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morrislab / phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.
GNU General Public License v3.0
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problem with compiling #132

Closed shaghayeghsoudi closed 3 years ago

shaghayeghsoudi commented 3 years ago

Hello, I am trying to install phyloWGS and getting the following error messages. I have installed all of the dependencies on a condo environment. So wonder what I am missing and how I can fix the problem. I appreciate the help /usr/bin/ld: warning: libcblas.so.3, needed by /home/ssoudi/miniconda3/envs/phylo/lib/libgsl.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libgfortran.so.5, needed by /home/ssoudi/miniconda3/envs/phylo/lib/libgslcblas.so, not found (try using -rpath or -rpath-link) /home/ssoudi/miniconda3/envs/phylo/lib/libgslcblas.so: undefined reference to _gfortran_etime@GFORTRAN_8' /home/ssoudi/miniconda3/envs/phylo/lib/libgslcblas.so: undefined reference to_gfortran_concat_string@GFORTRAN_8' collect2: error: ld returned 1 exit status

shaghayeghsoudi commented 3 years ago

The problem was the paths, and needed this:

g++ -O3 mh.cpp util.cpp -o mh.o \ -I/home/ssoudi/miniconda3/envs/phylo/include \ -L/home/ssoudi/miniconda3/envs/phylo/lib -lgsl -lgslcblas \ -Wl,-rpath,/home/ssoudi/miniconda3/envs/phylo/lib \ gsl-config --cflags --libs