Re: [Rpy] Using rpy2 with lib-apache2-mod-python
On Mon, 2008-10-20 at 21:12 -0700, Eric Bell wrote: Resolved ... or a least made to go away. It appears that the problem was caused in part due to loading another apache module supplied by R/Apache, as described at http://biostat.mc.vanderbilt.edu/rapache/ R/Apache is a project dedicated to embedding the R interpreter inside the Apache 2.0 (and beyond) web server I was looking through the apache error log, and noticed the lines: Error in .Call(R_isMethodsDispatchOn, onOff, PACKAGE = base) : Incorrect number of arguments (2), expecting 1 for R_isMethodsDispatchOn I don't know if the R/Apache r_module is causing this or rpy2, but I decided to disable the r_module and voila, my script works ... One possibility is that R gets initialized twice then (and R does not like that). I'll look into having rpy2 detect this kind of situation. well actually it doesn't, because now I get another error, but that's due to trying to use a call to JPEG, which requires that an X11 device be present, which it won't be running inside a web server. R's man page for jpeg() states it, and alternatives to use when no X11. --eric - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] Using rpy2 with lib-apache2-mod-python
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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Re: [Rpy] Using rpy2 with lib-apache2-mod-python
On Mon, 2008-10-20 at 12:39 -0700, Eric Bell wrote:
No change in behavior. I've simplifed my python script and added the
import rpy2.rinterface as instructed. I've stopped and started the
apache server as appropriate voodoo.
No change was expected: '--verbose' instructs R to tell a bit more of
what it is doing. Looking whether a hint appear when inspecting what it
tells is the way to go (although I am not sure that a hint appears, as
mentioned in a previous email).
Seems to me if I can't execute the library() call then it makes sense
that R functionality in the non-base libraries won't be available.
Other info: I'm running on Unbuntu Gusty ... I couldn't find a
packaged shared libraries version of R so I built it myself. I did
have R installed previously using the Synaptic package manager and
subsequently deinstalled when I built the shared library version. I've
just confirmed that Synatpic indicates that R is not installed. I
notice that if I do a printenv in a shell, there's no R_HOME variable
defined. Should there be? I recall having to futz with this when I was
trying to install the RSPython extension...the builds kept failing
because R_HOME was point to the wrong place.
I'm happy to run other tests if you tell me what to do.
Running the unit tests (see the documentation for rpy2) in order to
ensure that installation is otherwise proper is something recommended,
if not already done.
--eric
PYTHON SCRIPT
from mod_python import apache
import rpy2.rinterface as ri
# this must go before the import rpy2
ri.set_initoptions(('rpy2','--verbose','--vanilla','--nosave'))
import rpy2
from rpy2 import robjects
def handler(req):
r = robjects.r
r(library())
req.content_type = 'html'
req.write(HTMLBODYHello beautiful
World!BR/BODY/HTML)
return apache.OK
Traceback:
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/test1.py, line 14, 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
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Re: [Rpy] Using rpy2 with lib-apache2-mod-python
No change in behavior. I've simplifed my python script and added the
import rpy2.rinterface as instructed. I've stopped and started the
apache server as appropriate voodoo.
Seems to me if I can't execute the library() call then it makes sense
that R functionality in the non-base libraries won't be available.
Other info: I'm running on Unbuntu Gusty ... I couldn't find a packaged
shared libraries version of R so I built it myself. I did have R
installed previously using the Synaptic package manager and subsequently
deinstalled when I built the shared library version. I've just confirmed
that Synatpic indicates that R is not installed. I notice that if I do a
printenv in a shell, there's no R_HOME variable defined. Should there
be? I recall having to futz with this when I was trying to install the
RSPython extension...the builds kept failing because R_HOME was point to
the wrong place.
I'm happy to run other tests if you tell me what to do.
--eric
PYTHON SCRIPT
from mod_python import apache
import rpy2.rinterface as ri
# this must go before the import rpy2
ri.set_initoptions(('rpy2','--verbose','--vanilla','--nosave'))
import rpy2
from rpy2 import robjects
def handler(req):
r = robjects.r
r(library())
req.content_type = 'html'
req.write(HTMLBODYHello beautiful
World!BR/BODY/HTML)
return apache.OK
Traceback:
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/test1.py, line 14, 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
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Re: [Rpy] Using rpy2 with lib-apache2-mod-python
I performed the unit testing and here are my results: Note: Software Versions: R 2.7.2 Python 2.5.1 $ python Python 2.5.1 (r251:54863, Jul 31 2008, 23:17:40) [GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2 Type help, copyright, credits or license for more information. import rpy2.tests import unittest tr = unittest.TextTestRunner(verbosity = 1) suite = rpy2.tests.suite() tr.run(suite) ..Error in .Primitive([)(0:10, list(a, b, c)) : invalid subscript type 'list' E..FLoading required package: splines ..Error in function (x) : object y not found ...Error in .Primitive(sum)(c(a, b, c, d, e, f, g, h, i, : invalid 'type' (character) of argument ..F.. == ERROR: testNewString (rpy2.rinterface.tests.test_SexpVector.SexpVectorTestCase) -- Traceback (most recent call last): File /usr/lib/python2.5/site-packages/rpy2/rinterface/tests/test_SexpVector.py, line 95, in testNewString ri.NA_STRING[0] ValueError: Cannot handle type 9 == FAIL: testNewWithoutInit (rpy2.rinterface.tests.test_SexpVector.SexpVectorTestCase) -- Traceback (most recent call last): File /usr/lib/python2.5/site-packages/rpy2/rinterface/tests/test_SexpVector.py, line 37, in testNewWithoutInit self.assertTrue(False) # worked when tested, but calling endEmbeddedR causes trouble AssertionError == FAIL: testCallErrorWhenEndedR (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase) -- Traceback (most recent call last): File /usr/lib/python2.5/site-packages/rpy2/rinterface/tests/test_EmbeddedR.py, line 30, in testCallErrorWhenEndedR self.assertTrue(False) # worked when tested, but calling endEmbeddedR causes trouble AssertionError -- Ran 144 tests in 0.269s FAILED (failures=2, errors=1) unittest._TextTestResult run=144 errors=1 failures=2 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] Using rpy2 with lib-apache2-mod-python
Resolved ... or a least made to go away. It appears that the problem was caused in part due to loading another apache module supplied by R/Apache, as described at http://biostat.mc.vanderbilt.edu/rapache/ R/Apache is a project dedicated to embedding the R interpreter inside the Apache 2.0 (and beyond) web server I was looking through the apache error log, and noticed the lines: Error in .Call(R_isMethodsDispatchOn, onOff, PACKAGE = base) : Incorrect number of arguments (2), expecting 1 for R_isMethodsDispatchOn I don't know if the R/Apache r_module is causing this or rpy2, but I decided to disable the r_module and voila, my script works ... well actually it doesn't, because now I get another error, but that's due to trying to use a call to JPEG, which requires that an X11 device be present, which it won't be running inside a web server. --eric - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
