[BioC] Problem installing rmutil/repeated

[J-C. Marioni]

Hi,

I am trying to install the R libraries "rmutil" and "repeated" on a Mac OS 
X version 10.4.1 (which has the latest version of the Mac Developer tools 
installed) and I am having trouble compiling the libraries.

The error message I receive is as follows (I have only included the error 
message when I try and install the rmutil library):

............................


* Installing *source* package 'rmutil' ... ** libs gcc-3.3 -no-cpp-precomp 
-I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include 
-fno-common -g -O2 -c cutil.c -o cutil.o gcc-3.3 -no-cpp-precomp 
-I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include 
-fno-common -g -O2 -c dist.c -o dist.o g77 -fno-common -g -O2 -c gettvc.f 
-o gettvc.o gcc-3.3 -no-cpp-precomp 
-I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include 
-fno-common -g -O2 -c romberg.c -o romberg.o gcc-3.3 -no-cpp-precomp 
-I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include 
-fno-common -g -O2 -c toms614.c -o toms614.o gcc-3.3 -bundle 
-flat_namespace -undefined suppress -o rmutil.so cutil.o dist.o gettvc.o 
romberg.o toms614.o -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 
-lg2c -lSystem
         package successfully installed ld: dist.o has external relocation 
entries in non-writable section (__TEXT,__text) for symbols: restFP saveFP 
make: *** [rmutil.so] Error 1 ERROR: compilation failed for package 
'rmutil'

......................

When I remove the makefile (as suggested on Jim Lindsey's website) and try 
again, I get the following similar (but slightly different) output.

......................

* Installing *source* package 'rmutil' ... ** libs gcc-3.3 -no-cpp-precomp 
-I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include 
-fno-common -g -O2 -c cutil.c -o cutil.o gcc-3.3 -no-cpp-precomp 
-I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include 
-fno-common -g -O2 -c dist.c -o dist.o g77 -fno-common -g -O2 -c gettvc.f 
-o gettvc.o gcc-3.3 -no-cpp-precomp 
-I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include 
-fno-common -g -O2 -c romberg.c -o romberg.o gcc-3.3 -no-cpp-precomp 
-I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include 
-fno-common -g -O2 -c toms614.c -o toms614.o gcc-3.3 -bundle 
-flat_namespace -undefined suppress -L/usr/local/lib -o rmutil.so cutil.o 
dist.o gettvc.o romberg.o toms614.o 
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -lg2c -lSystem 
-framework R ** Removing 
'/Library/Frameworks/R.framework/Versions/2.1.1/Resources/library/rmutil' 
** Restoring previous 
'/Library/Frameworks/R.framework/Versions/2.1.1/Resources/library/rmutil'
         package successfully installed ld: dist.o has external relocation 
entries in non-writable section (__TEXT,__text) for symbols: restFP saveFP 
make: *** [rmutil.so] Error 1 ERROR: compilation failed for package 
'rmutil'

........................

I contacted Jim Lindsey (the package author) who wasn't able to suggest a 
solution. Hence, does anyone have an idea what could be causing this error 
or does anyone have a Mac binary for these libraries?

Thanks,

John Marioni

PS I know that these packages are not part of bioconductor, but they are 
pre-requisites for running the aCGH package of Jane Fridlyand. Hence, I 
thought it was appropriate to post this message (which I also sent to the R 
mailing list).

-- 
John Marioni
PhD Student
Computational Biology Group
Department of Applied Mathematics and Theoretical Physics
University of Cambridge
Wilberforce Road, Cambridge, CB3 0WA

Email: J.Marioni at damtp.cam.ac.uk
Phone: +44 (0)1223 763391