/man:/opt/local/share/man:/usr/share/man:/usr/local/share/man:/usr/X11/man:/usr/local/mysql/man
            MKL_NUM_THREADS=1
            OLDPWD=/Users/aaron/programs/CNVnator
            OLD_ROOTSYS=/Users/aaron/bin/root
            OPTERR=1
            OPTIND=1
            OSTYPE=darwin11
            PATH=/Users/aaron/programs/root-5.32/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python.framework/Versions/Current/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Users/aaron/programs/GenomeAnalysisTK-1.0.5336:/Users/aaron/programs/novocraft:/Users/aaron/programs/MUMmer3.22:/Users/aaron/bin:/Users/aaron/Dropbox/bin:/Users/aaron/bin/x86_64:/Users/aaron/programs/blast3:/usr/local/mysql/bin
            PERL5LIB=/Users/aaron/programs/vcftools_0.1.4a/perl
            PIPESTATUS=([0]="2")
            PPID=231
            PROMPT_COMMAND='update_terminal_cwd; '
            PS1='\u:\W '
            PS2='> '
            PS4='+ '
            PWD=/Users/aaron/programs/CNVnator/src
            PYTHONPATH=/Users/aaron/programs/root-5.32/lib:/Users/aaron/lib:/Users/aaron/Dropbox/lib:/Users/aaron/Dropbox/bin
            ROOTSYS=/Users/aaron/programs/root-5.32
            SECURITYSESSIONID=186a5
            SHELL=/bin/bash
            SHELLOPTS=braceexpand:emacs:hashall:histexpand:history:interactive-comments:monitor
            SHLIB_PATH=/Users/aaron/programs/root-5.32/lib
            SHLVL=1
            SSH_AUTH_SOCK=/tmp/launch-NrEVlu/Listeners
            TERM=xterm-256color
            TERM_PROGRAM=Apple_Terminal
            TERM_PROGRAM_VERSION=299
            TERM_SESSION_ID=3AC7B6C9-0A77-4377-8917-9F03FFF1BE39
            THIS=bin
            TMPDIR=/var/folders/1j/lkx2dg7d7tn6f4t4c6lwmt9r0000gq/T/
            UID=503
            USER=aaron
            _=make
            _GOOGLE_GILD_RUNTIME_FRAMEWORK_ABSOLUTE_PATH_=/Library/Google/Frameworks/Gild.framework
            __CF_USER_TEXT_ENCODING=0x1F7:0:0
            default_manpath=/Library/Frameworks/EPD64.framework/Versions/Current/share/man:/Library/Frameworks/Python.framework/Versions/Current/share/man:/opt/local/share/man:/usr/share/man:/usr/local/share/man:/usr/X11/man:/usr/local/mysql/man
            drop=/Users/aaron/bin/root/lib
            newpath=/Users/aaron/lib:/Users/aaron/Dropbox/lib:/Users/aaron/Dropbox/bin
            p=/Users/aaron/lib:/Users/aaron/Dropbox/lib:/Users/aaron/Dropbox/bin
            calc ()
            {
            awk "BEGIN{ print $* }"
            }
            drop_from_path ()
            {
            if test $# -ne 2; then
            echo "drop_from_path: needs 2 arguments";
            return 1;
            fi;
            p=$1;
            drop=$2;
            newpath=`echo $p | sed -e "s;:${drop}:;:;g" -e "s;:${drop};;g" -e "s;${drop}:;;g" -e "s;${drop};;g"`
            }
            update_terminal_cwd ()
            {
            local SEARCH=' ';
            local REPLACE='%20';
            local PWD_URL="file://$HOSTNAME${PWD//$SEARCH/$REPLACE}";
            printf '\e]7;%s\a' "$PWD_URL"
            }

            $ echo $LD_LIBRARY_PATH
            /Users/aaron/programs/root-5.32/lib:/usr/local/mysql/lib

            $ echo $ROOTSYS
            /Users/aaron/programs/root-5.32

            $ which root
            /Users/aaron/programs/root-5.32/bin/root

            $ make clean
            $ make
            g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
            g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c HisMaker.cpp -o obj/HisMaker.o
            g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c AliParser.cpp -o obj/AliParser.o
            g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c Genotyper.cpp -o obj/Genotyper.o
            g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c Genome.cpp -o obj/Genome.o
            g++ -pthread -m64 -o cnvnator obj/cnvnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Genome.o samtools/libbam.a -L/Users/aaron/programs/root-5.32/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lfreetype -pthread -lm -ldl
            Undefined symbols for architecture x86_64:
            "_deflateInit2_", referenced from:
            _deflate_block in libbam.a(bgzf.o)
            _razf_open_w in libbam.a(razf.o)
            "_deflate", referenced from:
            _deflate_block in libbam.a(bgzf.o)
            _razf_write in libbam.a(razf.o)
            __razf_write in libbam.a(razf.o)
            _razf_close in libbam.a(razf.o)
            "_deflateEnd", referenced from:
            _deflate_block in libbam.a(bgzf.o)
            _razf_close in libbam.a(razf.o)
            "_crc32", referenced from:
            _deflate_block in libbam.a(bgzf.o)
            "_inflateInit2_", referenced from:
            _bgzf_read_block in libbam.a(bgzf.o)
            __razf_open in libbam.a(razf.o)
            "_inflate", referenced from:
            _bgzf_read_block in libbam.a(bgzf.o)
            __razf_read in libbam.a(razf.o)
            "_inflateEnd", referenced from:
            _bgzf_read_block in libbam.a(bgzf.o)
            _razf_close in libbam.a(razf.o)
            __razf_open in libbam.a(razf.o)
            "_gzclose", referenced from:
            _sam_close in libbam.a(bam_import.o)
            _sam_header_read2 in libbam.a(bam_import.o)
            ___bam_get_lines in libbam.a(bam_import.o)
            "_gzdopen", referenced from:
            _sam_open in libbam.a(bam_import.o)
            _sam_header_read2 in libbam.a(bam_import.o)
            ___bam_get_lines in libbam.a(bam_import.o)
            "_gzopen", referenced from:
            _sam_open in libbam.a(bam_import.o)
            _sam_header_read2 in libbam.a(bam_import.o)
            ___bam_get_lines in libbam.a(bam_import.o)
            "_gzread", referenced from:
            _ks_getuntil in libbam.a(bam_import.o)
            _sam_header_read2 in libbam.a(bam_import.o)
            "_inflateReset", referenced from:
            _razf_seek in libbam.a(razf.o)
            _razf_jump in libbam.a(razf.o)
            "_deflateSetHeader", referenced from:
            _razf_open_w in libbam.a(razf.o)
            ld: symbol(s) not found for architecture x86_64
            collect2: ld returned 1 exit status
            make: *** [cnvnator] Error 1

            Comment


            • #7
              I suggest you try again from scratch. Use the included samtools. I am not familiar with the usage of libbam.a or how CNVnator utilizes it. But make sure that it was actually created (inside the samtools folder), did you check to see if it exists? Other than that I don't know what could be causing the problem, but right now I think it might be that if your using an external samtools then it wouldn't have libbam.a included in its source directory. So use the included one and 'make' from inside it and check if libbam.a is there.

              Comment


              • #8
                I'm assuming that libbam.a is used to read the bam files. It is definitely there. I also used nm to see if the offending symbol is present and it is:
                $ nm samtools/libbam.a |grep deflateInit2
                U _deflateInit2_
                U _deflateInit2_
                The compiled objects are indeed 64 bit:
                $ file samtools/bgzf.o
                samtools/bgzf.o: Mach-O 64-bit object x86_64

                Quite frustrating.

                Comment


                • #9
                  Looks like the problem runs quite deep, and I am not very good with libraries and linking them. You could try including your root/lib in your $PATH, I see you only have root/bin. Try that and if it doesn't work then contact the developer because this problem is most likely beyond me. Kind of a last ditch silly error fix, but who knows, its worth a shot.

                  -cheers

                  Comment


                  • #10
                    For the record, there seems to be a problem linking the libz libraries with OSX but CNVnator works fine if you tell it to ignore the linking problems by adding -Wl,-undefined,dynamic_lookup to the Makefile as:
                    cnvnator: $(OBJS)
                    $(CXX) -Wl,-undefined,dynamic_lookup -o [email protected] $(OBJS) $(SAMLIB) $(ROOTLIBS)

                    Much thanks to the author, Alex Abyzov, for helping me overcome this odd situation.

                    Comment


                    • #11
                      Hello, I followed the instructions given here and successfully installed root and setup the environment variables. The samtools in CNVnator_v0.2.5/src also compiled successfully.

                      I'm stuck at the final make step for CNVnator. I get the following error:

                      ~/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 samtools/libbam.a -lz -L/home/faraaz/root/lib -lNet -lCore -lCint -lRIO -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lMatrix -lPhysics -lMathCore -lThread -lGui -pthread
                      /home/faraaz/root/lib/libCint.so: undefined reference to `dlclose'
                      /home/faraaz/root/lib/libCint.so: undefined reference to `dlsym'
                      /home/faraaz/root/lib/libCint.so: undefined reference to `dlopen'
                      /home/faraaz/root/lib/libCint.so: undefined reference to `dlerror'
                      /home/faraaz/root/lib/libCore.so: undefined reference to `dladdr'
                      collect2: ld returned 1 exit status
                      make: *** [cnvnator] Error 1


                      I'm running this on Ubuntu 10.04. Can anyone help me to solve this? Thanks very much!

                      Comment


                      • #12
                        Ah I managed to fix my problem after searching around on google for a while.

                        I added in the term "-ldl" into the makefile so that it looks like this:

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

                        Comment


                        • #13
                          Good to know, thanks for the input!

                          Comment


                          • #14
                            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
                            Last edited by shriram; 03-23-2012, 05:47 AM.

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                            • #15
                              Thanks dmacmillan, this made my life so much easier!

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