> On 3 Nov 2015, at 05:07, Kevin Ushey <[email protected]> wrote: > > 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:
But the R-admin manual is very clear about this, and the posting guide does require checking the manual before posting .... > > 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 _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
