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

[Bela Tiwari]

Hello, 

Following up on Tony's message - he figured out that the problem he saw was due to a dependency on  the libpng12-dev package.   Recent images of Bio-Linux 5 should have that package pre-installed. For those of you that see the problem Tony reported, it probably means you don't have that package and need to install it.

Thanks for letting us know about this Tony.


Bela


*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


>>> A.J.Pemberton at bham.ac.uk 05/12/09 12:19 pm >>>
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
> 
> *************************
> 
> 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk 
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux 

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