Re: [Rd] R 2.5.0 MAC OS X version

From: Recai Yucel <yucel_at_schoolph.umass.edu>
Date: Wed, 30 May 2007 10:44:53 -0400

Right. I thought the problems might be obvious enough for MAC users, probably not!
I was mistaken with the GNU Fortran version, it is 4.0 as seen below. A specific example where I had problems is given below:

When I try to install a package called lmm (which was installed with no problem with the previous versions of R), I get the following messages, specifically on the make, chmod, etc.



trying URL 'http://cran.us.r-project.org/src/contrib/lmm_0.3-4.tar.gz' Content type 'application/x-tar' length 31471 bytes opened URL

downloaded 30Kb

WARNING: ignoring environment value of R_HOME tar: Read 4096 bytes from -

* Installing *source* package 'lmm' ...
** libs
** arch - i386

gfortran-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-fPIC -g -O2 -march=nocona -c lmm.f -o lmm.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib
-Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup
-single_module -multiply_defined suppress -L/usr/local/lib -o lmm.so
lmm.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.0 -lgfortran
-lgcc_s.10.4 -F/Library/Frameworks/R.framework/.. -framework R
/usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) object: /usr/local/lib/libgfortran.dylib malformed object (unknown load command 4)
/usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) object: /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown load command 4)
** arch - ppc
gfortran-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-fPIC -g -O2 -c lmm.f -o lmm.o
make: *** [lmm.so] Error 1
chmod:
/Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm/libs/i386/*: No such file or directory
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99
-dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup
-single_module -multiply_defined suppress -L/usr/local/lib -o lmm.so
lmm.o -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.0 -lgfortran
-lgcc_s.10.4 -lSystemStubs -F/Library/Frameworks/R.framework/..
-framework R

The downloaded packages are in

   /private/tmp/Rtmpe4c9Of/downloaded_packages ** Removing
'/Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm' ** Restoring previous
'/Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm' /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) object: /usr/local/lib/libgfortran.dylib malformed object (unknown load command 4)
/usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) object: /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown load command 4)
make: *** [lmm.so] Error 1
chmod:
/Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm/libs/ppc/*: No such file or directory
ERROR: compilation failed for package 'lmm'


Prof Brian Ripley wrote:

> And beyond that good advice, the mailing list for MacOS issues is 
> R-sig-mac.
>
> Are you really using 'GNU Fortran 4.2.0' (which was released well 
> after R 2.5.0), or some pre-release of it?  Such details do matter.
>
>
> On Wed, 30 May 2007, Roy Mendelssohn wrote:
>
>> Hi Recal:
>>
>> To save you from some possible flames, it would probably help if you
>> describe what the problems are, with specific examples and some of
>> the relevant error messages. It would be difficult to for someone to
>> know if they are seeing similar problems without knowing what the
>> problems are.
>>
>> I believe such information is in the posting guides, which do contain
>> good information on how to frame a question to the mail list that
>> will elicit useful responses.
>>
>> -Roy
>>
>>
>>
>>
>> On May 30, 2007, at 7:08 AM, Recai Yucel wrote:
>>
>>> Please accept my apologies if this was addressed before, I could not
>>> find any solution so I am posting my question here.
>>>
>>> I am having a lot of difficulties with installing and developing R
>>> packages with the latest version of R 2.5.0. I am using a MacBook
>>> Pro. I
>>> never had these problems with the previous versions of R. I think part
>>> of the problem is caused by the GNU Fortran 4.2.0 or my lack of
>>> knowledge...
>>>
>>> If anybody else had similar problems and found the solution, please
>>> let
>>> me know.
>>>
>>> Best.
>>>
>>> -- 
>>> Recai Yucel, Ph.D.
>>> Assistant Professor of Biostatistics
>>> Biostatistics and Epidemiology
>>> UMASS-Amherst
>

--

Recai Yucel, Ph.D.
Assistant Professor of Biostatistics
Biostatistics and Epidemiology
UMASS-Amherst



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