StatET – Setup and Installation

Errol StrainErrol.Strain@fda.hhs.gov

useR! July 20th 2010

Material to Cover

• 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