In the latest commit (7d3507a), the test on the Windows machine failed. It was noticed when no isobarics.txt was made. It threw the following error:
Error in .subset2(x, i, exact = exact) : subscript out of bounds
This happens within the function lapply on line 661.
At the end of this function the isobarics txt file should be made, therefore, the error breaks the function.
Based on what the log file stops writing the expected print statements, the last patient top_IEM pdf file seems to be never made. So it is expected that the problem is in the last item in the patient list when lapply loops over this list.

Testing on MacBook was successful with the same input files.

The separator 'qqq' is used for splitting isobaric compounds into a text file as a footnote. However, for some runs (pl coco run1 & pl pilot run10), the qqq is a name of a metabolite in the violin plots pdf. This is not supposed to happen, and it seems to happen to all stofgroup lists that contain a DiagnRatio. Also, more 'open circles', indicating the patients value, are in the qqq violin plot.

As long as this doesn't happen systematically, the error has no priority or risks.