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
