I am having an error updating several R bioconductor packages such as "genefilter". Each time I try updating it I get that error:

gfortran-4.8   -fPIC  -g -O2  -c AMD/Source/amd.f -o AMD/Source/amd.o

gfortran-4.8: warning: couldn’t understand kern.osversion ‘14.3.0
f951: internal compiler error: Illegal instruction: 4

f951: internal compiler error: Abort trap: 6
gfortran-4.8: internal compiler error: Abort trap: 6 (program f951)
make: *** [akj.o] Abort trap: 6
ERROR: compilation failed for package ‘gene filter’

I am using R version 3.2.2, Biovonductor 3.1 on Yosemite OS X

Any idea what the error means and how to solve it?

Thanks

You don't say how you are trying to install the package, but if you install it like this:

source("https://bioconductor.org/biocLite.R")
​biocLite("genefilter")

That should install the binary version by default which does not require compilation.