[R] Bioconductor package on linux machine

[James W. MacDonald]

Knut Krueger wrote:
> Hi together,
> we received a question about the bioconductor package,
> maybe anybody could help the guy and I will deliver the message over our 
> forum to him.
> If this way is allowed ...
> Regards Knut
> 
> Here the question:
> Hello,
> 
> I have installed R on a linux machine. I have then installed the 
> biocLite.R package from bioconductor.
> I wanted to install a few other packages - hgu133plus2cdf, rma .
> 
> I downloaded the source files and installed in the directory 
> /usr/lib64/R/library
> 
> but when i try using those files, they show as not installed.
> Anybody encounter this problem before OR is there something else i am 
> doing wrong?

The error is in the way you installed the packages. You cannot simply 
take the .tar.gz files and unpack them in the library directory using 
e.g. tar xvfz packagename.tar.gz. Instead you have to use the built in 
package handling system. Note that biocLite() is a script that among 
other things uses install.packages() to get things installed correctly.

What you want to do is:

source("http://www.bioconductor.org/biocLite.R")
biocLite("hgu133plus2cdf")

Alternatively you can install the already downloaded packages (assuming 
you downloaded the correct version for your version of R) using R CMD 
INSTALL at a terminal prompt.

Additionally, although this problem would occur with most R packages, 
enough of the details are strictly Bioconductor related so it is more 
appropriate to post this sort of question on the BioC listserv rather 
than R-help.

HTH,

Jim


> 
> Following is the sequence of stpes i used first:
> 1) library(affy)
> 
> 2) pcpc <- 
> ReadAffy(sampleNames=c("107762","110662","110682","110792","110802","111301","111611","111781","111801","154272","160881")) 
> 
> 
> 3) pc <- rma(pcpc)
> 
> Error in library("hgu133plus2cdf", lib.loc = NULL, character.only = TRUE) :
> 'hgu133plus2cdf' is not a valid package -- installed < 2.0.0?
> 
> ------------------------
> I tried all this when logged in as root.
> 
> 
> Any help will be appreciated.
> 
> thank you all..
> 
> sincerely
> Kiran
> Univ of Chicago
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623