From a.travis at abdn.ac.uk Thu Apr 9 10:17:06 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Thu, 09 Apr 2009 15:17:06 +0100 Subject: [Bio-Linux] Cleanup Message-ID: <49DE0362.1040408@abdn.ac.uk> Hello, I've just done a clean install of Bio-Linux 5.0.2 on a new machine, and I noticed that, after installation, the /root folder still contains the developer's .bash_history and other files that should have been purged from /root before mastering the DVD. There doesn't appear to be any sensitive information in the files, but I do think that these files should be removed if you're distributing Bio-Linux 5.0 to the public. Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt From tbooth at ceh.ac.uk Thu Apr 16 13:21:33 2009 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 16 Apr 2009 18:21:33 +0100 Subject: [Bio-Linux] IMPORTANT - All users of R on Bio-Linux 5 Message-ID: <1239902493.12679.117.camel@barsukas> Dear All, A new version of R (2.9.0) is due to be released tomorrow (April 17 2009). Because Bio-Linux 5 is set to pick up software updates from the CRAN package server in Bristol this update will be installed automatically. Unfortunately, several modules - notably those that are part of Bioconductor - are not yet officially updated to support this version. Therefore Bioconductor will be unavailable if the update goes ahead. If you are using Bioconductor right now you have three options: 1) Hold off the update by editing your sources.list. Give the command: nano -w /etc/apt/sources.list Place a hash (#) in front of the final line (the one referencing www.stats.bris.ac.uk/R/ ) and save the file. 2) If you do update R, you can install a pre-release of the new Bioconductor modules by using the package created by Philip de Groot. Download the file from here: http://nebc.nox.ac.uk/downloads/bio-linux/gp-bioc-2.4-0_i386.deb Then run 'sudo dpkg -i gp-bioc-2.4-0_i386.deb' 3) If you do not require the bioconductor modules in the next few days: Official support for Bioconductor in R 2.9 is due for release next week, on April 21st. Therefore over the next few days we will be preparing and testing full instructions for making a smooth upgrade to the official release and sending them out on this list and on our website. In the meantime, if you have any problems or concerns please contact us via the helpdesk address - helpdesk at nebc.nox.ac.uk. Thanks, Tim -- Tim Booth NERC Environmental Bioinformatics Centre at CEH Oxford +44 1865 281 975 From a.travis at abdn.ac.uk Sat Apr 18 18:22:37 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Sat, 18 Apr 2009 23:22:37 +0100 Subject: [Bio-Linux] IMPORTANT - All users of R on Bio-Linux 5 In-Reply-To: <1239902493.12679.117.camel@barsukas> References: <1239902493.12679.117.camel@barsukas> Message-ID: <49EA52AD.60200@abdn.ac.uk> Tim Booth wrote: > Dear All, > > A new version of R (2.9.0) is due to be released tomorrow (April 17 > 2009). Because Bio-Linux 5 is set to pick up software updates from the > CRAN package server in Bristol this update will be installed > automatically. Unfortunately, several modules - notably those that are > part of Bioconductor - are not yet officially updated to support this > version. Therefore Bioconductor will be unavailable if the update goes > ahead. If you are using Bioconductor right now you have three options: > [...] Hello, Tim. This is precisely why we have packaged R + Bioconductor ourselves in NuGO. Please contact my colleague Philip de Groot at Wageningen University directly for details of his most recent R + Bioconductor deb's, which we also use for GenePattern. Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt From btiwari at ceh.ac.uk Wed Apr 22 04:37:17 2009 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Wed, 22 Apr 2009 09:37:17 +0100 Subject: [Bio-Linux] Updating R and Bioconductor on Bio-Linux Message-ID: 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 *************************