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

[Rainer Johannes]

Dear Ludwig,

I tried to install that package and it compiled nicely on my system with 
> sessionInfo()
R Under development (unstable) (2015-10-20 r69547)
Platform: x86_64-apple-darwin15.0.0/x86_64 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.21.1

loaded via a namespace (and not attached):
[1] tools_3.3.0


I’m installing the fortran through homebrew, actually, fortran is part of the gcc “bottle” there, thus I installed
brew install gcc

and I’m building and compiling R always from source with:

/configure SHELL='/bin/bash' \
	    --prefix=$PREFIX \
	    r_arch=x86_64 \
	    --x-includes=/usr/X11/include/ \
	    --x-libraries=/usr/X11/lib/ \
	    CC="clang" \
	    CXX="clang++" \
	    OBJC="clang" \
	    F77="gfortran -arch x86_64" \
	    FC="gfortran -arch x86_64" \
	    --with-system-zlib \
	    --with-blas='-framework Accelerate' \
	    --with-lapack \
	    CPPFLAGS="-D__ACCELERATE__  \
	    --enable-R-framework=no \
	    --enable-memory-profiling \
	    --enable-R-shlib


I never had any problems anymore with missing fortran compilers on OS X

Hope that helps,

cheers, jo

> On 18 Nov 2015, at 12:12, Morgan, Martin <Martin.Morgan at roswellpark.org> wrote:
> 
> 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
> 
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