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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