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
[Bioc-devel] BioC packages - profileplyr
3 messages · Doug Barrows, Vincent Carey, Michael Shapiro
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 at 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
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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 user is running them, not like they're running inside the package.
On 7/12/2019 6:50 PM, Doug Barrows 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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