XCode / gcc / R compatibility issues on Yosemite with XCode 7 and on El Capitan

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.

 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.

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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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