ESMValTool: treatment of missing values

I noticed that missing values are treated differently in the ESMValTool REF installation and the stand-alone ESMValTool installation. In case of the REF installation, one single missing value will lead to a missing result when calculating e.g. area means across many grid cells. This is different from (my) stand-alone ESMValTool installation, where missing values are ignored in such cases.

This could potentially be related to the default behavior of some Python packages used in the ESMValTool installation, but I do not know how to pin this down.

Here is an example, the left plot show the results of a time series averaged over a region with (my) stand-alone ESMValTool installation, the right plot the results obtained with the REF installation of ESMValTool. Note the gaps in the time series marked with the red arrows. This is potentially quite concerning.