[R-SIG-Mac] value of FLIBS and installation of packages from source
Simon Urbanek
simon.urbanek at r-project.org
Tue Nov 3 00:03:32 CET 2015
> On Nov 2, 2015, at 4:50 PM, Chris Paciorek <paciorek at stat.berkeley.edu> wrote:
>
> 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.
>
Either should work - at least last time I checked it did. If I understand your report you didn't have *any* Fortran libraries installed, but you need Fortran to compile Fortran packages -- on CRAN it says
"GNU Fortran isNOT included (needed if you want to compile packages from sources that contain FORTRAN code) please see the tools directory."
That said, I guess it would be reasonable to provide a pkg for the Mavericks Fortran and add it to the tools as well.
Cheers,
Simon
>
> 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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>>
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