Hello,
My questions is in regards to using Rpy in the Pylons web framework to build
an online interface for microarray data analysis. If I simply include the
command "from rpy import *" in my pylons application controller, the server
throws the following error:
Module ?:*2* in <module> <http://127.0.0.1:5000/_debug/view/1191266866#>
<< <http://127.0.0.1:5000/_debug/view/1191266866#>*import* logging
*import* rpy
*from* firstapp*.*lib*.*base *import* ***>>
<http://127.0.0.1:5000/_debug/view/1191266866#>*import* rpy
Module rpy:*323* in <module>
<http://127.0.0.1:5000/_debug/view/1191266866#>
<< <http://127.0.0.1:5000/_debug/view/1191266866#>
# main instance
r *=* R*(**)*
# disable the printing of errors from within R, they will be handed by
>> <http://127.0.0.1:5000/_debug/view/1191266866#>r *=* R*(**)*
Module rpy:*266* in __init__
<http://127.0.0.1:5000/_debug/view/1191266866#>
<< <http://127.0.0.1:5000/_debug/view/1191266866#> _rpy*.*set_mode*(
*NO_DEFAULT*)*
self*.*get *=* _rpy*.*get_fun*(*'get'*)* # this must happen
before any calls to self or its methods!
self*(*"options(error = expression(NULL))"*)* # don't abort on
errors, just raise them!>> <http://127.0.0.1:5000/_debug/view/1191266866#>
self*.*get *=* _rpy*.*get_fun*(*'get'*)* # this must happen before any calls
to self or its methods!
*<class 'rpy.RException'>: R Function "get" not found*
If I open a shell, start python, and run "from rpy import*", this is what I
see:
>>> from rpy import *
RHOME= /Library/Frameworks/R.framework/Resources
RVERSION= 2.5.1
RVER= 2051
RUSER= /Users/Chris
Loading Rpy version 2051 .. Done.
Creating the R object 'r' .. Done
>>>
Any insight or suggestions that you can offer would be greatly appreciated.
Thanks!
Chris Parkin
Core Manager, Genomics
Tufts University Center for Neuroscience Research
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