[yuhao]

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?

[yuhao]

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

[japrin]

install libmpc.so.2 first

[maria.b]

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

[sachin]

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

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

[shriram]

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

[bhakti]

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

[sachin]

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/

[pascal]

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

[simobioinfo]

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?

[cyrielle]

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.