[R-gui] R-wxPython

[James Wettenhall]

Hi,

I've been playing with an R-inteface to wxPython which has 
potential to be more powerful than Tcl/Tk.  Currently it works 
on Windows, but so far, I haven't succeeded in getting it to 
work on Linux.  I haven't tried MacOS X.

http://bioinf.wehi.edu.au/folders/james/wxPython/

After I got back from useR!2004, I thought rather than 
emailing out straight away to let people know that my R-wxPython 
talk slides are available on the web, I would just wait until I 
got R-wxPython working on Linux (as well as Windows).  
"It should only take a day or two", I thought.  

Now, a few weeks later, I feel like I am still making 
progress, but it is very slow progress, so if there are any 
Linux-minded people out there who feel like collaborating, I 
would be very happy to work with you.

On Windows, you can just install Python, wxPython and RSPython 
from binaries, but it's a different story on Linux :-(

Here's how to get as far as I've got to date on Linux for 
R-wxPython:

1. Install R with the shared library enabled.  (This can be 
    done with "configure --enable-shlib" when installing R 
    from source.  The shared library will normally appear in
    /usr/local/lib/R/bin/libR.so)

2. Install Python 2.2.x from source.  (RSPython doesn't seem to 
    like 2.3.x, so don't install that.  The reason I say to 
    install from source, is that you will need to create a 
    python shared library: libpython2.2.so, and this doesn't 
    seem to be distributed in the python RPM.)

3. Install RSPython 0.5-3 or later, being careful to link it 
    with the shared Python library, not a static library.
    Check that RSPython.so depends on libpython2.2.so using
    "ldd RSPython.so", and check that you have an 
    RSInternal.so symbolic link to RSPython.so in the 
    R/library/RSPython/libs/ directory.  To get RSPython
    to link to libpython2.2.so, you may have to override the 
    automatic configure script, e.g. 
    "mv configure DONTconfigure" and manually edit Makefile, 
    Makevars, src/Makevars etc.

4. Build wxPython 2.5.x from source (by first building 
     wxWidgets, distributed with wxPythonSrc).  You need to modify 
     wxPython/config.py as follows:
       (i) Change self.root = "" to self.root = None
       (ii) Change newLFLAGS=[] to 
              newLFLAGS = ['libpython2.2.so']
     Copy libpython2.2.so to the wxPythonSrc/wxPython directory.
     Note that you probably don't need all of the 
     optional-extras like OpenGL support, so you can build with 
     "python setup.py build CORE_ONLY=1" or 
     "python setup.py install CORE_ONLY=1" to just install the 
     essentials.

5. Make sure that the new shared libraries are included in 
     LD_LIBRARY_PATH and have been registered with 
     /sbin/ldconfig.  Some Linux systems allow you to do this 
     without root privileges, while others don't.  I don't 
     have a root password, so I work mostly in my home area: 
     ~/usr/ etc. but occasionally I need to ask for help from 
     root.  

6. Run ldd on the wxPython shared libraries in
     /usr/local/lib/python2.2/site-packages/wx/ or wherever,
     to check that they depend on libpython2.2.so, otherwise you 
     will get errors like "Undefined symbol PyExc_IOError".

In R, type:
library(RSPython)

Ignore the following warning:
"the Python callback manager has been registered implicitly 
using the defaults (referenceManager())!"

[We will use the wxPython 2.4.x method of importing the wx 
module. In order understand the difference between 
importPythonModule("wxPython.wx") and importPythonModule("wx"), 
please read:
http://www.wxpython.org/migrationguide.php ]

Try importing the wxPython.wx module:

importPythonModule("wxPython.wx")

If it returns NULL with no errors, then it succeeded.  If it 
cannot be found, check your PYTHONPATH environment variable, 
and if necessary, modify the Python search path within R
as follows:
importPythonModule("sys")
.Python("path",.module="sys") # Check the current Python path.
path <- "/usr/local/lib/python2.2/site-packages/wx"
.PythonEval(paste("path.append('",path,"')",sep=""),.module="sys")
# Repeat for other paths you want to add.

Now create a simple wxPython module, testRwxPy.py :
-----------------------------
import wxPython.wx
from wxPython.wx import *

def wxRPyApp():
        app = wxApp()
        return app
-----------------------------

Make sure testRwxPy.py can be found in your Python search path, 
(using the technique above) and try:

.Python("wxRPyApp",.module="testRwxPy")

When running under R -d gdb, I get a segmentation fault which 
appears to come from gdk_init_check().  :-(

A few clues from Googling "gdk_init_check segmentation fault" 
and from running strace on R, suggested that it could make a 
difference whether I am running X11 from a remote Linux machine 
or actually sitting in front of the Linux machine.

I normally run Linux with XWin32 from Windows.  I am also trying 
to do some testing on a Linux machine which I am actually 
sitting in front of directly, but haven't been able to run ldconfig 
without root access.  I will ask my administrator to do it when 
he has a chance.

I hope this is of interest to a least some people on the list.

Regards,
James
 
--------------------------------------------------------------------------
James Wettenhall                                  Tel: (+61 3) 9345 2629
Division of Genetics and Bioinformatics           Fax: (+61 3) 9347 0852
The Walter & Eliza Hall Institute         E-mail: wettenhall at wehi.edu.au
 of Medical Research,                     Mobile: (+61 / 0 ) 438 527 921    
1G Royal Parade,
Parkville, Vic 3050, Australia
http://www.wehi.edu.au