[BioC] loading matchprobes

Wolfgang Huber huber at ebi.ac.uk
Wed Jul 20 11:40:01 CEST 2005

Hi Adam,

this does not look like a matchprobe-specific problem, rather one with 
your R installation / configuration. Within the matchprobes package, 
nowhere are those offending compiler options (-m32 -march=i386 
-mtune=pentium4) mentioned, they seem to be picked up from somewhere else.

I have no idea where from, though.
Did you compile R yourself, on the same machine as you are trying to 
install the package? Are you perhaps using a precompiled distribution of R?

Best wishes

> I am using BioC 1.6 on Linux RH 2.4.20-31.9. I was trying to load a probe library and it told me that I needed a newer matchprobes library. 
> Error: package 'matchprobes' 1.0.12 was found, but >= 1.0.20 is required by 'zebrafishprobe'
> Upon downloading and trying to install the newer match probes I got this error. I dont know wha this means. Any ideas?
> R CMD INSTALL -l /usr/lib/R/library ./matchprobes_1.0.22.tar.gz
> * Installing *source* package 'matchprobes' ...
> ** libs
> gcc -I/usr/lib/R/include  -I/usr/local/include   -fPIC  -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -c main.c -o main.o
> cc1: invalid option `tune=pentium4'
> make: *** [main.o] Error 1
> ERROR: compilation failed for package 'matchprobes'
> ** Removing '/usr/lib/R/library/matchprobes'
> ** Restoring previous '/usr/lib/R/library/matchprobes'

Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber

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