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
