Prev 58783 / 63424 Next

Strange behaviour of methods::slot() when returning a tibble

Fri, Jul 10, 2020 9:08 AM

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

	[[alternative HTML version deleted]]

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Thread (3 messages)

Stephen Martin Pederson Strange behaviour of methods::slot() when returning a tibble Jul 10 Duncan Murdoch Strange behaviour of methods::slot() when returning a tibble Jul 10 Stephen Martin Pederson Strange behaviour of methods::slot() when returning a tibble Jul 10