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dipetkov / eems

Estimating Effective Migration Surfaces
GNU General Public License v2.0
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Issue with installation #31

Closed nehasavant closed 5 years ago

nehasavant commented 5 years ago

Hi Dr. Petkova,

I'm having trouble with installing bed2diffs properly. I've downloaded the EEMS files and the plinkio files from Github (I put both master directories in one folder labeled "EEMS"). Then I edited the PLINKIO variable in the makefile in "src-wout-openmp" (I'm working on a Mac) to where I've downloaded the "libplinkio-master" directory. However, I'm getting this error when I run make darwin in terminal within the src-wout-openmp directory: 

Nehas-MacBook-Pro:src-wout-openmp nehasavant$ make darwin
c++ -I/Users/nehasavant/Dropbox/Columbia_New_York/Salamanders/Downstream_Analyses/EEMS/libplinkio-master//include -O3 -Wall -Werror -c bed2diffs_v1.cpp -o bed2diffs_v1.o
In file included from bed2diffs_v1.cpp:3:
./data.hpp:7:10: fatal error: 'plinkio/plinkio.h' file not found
#include <plinkio/plinkio.h>
         ^~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [bed2diffs_v1.o] Error 1

I'm not quite sure what I'm doing wrong. Any thoughts or advice would be much appreciated!

Thank you, Neha

nehasavant commented 5 years ago

I think the issue is that the new versions of plinkio do not contain the "include" folder that my error is saying I need. I had a colleague send me an older version of the plinkio folder which had the "include" folder and the command worked.

If anybody else is having this problem, feel free to message me for a link to an older version of plinkio.

dipetkov commented 5 years ago

Thanks for pointing this out. You are right that with the latest version of libplinkio, it is necessary to change the line

CXXFLAGS = -I${PLINKIO}/include -O3 -Wall -Werror

to

CXXFLAGS = -I${PLINKIO} -O3 -Wall -Werror

in the Makefile of bed2diffs.

Since libplinkio is on GitHub you can also get any older version by checking out its corresponding commit. For example, the current commit is 781e9ee37076... and to use that version of libplinkio in the future:

git clone https://github.com/mfranberg/libplinkio
cd libplinkio
git checkout 781e9ee37076

This should work now with bed2diffs since I've updated the c++ flags in the Makefile.