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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.

Ross
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Carmen Sandoval
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  • I had a clean install of Yosemite and installed XCode, XQuartz, command line tools. – Carmen Sandoval Jul 30 '15 at 00:40
  • But I was able to install it on two colleagues' Macs with Mavericks. – Carmen Sandoval Jul 30 '15 at 00:40
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    It is a not an error. It's a warning and can safely be ignored. I use that gfortran and compile R packages and have used it to create a standalone command line application in OS X Yosemite. As far as I can tell it's just a bug in gcc/gfortran. Maybe [this](https://gcc.gnu.org/bugzilla/show_bug.cgi?id=61407) helps . – Bhas Jul 30 '15 at 05:37
  • Of course I intended to write [this discussion](https://gcc.gnu.org/bugzilla/show_bug.cgi?id=61407). – Bhas Jul 30 '15 at 06:19
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    @Bhas, unfortunately, it is in fact an error. It causes the installation of the package to fail. – Carmen Sandoval Aug 01 '15 at 00:10
  • H'm. As I wrote I have that warning too and a package has not failed to install. And I use compiled CRAN packages for OS X Mavericks and higher. Without more details it's not possible to find out what's the matter. – Bhas Aug 02 '15 at 05:22

1 Answers1

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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

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burger
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