[BioC] Upgrading R

Bryan Hepworth bryan.hepworth at newcastle.ac.uk
Tue May 12 10:38:46 CEST 2009

>-----Original Message-----
>From: bioconductor-bounces at stat.math.ethz.ch 
>[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
>Sarmah, Chintanu Kumar
>Sent: 12 May 2009 06:45
>To: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Upgrading R
>Thanks to all of you (Robert, John, Steve, Bryan, Anna) for 
>your comments !
>Best Wishes,
>From: rgentlem at gmail.com [rgentlem at gmail.com] on behalf of 
>Robert Gentleman [rgentlem at fhcrc.org]
>Sent: 11 May 2009 17:23
>To: Sarmah, Chintanu Kumar
>Cc: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Upgrading R
>Hi Chintanu,
>  Basically no, there is no such path. You should always 
>upgrade R and reinstall all packages. biocLite will help you 
>to do that.
>  best wishes
>    Robert
>On Sat, May 9, 2009 at 4:33 PM, Sarmah, Chintanu Kumar 
><Chintanu.Sarmah2 at lincolnuni.ac.nz> wrote:
>> Hi,
>> Wonder if there is a way to upgrade R.
>> I'm currently using R 2.7.2, and wish to 'upgrade' to the 
>latest one via some process that doesn't make me reinstall all 
>the packages again !! Please let me know.
>> Thank you !
>> Chintanu

Hi Everyone

I'm curious to know people opinions on updates and would be grateful of some insight into this.

I recently did a rip and replace over a number of servers that are all now running RedHat 5. I updated R from the EPEL repository and then loaded up biocLite from R as it was a priority to get the packages on for work related tasks.

When the next release of R happens I was assuming rpm -Uvh R-2.9.1 then run the biocLite update from within R again.

I know there is work in progress on the Fedora packages to make the bioconductor packages an rpm too and I've been looking at doing a similar exercise with the EPEL repository, basically to make life simple for myself and ultimately my end users! I'm a sysadmin rather than an enduser if you hadn't gathered already :-)

Any comments most gladly welcomed.


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