[Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1

Morgan, Martin Martin.Morgan at roswellpark.org
Wed Nov 18 12:12:15 CET 2015

Probably the definitive answer will be the R-SIG-Mac mailing list


perhaps specifically this thread


which points to the R-admin manual and especially


From the discussion (especially the posts by Brian Ripley) it seems like it should be possible to use gfortran-5.2 via editing the R_HOME/etc/Makeconf or ~/.R/Makevars.


From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Ludwig Geistlinger [Ludwig.Geistlinger at bio.ifi.lmu.de]
Sent: Wednesday, November 18, 2015 5:53 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan      10.11.1


I am experiencing troubles installing "Hmisc", especially its dependency
"acepack", via

> biocLite("acepack")

in R-devel installed from the "R-devel-mavericks-signed.pkg" downloaded
from https://r.research.att.com/.

The error reads:

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable)
  (2015-11-16 r69640).
Installing package(s) ‘acepack’
Paket, das nur als Quelltext vorliegt und eventuell Übersetzung von
  C/C++/Fortran benötigt.: ‘acepack’
Do you want to attempt to install these from sources?
y/n: y
installing the source package ‘acepack’

versuche URL 'https://cran.rstudio.com/src/contrib/acepack_1.3-3.3.tar.gz'
Content type 'application/x-gzip' length 33590 bytes (32 KB)
downloaded 32 KB

* installing *source* package ‘acepack’ ...
** Paket ‘acepack’ erfolgreich entpackt und MD5 Summen überprüft
** libs
gfortran-4.8   -fPIC  -g -O2  -c ace.f -o ace.o
make: gfortran-4.8: No such file or directory
make: *** [ace.o] Error 1
ERROR: compilation failed for package ‘acepack’
* removing

which indicates that "gfortran-4.8" is missing.
I have however installed the recommended "gfortran-5.2" for El Capitan
from here:


Yesterday, I tried quite some time to install 4.8-versions of gfortran
available from the website above, however they are not compatible with El
Capitan (Error reads: kern.osversion not recognized: »15.0.0) and searched
through several newsgroups reporting on that issue, I was however not able
to fix that.

Did anyone of the community here experienced similar issues and have some
suggestions for me!?

Thank you very much!


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