Bugs in COMPASSContainerFromGatingSet

[gfinak]

Daryl reports that COMPASSContainerFromGatingSet is giving warnings:

Creating COMPASS Container
A COMPASSContainer with 112 samples from 8 individuals, containing data across 7 markers.
Warning message:
In if (!is.na(markers)) { :
  the condition has length > 1 and only the first element will be used

with the latest release of flowWorkspace and related tools.
He also gets an error:

Error in if (any(sapply(data, function(x) any(x < 0)))) { :
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In if (!is.na(markers)) { :
  the condition has length > 1 and only the first element will be used
2: '.local' is deprecated.
Use 'getSingleCellExpression' instead.
See help("Deprecated")

Presumably the API has changed somewhere and this did not get updated.
I don't think this is high priority since we can construct the objects by hand anyway.

[gfinak]

At the moment, we're going to try and rule out version discrepancies, etc.

[bneradil]

This issue renders COMPASSContainerFromGatingSet unusable starting from R version 4.2.0.

From R 4.2.0 release news: "Calling if() or while() with a condition of length greater than one gives an error rather than a warning."

Unless markers has a single element the function is bound to fail.