[Bioc-devel] BioC packages - profileplyr

[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 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
>
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