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• Minimum Installation– Java– Eclipse– StatET
• Recommended Installation– Apache, subversion, subclipse, LaTeX, Rtools
• Tricks and Troubleshooting
Java (and rJava)
• Sun Java (http://java.sun.com) for Linux & Windows– JRE 1.5 or higher– Eclipse/R/StatEt was crashing frequently with IBM java on
RHEL4 x86_64 (but this may be fixed in recent versions)– Eclipse can use local JRE if necessary
• Windows (32-bit)– CRAN binaries work in XP
• OS X– CRAN binaries (Snow Leopard)– http://r.research.att.com/– Forced to compile, use MacPorts
• Linux (RHEL and Ubuntu)– CRAN binaries (RHEL 5 & Lucid Lynx)– Shared/Dynamic Libraries, compile with “--enable-R-shlib”
R and Packages
• Setup tested using R 2.11.1 on XP and Snow Leopard
• rJava (version 8.4)
• rj (version 0.5.0-4)
– Needed for StatET RJ launch
– Not available on CRAN
– Download from http://www.walware.de/goto/statet
– Use the terminal/console to install
$ R CMD INSTALL --no-test-load rj_0.5.0-4.tar.gz
– R 2.10.1 does not have --no-test-load option
R Path
• StatET uses defined R environments, not the system R path in Windows and Linux
– Multiple R installations (Current version, previous working version, development version)
– Terminal/Console output and default StatET output be consistent
• Windows XP
– Settings -> Control Panel -> System -> Advanced -> Environment Variables, then edit Path variable to include C:\R\R-2.11.1\bin
– Or create symbolic link from C:\R\R to C:\R\R-2.11.1 and edit path to include C:\R\R\bin
• OS X and Linux
– /Users/username/.profile
– /home/username/.bashrc
Building Packages
• Compilers (gcc, mingw, Fortran), Perl, bitmap libraries, gzip, tar, etc.
• Windows– Use Rtools.exe– http://www.murdoch-sutherland.com/Rtools/
• OS X– XCode Developer Tools– http://r.research.att.com/tools/
• Linux (Ubuntu)– Use apt-get install r-base-dev
Eclipse IDE• Download Eclipse Classic (3.6) for your OS from www.eclipse.org
– Eclipse IDE for Java Developers is also supposed to work– Synaptic/Yum repository versions are usually a little behind
• Extract Files– One eclipse folder per user is easiest (config settings)– C:\eclipse\eclipse36 (Windows)– \home\user\eclipse\eclipse36 (Linux)– Applications Folder (OS X)
• Memory settings (eclipse/configuration/config.ini)– Modify/Add line to config.ini “-Xmx4096m”
• Select a Workspace– “C:\eclipse\workspace” or “\home\user\workspace” preferred – Makes it easier to switch machines and collaborate on projects
(absolute path names)– Multiple workspaces for different large, complex projects?
Plug-Ins
• Help -> Install New Software– If using Eclipse 3.5, add http://download.walware.de/eclipse-3.5– If using 3.6, download archive from
http://www.walware.de/goto/statet– Install StatET and related components
• Subclipse (uses subversion)– Help -> Install New Software– http://subclipse.tigris.org/update_1.6.x– Uncheck Mylyn and Revision Graph
• EGit (uses git)– Help -> Install New Software– http://download.eclipse.org/releases/helios/
Eclipse StatET/R Tutorial
• Installing Plug-Ins
• Create StatET project
• Specify Connector
– New Console, Classic Console, Rgui, Xterm
• Add R Environment
– Detect Default Properties/Settings
– Set as Default
• R Console Launch Configuration
• Launch the console
• R Index
Problems?
• Often Java Related– Check JRE under Run Configurations– Follow suggestions from
http://www.walware.de/goto/statet• In JRE tab, add to vm arguments:
"-Drjava.path=<path to rJava>"
• Snow Leopard– Complains about 32-bit R with 64-bit JRE
• Help -> About Eclipse -> Installation Details -> Configuration
• Building R from source?– R CMD javareconf
Latex and Sweave
• Statistical Analyses and Reproducible Research (Gentleman and Lang 2004)– http://www.bepress.com/bioconductor/paper2/
• MacTeX or MiKTeX• Copy style files from R-2.11.1/share/texmf to
your TeX path– Linux: $HOME/texmf/tex/latex– OS X: ~/Library/texmf/tex/latex
• Refresh LaTeX database– texhash
Sweave Setup
• Sweave Run Configurations (Eclipse 3.5)– Sweave Tab
• Sweave Document Processing• Run R CMD Sweave
– Create New
– LaTex Tab– Output Format: pdf
• Eclipse 3.6– Run inside console– *.Rnw file must be in working directory
• Latex Error– TeXClipse Highlighting– Run LaTeX from the Console
Troubleshooting SVN
• Conflicts, SVN corrupted R files with “<<<<<<<<< .mine“– Subversion attempts to merge files, resulting in *.mine, *.rXXX– Edit Conflicts, Mark Resolved
• Too many files, large files– 3000+ files in a folder is too many, 100 is okay
• Team Cleanup (svn cleanup)– Locked files
• Nuclear Option– Copy affected directories, delete *.svn folders– Replace with repository version– Copy/Replace workspace files with copies– Lose subversion history
Subversion Proxy• Subversion servers file on Windows
C:\Documents and Settings\Errol.Strain\Application Data\Subversion......[global]# http-proxy-exceptions = *.exception.com, www.internal-site.org# http-proxy-host = defaultproxy.whatever.com# http-proxy-port = 7000# http-proxy-username = defaultusername# http-proxy-password = defaultpassword
• Servers file is overwritten when updating eclipse/subclipse– Keep a backup of the working copy
• Where to look for help– http://subclipse.tigris.org/wiki/PluginFAQ– http://svnkit.com/kb/config-settings.html
Subversion Server Setup
• Requires Apache– OS X: /etc/apache2– Linux: /etc/httpd or /etc/apache2
• OS X Subversion Installation– http://www.sonzea.com/articles/subversion-trac.html– http://mrnovell.wordpress.com/2007/11/17/how-to-manage-your-
own-subversion-repository-in-leopard/
• Ubuntu: https://help.ubuntu.com/community/Subversion• Problems?
– Firewall settings– SVN repository permissions– Search for “apache dav svn”
Acknowledgements
• BD Technologies– Elaine McVey, Daniel Samarov, Julie
Leonard, Dylan Wilson, Perry Haaland
• StatET– Stephan Wahlbrink
• FDA – Center for Food Safety and Nutrition