R 2.5.0 MAC OS X version

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'
*************************************

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