From BioclipseWiki

Statistics plugins that allows interaction between Bioclipse and a R session.

Part of the Bioclipse.statistical repository.

Contents 1 TODO 2 Set up the correct system environment 2.1 Linux 2.1.1 Installing R packages on Ubuntu linux 2.1.2 Installing R packages on Debian linux 2.1.3 Installing R packages on openSUSE linux 3 Setup Bioclipse for R 3.1 get Bioclipse from hudson and R from updatesite 3.2 get Bioclipse & R from gitrepos 3.2.1 Get RServi from StatET 3.2.1.1 Using git command 3.2.1.2 Using eGit in Eclipse 3.2.1.3 continue 4 Setup Bioclipse with R from Debian 5 Currently working Status 5.1 Windows 5.2 Mac 5.3 Linux

TODO

• catch the quartz() command and give the user a message saying that quartz() is disabled for stability reasons and that x11 should bes used [Done]
• R sessions/history (look at Eclipse+StatET)

The work with the R console should be organized in the Bioclipse way - the user creates R project and the files associated with this project are stored stored in a directory in the bioclipse-workspace. R sessions are stored by the user project-wise. The default R wd is bioclipse-workspace => now session is loaded on startup.

• R scripts Not started
• multiple lines execution/";" separated commands execution (look at Eclipse+StatET) [Done]
• Quartz plotting Waiting for response
• q() command Not started
  • session saving prompt Not started
  • closing the view Not started
  • check about closing the connection with R?!?
• open help pages in the BC internal browser [Done]

• Check why [Done]

  R workspace:  "/Users/valentingeorgiev/bioclipse-workspace"
  Use load("file") and save.image("file")

is not printed in the R console on startup

• Reading Rhistory when loading R session file Not started

Set up the correct system environment

System install dependencies: R, rJava and RJ.

It is basically enough to install R. Standard Windows path: C:\Program Files\R\R-{version}\

Once R is installed, running Bioclipse-R installs rJava and RJ if they are missing (currently working on all platforms). For manual installation:

install from R:

  install.packages('rJava', repos='http://cran.stat.ucla.edu')
  install.packages('rj', repos='http://download.walware.de/rj-0.5')

or download rJava and RJ and

install from console:

 R CMD INSTALL --no-test-load rJava*.tar.gz
 R CMD INSTALL --no-test-load rj_0.5.5-4.tar.gz  

On a default R installation the R_HOME value is:

  /Library/Frameworks/R.framework/Resources on MacOSX
  ... on Windows
  ... on Linux

Linux

Look at this page for creating a personal R package library.

Installing R packages on Ubuntu linux

See [1]

Make sure you have Java Development Kit installed and correctly registered in R:

sudo R CMD javareconf

If you get something like this:

Java compiler    : not present
Java headers gen.: 
Java archive tool: 

instead of:

Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar

you need to install the Java Development Kit (JDK):

sudo apt-get install openjdk-6-jdk

and run javareconf again:

sudo R CMD javareconf

There are two options for installing the required R packages:

(i) install the required packages manually from within R

(ii) prepare the environment for the automatic Bioclipse installation (recommended)

...to be continued

Installing R packages on Debian linux

Follow the instructions here to install the latest R release to squeeze.

apt-get install openjdk-6-jdk

no need to run R CMD javareconf

rJava installs without problem

Installing R packages on openSUSE linux

JDK installed by default, but you need to install the gcc compiler and make (via YaST).

Setup Bioclipse for R

Choose one of the following two ways:

get Bioclipse from hudson and R from updatesite

• Download bioclise from latest successful build: Bioclipse 2.5.0.

When started go to Help/Install new software, Work with: "http://pele.farmbio.uu.se/jenkins/job/Bioclipse.statistics/lastSuccessfulBuild/artifact/buckminster.output/net.bioclipse.statistics_site_1.0.0-eclipse.feature/site.p2/", and press "Add". Name it R_console. Under uncategorized: select "Bioclipse-R integration", select Next and continue until it ask you to restart, and do so.

Go to "Window > Show View > Other.." under scripting you will find "R Console", and there you go.

Make sure you have set the system environment R_HOME to your R location.

Done!

get Bioclipse & R from gitrepos

Get RServi from StatET

Walware R GIT-repo

Using git command

git clone https://github.com/walware/rj-servi.git (rj-servi)
cd rj-servi
git checkout RJ-0.5.5

• import existing project and choose "de.walware.rj.servi" project

git clone https://github.com/walware/rj-core.git (rj-core)
cd rj-core
git checkout RJ.jri-0.5.5-4

• import existing project and choose "de.walware.rj.data" and "de.walware.rj.server" projects

git clone https://github.com/walware/rj-client.git (rj-client)
cd rj-client
git checkout RJ-0.5.5

• import existing project and choose "de.walware.rj.client" project

git clone https://github.com/walware/ecommons-coremisc.git (ecommons-coremisc)
cd ecommons-coremisc
git checkout StatET-0.9.2_E-3.6

• import existing project and choose "de.walware.ecommons.coremisc" project

---

Userinterface import, not in use! (maybe later)

• git clone https://github.com/walware/ecommons-uimisc.git (ecommons-uimisc)
  • import existing project and choose "de.walware.ecommons.uimisc" project

---

Using eGit in Eclipse

• Import.. Git > Projects from Git
• Clone URI: use the above URL:s, Next, Select ONLY the master branch, Next, Finish.
• Select the cloned git-repo, Next, Next, select ONLY the project needed.
• repeate for all the aboive URL:s

continue

• Download & Import bioclipse.statistical from Git Repo. [instructions]. But checkout and pull the R_console branch.

cd bioclipse.statistics
git checkout R_console
git pull

• Refresh net.bioclipse.r projects by selecting them in Package explorer and chooce "Refresh" (F5)

• Go to Run configuration, Plug-ins, select "net.bioclipse.r", "net.bioclipse.r.ui" and "Add required Plug-ins"

Now, just Run!

Setup Bioclipse with R from Debian

http://chem-bla-ics.blogspot.com/2011/02/diy-running-r-from-within-bioclipse.html

Currently working Status

• Include the rj package into the r-console
• the RJ packages are in target-platform
• different StatET binarys for R 2.13 and 2.12

Windows

• Windows XP(32 bit) (Valentin)
  • check rj  : works
  • install rj  : works (package version 0.5.5-4)
  • check rJava : works
  • install rJava : works
  • binary: installation of R console binaries works
  • plotting: works
  • eclipse: - how the eclipse dev environment setup works

• Windows 7 (64bit) (Christian)
  • check rj  : working(with UserLib)
  • check rJava: working(with UserLib)
  • binary:
  • eclipse: Works!
    • except for the plotting

• Windows Vista (puter @ bmc)

• Write restrictions on Program folder / Library - is this only Vista-related?

• • Create a user library, run R from terminal once and install any packages, and this i created.
  • Or use: dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)

Mac

only works with rj 0.5.5-4

• get R_HOME : using the default R path (if not set as system variable)
• check rj  : working
• install rj : working
• check rJava: working
• install rJava: working

• check Binary installation:
  • Mac OSX (32bit) Valentin: all works
  • Mac OSX (64bit) Christian

Linux

• get R_HOME : nothing done here
• check rj  : works
• install rj : works
• check rJava: works
• plotting  : works

• check Binary installation:
  • Linux (32bit)
  • Linux (64bit)