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 <[email protected]> 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: [email protected] > 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: > [email protected] > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
