value of FLIBS and installation of packages from source
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
<simon.urbanek at r-project.org> wrote:
On Nov 2, 2015, at 4:50 PM, Chris Paciorek <paciorek at stat.berkeley.edu> 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 <simon.urbanek at r-project.org> 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 <paciorek at stat.berkeley.edu> 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: paciorek at stat.berkeley.edu 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: paciorek at alumni.cmu.edu
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