[BioC] Package installation and Redifine.h

John Coulthard bahhab at hotmail.com
Thu Oct 16 13:39:03 CEST 2008

Dear All

Can you help me get biolite packages installed?  I seem to be missing Redifine.h.  

What I've tried...
Installed R-devel
I didn't have a copy of Redifine.h at all so I created one from the code on http://www.cs.kent.ac.uk/projects/cxxr/doc/html/Rdefines_8h-source.html and put it in /usr/local/include/  (it was a long shot, it didn't work!)

The error I'm getting is....

> source("http://bioconductor.org/biocLite.R")
> biocLite("affy")
Running biocinstall version 2.2.11 with R version 2.7.2 
Your version of R requires version 2.2 of BioConductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  argument 'lib' is missing: using '/usr/lib/R/library'

* Installing *source* package 'Biobase' ...
** libs
gcc -m32 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c anyMissing.c -o anyMissing.o
anyMissing.c:11:22: error: Rdefines.h: No such file or directory
anyMissing.c:14: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘anyMissing’
make: *** [anyMissing.o] Error 1
ERROR: compilation failed for package 'Biobase'

Linux version 2.6.25-14.fc9.i686 (mockbuild@) (gcc version 4.3.0 20080428 (Red Hat 4.3.0-8) (GCC) ) #1 SMP Thu May 1 06:28:41 EDT 2008

Many Thanks
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