I tried out codetoolsBioC for fun and found that it fails to report
(potentially necessary) method imports from packages that do not define the
generic (just add methods). A good example is "start" -- it will not be
reported for GenomicRanges under method imports. Of course, there is no way
to know whether a package is using start on a GRanges, IRanges, or a time
series for that matter, but it's best to be safe. Is there a maintainer
that can address this?
I did check-in one fix: findExternalDeps failed for cases where a package
(erroneously) imported methods without importing the generic (like
importMethodsFrom(GenomicRanges, "start<-") without the corresponding
import from IRanges). It now throws a more informative error message.
Michael
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