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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