> On Nov 2, 2015, at 4:50 PM, Chris Paciorek <[email protected]> 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 > <[email protected]> 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 <[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
