Hi Thomas,

I think you are running a to new version of gplot

http://blog.rstudio.org/2012/09/07/ggplot2-0-9-2/

opts is now deprecated and likely causes that error. Can you downgrade
the gplot version?
We are working on a R dependencies mechanism but we are not done yet,
sorry.

Hope that helps,
Bjoern

> Hey guys,
> 
>  
> 
> we are running a local galaxy instance (10200:fd4113962c32)with R
> version 3.0.1 and want to use Manhattan/qq, but we are missing the
> pval manhatan.pdf, only pval qqplot.pdf is generated and we are
> getting the following error:
> 
>  
> 
> Nonzero exit code = 1
> 
> [1] "### 11008 values read
> from /opt/galaxy/galaxy-dist/database/files/002/dataset_2408.dat read
> - now running plots"
> 
>  
> 
> 'opts' is deprecated. Use 'theme' instead. (Deprecated; last used in
> version 0.9.1)
> 
>  
> 
> Setting the plot title with opts(title="...") is deprecated.
> 
>  
> 
> Use labs(title="...") or ggtitle("...") instead. (Deprecated; last
> used in version 0.9.1)
> 
>  
> 
> Scale for 'x' is already present. Adding another scale for 'x', which
> will replace the existing scale.
> 
>  
> 
> Scale for 'y' is already present. Adding another scale for 'y', which
> will replace the existing scale.
> 
>  
> 
> [1] "## qqplot on pval done"
> 
>  
> 
> [1] "## manhattan on pval starting 1 2 3"
> 
>  
> 
> Error in structure(list(call = match.call(), aesthetics =
> aesthetics,  : 
> 
>  
> 
>   argument "values" is missing, with no default
> 
>  
> 
> Calls: rgqqMan ... scale_colour_manual -> manual_scale ->
> discrete_scale -> structure
> 
>  
> 
> Execution halted
> 
>  
> 
>  
> 
> At the galaxy-main ist working without any problems using the same
> input file.
> 
> All the necessary packages should be installed.
> 
>  
> 
> Any ideas? Thanks for your help.
> 
>  
> 
> Thomas
> 
> 
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