[BioC] Upgrading R

Sim, Fraser Fraser_Sim at URMC.Rochester.edu
Mon May 11 15:11:07 CEST 2009

It's very simple to maintain a small .R script file which runs a
combination of biocLite and install.packages(). You can have all the new
packages installed in about 30-60 mins on a typical connection. 

I've done this for a number of installs and it is very efficient.


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of john seers
Sent: Monday, May 11, 2009 7:39 AM
To: Sarmah, Chintanu Kumar; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Upgrading R

Hi Chintanu

I have struggled with this problem through several upgrades and I have
not found a consensus of the best way to do it. There are quite a lot of
suggestions and advice if you search around using RSiteSearch().

I think the most straightforward answer I have found is described here:


I have not investigated fully - perhaps copydir is the way to go?

But my last upgrade I used this:

Look for the README and the part that describes the alternative to

"An alternative to copydir is to reinstall all packages

	# Alternative to copydir.bat #1
	# this example is for moving from 2.4.1 to 2.5.0
	# run this in R 2.5.0
	ip <- installed.packages(lib.loc = "../R-2.4.1/library")
	ip <- ip[ip[,1]!="base" ,1]


I hope this helps.


John Seers

-----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: 10 May 2009 00:33
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Upgrading R

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 !

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