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rickhelmus / patRoon

Workflow solutions for mass-spectrometry based non-target analysis.
https://rickhelmus.github.io/patRoon/
GNU General Public License v3.0
61 stars 18 forks source link

Issues using docker image #18

Closed AldanaJ closed 3 years ago

AldanaJ commented 3 years ago

Hello,

First, I would like to thank you for all the effort in building this package. I consider it integrates non-vendor metabolomics software in a sophisticated way. I am using the latest Docker image of patRoon and its dependencies. I have experienced the following issues:

  1. When running genform

image

  1. When generating reportHTML() I got the following error and the final report never opens in the browser.

image

Thanks again

rickhelmus commented 3 years ago

Hello,

Thanks for the bug reports!

The first bug should be fixed now. It will take some time to let the Docker image rebuild (~1-2 hours from now).

The second issue is more involving. This seems to be related that Java (used by rcdk, which in turn is used to plot structures) assumes there is a graphical environment, but there is not. I created an issue (https://github.com/rocker-org/rocker-versioned/issues/249) to see what can be done. For now you can use an ugly work-around by executing the following before plotting any structures:

rJava::.jinit(); 
rJava::J("java.lang.System")$setProperty("java.awt.headless","true")

You may need to restart your R session before attempting this.

rickhelmus commented 3 years ago

The second issue should be resolved as well. Again, you may need to wait a bit for the Docker images to finish. Note that I also just released version 1.2, which marks some important changes related to suspect screening (see NEWS.md).

Feel free to re-open if you still find any issues!