<?xml version="1.0"?>
<!DOCTYPE MODE SYSTEM "xmode.dtd">

<MODE>
  <RULES IGNORE_CASE="FALSE">
        
    <SPAN_REGEXP MATCH_TYPE="MARKUP" 
      DELEGATE="java::MAIN" HASH_CHAR="&lt;">
      <BEGIN>&lt;script&gt;</BEGIN>
      <END>&lt;/script&gt;</END>
    </SPAN_REGEXP>
    
    <SPAN_REGEXP MATCH_TYPE="MARKUP" 
      DELEGATE="css::MAIN" HASH_CHAR="&lt;">
      <BEGIN>&lt;style&gt;</BEGIN>
      <END>&lt;/style&gt;</END>
    </SPAN_REGEXP>
    
    <IMPORT DELEGATE="xml::MAIN" />
  </RULES>

</MODE>

  <MODE NAME="jaxx"   FILE="jaxx.xml" FILE_NAME_GLOB="*.jaxx"  />

$ mkdir ~/opwrappers
$ cp -fr /usr/local/share/openturns/WrapperTemplates/wrapper_calling_shell_command ~/opwrappers/rwrapper
$ cd ~/opwrappers/rwrapper/
$ ll
total 300
-rw-r--r-- 1 romain romain     27 2009-01-23 11:54 AUTHORS
-rwxr-xr-x 1 romain romain   1304 2009-01-23 11:54 bootstrap
-rw-r--r-- 1 romain romain 199260 2009-01-23 11:54 ChangeLog
-rw-r--r-- 1 romain romain    216 2009-01-23 11:54 code_C1.data
-rw-rw-r-- 1 romain romain   1594 2009-01-23 12:42 configure.ac
-rw-r--r-- 1 romain romain  18002 2009-01-23 11:54 COPYING
-rwxr-xr-x 1 romain romain   1794 2009-01-23 11:54 customize
-rw-r--r-- 1 romain romain   9498 2009-01-23 11:54 INSTALL
drwxr-xr-x 2 romain romain   4096 2009-01-23 11:54 m4
-rw-rw-r-- 1 romain romain    571 2009-01-23 12:42 Makefile.am
-rw-r--r-- 1 romain romain    447 2009-01-23 11:54 myCFunction.c
-rw-r--r-- 1 romain romain    455 2009-01-23 11:54 myCFunction.h
-rw-r--r-- 1 romain romain      0 2009-01-23 11:54 NEWS
-rw-r--r-- 1 romain romain    925 2009-01-23 11:54 README
-rwxrwxr-x 1 romain romain    435 2009-01-23 12:03 rwrapper.R
-rw-rw-r-- 1 romain romain   3722 2009-01-23 12:42 rwrapper.xml.in
-rw-rw-r-- 1 romain romain   1442 2009-01-23 12:42 test.py
-rw-rw-r-- 1 romain romain   9349 2009-01-23 12:42 wrapper.c
-rw-r--r-- 1 romain romain     27 2009-01-23 11:54 AUTHORS

$ ./customize rwrapper

$ rm myCFunction.* 
$ rm code_C1.c
$ ll
total 288
-rw-r--r-- 1 romain romain     27 2009-01-23 11:54 AUTHORS
-rwxr-xr-x 1 romain romain   1304 2009-01-23 11:54 bootstrap
-rw-r--r-- 1 romain romain 199260 2009-01-23 11:54 ChangeLog
-rw-r--r-- 1 romain romain    216 2009-01-23 11:54 code_C1.data
-rw-rw-r-- 1 romain romain   1594 2009-01-23 12:42 configure.ac
-rw-r--r-- 1 romain romain  18002 2009-01-23 11:54 COPYING
-rwxr-xr-x 1 romain romain   1794 2009-01-23 11:54 customize
-rw-r--r-- 1 romain romain   9498 2009-01-23 11:54 INSTALL
drwxr-xr-x 2 romain romain   4096 2009-01-23 11:54 m4
-rw-rw-r-- 1 romain romain    571 2009-01-23 12:42 Makefile.am
-rw-r--r-- 1 romain romain      0 2009-01-23 11:54 NEWS
-rw-r--r-- 1 romain romain    925 2009-01-23 11:54 README
-rwxrwxr-x 1 romain romain    435 2009-01-23 12:03 rwrapper.R
-rw-rw-r-- 1 romain romain   3722 2009-01-23 12:42 rwrapper.xml.in
-rw-rw-r-- 1 romain romain   1442 2009-01-23 12:42 test.py
-rw-rw-r-- 1 romain romain   9349 2009-01-23 12:42 wrapper.c

#!/usr/bin/env Rscript

# grab arguments
argv <- commandArgs( TRUE )
datafile <- argv[1]
outfile  <- argv[2] 

# read data from data file 
rl <- readLines( datafile )
extract <- function( index = 1 ){
  rx <- sprintf( "^(I%d *= *)(.*)$", index )
  as.numeric( gsub( rx, "\\2", grep(rx, rl, value = TRUE ) ) ) 
}
x1 <- extract( 1 )
x2 <- extract( 2 )
x3 <- extract( 3 )

out <- x1 + x2 + x3
cat( "O1 = ", out, sep = "", file = outfile )

ACLOCAL_AMFLAGS = -I m4

wrapperdir          = $(prefix)/wrappers

wrapper_LTLIBRARIES = rwrapper.la
wcode_la_SOURCES    = wrapper.c
wcode_la_CPPFLAGS   = $(OPENTURNS_WRAPPER_CPPFLAGS)
wcode_la_LDFLAGS    = -module -no-undefined -version-info 0:0:0
wcode_la_LDFLAGS   += $(OPENTURNS_WRAPPER_LDFLAGS)
wcode_la_LIBADD     = $(OPENTURNS_WRAPPER_LIBS)

XMLWRAPPERFILE      = rwrapper.xml
wrapper_DATA        = $(XMLWRAPPERFILE)
EXTRA_DIST          = $(XMLWRAPPERFILE).in test.py code_C1.data

execbindir          = $(prefix)/bin
execbin_DATA        = rwrapper.R

        <variable id="O1" type="out">
          <comment>Output 1</comment>
          <unit>none</unit>
          <regexp>O1\S*=\S*(\R)</regexp>
        </variable>

      <!-- An output file -->
      <file id="result" type="out">
        <name>The output result file</name>
        <path>code_C1.result</path>
        <subst>O1</subst>
      </file>
 

    <command>Rscript @prefix@/bin/rwrapper.R code_C1.data code_C1.result</command>

$ ./bootstrap
$ ./configure --prefix=/home/romain/openturns --with-openturns=/usr/local
$ make 
$ make install

$ cp code_C1.data /tmp
$ cd /tmp

$ python
>>> from openturns import *
>>> p = NumericalPoint( (1,2,3))
>>> f = NumericalMathFunction( "rwrapper" )
>>> print f(p )
class=NumericalPoint name=Unnamed dimension=1 implementation=class=NumericalPointImplementation name=Unnamed dimension=1 values=[6]
>>> 1+2+3
6

• by writing the function in python and let python communicate with R (using rpy for instance)
• by writing a c wrapper that would initialize a connection to an R server when the function is created, and call it whenever the function needs to be called

• the listings package (somehow supported by the R package SweaveListingUtils
• Using highlight. I am using it in the graph gallery for example
• There are probably other ways ...

• The modified source of Code2HTML
• The actual jar file
• An example R file
• ... once translated into latex markup
• ... once compile with pdflatex

• do something about the gutter
• figure out how to invoke that from the command line
• write a sweave driver that would call it so that R code appears formatted in sweave documents

Introduction

After spending quite some time to install openturns on my fedora box, I feel I should post about it to spare the time of other people. The install page advertises for a forthcoming support for RPM packages available soon (we all know the real definition of soon don't we : it means "we don't need it for ourselves, so if you want it, do it", which is fair enough).

If I had more time, I would learn how to make rpms, and provide one for openturns, but this does not seem necessary for now as openturns installs fine from source, at least if you go round a few things. This post is absolutely not a replacement for the real install notes but maybe guidelines on how to read these notes from a fedora perspective.

Download

Grab the tar.gz from sourceforge and unzip it somewhere.

Dependencies

This is what the install notes say :

Till 0.12.1 included:

* GCC C, C++ and Fortran compilers (>= 3.3.5 except 4.0.x series, tested with 3.4.5, 3.4.6, 4.1.1, 4.1.2 & 4.2.2) * Python interpreter (>= 2.4.x) * R statistical language (>= 2.0) * Xerces-C XML parser (>= 2.6.0, tested with 2.7.0) * BOOST C++ library (>= 1.33.1) * LAPACK Linear Algebra library (>= 3.0) * Qt (3.3.x) * python-qt if you want to use the embedded image viewer ViewImage (TUI only)

Since 0.12.2:

* GCC C, C++ and Fortran compilers (>= 3.3.5 except 4.0.x series, tested with 3.3.5, 3.3.6, 3.4.5, 3.4.6, 4.1.1, 4.1.2, 4.2.2 & 4.3.1) * Python interpreter (>= 2.4.x) * R statistical language (>= 2.0) * Libxml2 XML library (>= 2.6.27) * LAPACK Linear Algebra library (>= 3.0) * python-qt if you want to use the embedded image viewer ViewImage (TUI only)

Here is what I have done on my fedora machine: python and gcc are already installed unless you really want them not to be, so nothing to do here, R is easy to compile from source, but you can get it with yum as well (yum install R)

For the other software, here is my list of yum calls :

# yum install -y xerces-c-devel
# yum install -y boost-devel
# yum install -y lapack-devel
# yum install -y qt3-devel
# yum install -y PyQt-devel
# yum install -y libxml2-devel

I also installed rpy and graphviz to have optional features as well:

# yum install -y rpy
# yum install -y graphviz-devel

After that, the ./configure call should be ok. Here is the summary I got which sounds good enough.

R Packages

Now you can install the R package rotRPackage which comes with openturns as described in the install page

# R CMD INSTALL utils/rotRPackage_1.4.4.tar.gz

You also need the sensitivity package, but at the time of writing the sensitivity package changed some of its API and openturns did not propagate, so you have to install version 1.3-1 as opposed to the current version.

The other problem I ran into was that I am using a custom ~/.Rprofile file which contains startup instructions such as requireing R packages, this caused the test cases of openturns to fail because the expected output was mixed with the standard error stream (which is where require writes its messages). So at least for running openturns tests, I have modified my .Rprofile file so that it does not load packages or write anything to the standard error stream.

Installing openturns

When this is ready, you can do :

$ make   # good opportunity to make some coffee while it compiles 
$ make check # everything should be ok
# make install
$ make installcheck # should be ok too

Loading the python module

Reading the FAQ is a good way to save yourself some time, specifically when trying to load the openturns python module. I have added these two lines to my .bash_profile file :

PYTHONPATH=/usr/local/lib/python2.5/site-packages/openturns
export PYTHONPATH

Then, you can start python and start using openturns, which is another story ...

$ python
Python 2.5.2 (r252:60911, Sep 30 2008, 15:41:38)
[GCC 4.3.2 20080917 (Red Hat 4.3.2-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from openturns import *

It is often useful when you close a bracket to know which bracket is the corresponding opening bracket, for this jedit has the StructureMatcher interface and the default implementation gives you this information, by surrounding the opening bracket when you type its associated closing bracket.

On the other hand, the XML plugin gives you a more useful information when closing an XML tag. Let's see it in action with this simple XML file from the w3c

On the left, the caret is within the </note> closing tag and so the entire opening <note> tag is being highlighted. Similarly, on the right, the caret is within the opening <heading> tag and consequently the closing </heading> gets highlighted. This is particularly useful when editing xml documents.

So the idea was to have the same sort of behaviour for R scripts. Here's a start, but I also plan to do something with the curly brackets to deal with for loops, function definitions and various apply calls, ... (see that post)

Standard Completion

The power editor supports completion of R code by relying on the CompletePlus function in the svMisc package. This function uses the completion engine that comes with R (formerly implemented in the rcompgen package and incorporated in utils in recent versions of R), and looks in documentation files for additional information related to each finding, for example when completing "rnorm( ", the CompletePlus function looks into the help page for rnorm and retrieves the description of each of the arguments :

R> require( svMisc )
Loading required package: svMisc
R> CompletePlus( "rnorm(" )
     [,1]      [,2]
[1,] "n = "    "rnorm"
[2,] "mean = " "rnorm"
[3,] "sd = "   "rnorm"
     [,3]
[1,] "number of observations. If 'length(n) > 1', the length is taken to be the number required."
[2,] "vector of means."
[3,] "vector of standard deviations."

The power editor plugin uses this information to display completion popups:

Completion of Colors

In special cases, instead of argument or function names, the engine will complete for colours using the current R palette :

or names of colors if you started to type a quote character

here the user started to type gre so the completion engine looks for colors having a name that matches the pattern gre. This is basically obtained as follows:

> head( grep( "gre", colors(), value = T ) )
[1] "darkgreen"       "darkgrey"        "darkolivegreen"  "darkolivegreen1"
[5] "darkolivegreen2" "darkolivegreen3"

Line Type completion

Usually the lty argument is associated with a line type, the completion engine suggests the basic line types as documented in ?par

Plot Character Completion

Same with the pch argument and the plotting character.

Edit Sweave Files with the Workbench

R> vignette( "grid", package = "grid")$file

Requirements

<MODE NAME="R"    FILE="r.xml" 
  FILE_NAME_GLOB="*.R" 
  FIRST_LINE_GLOB="#!/*{R,Rscript}" />
<MODE NAME="sweave"    
  FILE="sweave.xml" 
  FILE_NAME_GLOB="*.{R,S}nw" />

Coming Next

• allow preview of graphics when fig=TRUE is set, I need to understand some of the packages providing cache feature for Sweave
• have R completion when inside the code chunk , see this post
• completion of the options used by the sweave driver
• actions to weave and tangle the current file
• jump between sweave code chunks
• integrate this as a view
• support the html flavour of sweave