LOCKER:          r_v3.4.1

FILE:            /mit/r_v3.4.1/README.athena

CONTENTS:        R 3.4.1, RStudio 1.0.153, Bioconductor 3.5 version locker

DESCRIPTION:     R is a system for statistical computation and graphics, with
		 an internal programming language. It bears a passing 
                 resemblance to the S language developed at AT&T Bell 
                 Laboratories, and to the subsequent commercial Splus
                 application. ESS is a set of Emacs modes developed for
		 R and related statistical computation systems. RStudio
		 is a GUI for R.

HOW TO RUN:

 COMMAND: 	add r
	  	R (text-only version)
		or, from within Emacs, M-x R to start an R process
		rstudio (GUI version)

  FROM GNOME MENU: no

INTERFACES:	 command-line, GUI (rstudio)

VERSIONS:	 For Linux 32/64: R 3.4.1, Bioconductor 3.5
 
DEPENDENCIES:	 Java runtime, in "current" java locker for some functionality

DATAFILES:	 Platform-independent

LICENSE SERVER:	 no

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SUPPORT ISSUES --

I/S SUPPORT:

  CONSULTING:	 none

  TRAINING:	 none

  DOCUMENTATION: pdf docs in /mit/r_v3.4.1 directory, online html docs
                  Ipopt interface: https://ipopt_v3.12.6/doc/ipoptr.pdf

OTHER SUPPORT:

  CONSULTING:	 (none)

  TRAINING: much material is on the web, at the http://cran.r-project.org/
            site

  DOCUMENTATION: ESS documentation at http://ess.r-project.org/Manual/ess.html
                
  WEB PAGE:      http://www.r-project.org/ (R)
		 http://ess.r-project.org/ (ESS)
                 http://rstudio.org        (RStudio)

BUG REPORTS:	 Use sendbug

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LEGAL ISSUES -- 

STATUS: freely distributable under GPL; see 
        http://web.mit.edu/r_v3.4.1/COPYING for details

 SITES:         any
 
 RESTRICTIONS:  
 
 DOCUMENTATION:
                
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ABOUT THIS LOCKER --

MAINTAINER(S):	 3partysw (group), alexp

DIRECTORY STRUCTURE:

        arch      	- arch hierarchy
	bin		- link to bin dir, containing main binaries, others
	ess-16.10	- link to ess files (emacs modes for R)
	lib		- link to lib dirs (binaries, libraries, misc files)
        man		- man pages
	share		- link to misc helper files, man pages

MODIFY HISTORY:

       8/14/17  - Alex Prengel
                  Created this README.athena, initial locker setup

       1/18/18  - Alex Prengel
                  Updated R, Bioconductor packages to latest versions

-------------------------------------------------------------------------
To install additional R packages:

You will need to store these in a directory where you have write permission,
such as your home directory. Assuming your username is myusername and the
R package directory is R-packages, first create this directory if it doesn't 
exist already. Download the source package from 
http://cran.r-project.org/web/packages/index.html such as package.tar.gz.

Type at the Athena prompt:

R CMD INSTALL package.tar.gz -l /mit/myusername/R-packages/

To load the package within R, type:

> library("packagename", lib.loc="/mit/myusername/R-packages/")

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MISCELLANEOUS:

You may get error messages at RStudio launch like:

load glyph failed err=6 face=0x2c93720, glyph=2680
QApplication::qAppName: Please instantiate the QApplication object first

This should be harmless and can be ignored.

The R FAQ at http://cran.r-project.org/doc/FAQ/R-FAQ.html is an excellent
source of information about R.

There is an Emacs mode for R available through the ESS package
(installed in the locker). To enable it, you must add the following
line to your ~/.emacs file (create the file if it does not already
exist):

(load "/afs/athena/software/r_v3.4.1/ess-16.10/lisp/ess-site")

To use it, type

add r

then, start Emacs after adding the line above to your .emacs file,
and from within Emacs:

M-x R

Help on ESS is available with Emacs after you invoke an R process by
typing:

C-h m

Many add on packages are available. We will consider adding additional ones 
requested by MIT users (send requests to the 3partysw@mit.edu mailing list).

To see the ones that are currently installed, type:

> library()

at the R > prompt. pdf manuals for the add-on packages are in the
lib/R/doc/extra-packages directory.

A package for using the ipopt non-linear solver has been added (64 bit only).

to access it within R:
add r; R
> library(ipoptr)

To get documentation:

> ?ipoptr
        
For extended documentation see https://web.mit.edu/ipopt_v3.12.6/doc/ipoptr.pdf