[R-SIG-Mac] library problem (leopard v. tiger)

[Andrew Beckerman]

Dear all -

10.5.1, R 2.6.1.

I am trying to get a biocinductor package called GeneticsPed to work  
with leopard and R2.6.1.  It worked on Tiger with 2.5.

I have tried to install via Bioconductor, via the binary as a  
download, and as a source file.

Before documenting the behaviours, please note, that I have the latest  
Xcode installed, and also the latest GCC and gfortran installed  
through HPC.

1) Bioconductor can't find it, and that's ok, because it only exists  
now in the Devel version.

2) When I try and load the installed binary, I get the following error  
(note that it appeast to be built against 2.5?).

 > library(GeneticsPed)
Loading required package: gdata

Attaching package: 'gdata'


	The following object(s) are masked from package:Hmisc :

	 combine,
	 reorder.factor

Error in dyn.load(file, ...) :
   unable to load shared library '/Library/Frameworks/R.framework/ 
Resources/library/GeneticsPed/libs/i386/GeneticsPed.so':
   dlopen(/Library/Frameworks/R.framework/Resources/library/ 
GeneticsPed/libs/i386/GeneticsPed.so, 6): Library not loaded: /Library/ 
Frameworks/R.framework/Versions/2.5/Resources/lib/libgfortran.2.dylib
   Referenced from: /Library/Frameworks/R.framework/Resources/library/ 
GeneticsPed/libs/i386/GeneticsPed.so
   Reason: image not found
Error: package/namespace load failed for 'GeneticsPed'
 >

3) When I try and install via source, I get the following error  
(indicating use of the 10.4SDK?):

/Library/Frameworks/R.framework/Resources/library
* Installing *source* package 'GeneticsPed' ...
** libs
** arch - i386
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386  -msse3    -fPIC  -g -O2 -march=nocona -c ainverse.cc -o ainverse.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
i386  -msse3    -fPIC  -g -O2 -march=nocona -c eibd.cc -o eibd.o
gfortran -arch i386  -isysroot /Developer/SDKs/MacOSX10.4u.sdk   - 
fPIC  -g -O2 -march=nocona -c ggmatmult.f -o ggmatmult.o
** arch - ppc
g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
ppc  -I/usr/local/include    -fPIC  -g -O2 -c ainverse.cc -o ainverse.o
f951: error: unrecognized command line option "-arch"
make: *** [ggmatmult.o] Error 1
chmod: /Library/Frameworks/R.framework/Resources/library/GeneticsPed/ 
libs/i386/*: No such file or directory
g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
ppc  -I/usr/local/include    -fPIC  -g -O2 -c eibd.cc -o eibd.o
gfortran -arch ppc  -isysroot /Developer/SDKs/MacOSX10.4u.sdk   -fPIC   
-g -O2 -c ggmatmult.f -o ggmatmult.o
** Removing '/Library/Frameworks/R.framework/Resources/library/ 
GeneticsPed'
** Restoring previous '/Library/Frameworks/R.framework/Resources/ 
library/GeneticsPed'
f951: error: unrecognized command line option "-arch"
make: *** [ggmatmult.o] Error 1
chmod: /Library/Frameworks/R.framework/Resources/library/GeneticsPed/ 
libs/ppc/*: No such file or directory
ERROR: compilation failed for package 'GeneticsPed'

Any advice or obvious comments on what to do?

Cheers
andrew
---------------------------------------------------------------------------------
Dr. Andrew Beckerman
Department of Animal and Plant Sciences, University of Sheffield,
Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
ph +44 (0)114 222 0026; fx +44 (0)114 222 0002
http://www.beckslab.staff.shef.ac.uk/