I may have been unclear in my original message -- I had gfortran 4.2.3 installed previously and was having the problem with that older version installed. With 4.2.3, if I _manually_ set FLIBS in etc/Makeconf to point to /usr/local/gfortran/lib, then the problem went away.
Once I installed 4.8.2, things were fine without having to change FLIBS in etc/Makeconf. chris On Mon, Nov 2, 2015 at 3:03 PM, Simon Urbanek <[email protected]> wrote: > >> 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
