[BioC] Affy packages
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
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
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
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
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 ?
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