On 10/1/07, Chris Parkin <[EMAIL PROTECTED]> wrote:
>
> 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!
Hi, Chris. As what user are you running your Pylons app? If it is not the
same user as you (as root, for example), that may be problematic.
Sean
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