[BioC] Installation of a custom cdf hs133phsentrezgcdf
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 install
> R -> /usr/bin/R/2.9.0/bin/R
> I suspect there are permission issues, as I get these warning messages in R.
> 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.
> 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
> 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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