[R-SIG-Mac] value of FLIBS and installation of packages from source

[Chris Paciorek]

Thanks, that worked. But is it a concern that users can't easily
install a package on OS X from source? Perhaps not since there should
be Mac binaries for packages on CRAN?

In particular, on CRAN (https://cran.r-project.org/bin/macosx/tools/)
I was seeing gfortran 4.2.3 and overlooked the note about more recent
Fortran binaries.  But even in clicking on that link to get to
http://r.research.att.com/tools/, I don't see the 4.8.2 version.
Should any of these items be updated?  It's not clear to me how one
would find 4.8.2 if one didn't know where to look.


chris

On Mon, Nov 2, 2015 at 1:31 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
> Chris,
>
> it seems that you didn't install the necessary Fortran compiler from
> http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
>
> Cheers,
> Simon
>
>
>> On Nov 2, 2015, at 2:03 PM, Chris Paciorek <paciorek at stat.berkeley.edu> wrote:
>>
>> I'm having trouble installing a number of R packages from source on
>> Mac OS X (Yosemite) when the packages reference FLIBS in their
>> src/Makevars.
>>
>> I have what I think is a fairly standard R install on Yosemite -
>> installed from R-3.2.2.pkg.
>>
>> Here's where an example install fails (in this case the 'actuar' package):
>> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
>> dynamic_lookup -single_module -multiply_defined suppress
>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
>> actuar.so beta.o burr.o chisq.o dpq.o dpqphtype.o exp.o gamma.o
>> genbeta.o genpareto.o hierarc.o init.o invburr.o invexp.o invgamma.o
>> invgauss.o invparalogis.o invpareto.o invtrgamma.o invweibull.o
>> lgamma.o llogis.o lnorm.o names.o normal.o panjer.o paralogis.o
>> pareto.o pareto1.o phtype.o random.o randomphtype.o trbeta.o trgamma.o
>> unif.o util.o weibull.o
>> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack
>> -L/Library/Frameworks/R.framework/Resources/lib -lRblas
>> -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran
>> -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R
>> -Wl,-framework -Wl,CoreFoundation
>> ld: warning: directory not found for option
>> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
>> ld: library not found for -lgfortran
>> clang: error: linker command failed with exit code 1 (use -v to see invocation)
>>
>> Some likely relevant facts:
>>
>> 1)
>> /Library/Frameworks/R.framework/Resources/etc/Makeconf has
>> FLIBS = -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2
>> -lgfortran -lquadmath -lm
>> but /usr/local/lib/gcc does not exist on my machine.
>>
>> 2) libquadmath.0.dylib and libgfortran.3.dylib exist in
>> /Library/Framework/R.framework/Resources/lib
>> The following kludge allows the 'actuar' package to be installed from source:
>> cd /Library/Framework/R.framework/Resources/lib
>> ln -s libgfortran.3.dylib libgfortran.dylib
>> ln -s libquadmath.0.dylib libquadmath.dylib
>>
>> albeit of course still with the warning about the nonexistent
>> /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2
>>
>> 3) Alternatively I can install the gfortran Mac package provided by
>> CRAN and manually set FLIBS in Makeconf to point to
>> /usr/local/gfortran/lib
>>
>> So, any ideas why R is being installed such that FLIBS points to a
>> non-existent directory? And for packages that don't need the fortran
>> compiler, but merely libgfortran, is there a way to install packages
>> that have FLIBS in their Makevars without installing the gfortran
>> package and monkeying with FLIBS in Makeconf?
>>
>> I'll note that this is occurring on a few machines I have access to,
>> including a new Macbook Air purchased in June 2015, with R and Xcode
>> installed thereafter. So it doesn't seem that it is a result of having
>> versions of OS X and command line tools from before Yosemite.
>>
>> I have command line tools installed:
>>
>> paciorek:/tmp> gcc --version
>> Configured with:
>> --prefix=/Applications/Xcode.app/Contents/Developer/usr
>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>> Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn)
>> Target: x86_64-apple-darwin14.3.0
>> Thread model: posix
>>
>>
>> Here's sessionInfo():
>>
>>> sessionInfo()
>> R version 3.2.2 (2015-08-14)
>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> Running under: OS X 10.10.3 (Yosemite)
>>
>> 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
>>
>>
>> thanks,
>> Chris
>>
>> ----------------------------------------------------------------------------------------------
>> Chris Paciorek
>>
>> Associate Research Statistician, Lecturer, Statistical Computing Consultant
>>
>> Office: 495 Evans Hall                      Email: paciorek at stat.berkeley.edu
>> Mailing Address:                            Voice: 510-842-6670
>> Department of Statistics                    Fax:   510-642-7892
>> 367 Evans Hall                              Skype: cjpaciorek
>> University of California, Berkeley          WWW:
>> www.stat.berkeley.edu/~paciorek
>> Berkeley, CA 94720 USA                      Permanent forward:
>> paciorek at alumni.cmu.edu
>>
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