[galaxy-dev] Failure to prepare job error

Hello,

I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I
import a package I've installed called PypeR. My tool works fine from the
command line, but when I try to run it on my Amazon instance, it gives me
this error:

Traceback (most recent call last):
File "/nfs/software/galaxy/lib/galaxy/jobs/runners/local.py", line
61, in run_job
job_wrapper.prepare()
File "/nfs/software/galaxy/lib/galaxy/jobs/__init__.py", line 371, in prepare
self.command_line = self.tool.build_command_line( param_dict )
File "/nfs/software/galaxy/lib/galaxy/tools/__init__.py", line 1543,
in build_command_line
command_line = fill_template( self.command, context=param_dict )
File "/nfs/software/galaxy/lib/galaxy/util/template.py", line 9, in
fill_template
return str( Template( source=template_text, searchList=[context] ) )
File "/nfs/software/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-i686-ucs4.egg/Cheetah/Template.py",
line 1004, in __str__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1311891781_86_41894.py",
line 83, in respond
EOFError: EOF when reading a line

With the additional caption "failure to prepare job".
I've been struggling with this for days, and I'm pretty sure I don't
have a typo in my .xml file. How can I solve this?