My understanding is that gfortran 4.2.3 was used with CRAN R built with pre-Mavericks OSes (ie, before Apple made the move from gcc to clang); nowadays gfortran 4.8.2 is used. Considering that you're on Yosemite, you want to be installing gfortran 4.8.2.
Unfortunately, this information is not very well advertised on the tools pages; it would be helpful if these pages were updated: https://cran.r-project.org/bin/macosx/tools/ http://r.research.att.com/tools/ Best, Kevin On Mon, Nov 2, 2015 at 7:31 PM, Chris Paciorek <[email protected]> wrote: > Yes, good point, I think on one of my machines I did have gfortran > from a different source. > > That said, on a different machine, I had Xcode and R installed but not > gfortran. So I just now installed the 4.2.3 gfortran from CRAN, and as > seen below, FLIBS is still pointing to a non-existent directory and > while libgfortran.dylib is now available, libquadmath.dylib is not, so > any installation from source of a package that uses FLIBS will fail > (and will also warn about the non-existing > /usr/local/lib/gcc/x86_64-apple-darwin13.0.0). That was with R 3.2.0. > I also tried installing R 3.2.2 after gfortran 4.2.3 was already > installed and FLIBS is still pointing to the non-existent location. > (I'm guessing > FLIBS in etc/Makeconf is being set based on the OS X version and > not based on any looking for gfortran on the user's system.) > > So am I misreading things that the 4.2.3 gfortran provided by R is not > fully compatible with R on recent OS X versions and that installing > FLIBS-reliant packages from source will generally fail unless one gets > the 4.8.2 gfortran? If that is the case, I do think it would be > helpful if you could provide the 4.8.2 gfortran as the default so that > users who try to install FLIBS-reliant packages from source will be > able to. > > chris > > =================== > > paciorek@glinda:~/Downloads> R CMD config FLIBS > -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm > > paciorek@glinda:~/Downloads> ls /usr/local/lib/gcc > i686-apple-darwin8 powerpc-apple-darwin8 > > paciorek@glinda:~/Downloads> ls /usr/local/lib/libgfortran* > /usr/local/lib/libgfortran.2.0.0.dylib /usr/local/lib/libgfortran.dylib > /usr/local/lib/libgfortran.2.dylib /usr/local/lib/libgfortran.la > /usr/local/lib/libgfortran.a > > paciorek@glinda:~/Downloads> ls /usr/local/lib/libquadmath* > ls: /usr/local/lib/libquadmath*: No such file or directory > > On Mon, Nov 2, 2015 at 6:35 PM, Simon Urbanek > <[email protected]> wrote: >> >> On Nov 2, 2015, at 6:31 PM, Chris Paciorek <[email protected]> >> wrote: >> >>> 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. >>> >> >> ... but that is *not* what the CRAN Fortran uses - so I guess you had >> different Fortran installed - which is why it didn't work. I suspect that if >> you had actually [re?]installed the Fortran from Tools it would work, but >> you [or some script] have possibly removed the libraries from /usr/local/lib >> or had a different Fortran which is why you got the error. >> >> Cheers, >> Simon >> >> >>> 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 _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
