[R-pkg-devel] Checking timings of packages
Ben Bolker
bbo|ker @end|ng |rom gm@||@com
Tue Mar 14 15:42:33 CET 2023
I would try running them on https://win-builder.r-project.org/ . If
the Windows timings are OK on that platform I think you can make a good
case to CRAN that you've done your best ...
On 2023-03-14 9:52 a.m., Chris Brien wrote:
> 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
>
> ______________________________________________
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--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
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