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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Installation error #103

Closed waqasuddinkhan closed 3 years ago

waqasuddinkhan commented 6 years ago

Hi,

My system has:

gcc --version
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.6) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
g++ --version
g++ (Ubuntu 5.4.0-6ubuntu1~16.04.6) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

and

Welcome to ROOT 6.13/01                        http://root.cern.ch |
  |                                       (c) 1995-2017, The ROOT Team |
  | Built for linuxx8664gcc                                            |
  | From heads/master@v6-11-02-1533-gee46575, févr. 08 2018, 11:51:05 |
  | Try '.help', '.demo', '.license', '.credits', '.quit'/'.q'

I used the following export commands:

export ROOTSYS=/home/wuk/software/root/build/bin/root
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$/home/wuk/software/root/build/bin/root

When I tried to run make within the src folder of CNVnator_v0.3, I received the following error:

make
g++ -m64 -DCNVNATOR_VERSION=\"v0.3\" -I/home/wuk/software/root/build/bin/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
cc1plus: error: /home/wuk/software/root/build/bin/root/include: Not a directory
Makefile:34: recipe for target 'obj/cnvnator.o' failed
make: *** [obj/cnvnator.o] Error 1

Is it version compatibility issue? or export issue of root? Any help is highly appreciated...,,,!!!!!

Thanks,

Waqas.

abyzov commented 6 years ago

Hi, from the message that you send it looks like there is a problem with directories in ROOT installation location

cc1plus: error: /home/wuk/software/root/build/bin/root/include: Not a directory

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745