[R-SIG-Mac] R compile from sources: error in make with gcc-4.7

[Simon Zehnder]

Hi guys,

I want to make a last comment on compiling R on a Mac OS with the GNU 4.7.1 compiler. I solved all my problems and I would like to present my way here for other users who may find it helpful.

I am using Mountain Lion 10.8.2 and followed: http://solarianprogrammer.com/2012/02/20/living-on-the-edge-building-gcc-4-7-on-mac-osx-lion/  for the installation of gcc-4.7.1. Furthermore I downloaded the latest version of XQuartz (http://xquartz.macosforge.org/landing/).

Next step: I downloaded the latest R-patched version 2.15.1 here (thanks for the tip Simon!): http://r.research.att.com. 

Then the following commands have been made: 

In the untared R-patched folder:

mkdir build && cd build

../configure CC=gcc-4.7 CXX=g++-4.7 F77=gfortran-4.7 FC=gfortran-4.7 OBJC=clang CFLAGS="-DOS_OBJECT_USE_OBJC=0" CPPFLAGS="-D__ACCELERATE__" --with-lapack --with-blas='-framework Accelerate' --with-x

sudo make 

sudo make install

Now R runs much faster on my Mac then before and without any problem. The only unsolved task yet is, that the R.framework - especially the library folder below Resources/ is not accessible by default. So installing a package results in an exception. I solved this task by simply changing the permissions on the folder. 

The solution to my problem has been brought up by a friend of mine in the HPC team at the Computing Center RWTH Aachen University (Germany), Hriesto Iliev (http://www.rz.rwth-aachen.de/aw/cms/rz/Themen/hochleistungsrechnen/hilfen_kurse_und_veranstaltungen/~svf/und_das_sind_wir/?lang=de or on stackoverflow: http://stackoverflow.com/users/1374437/hristo-iliev). 

In his words: The reason why compilation of aqua.c fails is due to a change possibly introduced in the 10.8 SDK. Several system header files now use by default some Obj-C constructs with extensions (code blocks), only supported by clang and Apple's version of GCC. The workaround is given via the C flag -DOS_OBJECT_USE_OBJC=0". 
The veLib problem can be used in two different ways: 

1. Simon Urbanek suggests to use the CPP flag -D__ACCELERATE__

2. Hriesto solved the problem via changing #include<vecLib/vecLib.h> to #include<Accelerate/Accelerate.h> in ../src/modules/lapack/vecLib95c.c (relative to the build directory).  

As vecLib is deprecated it should also be used --with-blas="-framework Accelerate" instead of --with-blas="-framework vecLib" (but both options seem to work).

Unfortunately there is another part that prevents one from building R with gcc-4.7: The Quartz graphics device must be compiled with the Objective-C compiler from Apple as (again) code blocks are used extensively in the OS X SDK and this time there is no workaround. Clang is a good candidate and as high performance libraries like OpenMP are not used in the graphics device, Xcode's default can be used without matters. So one simply changes the Obj-C compiler to clang: OBJC=clang. 
Following Hristo it is also unnecessary to specify "-arch x86_64" as the compiler is already producing 64-bit code by default. 

We are still not sure if we need the X11 graph device, as the Quartz one should be more capable (graphics in R work fine). Any comments are welcome. 

As I use R either on the command line or in RStudio I have not installed the R.app. If one wants to install it, one have to build R as a dynamic library to be later used by R.app. Doing so one needs the --enable-R-framework directive in the configure step above following the manual, but we got it by default...

With the building steps above one can now use R - or rather R extensions - with OpenMP 3.0 as well as other very helpful developments in the C++11 standard. I do not know other mathematical or hpc libraries, but as the compiler is the latest version everything should run.  

At the end I want to thank everyone here for his helpful comments and Hristo for his time - even if he is not connected to R (yet:))

Best

Simon 


On Sep 16, 2012, at 3:10 PM, Simon Zehnder <szehnder at uni-bonn.de> wrote:

> Hi Simon,
> 
> below you find my configure and my make output while building R from sources with gcc-4.7.1 and including aqua (I used the R-patched). 
> 
> 1. (Configure) Output: http://pastebin.com/GJ5DZncU
> 
> 2. (Make) Output: http://pastebin.com/SHZWgA4P
> 
> Best regards
> 
> Simon
> 
> On Sep 16, 2012, at 3:16 AM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
> 
>> Simon,
>> 
>> On Sep 15, 2012, at 6:56 PM, Simon Zehnder wrote:
>> 
>>> That is correct! My fault! Simon, I didn't want to blame you with this one. 
>>> 
>>> It compiles know and it works perfectly on the console. I am still interested, why it does not compile with aqua. Can somebody explain me why? 
>>> 
>> 
>> Can you sent me the full output? I don't have the time to compile gcc from scratch right now and none of the usual suspects supports ObjC - that alone is a sign that no one really uses gcc on OS X (other than for ports) since Apple has abandoned it. My guess would be that the ObjC support is not as complete as in Apple's version - it's probably more geared toward GNUstep - but that's just a guess.
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> Best regards
>>> 
>>> Simon
>>> 
>>> On Sep 14, 2012, at 4:38 PM, Berend Hasselman <bhh at xs4all.nl> wrote:
>>> 
>>>> 
>>>> On 14-09-2012, at 16:01, Simon Zehnder wrote:
>>>> 
>>>>> Running through the errors of my make output on http://pastebin.com/HXqLgH4b (without aqua) pulled my attention to the following error: 
>>>>> 
>>>>> In file included from ../../../../src/modules/lapack/vecLibg95c.c:5:0:
>>>>> /System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:22:4: error: #error "<vecLib/vecLib.h> is deprecated.  Please #include <Accelerate/Accelerate.h> and link to Accelerate.framework."
>>>>> 
>>>>> This error is, I think from you Simon, already commented on http://permalink.gmane.org/gmane.comp.lang.r.mac/7293. So I followed your advice there and added the flag CPPFLAGS=-D ACCELERATE to my configure command:
>>>>> 
>>>>> 1. (Configure) The whole command is:
>>>>> 
>>>>> ../configure CC="gcc-4.7 -arch $arch" CXX="g++-4.7 -arch $arch" F77="gfortran-4.7 -arch $arch" FC="gfortran-4.7 -arch $arch" OBJC="gcc-4.7 -arch $arch" --x-includes=/usr/X11/include/ --x-libraries=/usr/X11/lib/ --with-blas='-framework libVec' --with-lapack --without-aqua CPPFLAGS="-D ACCELERATE"
>>>>> 
>>>>> All runs fine - no errors nor warnings.
>>>>> 
>>>>> 2. (Make) I run the make via:
>>>>> 
>>>>> make -j 8
>>>>> 
>>>>> and I get the following errors: http://pastebin.com/5UfaMK6r
>>>>> 
>>>>> It seems that the flag CPPFLAGS=-D ACCELERATE does not modify the compilers work. 
>>>>> 
>>>>> Any suggestions here?
>>>> 
>>>> Reading the reply by Simon tells me that your CPPFLAGS doesn't agree with Simon's fix. It should be  CPPFLAGS=-D__ACCELERATE__
>>>> 
>>>> Berend
>>>> 
>>> 
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>> 
> 
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