[R-SIG-Mac] [Caution: Message contains Suspicious URL content] R 3.0.1 build from sources: Wrong library paths

[Simon Urbanek]

On Sep 13, 2013, at 6:16 AM, Simon Zehnder wrote:

> Dear Brian,
> 
> if it is able to test the compilation of the quartz device by calling quartz() in R - this works. Calling xcodebuild -version gives me: Xcode 4.6.3 and clang --version gives me LLVM 3.2svn indeed. My prime target was to be able to use OpenMP 3.1 which is actually only available (freely) in gcc >= 4.7.

That's not true - Intel OpenMP RTL (http://www.openmprtl.org/ ) is free (BSD license), goes even up to OpenMP 4.0 features and has much better performance. GOMP has terrible performance on OS X (one of the two reasons why we disable it in the binaries), so if you care about OMP you probably don't want to use gcc anyway (or plug out GOMP for the Intel one).


> Is there a possibility to install, check and reinstall all CRAN packages in R? 
> 

Install is easy - you feed install.packages() with package list from available.packages() and you can even use Ncpus. Check is annoying since there is no equivalent R function (AFAIK). All of us have their own functions they use for this. But what's more complicated is that you'll need to install all dependent libraries in the system - and there are a lot of them.

Cheers,
Simon



> Best
> 
> Simon
> 
> 
> On Sep 13, 2013, at 10:52 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
> 
>> On 13/09/2013 07:52, Anirban MUKHERJEE wrote:
>>> Hi Simon,
>>> 
>>> On a related note, there has been progress on openmp in llvm/clang:
>>> 
>>> http://www.phoronix.com/scan.php?page=news_item&px=MTQ0NjQ
>>> 
>>> http://lists.cs.uiuc.edu/pipermail/llvmdev/2013-August/065169.html
>>> 
>>> http://clang-omp.github.io/
>>> 
>>> That might be an alternative route to consider if needed. Clang (I have not openmp/clang) usually builds easily on Mac OS.
>> 
>> We know (I believe it has been mentioned here before).  But please remember that only the Apple clang is easy to use (does your self-build compile the quartz device? -- mine did not), and Apple lags a long way behind.  The current Xcode version says it is '3.2svn' but lacks even 3.1 features such as AddressSanitizer.  We will see what Xcode 5 brings when it is released.
>> 
>> I don't think people appreciated Simon's comments about the stability needed.  If you can check all of CRAN with no more than 10 issues with gcc 4.7 or 4.8, then let us know.  That is about where we are with llvm-gcc 4.2 and clang 3.2- from Xcode 4.6.3.  When I tried 4.7.x prior to R 3.0.0 I had over 50 failures (and CRAN is reqularly checked with 4.7.x on other platforms).
>> 
>> And we are only in that good a state because a lot of (literally) thankless work has been done to get CRAN/BioC packages to compile with clang.
>> 
>> -- 
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>> 
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