Re: [R-pkg-devel] How to reduce examples in a package that takes more than 5 seconds to run?
On 12/15/22 9:02 AM, Ben Bolker wrote:
On 2022-12-15 9:57 a.m., Brian G. Peterson wrote:
On 12/15/22 08:34, Ismail Otoakhia wrote:
The R package 'ardl.nardl' has some examples that take more than 5
seconds
to run. I was advised by the CRAN team to reduce the run time to less
than
5 seconds.
How can this be achieved?
- you can lower the amount of data in the example
- you can use a faster method than your default method
- you can wrap the example in a dontrun tag so it will not run during
checking
If your example involves something like a fitted model object that
takes a long time to compute, you can pre-compute the model fit and
store the object in an inst/testdata directory, then use something like
fitted_model <- readRDS(system.file("testdata", "my_example.rds",
package = "mypackage"))
to retrieve it
The "sos" package includes a function "CRAN", which is used for that
purpose. The examples section in "findfn.Rd" includes the following:
# Skip these tests on CRAN,
# because they take more than 5 seconds
if(!CRAN()){
...
}
I know that some on this list do not like this construct, but it has
helped me manage this problem for several years. NOTE: This CRAN
function is NOT maintained by anyone on CRAN, so it is NOT guaranteed to
work. However, the "sos" package is currently on CRAN, and I have not
seen an email asking me to avoid it ;-)
https://github.com/sbgraves237/sos/blob/master/man/findFn.Rd
Hope this helps.
Spencer Graves
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] How to reduce examples in a package that takes more than 5 seconds to run?
On 2022-12-15 9:57 a.m., Brian G. Peterson wrote:
On 12/15/22 08:34, Ismail Otoakhia wrote:
The R package 'ardl.nardl' has some examples that take more than 5
seconds
to run. I was advised by the CRAN team to reduce the run time to less
than
5 seconds.
How can this be achieved?
- you can lower the amount of data in the example
- you can use a faster method than your default method
- you can wrap the example in a dontrun tag so it will not run during
checking
If your example involves something like a fitted model object that
takes a long time to compute, you can pre-compute the model fit and
store the object in an inst/testdata directory, then use something like
fitted_model <- readRDS(system.file("testdata", "my_example.rds",
package = "mypackage"))
to retrieve it
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
> E-mail is sent at my convenience; I don't expect replies outside of
working hours.
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] How to reduce examples in a package that takes more than 5 seconds to run?
On 12/15/22 08:34, Ismail Otoakhia wrote: The R package 'ardl.nardl' has some examples that take more than 5 seconds to run. I was advised by the CRAN team to reduce the run time to less than 5 seconds. How can this be achieved? - you can lower the amount of data in the example - you can use a faster method than your default method - you can wrap the example in a dontrun tag so it will not run during checking __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] How to reduce examples in a package that takes more than 5 seconds to run?
The R package 'ardl.nardl' has some examples that take more than 5 seconds to run. I was advised by the CRAN team to reduce the run time to less than 5 seconds. How can this be achieved? E. I Otoakhia [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE about use of `:::`
If you want the name of the function to appear, then you can put the
function in an environment whose parent is where most of the evaluation
should take place. For example,
f <- function(...) {
call <- match.call(expand.dots = TRUE)
call[[1]] <- quote(parse_args)
envir <- new.env(parent = parent.frame())
envir$parse_args <- parse_args
eval(call, envir)
}
parse_args <- function(...) {
cat("args were ", names(list(...)), "\n")
stop("Error in parse_args")
}
f(a = 1, b = 2)
#> args were a b
#> Error in parse_args(a = 1, b = 2): Error in parse_args
Duncan Murdoch
On 14/12/2022 8:35 p.m., David Kepplinger wrote:
Thank you both for the suggestions. I would prefer a clean stack trace in
case of errors as input errors are caught by this function and hence users
might very well see errors emitted from it. It seems more informative to me
if the error message would say "Error in .parse_args…" than "Error in
new.env(…". But since this solution was suggested by both of you it is
likely that CRAN too would demand this or a similar approach instead of
using `:::`. I know `:::` is expansive, but the computations that follow
are typically at least a few minutes so anything that takes less than a few
seconds won't be noticeable.
I also thought about using `...` before, but then the signature of the
user-facing functions would be incomplete and IDEs won't be able to provide
suggestions.
Thanks for the help!
-- David
On Wed, Dec 14, 2022 at 7:11 PM Simon Urbanek
wrote:
David,
why not
call[[1]] <- parse_args
The assignment is evaluated in your namespace so that makes sure the call
is that of your function. The only downside I see is that in a stack trace
you'll see the definition instead of the name.
Or possibly
do.call(parse_args, as.list(call[-1]))
Cheers,
Simon
PS: Note that ::: is expensive - it probably doesn't matter here, but
would in repeatedly called functions.
On 15/12/2022, at 12:19 PM, David Kepplinger
wrote:
Dear List,
I am working on updating the pense package and refactored some of the
methods. I have several functions which take the same arguments, hence
I'm
sending all these arguments to an internal function, called
`parse_args()`.
Since I want to evaluate the arguments in the caller's environment, I'm
using the following code
call <- match.call(expand.dots = TRUE)
call[[1]] <- quote(pense:::parse_args)
args <- eval.parent(call)
Of course, R CMD CHECK complains about the use of `:::`, as it's almost
never needed. I think the above usage would fall into that area of
"almost", but I'm not sure if (a) there's a better approach and (b) the
CRAN team would agree with me. I would have to test (b) by submitting and
working with the CRAN team, but I wanted to ask the list first to see if
I'm missing something obvious. I don't want to export the function
parse_args() as it's not useful for a user, and the use is truly
internal.
Thanks and all the best,
David
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
