Monday, August 26, 2013

Bioconductor is out-of-date: update R to version 3.0 in ubuntu

I wanted to install cummeRbund into a new workstation, per the protocol of TopHat and Cufflinks (Trapnell et al 2012), however I ran into a problem with R version and bioconductor. This may not be relevant soon as we believe that R 3.0 will soon be put into the repository for apt-get, but who knows it may be useful: Here is the error that I got: After going into R:
$ R
$ source("http://bioconductor.org/biocLite.R")
I got the error:
Your Bioconductor is out-of-date, upgrade to version %s by following instructions at http://bioconductor.org/install
However for me this was not the case, and following instructions on Bioconductor's website did not help. I found that updating my version of R from 2.14 to 3.0 solved my problems. The instructions to update R to 3.0 can be found on the R website . Here is what I did: 1. removed older version of R
$ sudo apt-get remove r-base-core
2. Add deb to sources.list using vim: 2a. open sources.list using vim
$ sudo vim /etc/apt/sources.list
2b. scroll down to the bottom holding down Ctrl + F
2c. type "I" to insert text, and type in the following
## yourname modification on date    
deb http://cran.rstudio.com/bin/linux/ubuntu percise/
(my ubuntu version is precise) 2d. push "Esc" button to exit insert mode
2e. type ":w" and "Enter" to save
2f. type ":q" and "Enter" to exit vim editor
3. Add key to sign CRAN packages
$ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
4. Add specific PPA to the system
$ sudo add-apt-repository ppa:marutter/rdev
$ sudo apt-get update
$ sudo apt-get upgrade
5. Install latest version of R:
$ sudo apt-get install r-base
Now I had the right version of R, so I could install bioconductor and then cummeRbund: 1. open R
$ R
2. Install CummeRbund package:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite('cummeRbund')
3. load CummeRbund library:
> library(cummeRbund)
4. Now you should be able to use the cummeRbund package as described in the protocol!

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