date:20220829

Re: [R-pkg-devel] [Solved, sort-of] CRAN valgrind reports with zero leaks - actionable?

2022-08-29 Thread Dirk Eddelbuettel



Based on further (off-list) follow-ups with Simon and Uwe, the situation can
now be summarized as follows:

 - there appears to be no word about non-leak errors reported by valgrind in
   the official documentation; I will have to plead that those with the power
   to amend these documents maybe address that one day

 - it has been confirmed that when such a valgrind report is present, there
   is no auto-processing of the package and a manual re-check is done; as a
   package maintainer I rather avoid that to minimize manual interventions by
   both the CRAN team and the package maintainer (i.e. myself)

 - using `VALGRIND_OPTS="-s" R -d valgrind -f nameOfTheFile.R` is helpful,
   especially for the test framework I use where test files are standard R
   scripts; this helps in locating the issue

 - in the case that spawned this, the error actually comes from just one test
   and is tickled by a third-party system library so there is nothing for us
   to do here, besides not to run the test

 - so I moved the test into a testfile matching 'test_.*_extra.R' and now
   exclude files with that pattern via .Rbuildignore; that gives us a fuller
   test surface when testing locally via the full the test directory yet
   permits to isolate-away tests we would rather not be running at CRAN.

My thanks to everybody who helped with the question and clarified the context.

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] Dispatch for S3 and Ordinary Function with Same Name

2022-08-29 Thread Alexandre Courtiol

Hi Dario,
I would have suggested using randomForest::predict.randomForest but you
cannot because it is not exported by randomForest :-(
There is probably a better way but my workaround would be for you to define
your own class to avoid the ambiguity in scope.
Whenever you want to use the predict from randomForest rather than yours, I
would just strip out your specific class name.
Hopefully someone will advise something more elegant to force the scoping...
++



On Mon, 29 Aug 2022 at 17:00, Dario Strbenac 
wrote:

> Good day,
>
> If there is a function named predict in my package and another in another
> package, such as randomForest, which is also called in a particular wrapper
> function in my package, how may I ensure that the call to predict inside of
> the wrapper function will call randomForest's prediction function and not
> the predict function defined elsewhere in my package? To illustrate
>
> randomForestPredictInterface <- function(forest, measurementsTest, ...)
> {
>   predictions <- predict(forest, measurementsTest) # Currently, executes
> predict defined in my package.
>
> --
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> __
> R-package-devel@r-project.org mailing list
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>


-- 
Alexandre Courtiol, www.datazoogang.de

[[alternative HTML version deleted]]

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Re: [R-pkg-devel] dates in NEWS.Rd headers are ignored

2022-08-29 Thread Uwe Ligges





On 29.08.2022 13:06, Adelchi Azzalini wrote:

Thanks, Uwe. What you write illustrates in greater detail the state of affairs,
but from here I cannot see a way of sorting out the problem, which is as follows
(as I see it):

1. the inst/NEWS.Rd file contains the required dates;
2. when the package is built and installed, the dates do not show, specifically 
by
help(package="sn”), followed by a click on “Package NEWS;
3. I do not know how to control the proper translation from Rd to HTML.

So the specific question is: how can I enforce the presence on the dates show by
  help(package="sn”) + click on “Package NEWS ?


Currently you cannot, as the code that translates to html does not 
handle the dates. We will discuss this.


Best,
Uwe




Best wishes,

Adelchi



On 29 Aug 2022, at 12:36, Uwe Ligges  wrote:



On 29.08.2022 11:01, Adelchi Azzalini wrote:

Hi. In the last version of package ’sn’ (v. 2.1.0) the old NEWS text file
has been converted to inst/NEWS.Rd. The headers in this file are of the form
\section{Changes in sn version 2.1.0 (2022-07-30)}
\section{Changes in sn version 2.0.2 (2022-03-07)}
and so on
However, when I now look at the package documentation in the HTML rendering,
the “NEWS in packages ’sn’”  does NOT display the dates!
Details on the session are reported below, in case they are relevant.
Can anyone explain how show these dates?


In an interacticve session news(package="sn")  open a web page in some web 
browser and the html code does not contain the dates, but the text form does:

print(news(package="sn"), doBrowse=FALSE)

To analyzse more precisely, we can directly look at the database if the format 
was read correctly:

db <- news(package="sn")
str(db)
db$Date

and all dates were read correctly.

Best,
Uwe Ligges


---
Adelchi Azzalini
http://azzalini.stat.unipd.it
R> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.5.1
Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
Random number generation:
  RNG: Mersenne-Twister
  Normal:  Inversion
  Sample:  Rounding
  locale:
[1] en_US.UTF-8/UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid  stats4stats utils datasets  grDevices graphics  
methods   base
other attached packages:
[1] gtable_0.3.0  ggplot2_3.3.6 sn_2.1.0
loaded via a namespace (and not attached):
  [1] Rcpp_1.0.8.3highr_0.9   pillar_1.7.0compiler_4.2.1
  [5] tools_4.2.1 digest_0.6.29   evaluate_0.15   
lifecycle_1.0.1
  [9] tibble_3.1.7lattice_0.20-45 pkgconfig_2.0.3 rlang_1.0.2
[13] Matrix_1.4-1cli_3.3.0   xfun_0.31   stringr_1.4.0
[17] withr_2.5.0 dplyr_1.0.9 knitr_1.39  generics_0.1.2
[21] vctrs_0.4.1 isoband_0.2.5   tidyselect_1.1.2glue_1.6.2
[25] R6_2.5.1fansi_1.0.3 purrr_0.3.4 farver_2.1.0
[29] magrittr_2.0.3  scales_1.2.0ellipsis_0.3.2  mnormt_2.1.0
[33] colorspace_2.0-3numDeriv_2016.8-1.1 labeling_0.4.2  utf8_1.2.2
[37] stringi_1.7.6   munsell_0.5.0   crayon_1.5.1
R>
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Re: [R-pkg-devel] dates in NEWS.Rd headers are ignored

2022-08-29 Thread Uwe Ligges





On 29.08.2022 11:01, Adelchi Azzalini wrote:

Hi. In the last version of package ’sn’ (v. 2.1.0) the old NEWS text file
has been converted to inst/NEWS.Rd. The headers in this file are of the form

\section{Changes in sn version 2.1.0 (2022-07-30)}
\section{Changes in sn version 2.0.2 (2022-03-07)}
and so on

However, when I now look at the package documentation in the HTML rendering,
the “NEWS in packages ’sn’”  does NOT display the dates!

Details on the session are reported below, in case they are relevant.

Can anyone explain how show these dates?


In an interacticve session news(package="sn")  open a web page in some 
web browser and the html code does not contain the dates, but the text 
form does:


print(news(package="sn"), doBrowse=FALSE)

To analyzse more precisely, we can directly look at the database if the 
format was read correctly:


db <- news(package="sn")
str(db)
db$Date

and all dates were read correctly.

Best,
Uwe Ligges


---
Adelchi Azzalini
http://azzalini.stat.unipd.it



R> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.5.1

Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

Random number generation:
  RNG: Mersenne-Twister
  Normal:  Inversion
  Sample:  Rounding
  
locale:

[1] en_US.UTF-8/UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid  stats4stats utils datasets  grDevices graphics  
methods   base

other attached packages:
[1] gtable_0.3.0  ggplot2_3.3.6 sn_2.1.0

loaded via a namespace (and not attached):
  [1] Rcpp_1.0.8.3highr_0.9   pillar_1.7.0compiler_4.2.1
  [5] tools_4.2.1 digest_0.6.29   evaluate_0.15   
lifecycle_1.0.1
  [9] tibble_3.1.7lattice_0.20-45 pkgconfig_2.0.3 rlang_1.0.2
[13] Matrix_1.4-1cli_3.3.0   xfun_0.31   stringr_1.4.0
[17] withr_2.5.0 dplyr_1.0.9 knitr_1.39  generics_0.1.2
[21] vctrs_0.4.1 isoband_0.2.5   tidyselect_1.1.2glue_1.6.2
[25] R6_2.5.1fansi_1.0.3 purrr_0.3.4 farver_2.1.0
[29] magrittr_2.0.3  scales_1.2.0ellipsis_0.3.2  mnormt_2.1.0
[33] colorspace_2.0-3numDeriv_2016.8-1.1 labeling_0.4.2  utf8_1.2.2
[37] stringi_1.7.6   munsell_0.5.0   crayon_1.5.1
R>
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Re: [R-pkg-devel] [Solved, sort-of] CRAN valgrind reports with zero leaks - actionable?

Re: [R-pkg-devel] Dispatch for S3 and Ordinary Function with Same Name

Re: [R-pkg-devel] dates in NEWS.Rd headers are ignored

Re: [R-pkg-devel] dates in NEWS.Rd headers are ignored

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