[BioC] Installation of a custom cdf hs133phsentrezgcdf

Min-Han Tan minhan.tan at gmail.com
Fri May 29 00:34:05 CEST 2009

Good morning,

Sorry to trouble the list.

My overall goal is to obtain a normalized data set.I would like to do
it using a custom cdf. hs133phsentrezgcdf. I am using R 2.9.0 on SUSE
Linux 10.1. (newbie to Linux, would prefer to use Windows, but it
can't manage the memory requirements for 150 HGU133Plus2.0 CEL files).
I have installed the cdf in Windows without problems, I just moved it
to the library directory there. I am however struggling over
installation of this cdf in Linux.

In terms of directories, to install R, have done
./configure --prefix=/usr/bin/R/2.9.0
make install

R -> /usr/bin/R/2.9.0/bin/R

I suspect there are permission issues, as I get these warning messages in R.
> install.packages("survival")
Warning in install.packages("survival") :
  argument 'lib' is missing: using
However, there are no issues installing packages otherwise, and they
seem to work fine.

I have downloaded the CDF hs133phsentrezgcdf version 10, tar xvf done,
and moved the directory to

However, I get this error.
> library(hs133phsentrezgcdf)
Error in library(hs133phsentrezgcdf) :
  'hs133phsentrezgcdf' is not a valid installed package

Ideally, I would like to do
    biocLite("hs133phsentrezgcdf") as was possible in past versions
but package hs133phsentrezgcdf is not available in this version, I think.

Your help is much appreciated! Apologies for this question!


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