[BioC] Re: Installing Bioconductor on R 1.9.1

[Wolfgang Huber]

M. K. wrote:
 > Dear Sir,
 >
 > Our unix cluster have R version 1.9.0. When I type
 > /source("http://www.bioconductor.org/getBioC.R")/  and /getBioC()/, I
 > get the following message: "You are currently running R version 1.9.0,
 > however R version 2.0.0 is required". Our system-add-min is not willing
 > to install the  newest version (2.0.1) of the R, so is it possible to
 > install the bioconductor packages wihtout changing the R version ?
 >
 > For example, can I delete the version check in getBioC.R-code or
 > manually install the packages ?
 >

Hi,

the best place to ask these questions is the bioconductor mailing list.

Do not simply elimate the version check. It is there for a reason and 
Bioconductor release 1.5 will not run on anything before R 2.0.0!

You could try to revert back to release 1.4 of Bioconductor. I am not 
sure how to do this best, maybe by making some changes to the getbioC.R 
script, or by manually getting all required packages from
http://www.bioconductor.org/repository/release1.4/package/html/index.html

But the recommended solution is: Install your own R in your home 
directory! This is has many advantages, and it is not difficult. Simply 
get R-2.0.1.tar.gz, untar, run './configure' and 'make'. More detailed 
instruction are on the Biocondutor and R-project websites. For some 
options you may need to install additional libraries (e.g. on Suse 
"readline-devel" for nicer command-line editing, or libpng for PNG 
graphics, but these are second-order cosmetics.)

If you want to seriously use R/Bioconductor, this is much better than 
relying on an unhelpful sysad. Also, in principle installing R and R 
packages as a user is more secure than as root! Although I have never 
heard of any cases, a malevolent package author could to bad things when 
you let the package installation run with superuser permissions...

Best regards
  Wolfgang


-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber