mfranberg/besiq

Genetic interaction analysis

besiq's Issues

Compiling on mac os

Running on Mac OS X 10.14.4 I installed the Armadillo pkg through homebrew:

brew install armadillo

Then the cmake worked alright. However, when running "make" I ran into the following problem:

Scanning dependencies of target gene_environment
[ 67%] Building CXX object src/CMakeFiles/gene_environment.dir/gene_environment.cpp.o
clang: error: no such file or directory: 'NOTFOUND'
make[2]: *** [src/CMakeFiles/gene_environment.dir/gene_environment.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/gene_environment.dir/all] Error 2
make: *** [all] Error 2

When looking at flags.make in the gene_environment folder I saw the following:

CXX_FLAGS = -std=c++11 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk NOTFOUND I have no clue how the NOTFOUND ended up there. It's also in the link.txt. Had to manually delete it in the two files and then this part worked. There were 2-3 more folders where I had to do the same: remove NOTFOUND in CXX_FLAGS of flags.make and in link.txt. Then it compiled.

Any idea where this came from? It's not important, in particular because it looks like a Mac specific problem, but maybe others running into the same problem might benefit from this issue.

Any test data available?

The Readme file in the section "For the impatient" contains the following block:

ls /data/
dataset.pair
dataset.bim
dataset.fam
dataset.bed

So these data apparently are located outside the project, so as an outsider it's not possible to run this - hence, this is unfortunately not very helpful. I understand that some data cannot be shared, but I definitely miss a statement about this in the README file. Furthermore, it would be nice to include any real "trial" data as part of the program so I could at least try out the software? :-(