[Rd] R, Macports and C++ streams
simon.urbanek at r-project.org
Wed Jul 30 20:23:13 CEST 2008
On Jul 30, 2008, at 13:16 , Ernest Turro wrote:
> On 30 Jul 2008, at 18:04, Simon Urbanek wrote:
>> On Jul 30, 2008, at 12:32 , Ernest Turro wrote:
>>> On 30 Jul 2008, at 15:46, Simon Urbanek wrote:
>>>> On Jul 30, 2008, at 9:45 , Ernest Turro wrote:
>>>>> Dear all,
>>>>> R on Macports relies on GCC 4.3 to build packages. I find that
>>>>> packages with shared objects that use C++ streams crash R if
>>>>> they're compiled using Macports' gcc43, but work fine if
>>>>> compiled in exactly the same way using Apple-supplied GCC 4.2.
>>>>> Has anyone here had the same issue/know what is causing this
>>>> Using compilers from MacPorts and similar suites (Darwin ports,
>>>> Fink etc.) is strongly discouraged (and outright not supported by
>>>> the CRAN binary) since they have been known to be badly broken in
>>>> the past and when whenever tested so far they were incomplete and
>>>> incompatible. You have to re-compile R yourself with those tools
>>>> (and you're entirely on your own) if you really want to use them.
>>>> CRAN binaries work only with Apple's gcc branches, if you want to
>>>> use anything else, you have to follow the unix R instructions and
>>>> compile everything from sources.
>>> Dear Kjell,
>>> As you can see above, your R port on Macports appears to be broken
>>> and has a reputation of having been broken for a while. I for one
>>> have experienced odd problems as described above. To avoid further
>>> issues with unsuspecting Macports users, perhaps it would be good
>>> to pull the port from the repository until a decent level of
>>> reliability can be provided ?
>> Although I do agree on your last point, I just want to clarify that
>> I was talking about supported R for Mac setup (as provided in
>> binary form on CRAN).
> Having installed the R binary for Mac, I've noticed that it uses
> Apple's default gcc 4.0.1.
That is not exactly true - it uses whatever your gcc version is. You
can use Apple's gcc 4.0 or 4.2, they both work.
> The problem with this is that there is no OpenMP support in gcc
> until version 4.2, which is available as a preview from apple on ADC.
FYI it's part of Xcode 3.1 ...
> Changing gcc and g++ to gcc-4.2 and g++-4.2 in the default Makeconf
> isn't quite enough, as R also needs to look in the appropriate
> header paths, etc...(e.g. to find omp.h). Could you recommend an
> easy way of getting a binary R installation to work with apple-
> supplied gcc 4.2 instead of 4.0 ?
I suspect you're confusing several separate issues here - the include
paths for OMP have nothing to do with R, they are part of the gcc and
as such added regardless of the include flags. Just try
gcc-4.2 omp.c -o omp -fopenmp
which specifies no include flags and works just fine.
The real issue here is that Apple doesn't provide gcc-4.2 support for
Tiger, so you cannot use 10.4 SDK unless you also install the
corresponding libraries. Hence you have two choices:
1) install gcc-4.2 libraries in 10.4u SDK
2) build for Leopard-only
As for 1) you can get just the SDK files for Tiger from
(you'll need to symlink darwin8 directory to darwin9)
As for 2) you can use the Leopard binaries from
>> Although it should be possible to build R with non-Apple gcc, but
>> it must be done very carefully, because there are many dangers
>> lurking in the interaction of system libraries with those from non-
>> Apple tools. This has nothing to do with R, it's about knowledge
>> how things work in OS X and it is very important when compilers are
>> involved [unfortunately there are many binaries around from people
>> that don't understand the intricacies of OS X well enough and think
>> it's almost like a Linux box - I'm not talking about MacPorts in
>> particular, it's just a general observation].
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