[R-SIG-Mac] XCode / gcc / R compatibility issues on Yosemite with XCode 7 and on El Capitan
Berend Hasselman
bhh at xs4all.nl
Tue Oct 13 17:07:54 CEST 2015
> On 13 Oct 2015, at 16:14, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
>
> On 13/10/2015 14:36, Simon Urbanek wrote:
>>
>> On Oct 12, 2015, at 4:22 PM, Jenny Brown <jennybrown8 at 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 <ripley at 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 <jennybrown8 at 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]]
>>>>>>
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>>>>>>
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>>>>>
>>>>
>>>> --
>>>> Brian D. Ripley, ripley at stats.ox.ac.uk
>>>> Emeritus Professor of Applied Statistics, University of Oxford
>>>> 1 South Parks Road, Oxford OX1 3TG, UK
>>>>
>>>>
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>>
>
>
> --
> Brian D. Ripley, ripley at stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 1 South Parks Road, Oxford OX1 3TG, UK
>
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