[BioC] Affy packages

Jason Skelton jps at sanger.ac.uk
Thu Nov 4 15:15:22 CET 2004

Hi All (wasn't sure if this should go to r-help or bioconductor)

We have recently installed R 2.0 and the Bioconductor bundle was 
installed using getBioC()
(A systems administrator compiled it so unfortunately I'm not sure what 
they have done)
However there appears to be a few compiling errors with a few of the 
affy packages

This appears to be affecting

basically when you try to attach the packages they all return errors 
with messages related to compilation.
I've try to install myself using R CMD INSTALL packages individually but 
again have compilation errors
I'm wondering if this a problem with the affy related packages OR more 
likely with the Build of R that we
have been given ?

[jps at bc-1-2-03 /]$ /nfs/farm/R/bin/R CMD INSTALL -l  
For X functions to work, this machine needs to be authorised
to access deskpro179:0.0.  I will test this now (this may take a
few seconds.
This is unning remotely on a blade somewhere so I don't know much about 
the machine its running on:

Job <576812> is submitted to default queue <normal>.
<<Waiting for dispatch ...>>
<<Starting on bc-3-2-12>>
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... /lib/cpp
checking for main in -lz... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/nfs/farm/R/Linux-i686/lib/R/include   -D__NO_MATH_INLINES 
-mieee-fp  -fPIC  -O2 -march=pentium3 -c chipbackground.c -o 
make: gcc: Command not found
make: *** [chipbackground.o] Error 127
ERROR: compilation failed for package 'affy'

other packages that came from the same bundle work fine
& also packages I have obtained seperately like limma, gregmisc etc all 
work with this method
apologies for my lack of linux/unix experiance, any help will be 
greatfully recieved
If these errors mean anything to anyone could they explain them please
all the packages mentioned appear to be looking for gcc which I'm 
guessing is being effected by how R was built ?

best regards


Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919

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