I will echo the general usefulness; I have been using it a lot for the
exact same reason.  I only use the namespace functionality.

Kasper


On Thu, Dec 19, 2013 at 5:58 PM, Michael Lawrence <lawrence.michael@gene.com
> wrote:

> Would be nice to get it cleaned up. I ran it this morning on rtracklayer,
> ggbio, etc, and found tons of previously unexposed missing import bugs.
> It's super useful, despite it being not quite right.
>
>
> On Thu, Dec 19, 2013 at 7:46 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:
>
> > 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.
> >
> > Martin
> >
> >
> > 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@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
> >>>
> >>>
> >>>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
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> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> >
> > --
> > Computational Biology / Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N.
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> >
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> >
>
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