[Bioc-devel] BioC packages - profileplyr

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Fri Jul 12 20:25:31 CEST 2019

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.barrows using 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]]
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