[R-pkg-devel] Checking timings of packages

[Chris Brien]

Dear list members.

I have run into a problem with examples from my package growthPheno (https://github.com/briencj/growthPheno) that take more than 10 s to execute on two flavours under r-devel. The following is the details.log:

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
  Maintainer: 'Chris Brien mailto:chris.brien using adelaide.edu.au'

Flavor: r-devel-windows-x86_64
Check: examples, Result: NOTE
  Examples with CPU (user + system) or elapsed time > 10s
                               user system elapsed
  probeSmooths 13.56     0.15     13.73
  traitSmooth     13.03     0.10     13.13

When I run the examples on laptop and a desktop running Windows 10 under r-devel with all packages updated, the elapsed times were 4.26 and 4.45, respectively i.e. much less than on the CRAN platforms. These timings were achieved using the following function call from RStudio (2022.12.0 Build 353):

> devtools::check("growthPheno", manual=FALSE, check_dir="D:/Analyses/R",
+                 args="--as-cran", env_vars = c(NOT_CRAN = "false"))

I have also submitted the package to rhub using the following command:

 rhub::check_for_cran(path = "growthPheno_2.1.18.tar.gz",
               env_vars = c(`_R_CHECK_FORCE_SUGGESTS_` = "false",
               `_R_CHECK_CRAN_INCOMING_USE_ASPELL_` = "false"),
               email = "chris.brien using adelaide.edu.au") with the following results for timing:

The timing results were:

   Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
    probeSmooths   6.50     0.09       6.64
   traitSmooth         6.02     0.03      6.04

While these are higher than the timings on my machines, they are half those reported on in the details.log resulting from my CRAN submission.

In order to be able to pass the CRAN tests, I have reduced the examples so that the timings on my laptop are (sessionInfo is below):

                              user system elapsed
probeSmooths    2.32    0.06    2.45
traitSmooth     3.47    0.09    3.73

and, using rhub::check_for_CRAN, the timings > 5 s are:

                            user system elapsed
probeSmooths 5.16      0.07     6.42

The difficulty I am having is that I cannot be sure that the timings for r-devel-linux-x86_64-debian-gcc and r-devel-windows-x86_64 will be under 10 s, as seems to be required, if I were to resubmit the package to CRAN with the reduced examples.

I would be grateful to anyone who can suggest how I might go about determining the CRAN timings without submitting the package to CRAN.

Cheers,

 Chris

Chris Brien
Adjunct Associate Professor in Statistics, UniSA STEM| web page
Senior Biostatistician, Australian Plant Phenomics Facility | researcher profile

---------------
> sessionInfo()
R Under development (unstable) (2023-03-13 r83977 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default


locale:
[1] LC_COLLATE=English_Australia.utf8  LC_CTYPE=English_Australia.utf8
[3] LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Australia.utf8

time zone: Australia/Adelaide
tzcode source: internal

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

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0   viridisLite_0.4.1  dplyr_1.1.0        viridis_0.6.2      fields_14.1
 [6] fastmap_1.1.1      xopen_1.0.0        promises_1.2.0.1   digest_0.6.31      rpart_4.1.19
[11] dotCall64_1.0-2    mime_0.12          lifecycle_1.0.3    cluster_2.1.4      ellipsis_0.3.2
[16] processx_3.8.0     magrittr_2.0.3     compiler_4.3.0     rlang_1.0.6        Hmisc_5.0-1
[21] tools_4.3.0        utf8_1.2.3         yaml_2.3.7         data.table_1.14.8  knitr_1.42
[26] prettyunits_1.1.1  htmlwidgets_1.6.1  curl_5.0.0         pkgbuild_1.4.0     dae_3.2.15
[31] plyr_1.8.8         RColorBrewer_1.1-3 JOPS_0.1.15        pkgload_1.3.2      miniUI_0.1.1.1
[36] foreign_0.8-84     withr_2.5.0        purrr_1.0.1        desc_1.4.2         nnet_7.3-18
[41] grid_4.3.0         fansi_1.0.4        urlchecker_1.0.1   profvis_0.3.7      xtable_1.8-4
[46] colorspace_2.1-0   ggplot2_3.4.1      scales_1.2.1       MASS_7.3-58.3      cli_3.6.0
[51] rmarkdown_2.20     crayon_1.5.2       generics_0.1.3     remotes_2.4.2      rstudioapi_0.14
[56] sessioninfo_1.2.2  cachem_1.0.7       SemiPar_1.0-4.2    stringr_1.5.0      maps_3.4.1
[61] base64enc_0.1-3    vctrs_0.5.2        devtools_2.4.5     callr_3.7.3        rcmdcheck_1.4.0
[66] Formula_1.2-5      htmlTable_2.4.1    testthat_3.1.7     SpATS_1.0-18       glue_1.6.2
[71] spam_2.9-1         ps_1.7.2           stringi_1.7.12     gtable_0.3.1       later_1.3.0
[76] munsell_0.5.0      tibble_3.2.0       pillar_1.8.1       htmltools_0.5.4    brio_1.1.3
[81] R6_2.5.1           rprojroot_2.0.3    evaluate_0.20      shiny_1.7.4        lattice_0.20-45
[86] backports_1.4.1    memoise_2.0.1      httpuv_1.6.9       Rcpp_1.0.10        gridExtra_2.3
[91] nlme_3.1-162       checkmate_2.1.0    xfun_0.37          fs_1.6.1           usethis_2.1.6
[96] pkgconfig_2.0.3