Hi all, I'm working on integrating cummeRbund[1] into Galaxy. This is a very helpful tool for analysis and visualization of cuffdiff output. My problem is any text output from running R code, puts the galaxy output in error state. Even if everything is working correctly and the outputs are generated as intended. I tried this code from 'tools/plotting/xy_plot.xml': ## Setup R error handling to go to stderr options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) But it didn't help. Even for loading the library I had to go with: suppressPackageStartupMessages(library("cummeRbund")) Nothing else would work. Now the tool is outputting some messages while running R functions, which is putting the output in galaxy in error state. I'm thinking about asking the upstream developer to provide a way to run the functions in the library in 'quite' mode. Is there any other option? Right now I'm using the path of creating a R script in the XML file and using r_wrapper.sh to run it. I tried first with rpy, as it would give me more freedom, but cummeRbund use ggplot2 which seems to be supported only on rpy2. [1]http://compbio.mit.edu/cummeRbund/ Thanks in advance, Carlos