[Bio-Linux] Updating R and Bioconductor on Bio-Linux

[Anthony Pemberton]

Bela,

I still had a problem updating the rgl under R after installing the
libraries you mentioned below. There appeared to be a header file still
required pngpixmap.h. I could not locate a deb for this with 

# apt-file search pngpixmap.h

Any ideas as to the source of the problem?

Regards,

Tony Pemberton


> -----Original Message-----
> From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [mailto:bio-linux-
> bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Bela Tiwari
> Sent: 22 April 2009 09:37
> To: bio-linux at envgen.nerc-oxford.ac.uk
> Subject: [Bio-Linux] Updating R and Bioconductor on Bio-Linux
> 
> Hello,
> 
> This email is to follow up on our email last week about R and
> Bioconductor on Bio-Linux.
> 
> R 2.9.0 and Bioconductor 2.4 are now available. If you wish to ensure
> that all your R and Bioconductor libraries are up to date, you can run
> the commands below. If you chose option 1 in the previous email, and
> stopped the updates from happening, you should remove the hash you put
> in front of the line that includes www.stats.bris.ac.uk/R/, then
update
> R, or wait until the updates are run overnight. Then follow the
> instructions below.  If you chose option 2, and installed Philip de
> Groot's package, there
> are a few notes about that package at the very end of this email.
> 
> Commands to run:
> 
> sudo R
> 
> Then at the R command prompt, type:
> 
> source("http://bioconductor.org/biocLite.R")
> update.packages(repos=biocinstallRepos(), ask=FALSE)
> 
> The update will take some time. You may see errors at the end when the
> rgl package attempts to update. This package was originally installed
> using the r-cran-rgl package. If you don't use rgl, or are happy with
> version 0.76, which is currently installed, then you can ignore this.
> 
> If you want the latest version, which is 0.84, then instructions
> follow:
> 
> Installing rgl via R:
> You can get the latest version of rgl by using the R command
> install.packages("rgl")
> However, BEFORE you do this, you will need to install some libraries.
> You can do this by typing on a terminal command line (not R):
> 
> sudo apt-get install libglu1-mesa-dev
> 
> (This will install the libglu1-mesa-de, libgl1-mesa-dev and
> mesa-common-dev packages.)
> 
> If you choose to update rgl this way, it should not conflict with the
> version installed via the deb package r-cran-rgl on a standard Bio-
> Linux
> system, and the version you installed from within R should take
> precedence. Note that the r-cran-rgl package is required by
Rcommander,
> so is best left installed if you or other users of your system use
> Rcommander.
> 
> 
> Further notes about Philip de Groot's package:
> Philip has just informed us that 2 of the R libraries in his package
> have slight alterations compared to the version from CRAN. These are:
> 
>  - simpleaffy - changed so that tab characters are interpreted as
> proper separators when loading a covdesc file.
>  - q-value - removal of the tcltk dependency so that servers without
> X11 output do not crash when loading this library
> 
> 
> 
> *************************
> Dr. Bela Tiwari
> Lead Bioinformatician
> NERC Environmental
> Bioinformatics Centre
> 
> CEH Oxford
> Mansfield Road
> Oxford, OX1 3SR
> 01865 281975
> 
> *************************
> 
> 
> 
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