[BioC] Installation of a custom cdf hs133phsentrezgcdf

Martin Morgan mtmorgan at fhcrc.org
Mon Jun 1 15:38:50 CEST 2009

Hi Min-Han --

Min-Han Tan <minhan.tan at gmail.com> writes:

> 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
> su
> make install
> exit()
> 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
> '/home/minhan/R/x86_64-unknown-linux-gnu-library/2.9'
> 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
> /home/minhan/R/x86_64-unknown-linux-gnu-library/2.9
> However, I get this error.
>> library(hs133phsentrezgcdf)
> Error in library(hs133phsentrezgcdf) :
>   'hs133phsentrezgcdf' is not a valid installed package

Use something like

  R CMD INSTALL --clean hs133phsentrezgcdf.tar.gz

to install packages from the command line. I'm not really sure why
this cdf is not available via biocLite, but will try to find out.


> Ideally, I would like to do
>   source("http://bioconductor.org/biocLite.R")
>     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!
> Min-Han
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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