Release jlmerclusterperm 1.0.0

[yjunechoe]

First release:

• usethis::use_cran_comments()
• Update (aspirational) install instructions in README
• Proofread Title: and Description:
• Check that all exported functions have @return and @examples
• Check that Authors@R: includes a copyright holder (role 'cph')
• Check licensing of included files
• Review https://github.com/DavisVaughan/extrachecks

Prepare for release:

• git pull
• Check if any deprecation processes should be advanced, as described in Gradual deprecation
• devtools::build_readme()
• urlchecker::url_check()
• devtools::check(remote = TRUE, manual = TRUE)
• devtools::check_win_devel()
• rhub::check_for_cran()
• git push
• Draft blog post

Submit to CRAN:

• usethis::use_version('major')
• devtools::submit_cran()
• Approve email

Wait for CRAN...

• Accepted 🎉
• git push
• usethis::use_github_release()
• usethis::use_dev_version()
• Readme badges
• git push
• Finish blog post
• Tweet
• Add link to blog post in pkgdown news menu

[yjunechoe]

CRAN comments:

\dontrun{} should only be used if the example really cannot be executed
(e.g. because of missing additional software, missing API keys, ...) by
the user. That's why wrapping examples in \dontrun{} adds the comment
("# Not run:") as a warning for the user.
Does not seem necessary.
Please unwrap the examples if they are executable in < 5 sec, or create
additionally small toy examples to allow automatic testing.
(You could also replace \dontrun{} with \donttest, if it takes longer
than 5 sec to be executed, but it would be preferable to have automatic
checks for functions. Otherwise, you can also write some tests.)

Tracked in the as-donttest branch. Pending response on whether this is the right approach:

Please ensure that you do not use more than 2 cores in your examples,
vignettes, etc.

Fixed in e6ca9e2

[yjunechoe]

CRAN comments:

• long run times with \donttest{} approach:

  Fine if in \donttest

• whether to run the lengthy tests on cran:

  Test may take longer. Ovberall checktime should not exceed 10 min.

• special considerations for Julia/JuliaConnectoR

  Julia is the issue here, as it is not available on all machines.
  I see no SystemRequirements field that decalres that Julia is needed?

[yjunechoe]

Check log after applying fixes for above:

* using log directory 'd:/RCompile/CRANincoming/R-devel/jlmerclusterperm.Rcheck'
* using R Under development (unstable) (2023-06-07 r84523 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'jlmerclusterperm/DESCRIPTION' ... OK
* this is package 'jlmerclusterperm' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'June Choe <jchoe001@gmail.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  Oostenveld (8:62)
  interpretability (12:39)
  timewise (10:61)
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'jlmerclusterperm' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [421s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                            user system elapsed
permute_timewise_statistics 0.22   0.00   31.31
permute_by_predictor        0.15   0.02   29.25
to_jlmer                    0.14   0.01   29.93
walk_threshold_steps        0.13   0.02   29.91
calculate_clusters_pvalues  0.08   0.01   30.06
extract_empirical_clusters  0.05   0.02   30.16
julia_model_tidiers         0.05   0.02   31.21
clusterpermute              0.06   0.00   29.19
julia_rng                   0.04   0.02   30.08
compute_timewise_statistics 0.04   0.01   29.64
extract_null_cluster_dists  0.05   0.00   28.67
jlmer                       0.04   0.01   29.22
cluster_permutation_tidiers 0.02   0.02   29.77
julia_progress              0.03   0.01   29.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [96s] OK
  Running 'testthat.R' [96s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [18s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 NOTEs