Thanks Duncan. Much appreciated & I can now see it's
ellipsis::check_dots_empty() causing the trouble. I'll take the question to the
github issues page for that package.
All the best,
Steve
________________________________
From: Duncan Murdoch <murdoch.dun...@gmail.com>
Sent: Saturday, 11 July 2020 1:38 AM
To: Stephen Martin Pederson <stephen.peder...@adelaide.edu.au>;
r-devel@r-project.org <r-devel@r-project.org>
Subject: Re: [Rd] Strange behaviour of methods::slot() when returning a tibble
I don't get any warning (but am using slightly different versions of
everything than you are).
You can find where that message is coming from by running
options(warn=2) first, which will convert it to an error.
Duncan Murdoch
On 10/07/2020 11:54 a.m., Stephen Martin Pederson wrote:
> I have an S4 object class defined in a Bioconductor package which contains
> multiple slots, some of which are tibbles, whilst others are vectors. If I
> call
>
> slot(object, name)
>
> where 'name' is an slot that contains a vector, everything works as expected.
> However, when I call slot(object, name) where 'name' is an slot that contains
> a tibble I get the following warning:
>
>
> Warning message:
> `...` is not empty.
>
> We detected these problematic arguments:
> * `needs_dots`
>
> These dots only exist to allow future extensions and should be empty.
> Did you misspecify an argument?
> Making 'packages.html' ... done
>
> Wrapping the call in suppressWarnings() doesn't stop this, and this warning
> is printed every time the resultant object is called, e.g. df <- slot(object,
> name); df, would not print the error on the first call, but would print the
> warning every time df is printed.
>
> For an MWE
>
>
> setClass("track", slots = c(x="numeric", y="data.frame"))
> myTrack <- new("track", x = -4:4, y = tibble(y = 1))
>
> myTrack
>
> df <- slot(myTrack, "y")
> df
>
> The package passes R CMD check even though this warning is produced in most
> examples. Changing to a generic S3 data.frame also doesn't produce this
> error. I'm running the following configuration:
>
>
> R version 4.0.2 (2020-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.4 LTS
>
> Matrix products: default
> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
>
> locale:
> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
> LC_TIME=en_AU.UTF-8
> [4] LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8
> LC_MESSAGES=en_AU.UTF-8
> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C
> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] ngsReports_1.5.3 tibble_3.0.2 ggplot2_3.3.2
> BiocGenerics_0.34.0
>
> Thanks in advance,
>
> Steve
>
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>
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