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.br...@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.br...@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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