Contra the usage example in the "Quality control with scater" vignette, calculateQCmetrics doesn't accept numeric feature_controls:

example_sce = calculateQCMetrics(example_sce, feature_controls = 1:40)

Error in calculateQCMetrics(example_sce, feature_controls = 1:40) :
  feature_controls should be named

This line in the vignette has eval = FALSE so it's not caught when the vignette is built.

Thanks Andrew. The problem is actually worse than having eval=FALSE; the vignette will happily compile even with errors in evaluated code, because error=TRUE in the knitr settings. The immediate problems have been fixed on Github, though bringing the vignettes (back) up to Bioconductor standard will be a long struggle.