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
