[BioC] Re: Installing Bioconductor on R 1.9.1

[Marion Hakanson]

Wolfgang Huber <huber at ebi.ac.uk> wrote:
> . . .
> 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


Having been down this road myself, I can confirm that the above will
work, but with one major deficiency:  I have been unable to get hold of
most of the metadata packages which go with release 1.4.  In the end,
I gave up on this approach and have upgraded to R-2.0.1 & BioC-1.5, etc.


> . . .
> 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...

Please pardon as I veer slightly farther off-topic here:

Being a sysadmin myself (and not a BioC user), I'll mention that this
security concern can easily be dealt with by a number of techniques.
And I'll add that you might be better served if you advocated for your 
organization's getting more sysadmin's to take care of your research tools
for you, instead of having each and every researcher go off and spend hours
of their time learning the nuts and bolts of compilers and operating systems.  
Unless of course you enjoy doing that sort of thing and have someone willing
to pay you to do it (:-).

Regards,

-- 
Marion Hakanson