On 30 Aug 2012, at 17:10, Simon Urbanek <[email protected]> wrote:
> > On Aug 30, 2012, at 11:42 AM, Federico Calboli <[email protected]> > wrote: > >> On 30 Aug 2012, at 16:26, Simon Urbanek <[email protected]> wrote: >> >>> >>> On Aug 30, 2012, at 11:19 AM, Federico Calboli <[email protected]> >>> wrote: >>> >>>> On 22 Aug 2012, at 15:12, Simon Urbanek <[email protected]> >>>> wrote: >>>> >>>>> >>>>> On Aug 22, 2012, at 6:34 AM, Federico Calboli <[email protected]> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I used to be able to use the Fortran binaries provided by Simon for both >>>>>> R and Julia, but alas this will not be possible anymore: >>>>>> >>>>>> "The problem is not BLAS, but your version of gfortran. Mac provides a >>>>>> built-in system blas, so it is not required to build our own. However, >>>>>> "checking for Fortran 77 name-mangling scheme... unknown" is a problem. >>>>>> It appears that the R version of gfortran is too old to build arpack (a >>>>>> quick google search reveals that gfortran older than 4.4 won't build >>>>>> code properly on 64 bit -- yours is 4.2.3) ." >>>>>> >>>>>> I could install the GFortran from here: >>>>>> http://gcc.gnu.org/wiki/GFortranBinaries#MacOS. but (1) they will >>>>>> overwrite /usr/local/bin/gfortran (with a symlink) and (2) I don't know >>>>>> if it will work for R. >>>>>> >>>>>> So, will the GCC binary work for R, or is it going to be utter PITA? >>>>>> I'm on 10.8, Xcode 4.4.1 + CLI add-ons and all the other bells and >>>>>> whistles. >>>>>> >>>>> >>>>> They won't work with CRAN R binaries because they don't use Apple >>>>> driver-drivers (i.e. they don't support -arch etc.)*. If you compile R >>>>> from sources, you can use any Fortran binary you want - it will be tied >>>>> to your particular runtime (and you can't use -arch). >>>> >>>> I use the CRAN R binary and CRAN binary packages >>>>> >>>>> BTW: The FSF Fortran installs in /usr/local/gfortran so it can peacefully >>>>> co-exist with out CRAN Fortran -- even in our Fortran gfortran is just a >>>>> symlink to gfortran-4.2 so you can easily restore it with >>>>> sudo ls -sfn gfortran-4.2 /usr/local/bin/gfortran >>>>> if you wish. >>>> >>>> Given the above, can I leave gfortran to point to the GCC fortran? >>> >>> Not for CRAN binary unless you do sed 's:gfortran -arch:gfortran-4.2 >>> -arch:g' on both Makeconf files … >> >> are you saying the binaries (R + whatever libraries I install) using fortran >> will not work with GCC fortran? I am confused. >> > > The *binaries* don't care about the Fortran as R comes with its own gfortran > runtime, but you can't compile packages that have Fortran code with FSF > Fortran as it doesn't understand Apple flags. > > >>>> if I do not, julia throws a hissy fit every time I compile it, >>> >>> Can't you just set FC and F77 to gfortran-4.2 when configuring Julia? >> >> It used to be possible (I did successfully build julia on Lion with the R >> gfortran add on for Lion), though now I am on ML and julia has a fit trying >> to build arpack with a fortran < 4.4. As I posted above from the julia dev >> conversation I started: >> >> "The problem is not BLAS, but your version of gfortran. Mac provides a >> built-in system blas, so it is not required to build our own. However, >> "checking for Fortran 77 name-mangling scheme... unknown" is a problem. It >> appears that the R version of gfortran is too old to build arpack (a quick >> google search reveals that gfortran older than 4.4 won't build code properly >> on 64 bit -- yours is 4.2.3) ." >> > > > But then it's using the wrong compiler ... did you change FC to gfortran-4.2 > in Make.inc? I didn't realize that julia doesn't even have a reasonable build > system, so you have to edit it by hand … Just to test, I removed julia altogether, cloned the git repo, edited Make.inc to have FC = gfortran-4.2 and I get: … … i686-apple-darwin8-gfortran-4.2: unrecognized option '-shared' Undefined symbols for architecture i386: "_MAIN__", referenced from: _main in libgfortranbegin.a(fmain.o) ld: symbol(s) not found for architecture i386 collect2: ld returned 1 exit status make[2]: *** [amos/libamos.dylib] Error 1 make[1]: *** [julia-release] Error 2 make: *** [release] Error 2 So it looks like there is no way of building julia with R gfortran. Cheers F PS > > Cheers, > Simon > > > >> >>> >>> >>>> though I use and need R *much more than julia*, so I'd like to avoid R >>>> binaries of any sort having a hissy fit if gfortran points to something >>>> else than gfortran-4.2. Between R and julia I'm with R. >>>> >>> >>> Binaries will be fine, but compiling won't work (because FSF gfortran >>> doesn't understand Apple flags). >>> >>> Cheers, >>> Simon >>> >>> >>> >>>> Cheers >>>> >>>> Federico >>>> >>>> >>>> >>>>> Cheers, >>>>> Simon >>>>> >>>>> --- for advanced users only - if you have no idea what I'm talking about, >>>>> don't do it --- >>>>> >>>>> * - in theory you can use the Apple driver-driver of our Fortran to drive >>>>> FSF-build Fortran. For example if you take the CRAN Fortran then renaming >>>>> your FSF Fortran to i686-apple-darwin8-gfortran-4.2 and putting our >>>>> driver instead of gfortran then you may have some luck using CRAN R with >>>>> your FSF Fortran (obviously, -arch ppc won't work but fewer people care >>>>> now ;)). There are some potential issues, though, for example the FSF >>>>> binaries use purely dynamic setup so anything you compile can only be >>>>> used on your machine. Also in theory you can have runtime version >>>>> mismatch issues (two different versions of gfortran and gcc runtimes) - >>>>> so your mileage may vary. >>>>> >>>>> >>>>>> BW >>>>>> >>>>>> F >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Federico C. F. Calboli >>>>>> Neuroepidemiology and Ageing Research >>>>>> Imperial College, St. Mary's Campus >>>>>> Norfolk Place, London W2 1PG >>>>>> >>>>>> Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 >>>>>> >>>>>> f.calboli [.a.t] imperial.ac.uk >>>>>> f.calboli [.a.t] gmail.com >>>>>> >>>>>> _______________________________________________ >>>>>> R-SIG-Mac mailing list >>>>>> [email protected] >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>>> >>>>>> >>>>> >>>> >>>> -- >>>> Federico C. F. Calboli >>>> Neuroepidemiology and Ageing Research >>>> Imperial College, St. Mary's Campus >>>> Norfolk Place, London W2 1PG >>>> >>>> Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 >>>> >>>> f.calboli [.a.t] imperial.ac.uk >>>> f.calboli [.a.t] gmail.com >>>> >>>> >>> >> >> -- >> Federico C. F. Calboli >> Neuroepidemiology and Ageing Research >> Imperial College, St. Mary's Campus >> Norfolk Place, London W2 1PG >> >> Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 >> >> f.calboli [.a.t] imperial.ac.uk >> f.calboli [.a.t] gmail.com >> >> > -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
