Hi all,

Just upgraded both the R and R-devel. Tried to download and install the
default packages of biocLite, I get the following error for the installation
of affyPLM:

for R -

>biocLite("affyPLM", type="source")
Running biocinstall version 2.1.7 with R version 2.6.0 (under development)
Your version of R requires version 2.1 of Bioconductor.
trying URL '
http://bioconductor.org/packages/2.1/bioc/src/contrib/affyPLM_1.13.16.tar.gz
'
Content type 'application/x-gzip' length 6437455 bytes (6.1 Mb)
opened URL
==================================================
downloaded 6.1 Mb

* Installing *source* package 'affyPLM' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386  -msse3
-I"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/preprocessCore/include"
-fPIC  -g -O2 -std=gnu99 -march=nocona -c LESN.c -o LESN.o
i686-apple-darwin8-gcc-4.0.3: unrecognized option '-no-cpp-precomp'
/var/tmp//cccIEpjo.s:919:indirect jmp without `*'
/var/tmp//cccIEpjo.s:934:indirect jmp without `*'
/var/tmp//cccIEpjo.s:949:indirect jmp without `*'
/var/tmp//cccIEpjo.s:964:indirect jmp without `*'
/var/tmp//cccIEpjo.s:979:indirect jmp without `*'
/var/tmp//cccIEpjo.s:994:indirect jmp without `*'
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386  -msse3
-I"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/preprocessCore/include"
-fPIC  -g -O2 -std=gnu99 -march=nocona -c PLM_avg_log.c -o PLM_avg_log.o
i686-apple-darwin8-gcc-4.0.3: unrecognized option '-no-cpp-precomp'
PLM_avg_log.c:33:51: error: avg_log.h: No such file or directory
PLM_avg_log.c: In function 'AverageLog_threestep':
PLM_avg_log.c:66: warning: implicit declaration of function 'AverageLog'
PLM_avg_log.c: In function 'AverageLog_PLM':
PLM_avg_log.c:82: warning: implicit declaration of function
'averagelog_no_copy'
make: *** [PLM_avg_log.o] Error 1
chmod:
/Library/Frameworks/R.framework/Versions/2.6/Resources/library/affyPLM/libs/i386/*:
No such file or directory
** arch - ppc
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99
-no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I/usr/local/include
-I"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/preprocessCore/include"
-fPIC  -g -O2 -c LESN.c -o LESN.o
powerpc-apple-darwin8-gcc-4.0.3: unrecognized option '-no-cpp-precomp'
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99
-no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I/usr/local/include
-I"/Library/Frameworks/R.framework/Versions/2.6/Resources/library/preprocessCore/include"
-fPIC  -g -O2 -c PLM_avg_log.c -o PLM_avg_log.o
powerpc-apple-darwin8-gcc-4.0.3: unrecognized option '-no-cpp-precomp'
PLM_avg_log.c:33:51: error: avg_log.h: No such file or directory
PLM_avg_log.c: In function 'AverageLog_threestep':
PLM_avg_log.c:66: warning: implicit declaration of function 'AverageLog'
PLM_avg_log.c: In function 'AverageLog_PLM':
PLM_avg_log.c:82: warning: implicit declaration of function
'averagelog_no_copy'
make: *** [PLM_avg_log.o] Error 1
chmod:
/Library/Frameworks/R.framework/Versions/2.6/Resources/library/affyPLM/libs/ppc/*:
No such file or directory
ERROR: compilation failed for package 'affyPLM'
** Removing
'/Library/Frameworks/R.framework/Versions/2.6/Resources/library/affyPLM'
** Restoring previous
'/Library/Frameworks/R.framework/Versions/2.6/Resources/library/affyPLM'

> sessionInfo()
R version 2.6.0 RC (2007-10-02 r43058)
i386-apple-darwin8.10.1

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15 tools_2.6.0

I get the same error for R-devel. Can anyone reproduce this error on their
macs..on other platforms? I think it might have something to do with my
c-complier, but I have no idea what that would be.

Thanks,
--Tony

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