Re: [Bioc-devel] BioC packages - profileplyr

2019-07-12 Thread michael shapiro
Is the failure in your code or in the vignettes?  I ran into a situation where I was @importFrom-ing function and my devtools::check() was failing because the @examples code wasn't seeing the imported functions.  This actually makes sense as a behavior because examples should act like the

Re: [Bioc-devel] BioC packages - profileplyr

2019-07-12 Thread Vincent Carey
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

[Bioc-devel] BioC packages - profileplyr

2019-07-12 Thread Doug Barrows
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