On Mon, 2008-10-20 at 09:55 -0700, Eric Bell wrote:
> I want to be able to call R from python scripts that are being executed
> via lib-apache2-mod-python. Should this be doable?
In theory, yes.
It might have limited testing, still.
> My python script can access some R functionality but it is very limited.
> It *appears* that only the functionality in the base R package is being
> loaded.
>
> from mod_python import apache
>
# is the line below needed at ?
> import rpy2
# try adding here:
import rpy2.rinterface as ri
ri.set_initoptions(('rpy2', '--verbose', '--vanilla', '--no-save'))
# and run the rest, looking at what the output is...
# (I don't think it will help but well, one never knows).
Otherwise, there might also be entanglements when the apache process is
trying to access R files (libraries) located in directories where is not
configured to go (just a wild guess).
Let us know what is happening.
L.
> from rpy2 import robjects
>
> import math
> import array
>
> def handler(req):
> r = robjects.r
>
> r("y <- (1:10)")
> r("x <- (1:10)")
>
> r('jpeg("/var/www/apache2-default/images/testplot.jpg")')
> #r.plot(r.runif(10),y,xlab="runif",ylab="foo/bar",col="red")
>
> #r._dotter = True
> #r.dev_off()
>
>
> req.content_type = 'html'
> req.write("<HTML>")
> req.write("<BODY>")
>
> req.write("Hello beautiful World!<BR>")
>
> req.write('<img src="/apache2-default/images/test123.jpg" />')
>
> req.write("</BODY>")
> req.write("</HTML>")
>
> return apache.OK
>
>
> When I access the page, mod_pthon generates the following error
> information:
>
> Traceback (most recent call last):
>
> File "/usr/lib/python2.5/site-packages/mod_python/importer.py",
> line 1537, in HandlerDispatch
> default=default_handler, arg=req, silent=hlist.silent)
>
> File "/usr/lib/python2.5/site-packages/mod_python/importer.py",
> line 1229, in _process_target
> result = _execute_target(config, req, object, arg)
>
> File "/usr/lib/python2.5/site-packages/mod_python/importer.py",
> line 1128, in _execute_target
> result = object(arg)
>
> File "/var/www/apache2-default/test_python/mptest.py", line 16, in
> handler
> r('jpeg("/var/www/apache2-default/images/testplot.jpg")')
>
> File "/usr/lib/python2.5/site-packages/rpy2/robjects/__init__.py",
> line 501, in __call__
> res = self.eval(p)
>
> File "/usr/lib/python2.5/site-packages/rpy2/robjects/__init__.py",
> line 381, in __call__
> res = super(RFunction, self).__call__(*new_args, **new_kwargs)
>
> RRuntimeError: Error in eval(expr, envir, enclos) : could not find
> function "jpeg"
>
> ------------------------
>
> If I modify my python script to call the R library() function, I get a
> different error message.
>
> def handler(req):
> r = robjects.r
>
> r("library()")
> .
> .
> .
>
> Generates:
>
> Traceback (most recent call last):
>
> File
> "/usr/lib/python2.5/site-packages/mod_python/importer.py", line
> 1537, in HandlerDispatch
> default=default_handler, arg=req, silent=hlist.silent)
>
> File
> "/usr/lib/python2.5/site-packages/mod_python/importer.py", line
> 1229, in _process_target
> result = _execute_target(config, req, object, arg)
>
> File
> "/usr/lib/python2.5/site-packages/mod_python/importer.py", line
> 1128, in _execute_target
> result = object(arg)
>
> File "/var/www/apache2-default/test_python/mptest.py", line
> 13, in handler
> r("library()")
>
> File
> "/usr/lib/python2.5/site-packages/rpy2/robjects/__init__.py",
> line 501, in __call__
> res = self.eval(p)
>
> File
> "/usr/lib/python2.5/site-packages/rpy2/robjects/__init__.py",
> line 381, in __call__
> res = super(RFunction, self).__call__(*new_args,
> **new_kwargs)
>
> RRuntimeError: Error in gzfile(file, "rb") : invalid 'encoding'
> argument
>
> Any ideas?
>
> --eric
>
>
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