Updates for R-CMD-check-occasional to pass with minimal CI noise

[MichaelChirico]

The work here represents diagnosis+fix mainly by Gemini, with some back-and-forth + my input. I didn't quite keep all the commits from Gemini strictly pristine, but anything where there's any Gemini authorship has the commit message prefixed with Gemini: (with possible clean-up edits by me). The most crucial logjam was broken w.r.t. _R_CHECK_DEPENDS_ONLY_, as described by Gemini below:

---

Setting _R_CHECK_DEPENDS_ONLY_: false in .github/workflows/R-CMD-check-occasional.yaml overrides a default behavior of --as-cran in R CMD check that hides optional packages from the test suite:

1. Default Behavior of --as-cran in R CMD check

Under --as-cran, R automatically enables _R_CHECK_DEPENDS_ONLY_=true:

data.table/.github/workflows/R-CMD-check-occasional.yaml

Line 117 in fae95de

check_args = c("--no-manual", "--as-cran")

When active, R creates a restricted, temporary library (.libPaths()) during the check containing only the packages explicitly listed in DESCRIPTION (Depends, Imports, Suggests, and Enhances), plus base/recommended R packages. Any other packages installed on the system are hidden from the search path during test execution.

2. Why This Broke other.Rraw in CI

In step 82 of R-CMD-check-occasional.yaml, the workflow installs "fully optional packages" (other_pkgs such as caret, dplyr, ggplot2, sf, vctrs, etc.) so they can be tested for interoperability in inst/tests/other.Rraw. These optional packages are intentionally not listed in data.table's DESCRIPTION file.

Because they are omitted from DESCRIPTION, --as-cran stripped them from .libPaths() during check execution. Even though the step successfully installed all 19 optional packages and set TEST_DATA_TABLE_WITH_OTHER_PACKAGES=TRUE, inside R CMD check, other.Rraw could not find them and aborted across all CI runners with:

test.data.table('other.Rraw') failed to attach required package(s): caret, DBI, dplyr, gdata, ggplot2, hexbin, knitr, nanotime, nlme, plyr, RSQLite, sf, vctrs.

3. Effect of the Change

By explicitly setting _R_CHECK_DEPENDS_ONLY_: false, we prevent R CMD check from isolating the check library strictly to DESCRIPTION dependencies. This allows other.Rraw to see and attach the optional packages installed in the runner library during the check.

[github-actions]

• HEAD=occasional-fix much slower for transform improved in #5493
• HEAD=occasional-fix faster P<0.001 for DT[by,verbose=TRUE] improved in #6296
• HEAD=occasional-fix slower P<0.001 for memrecycle regression fixed in #5463
  

Generated via commit 150737f

Download link for the artifact containing the test results: ↓ atime-results.zip

Task	Duration
R setup and installing dependencies	3 minutes and 4 seconds
Installing different package versions	50 seconds
Running and plotting the test cases	6 minutes and 53 seconds

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.01%. Comparing base (f3bde87) to head (03cd5af).

Additional details and impacted files

@@                Coverage Diff                @@
##           utf8-old-windows    #7832   +/-   ##
=================================================
  Coverage             99.01%   99.01%           
=================================================
  Files                    88       88           
  Lines                 17286    17286           
=================================================
  Hits                  17116    17116           
  Misses                  170      170           

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[MichaelChirico]

Merging: this only touches the R-CMD-check-occasional GHA config, which should be in good shape starting from the next monthly run.