Problem with tool in R

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Problem with tool in R

Ramon Tiburski
I have a problem with a tool in R. I can't load the RPostgreSQL library that I get the following error:

ERROR: carregando pacotes exigidos: dbi

My xml is this:

<command interpreter="bash">r_wrapper.sh $script_file</command>

<configfiles>
<configfile name="script_file">
library(RPostgreSQL)
...
</configfile>
</configfiles>

I have this library installed at my system, what can I do?

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Re: Problem with tool in R

Nate Coraor (nate@bx.psu.edu)
On Jun 3, 2013, at 10:13 AM, Ramon Tiburski wrote:

> I have a problem with a tool in R. I can't load the RPostgreSQL library that I get the following error:
>
> ERROR: carregando pacotes exigidos: dbi
>
> My xml is this:
>
> <command interpreter="bash">r_wrapper.sh $script_file</command>
>
> <configfiles>
> <configfile name="script_file">
> library(RPostgreSQL)
> ...
> </configfile>
> </configfiles>
>
> I have this library installed at my system, what can I do?

Hi Ramon,

Have you checked to make sure that the user that Galaxy runs as is able to find the library? Is it possible that it is installed for a single user or in a non-standard path that has not been configured for the Galaxy user?  Does the script work if run directly on the command line as the Galaxy user?

--nate

> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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