Stephen Martin Pederson
2020-Jul-10 15:54 UTC
[Rd] Strange behaviour of methods::slot() when returning a tibble
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]]
Duncan Murdoch
2020-Jul-10 16:08 UTC
[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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
Stephen Martin Pederson
2020-Jul-10 16:16 UTC
[Rd] Strange behaviour of methods::slot() when returning a tibble
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.duncan at gmail.com> Sent: Saturday, 11 July 2020 1:38 AM To: Stephen Martin Pederson <stephen.pederson at adelaide.edu.au>; r-devel at r-project.org <r-devel at 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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >[[alternative HTML version deleted]]