[R-SIG-Mac] XCode / gcc / R compatibility issues on Yosemite with XCode 7 and on El Capitan

Prof Brian Ripley ripley at stats.ox.ac.uk
Tue Oct 13 17:30:55 CEST 2015 

On 13/10/2015 16:07, Berend Hasselman wrote:
>
>> 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?

Yes (but that was only meant as an illustration of what can be done).

> 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?

It can.  The CRAN R binary is self-contained (it contains libgfortran 
etc in R_HOME/lib).  You can use any Fortran compiler with it to compile 
a Fortran-using package.  (There might be problems with finding the 
runtime components such as libgfortran.dylib from 
/usr/local/gfortran/lib, but this seems usually to just work and the way 
we use the OS X linker the absolute paths are captured at link time.)


>
> 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]]
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> R-SIG-Mac at r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>
>>>> 	[[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>
>>
>>
>> --
>> 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
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>


-- 
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

More information about the R-SIG-Mac mailing list