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

[Simon Urbanek]

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
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