On Wed, Nov 27, 2013 at 8:00 AM, Horne, Nigel (NIH/NLM/NCBI) [C] <
nigel.horne@nih.gov> wrote:

>  Sean,
>
> On Tue, Nov 26, 2013 at 12:09 PM, Horne, Nigel (NIH/NLM/NCBI) [C] <
> nigel.horne@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!
>
>
Hi, Nigel.

Sorry for the confusion, but suffice it to say that the Bioconductor
releases are coordinated to R so that a specific version of Bioconductor is
tied to the associated R release.  Some packages may run in earlier
versions of R (hence, the R>=2.10 in the package DESCRIPTION), but that use
case is not supported by Bioconductor.  Following the installation
instructions on the Bioconductor website minimizes the chance of getting
into trouble with non-matching package versions.

In any case, if the user wants to use a specific version of R, the
appropriate package version should always be installed using biocLite as
detailed on the Bioconductor website.

Sean

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