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

[Morgan, Martin]

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

  https://stat.ethz.ch/mailman/listinfo/r-sig-mac

perhaps specifically this thread

  https://stat.ethz.ch/pipermail/r-sig-mac/2015-October/011641.html

which points to the R-admin manual and especially

  https://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X

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.

Martin


________________________________________
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

Hi,

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
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/acepack’


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

https://gcc.gnu.org/wiki/GFortranBinaries#MacOS

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!

Best,
Ludwig

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.