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.mich...@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 <mtmor...@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 <micha...@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]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > >> > > > > -- > > Computational Biology / Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. > > PO Box 19024 Seattle, WA 98109 > > > > Location: Arnold Building M1 B861 > > Phone: (206) 667-2793 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
