如何从rJython导入站点包？

Question

I am trying to call some functions in openopt package for Python from R using the rJython package. I have the NumPy, SciPy, and OpenOpt installed for Python 2.7.4 on my 64 bit windows 7. Importing openopt from Python is OK.

However, when I run the codes:

library(rJython)
rJython <- rJython(modules='openopt')
rJython$exec("from openopt import GLP")

I got errors:

.jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named openopt

Of course I checked the sys.path values for the Python environment:

rJython$exec("import sys")
rJython$exec("pname = sys.path")
jython.get(rJython, "pname")

but I got:

[1] "C:\\Users\\myname\\Documents\\R\\win-library\\2.15\\rJython\\Lib"            
[2] "C:\\Users\\myname\\Documents\\R\\win-library\\2.15\\rJython\\jython.jar\\Lib"
[3] "__classpath__"                                                                 
[4] "__pyclasspath__/"                                                              
[5] "openopt"                                                                       
[6] "C:/Users/myname/Documents/R/win-library/2.15/rJython" 

These are absolutely not like the values of sys.path in Python itself. So I extended the sys.path by:

rJython$exec("sys.path.extend(['C:\\Python27\\lib\\site-packages\\openopt-0.45-py2.7.egg'])")

Then it seems that I need to add the numpy to sys.path:

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Python27\lib\site-packages\openopt-0.45-py2.7.egg\openopt\__init__.py", line 10, in <module>
    from oo import *
File "C:\Python27\lib\site-packages\openopt-0.45-py2.7.egg\openopt\oo.py", line 4, in <module>
    from LP import LP as CLP
File "C:\Python27\lib\site-packages\openopt-0.45-py2.7.egg\openopt\kernel\LP.py", line 1, in <module>
    from baseProblem import MatrixProblem
File "C:\Python27\lib\site-packages\openopt-0.45-py2.7.egg\openopt\kernel\baseProblem.py", line 2, in <module>
    from numpy import *
ImportError: No module named numpy

I then extended everything in the sys.path list of Python in rJython. But I still get further information:

Erro in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Python27\lib\site-packages\openopt-0.45-py2.7.egg\openopt\__init__.py", line 10, in <module>
    from oo import *
  File "C:\Python27\lib\site-packages\openopt-0.45-py2.7.egg\openopt\oo.py", line 4, in <module>
    from LP import LP as CLP
  File "C:\Python27\lib\site-packages\openopt-0.45-py2.7.egg\openopt\kernel\LP.py", line 1, in <module>
    from baseProblem import MatrixProblem
  File "C:\Python27\lib\site-packages\openopt-0.45-py2.7.egg\openopt\kernel\baseProblem.py", line 2, in <module>
    from numpy import *
  File "C:\Python27\lib\site-packages\numpy\__init__.py", line 154, in <module>
    import add_newdocs
  File "C:\Python27\lib\site-packages\numpy\add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "C:\Python27\lib\site-packages\numpy\lib\__init__.py", line 4, in <module>
    from type_check import *
  File "C:\Python27\lib\site-packages

OK. The main question is: it seems like I cannot import a module from the site-packages. I can absolutely import basic modules in Python2.7.4. Any suggestion?

Answer 1

rJython is a package that does not call Python but Jython , which is not exactly the same thing. In particular, Jython programs cannot currently use CPython extension modules written in C , only those in pure Python.

This is why neither NumPy nor SciPy can be invoked via rJython.

However, rPython , a package with exactly the same interface as rJython does interact with the true Python. You should try that.

There is a caveat, though: it currently only runs on UNIX (Linux/Mac/...) environments, not on Windows. It is possible to have it installed on Windows and there are some instructions as to install it on such platform, but involves some manual configuration of scripts (essentially, to indicate which version of Python is to be used and the path where it is located) and compilation.