> On 13 Oct 2015, at 16:14, Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote: > > On 13/10/2015 14:36, Simon Urbanek wrote: >> >> On Oct 12, 2015, at 4:22 PM, Jenny Brown <jennybro...@gmail.com> wrote: >> >>> Thank you to both of you. I believe my issue is solved by using the binary >>> distribution of gfortran libraries, as it was dynamic linking that was >>> causing me the most headache. And that seems to solve that. >>> >>> I still have to modify the etc/Makeconf file to use the right directory for >>> -L and the right library name for gfortran .... it comes written as >>> gfortran-4.8 in the Makeconf but that gives a not-found on my system. >> >> >> It means you're not using the Fortran we use (as I said below) - see >> http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 > > Also, you do not need to modify etc/Makeconf ... the manual says > > 'The default compilers specified in > /Library/Frameworks/R.framework/Resources/etc/Makeconf depend on the version > of OS X under which R was installed, and are appropriate to the latest > version of the command-line tools for that version of OS X. The settings can > be changed, either by editing that file or in a file such as ~/.R/Makevars > (see the next section).' > > I have in ~/.R/Makevars on my laptop > > F77 = /usr/local/gfortran/bin/gfortran > FC = /usr/local/gfortran/bin/gfortran > FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin14/5.2.0 > -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm > >
This is Coudert’s gfortran, I presume? Can it be used together with R binary provided by CRAN and Simon? Or would one have to recompile R from scratch using Coudert’s gfortran? Berend > >> >> Cheers, >> Simon >> >> >> >>> I'm >>> not entirely clear on when the Makeconf is initially written during a >>> binary install of R. But it does seem that I can adjust the lines related >>> to fortran and get it to work for compiling my source packages. >>> >>> Thanks! >>> >>> >>> >>> >>> On Thu, Oct 8, 2015 at 1:33 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk> >>> wrote: >>> >>>> On 08/10/2015 02:37, Simon Urbanek wrote: >>>> >>>>> Jenny, >>>>> >>>>> I suspect you may not have the correct information. The CRAN Mavericks >>>>> binary of R is not built with gcc, it's actually build using Apple clang >>>>> and we're neither using nor requiring homebrew, so most of what you are >>>>> describing doesn't make sense to me. I have tested Xcode 7 with the >>>>> gfortran-4.8 we supply and it works just fine on 10.11 (tested on Hmisc). >>>>> I >>>>> have only 10.6, 10.9 and 10.11 so I can't check 10.10, but I would >>>>> certainly recommend building on 10.9 with Xcode 6 for compatibility >>>>> (that's >>>>> what we do for CRAN). If you don't care about binary compatibility then >>>>> Xcode 7 on 10.11 is fine (FWIW Hmisc package compiled on 10.11 actually >>>>> works for me on 10.9 so it could even be that you may get away with using >>>>> 10.11 if you don't use system dependencies with higher versions). >>>>> >>>> >>>> It also works for me on 10.10. If the 'Command Line Tools OS X 10 for >>>> Xcode 7' Apple package is installed on 10.10 (specifically file >>>> http://adcdownload.apple.com/Developer_Tools/Command_Line_Tools_OS_X_10.10_for_Xcode_7/Command_Line_Tools_OS_X_10.10_for_Xcode_7.dmg), >>>> it installs >>>> >>>> % clang --version >>>> Apple LLVM version 7.0.0 (clang-700.0.74) >>>> Target: x86_64-apple-darwin14.5.0 >>>> >>>> hence targets OS X 10.10 aka Darwin 14. My 10.10 machine does not have >>>> Xcode installed, only the CLT: you do not need Xcode's SDKs to compile R >>>> nor any CRAN package. (You do need Xcode to compile R.app.) >>>> >>>> For Fortran on Yosemite/El Capitan I use the gfortran 5.2 build at the >>>> sites given in the current R-admin manual ('Other builds of gfortran are >>>> available: see https://gcc.gnu.org/wiki/GFortranBinaries and >>>> http://coudert.name/software.html'). My recollection is that the >>>> 'gfortran-4.8 for Mavericks' on r.research.att.com does compile all but >>>> one of the CRAN packages on Yosemite (SWATmodel which compiles executables >>>> from Fortran code), in some cases with warnings. >>>> >>>> Note that any recent(ish) build of gfortran will have dynamic libgfortran >>>> and libquadmath libraries, and installations of most Fortran-using packages >>>> will link to these. So you either need to install those libraries on all >>>> the machines or arrange for the packages you distribute to point to the >>>> copies in the CRAN build (in R_HOME/lib) as is done for the CRAN binary >>>> packages. (I believe they are post-processed by >>>> https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Simon/packages/1.fixr >>>> .) My recollection is that a very few packages also link to libgcc_s, also >>>> in R_HOME/lib. >>>> >>>> >>>> >>>> Cheers, >>>>> Simon >>>>> >>>>> >>>>> On Oct 7, 2015, at 10:47 AM, Jenny Brown <jennybro...@gmail.com> wrote: >>>>>> >>>>>> I am maintaining R installations and packages for a large number of OS X >>>>>> machines. A recent change from Apple is making the R installation more >>>>>> awkward, and I'm trying to determine the best path forward with minimal >>>>>> maintenance headaches. >>>>>> >>>>>> >>>>>> Recently, XCode 7's release on Yosemite 10.10 broke compilation of "brew >>>>>> install --with-fortran gcc48" which is a pre-requisite for compiling >>>>>> third >>>>>> party R packages that use fortran. (XCode 7 eliminates the 10.9 and >>>>>> 10.10 >>>>>> SDKs and only provides 10.11 which is El Capitan's... so even though >>>>>> XCode >>>>>> 7 installs on Yosemite, it can not build for Yosemite, which causes gcc >>>>>> trouble. Lots of opensource devs are commenting on this on various >>>>>> projects.) >>>>>> >>>>>> It appears that the binary installs of R for OS X (3.1 through 3.2.2) >>>>>> were >>>>>> all built against gcc 4.8. I've discovered that gcc 5.2 builds properly >>>>>> on >>>>>> Yosemite, even with XCode 7, and R can be compiled with gcc 5.2. >>>>>> >>>>>> However, even the latest R (3.2.2) on cran.rstudio.com appears to be >>>>>> built >>>>>> by default with gcc 4.8 -- are there plans to move to gcc 5.2? >>>>>> Presumably >>>>>> the breakage I'm seeing where gcc 4.8 can't use the xcode 7 10.11 SDK >>>>>> would >>>>>> also occur on El Capitan, so gcc 5.2 would be a necessary upgrade there >>>>>> too. >>>>>> >>>>>> Right now my choices for getting R to work with my third-party fortran >>>>>> packages appear to be: manually downgrade xcode to 6.4 for Yosemite; or, >>>>>> maintain my own compilation of R against gcc 5.2, for each of Yosemite >>>>>> and >>>>>> El Capitan. Both have their downsides, and I hope to be able to return >>>>>> to >>>>>> the normal public binary R distribution sooner rather than later. >>>>>> >>>>>> What's on the roadmap for upcoming upgrades and compatibility? Thanks. >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> R-SIG-Mac mailing list >>>>>> R-SIG-Mac@r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> R-SIG-Mac mailing list >>>>> R-SIG-Mac@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>> >>>>> >>>> >>>> -- >>>> Brian D. Ripley, rip...@stats.ox.ac.uk >>>> Emeritus Professor of Applied Statistics, University of Oxford >>>> 1 South Parks Road, Oxford OX1 3TG, UK >>>> >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> > > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Emeritus Professor of Applied Statistics, University of Oxford > 1 South Parks Road, Oxford OX1 3TG, UK > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac