Hi, I'm executing a R script via Python's os.system() (using Rscript executable which allow executing R script in the command line). This script makes use of library that will attempt to load up Tcl/Tk interface. Though I don't see anything even if I'm running the commands on Windows interactive R console, it will attempt to connect to the display server unsuccessfully during Galaxy's execution (and fail because $DISPLAY is not set). The program runs just fine since I have the output I wanted. But Galaxy sees error, and I'm suspecting it's because of this DISPLAY thing. I don't understand how Galaxy detects something goes wrong. If anything I thought it's my Python script return code that should matter. But how does Galaxy know?! And how do I fix it? Timothy
On Wed, Jan 4, 2012 at 5:24 AM, Timothy Wu <2huggie@gmail.com> wrote:
Hi,
I'm executing a R script via Python's os.system() (using Rscript executable which allow executing R script in the command line). This script makes use of library that will attempt to load up Tcl/Tk interface. Though I don't see anything even if I'm running the commands on Windows interactive R console, it will attempt to connect to the display server unsuccessfully during Galaxy's execution (and fail because $DISPLAY is not set). The program runs just fine since I have the output I wanted. But Galaxy sees error, and I'm suspecting it's because of this DISPLAY thing.
I don't understand how Galaxy detects something goes wrong. If anything I thought it's my Python script return code that should matter. But how does Galaxy know?! And how do I fix it?
Timothy
Currently you must suppress any warning messages to stderr, see https://bitbucket.org/galaxy/galaxy-central/issue/325/ Peter
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Timothy Wu