I don't see any mention in the admin manual that GCC add-ons are no longer recommended. The section you linked to says: "Other compilers from http://r.research.att.com/tools/ can also be used." That tools page further says: "Note: If you are interested in cutting-edge compilers and/or integration of GNU Fortran and Apple's compilers see gcc 4.2 section below." That's what I was using, "gcc-4.2 (Apple build 5666.3) with GNU Fortran 4.2.4 for Mac OS X 10.7 (Lion)", since I use XCode and liked the integration. I should have noted that in my message, although I didn't know that the path would be different.
Davor On 2013-05-08, at 11:40 PM, Prof Brian Ripley wrote: > Note that the recommended CRAN gfortran *does* go into /usr/local. This one: > http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg as described at > http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X . > > That's for R 3.0.0: other versions were recommended for earlier versions as > add-ons to gcc versions which are no longer recommended. > > If you are not using the recommended compiler with a CRAN binary build you > should set some variables in ~/.R/Makevars: see > http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages . > > On 08/05/2013 23:28, Davor Cubranic wrote: >> I don't see this on my machine: >> >>> install.packages('fields', type='source') >> * installing *source* package 'fields' ... >> ** package 'fields' successfully unpacked and MD5 sums checked >> ** libs >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c css.f -o css.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c csstr.f -o csstr.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c cvrf.f -o cvrf.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c dchold.f -o dchold.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c dcopy.f -o dcopy.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c ddfind.f -o ddfind.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c ddot.f -o ddot.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c derrb.f -o derrb.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c dlv.f -o dlv.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c dmaket.f -o dmaket.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c drdfun.f -o drdfun.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c dsetup.f -o dsetup.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c evlpoly.f -o evlpoly.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c evlpoly2.f -o evlpoly2.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c expfn.f -o expfn.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c ifind.f -o ifind.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c igpoly.f -o igpoly.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c inpoly.f -o inpoly.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c mltdrb.f -o mltdrb.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c mltdtd.f -o mltdtd.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c multeb.f -o multeb.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c multrb.f -o multrb.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c radbas.f -o radbas.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c radfn2.f -o radfn2.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c radfun.f -o radfun.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c rcss.f -o rcss.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c rcssr.f -o rcssr.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c rcsswt.f -o rcsswt.o >> gfortran-4.2 -arch x86_64 -fPIC -g -O2 -c sortm.f -o sortm.o >> llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib >> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module >> -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o fields.so >> css.o csstr.o cvrf.o dchold.o dcopy.o ddfind.o ddot.o derrb.o dlv.o dmaket.o >> drdfun.o dsetup.o evlpoly.o evlpoly2.o expfn.o ifind.o igpoly.o inpoly.o >> mltdrb.o mltdtd.o multeb.o multrb.o radbas.o radfn2.o radfun.o rcss.o >> rcssr.o rcsswt.o sortm.o >> -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 >> -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran >> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework >> -Wl,CoreFoundation >> ld: warning: directory not found for option >> '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64' >> ld: warning: directory not found for option '-L/usr/local/lib/x86_64' >> ld: warning: directory not found for option >> '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3' >> installing to /private/tmp/library/fields/libs >> ** R >> ** data >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices >> ** testing if installed package can be loaded >> * DONE (fields) >> >> I'm also running R-3.0.0 and OS X 10.7.5, so I think the issue is your >> environment. Why do you have gfortran in /usr/local anyways? CRAN's fortran >> goes into /usr/bin. >> >> Note that you set FC and F77 to "gfortran-4.2" (no path), so that will look >> for it in your PATH, and you probably have /usr/local/gfortran/bin before >> /usr/bin. Try either removing /usr/local/gfortran directory or make sure the >> one in /usr/bin is found first. >> >> Davor >> >> On 2013-05-07, at 4:30 PM, Andy Jacobson (NOAA Affiliate) wrote: >> >>> Howdy, >>> >>> I am attempting to install the fields_6.7.6 package under R-3.0.0 on OS X >>> 10.7.5. I think the install process is calling the wrong gfortran >>> compiler. The compiler being called is /usr/local/gfortran/bin/gfortran, >>> which is "GNU Fortran (GCC) 4.4.0 20090321 (experimental) [trunk revision >>> 144983]". I've installed the gfortran-4.2.3.pkg package from >>> http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg. >>> >>> The /Library/Frameworks/R.framework/Versions/3.0/Resources/etc/Makeconf >>> file specifies: >>> >>> FC = gfortran-4.2 -arch x86_64 >>> and >>> F77 = gfortran-4.2 -arch x86_64 >>> >>> The text output from install.packages() shows lots of -c compilation using >>> this wrong gfortran, then attempts to link with llvm-gcc-4.2. The linking >>> step complains about the .o files being architecture i386, which is >>> probably wrong output from the gfortran-4.4.0 compiler: >>> >>>> /usr/local/gfortran/bin/gfortran -fPIC -g -O2 -c sortm.f -o sortm.o >>>> llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib >>>> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module >>>> -multiply_defined suppress -L/usr/local/gfortran/lib/ -o fields.so css.o >>>> csstr.o cvrf.o dchold.o dcopy.o ddfind.o ddot.o derrb.o dlv.o dmaket.o >>>> drdfun.o dsetup.o evlpoly.o evlpoly2.o expfn.o ifind.o igpoly.o inpoly.o >>>> mltdrb.o mltdtd.o multeb.o multrb.o radbas.o radfn2.o radfun.o rcss.o >>>> rcssr.o rcsswt.o sortm.o >>>> -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 >>>> -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 >>>> -lgfortran -F/Library/Frameworks/R.framework/.. -framework R >>>> -Wl,-framework -Wl,CoreFoundation >>>> ld: warning: ld: warning: ignoring file css.o, file was built for i386 >>>> which is not the architecture being linked (x86_64): css.oignoring file >>>> csstr.o, file was built for i386 which is not the architecture being >>>> linked (x86_64): csstr.o >>> >>> >>> >>> There's no Makefile in the fields package, so FC and F77 are not being >>> overridden by the package itself, I believe. The FC and F77 variables from >>> R's Makeconf are not being respected, and I've tried to specify alternative >>> gfortran compilers with syntax like: >>> >>> >>> install.packages("fields",type="source",repos="http://cran.us.r-project.org",clean=TRUE,configure.vars=list(F77="gfortran-4.2 >>> -arch x86_64",FC="gfortran-4.2 -arch x86_64")) >>> >>> Nothing I do seems to tell the fields package to use the proper gfortran >>> compiler. I have no environment variables like FC or F77 defined. I have >>> to admit that I do have four different gfortran versions installed on this >>> machine: in addition to the R pkg version and the gfortran-4.4.0, there's >>> a fink /sw/bin/gfortran 4.6.2, and a /usr/bin/gfortran-4.2 which claims to >>> come from Apple (GNU Fortran (GCC) 4.2.1 (Apple Inc. build 5566)). I'm up >>> to date with Xcode. >>> >>> Any advice about how to do this correctly would be much appreciated! >>> >>> Thanks, >>> >>> Andy >>> -- >>> Andy Jacobson >>> [email protected] >>> >>> NOAA Earth System Research Lab >>> Global Monitoring Division >>> 325 Broadway R/GMD1 >>> Boulder, Colorado 80305 >>> >>> 303/578-2237 >>> >>> _______________________________________________ >>> 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 >> > > > -- > Brian D. Ripley, [email protected] > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > _______________________________________________ > 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
