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
