Hi Doug, I think you've written a method of "[" for class "profileplyr" that is using certain aspects of the Assays API that are not guaranteed to be stable. It would be good to have a simple reproducible example -- I can run your vignette and see that certain uses of "$" cause errors but pinpointing how you have to update your code would take some work. My gut feeling is that you do not have to write as much of a "[" method as you have ... let RangedSummarizedExperiment infrastructure do everything it can, and only when one of your extensions really needs to be fiddled with by "[" do you add that operation. Learning how to use callNextMethod may be helpful.
On Fri, Jul 12, 2019 at 1:51 PM Doug Barrows <doug.barr...@gmail.com> wrote: > Hi, > > Our package - profileplyr - is failing on the development branch with an > error when it tries to subset a RangedSummarizedExperiment object with > brackets ([ ]). Within our package we build a slightly modified > RangedSummarizedExperiment object with a few additional slots and features, > and often will subset this object using the brackets in both the functions > and in the vignette. When trying to subset (e.g. object[1:10, 1:10]) we get > the error "Error: $ operator not defined for this S4 class". This is a new > error, so I wanted to check if this kind of subsetting functionality is no > longer supported with RangedSummarizedExperiment objects in general, or > whether this is likely something specific to our package. Any insight you > may have would be greatly appreciated - thanks! > > Bestm > Doug > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel