gfortran 4.8 error within R on OS X Yosemite

Question

I have been using this R package for single-cell analysis (SCDE) for the past few months on a Linux machine without any problems.

I have been having a lot of trouble getting it to work on my Mac, though. Installing on Mavericks seems to work fine, but I've tried on two Macs with Yosemite to no avail.

The problem seems to be with gfortran 4.8 not playing nice with Yosemite; I get this error:

gfortran-4.8   -fPIC  -g -O2  -c dqrdc.f -o dqrdc.o
gfortran-4.8: warning: couldn’t understand kern.osversion ‘14.1.1

Many people get this error on Yosemite while trying to use gfortran outside of R, and the solution they have found is to upgrade to gfortran 5.0 , which has been fixed to work well with Yosemite.

However, R calls a specific version of gfortran (4.8) , so I'm kind of stuck here. I can't really upgrade to gfortran 5.0 because R won't recognize it, and gfortran 4.8 doesn't work well with my OS.

Any help would be much appreciated.

Answer 1

If you have Homebrew, you can install gcc/gfortran 4.8 alongside newer gfortran like this:

brew install gcc48 --with-fortran

Same issue discussed in more detail here: OS X package installation depends on gfortran-4.8