[BioC] Package installation and Redifine.h

[Martin Morgan]

John Coulthard <bahhab at hotmail.com> writes:

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

Likely you've used a linux package installer that separates the header
files from the rest of the distribution, probably in a 'devel'
package. This thread might be relevant.

http://tolstoy.newcastle.edu.au/R/e4/help/08/07/16589.html

though not directly Red Hat related

Martin

> 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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