[Bioc-devel] codetoolsBioC does not suggest methods from packages not defining generic

Martin Morgan mtmorgan at fhcrc.org
Thu Dec 19 16:46:02 CET 2013

Thanks Michael for this fix; codetoolsBioC is in need of some work (maybe not a 
lot) but I don't think anyone in the Seattle group will be taking this up in the 
near future. If you or someone in the broader community (this kind of facility 
is useful in R generally) is interested in taking over active maintainership 
please let me know.


On 12/19/2013 06:55 AM, Michael Lawrence wrote:
> PS: the case that I fixed probably shouldn't be an error at all, rather it
> should just suggest the necessary imports.
> On Thu, Dec 19, 2013 at 6:45 AM, Michael Lawrence <michafla at gene.com> wrote:
>> 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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