Issues using docker image

[AldanaJ]

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

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

Thanks again

[rickhelmus]

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 (rocker-org/rocker-versioned#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]

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!