[BioC] Building GenomicRanges1.14.3 on Centos6

[Horne, Nigel (NIH/NLM/NCBI) [C]]

Sean,

On Tue, Nov 26, 2013 at 12:09 PM, Horne, Nigel (NIH/NLM/NCBI) [C] <nigel.horne at nih.gov<mailto:nigel.horne at nih.gov>> wrote:
I am a system admin who has been asked by a user to install GenomicRanges, however it is failing.  I know absolutely nothing about R, so I'd like some (gentle!) help on how to install it.

This is on CentOS6, with gcc 4.4.7, R2.15.1.  The error I get is:

bash-4.1$ /usr/local/R/2.15.1/lib64/R/bin/Rcmd INSTALL GenomicRanges_1.14.3.tar.gz

Hi, Nigel.

It turns out that the Bioconductor packages (of which GenomicRanges is one) are matched to the version of R.  You are trying to install on a fairly old version of R and the GenomicRanges version does not match.  While R does not change too quickly, Bioconductor does continue to add features, so my suggestion is to first install the most recent version of R (3.0.2, I believe) so that your users have the most updated release.   Then install using the instructions here:

http://www.bioconductor.org/packages/2.13/bioc/html/GenomicRanges.html


Thanks for your answer.  I wondered if that could be the case, though the page you mentioned says it works with "R (>= 2.10)",  so I assumed it would work with 2.15.1.  I will try to convince the user to use a different version – wish me good luck on that one!  Perhaps I could also suggest that the page correctly reflect the minimum version of R that's required?  That would make my life easier when trying to convince her!

Regards,

-Nigel