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Wolfgang Huber
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@wolfgang-huber-3550
Last seen 12 days ago
EMBL European Molecular Biology Laborat…
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.h
tml
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