From yucel at schoolph.umass.edu  Wed May 30 16:44:53 2007
From: yucel at schoolph.umass.edu (Recai Yucel)
Date: Wed, 30 May 2007 10:44:53 -0400
Subject: [Rd] R 2.5.0 MAC OS X version
In-Reply-To: <Pine.LNX.4.64.0705301535420.25280@gannet.stats.ox.ac.uk>
References: <465D854D.6060501@schoolph.umass.edu>
	<E72C4C2A-748F-4ED2-BCB6-51001EF22BC8@noaa.gov>
	<Pine.LNX.4.64.0705301535420.25280@gannet.stats.ox.ac.uk>
Message-ID: <465D8DE5.8040104@schoolph.umass.edu>

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



[Rd] R 2.5.0 MAC OS X version
Recai Yucel