[R-pkg-devel] Submission after archived version

[Ivan Krylov]

В Mon, 11 Mar 2024 23:45:13 +0100
Nils Mechtel <nils.mech using gmail.com> пишет:

> Despite R CMD check not giving any errors or warnings, the package
> doesn’t pass the pre-tests:

If your question was more about the reasons for the difference between
your R CMD check and the pre-tests, most of it is due to --as-cran:

(Using commit ffe216d from https://github.com/nilsmechtel/MetAlyzer as
the basis for the example, which seems to be different from the
incoming pretest from the link you've shared.)

$ R-devel CMD check MetAlyzer_1.0.0.tar.gz
<...>
Status: OK	
$ R-devel CMD check --as-cran MetAlyzer_1.0.0.tar.gz
<...>
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories: ‘metabolomics_data.csv’
<...>

It's less wasteful to run checks without --as-cran in CI (as you
currently do), but you need to perform additional testing before making
a release. The incoming pre-tests use a custom set of environment
variables that go a but further than just --as-cran:
https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Kurt/lib/R/Scripts/check_CRAN_incoming.R

In particular, _R_CHECK_CRAN_INCOMING_USE_ASPELL_=true enables the
check for words that are possibly misspelled:

(Using an extra environment variable because your package has been
already published and R filters out "misspellings" found in the CRAN
version of the package. Congratulations!)

$ env \
 _R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_MAYBE_=FALSE \
 _R_CHECK_CRAN_INCOMING_USE_ASPELL_=true \
 R-devel CMD check --as-cran MetAlyzer_1.0.0.tar.gz
<...>
Possibly misspelled words in DESCRIPTION:
  metabolomics (15:78)
<...>

Yet another way to avoid false misspellings is to create a custom
dictionary:
http://dirk.eddelbuettel.com/blog/2017/08/10/#008_aspell_cran_incoming

$ mkdir -p .aspell
$ echo '
 Rd_files <- vignettes <- R_files <- description <- list(
  encoding = "UTF-8",
  language = "en",
  dictionaries = c("en_stats", "dictionary")
 )
' > .aspell/defaults.R
$ R -q -s -e '
 saveRDS(c(
  "metabolomics" # , extra words go here
 ), file.path(".aspell", "dictionary.rds"))
'
$ R CMD build .
$ env \
 _R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_MAYBE_=FALSE \
 _R_CHECK_CRAN_INCOMING_USE_ASPELL_=true \
 R-devel CMD check --as-cran MetAlyzer_1.0.0.tar.gz
# No more "Possibly misspelled words in DESCRIPTION"!

Some day, this will be documented in Writing R Extensions, or maybe in
R Internals (where the other _R_CHECK_* variables are documented), or
perhaps in the CRAN policy. See also:
https://stat.ethz.ch/pipermail/r-package-devel/2024q1/010558.html

-- 
Best regards,
Ivan