[IPython-dev] Rmagic under Debian Squeeze problem
Javier Martínez-López
javi.martinez.lopez at gmail.com
Mon Jan 21 04:11:17 EST 2013
*Dear all,
I need to run R code with the IPython notebook in my Debian squeeze desktop
computer. **I can apparently load the rmagic extension but when I try to
run R code I get the following error message:
*AttributeError Traceback (most recent call last)
<ipython-input-4-9de0d21a54a2> in <module>()
----> 1 get_ipython()._run_cached_cell_magic(u'R', u'')
/home/user/ipython/IPython/core/interactiveshell.pyc in
_run_cached_cell_magic(self, magic_name, line)
2550 cell = self._current_cell_magic_body
2551 self._current_cell_magic_body = None
-> 2552 return self.run_cell_magic(magic_name, line, cell)
2553
2554 def run_cell(self, raw_cell, store_history=False, silent=False,
shell_futures=True):
/home/user/ipython/IPython/core/interactiveshell.pyc in
run_cell_magic(self, magic_name, line, cell)
2130 magic_arg_s = self.var_expand(line, stack_depth)
2131 with self.builtin_trap:
-> 2132 result = fn(magic_arg_s, cell)
2133 return result
2134
<string> in R(self, line, cell, local_ns)
/home/user/ipython/IPython/core/magic.pyc in <lambda>(f, *a, **k)
189 # but it's overkill for just that one bit of state.
190 def magic_deco(arg):
--> 191 call = lambda f, *a, **k: f(*a, **k)
192
193 if callable(arg):
/home/user/ipython/IPython/extensions/rmagic.py in R(self, line, cell,
local_ns)
550 return_output = False
551 else:
--> 552 text_result, result = self.eval(code)
553 text_output += text_result
554
/home/user/ipython/IPython/extensions/rmagic.py in eval(self, line)
156 ri.set_writeconsole(self.write_console)
157 try:
--> 158 value = ri.baseenv['eval'](ri.parse(line))
159 except (ri.RRuntimeError, ValueError) as exception:
160 warning_or_other_msg = self.flush() # otherwise next
return seems to have copy of error
AttributeError: 'module' object has no attribute 'arse'
*After an iptest, I get:*
Status:
ERROR - 3 out of 10 test groups failed.
----------------------------------------
Runner failed: IPython.core
You may wish to rerun this one individually, with:
/usr/bin/python
/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/testing/iptest.py
IPython.core
----------------------------------------
Runner failed: IPython.extensions
You may wish to rerun this one individually, with:
/usr/bin/python
/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/testing/iptest.py
IPython.extensions
----------------------------------------
Runner failed: IPython.utils
You may wish to rerun this one individually, with:
/usr/bin/python
/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/testing/iptest.py
IPython.utils
*
And after the specific test for extensions**, I get:*
ERROR: IPython.extensions.tests.test_rmagic.test_Rconverter
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/lib/python2.6/dist-packages/nose-1.2.1-py2.6.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/extensions/tests/test_rmagic.py",
line 31, in test_Rconverter
v = ip.run_line_magic('Rget', '-d datapy')
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/core/interactiveshell.py",
line 2062, in run_line_magic
result = fn(*args)
File "<string>", line 2, in Rget
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/core/magic.py",
line 191, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/extensions/rmagic.py",
line 299, in Rget
return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe)
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/extensions/rmagic.py",
line 107, in Rconverter
if cols != ri.NULL:
AttributeError: 'module' object has no attribute 'NULL'
======================================================================
ERROR: IPython.extensions.tests.test_rmagic.test_cell_magic
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/usr/local/lib/python2.6/dist-packages/nose-1.2.1-py2.6.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/extensions/tests/test_rmagic.py",
line 60, in test_cell_magic
ip.run_cell_magic('R', '-i x,y -o r,xc a=lm(y~x)', snippet)
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/core/interactiveshell.py",
line 2093, in run_cell_magic
result = fn(line, cell)
File "<string>", line 2, in R
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/core/magic.py",
line 191, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/extensions/rmagic.py",
line 516, in R
text_result, result = self.eval(code)
File
"/usr/local/lib/python2.6/dist-packages/ipython-0.13.1-py2.6.egg/IPython/extensions/rmagic.py",
line 158, in eval
value = ri.baseenv['eval'](ri.parse(line))
AttributeError: 'module' object has no attribute 'parse'
----------------------------------------------------------------------
Ran 16 tests in 1.177s
FAILED (errors=2)
*... Does anyone has a clue?*
*Thank you very much!*
Kind regards,
Javier
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