Pre-CRAN polish for 0.3.0 (+ keep Colin as maintainer) by VincentGuyader · Pull Request #115 · ThinkR-open/dockerfiler

VincentGuyader · 2026-05-12T07:06:59Z

Summary

Pre-submission cleanup for the 0.3.0 CRAN release. Two commits:

chore: keep Colin Fay as the package maintainer (was PR chore: keep Colin Fay as the package maintainer #114 — supersedes and closes it). Reverts the cre swap from docs(cran-prep): switch maintainer to Vincent + rewrite cran-comments.md for 0.3.0 #111: Colin Fay stays the maintainer; Vincent Guyader goes back to aut. cran-comments.md's "Maintainer change" section is removed (no maintainer change → no "New maintainer" note from CRAN).
docs+chore: pre-CRAN polish for 0.3.0 — the result of a dedicated documentation review + a coverage pass:

dock_from_desc() — flip default repos to PPM (consistency with dock_from_renv()): default is now c(CRAN = "https://p3m.dev/cran/latest"), and .patch_rprofile_for_ppm() is wired into the generated Rprofile.site RUN so the build pulls pre-compiled Linux binaries (the __linux__/$VERSION_CODENAME/ rewrite + the strict HTTPUserAgent PPM requires). Pass repos = c(CRAN = "https://cran.rstudio.com/") to opt out. Breaking change to the generated Dockerfile; NEWS updated. Tests added (red-first): the default repos formal is the PPM URL; a default dock_from_desc() invocation produces the rewritten Rprofile line.

Documentation:
- README: the renv.lock section now shows the bare dock_from_renv(lockfile = ...) call and spells out the 0.3.0 defaults (multi-arch rocker/r-ver, p3m.dev binaries, rstudio user) and how to opt out; a parse_dockerfile() section is added; README links to vignette("dockerfiler").
- Vignette: adds dock_from_renv() and parse_dockerfile() sections; fixes the r(install.packages(..., repo = ...)) typo (repos =); notes the generators' default FROM/repos.
- dock_from_desc() roxygen: @examples + @details (explaining build_from_source/update_tar_gz); documents the new repos default + PPM rewrite; fixes the AS "Default it NULL" typo; clarifies AS is a build-stage name.
- Dockerfile$new() roxygen: @param FROM states the default; @param AS described as a build-stage name.
- Dockerfile$ENV() roxygen: @param key,value said "label" (copy-paste from LABEL()) → "environment variable".
- r() roxygen: clearer @description/@param/@return (captures an R expression unevaluated, returns a shell-quoted R -e '...' string); fixes the example's repo = typo.
- get_sysreqs() roxygen: @examples.
- NEWS: split the dense "Small polish bundle" bullet into readable user-facing lines; widen the FROM/repos breaking-change bullets to cover dock_from_desc().
- man/*.Rd regenerated (devtools::document(); bumps RoxygenNote 7.3.2 → 7.3.3 to match the installed roxygen2).
Coverage: tests/testthat/test-utils.R gains direct tests for the type/length/NA/format guards of every .validate_* helper (these guards are part of the security contract — the argument is interpolated into a generated Dockerfile directive — but were only exercised via the format-regex branch). Package coverage is back to 99.65% (R/utils.R 99.10%, was 80.18%); cran-comments.md updated with the real figure.

Verification

devtools::test(): 0 failures (3 pre-existing warnings only — 2 deliberate "warns when path missing" tests + an rlang lifecycle deprecation from a dependency).
covr::package_coverage(): 99.65%.
Fast R CMD check (Rd / NAMESPACE / DESCRIPTION / cross-references): all OK. (A full --as-cran run on this box is unusually slow due to networked tests + competing processes — CI is the authoritative check; the same --as-cran run on the maintainer-revert-only branch was 0/0/1, the NOTE being the transient "unable to verify current time" host clock.)
New roxygen cross-refs ([dock_from_desc()], [base::shQuote()], [Dockerfile]) resolve (checking Rd cross-references ... OK).

Test plan

dock_from_desc default repos flip — red-first tests, green after.
validator-guard tests — R/utils.R 80.18% → 99.10%.
devtools::test() 0 failures.
Rd cross-references OK.
CI (R-CMD-check) green — authoritative.
pr-reviewer + Copilot.

Closes #114.

Revert the maintainer (`cre`) swap from #111: Colin Fay (`contact@colinfay.me`) stays the `cre`, Vincent Guyader goes back to `aut`. Both remain listed as authors. No "New maintainer" note will be emitted by CRAN's submission system, so the corresponding section of `cran-comments.md` is removed.

VincentGuyader · 2026-05-12T07:07:08Z

/copilot review

Bundled pre-submission cleanup, the result of a dedicated documentation review plus a coverage pass. dock_from_desc(): flip the default `repos` to `c(CRAN = "https://p3m.dev/cran/latest")`, matching dock_from_renv(), and wire `.patch_rprofile_for_ppm()` into the generated Rprofile.site RUN so the build pulls pre-compiled Linux binaries (the `__linux__/$VERSION_CODENAME/` rewrite + the strict `HTTPUserAgent` PPM requires). Pass `repos = c(CRAN = "https://cran.rstudio.com/")` to opt out. Breaking change (behaviour of the generated Dockerfile); NEWS updated. Tests added (red-first): the default `repos` formal is the PPM URL, and a default `dock_from_desc()` invocation produces the rewritten Rprofile line. Documentation: - README: the renv.lock section now shows the bare `dock_from_renv(lockfile = ...)` call and spells out the 0.3.0 defaults (multi-arch `rocker/r-ver`, p3m.dev binaries, `rstudio` user) and how to opt out; a `parse_dockerfile()` section is added; the README links to `vignette("dockerfiler")`. - Vignette: adds `dock_from_renv()` and `parse_dockerfile()` sections, fixes the `r(install.packages(..., repo = ...))` typo (`repos =`), and notes the generators' default `FROM` / `repos`. - `dock_from_desc()` roxygen: add `@examples` and `@details` (explaining the `build_from_source` / `update_tar_gz` interplay), document the new `repos` default + PPM rewrite, fix the `AS` "Default it NULL" typo, clarify `AS` is a build-stage name. - `Dockerfile$new()` roxygen: `@param FROM` now states the default (`"rocker/r-base"`, and that the high-level generators differ); `@param AS` describes it as a build-stage name. - `Dockerfile$ENV()` roxygen: `@param key,value` said "label" (copy-paste from `LABEL()`); now "environment variable". - `r()` roxygen: clearer `@description` / `@param` / `@return` (it captures an R *expression* unevaluated and returns a shell-quoted `R -e '...'` string), fix the example's `repo =` typo. - `get_sysreqs()` roxygen: add `@examples`. - NEWS: split the dense "Small polish bundle" bullet into readable, user-facing lines; widen the FROM/repos breaking-change bullets to cover `dock_from_desc()`. - regenerated `man/*.Rd` (`devtools::document()`; bumps `RoxygenNote` 7.3.2 -> 7.3.3 to match the installed roxygen2). Coverage: - `tests/testthat/test-utils.R`: direct tests for the type/length/NA/format guards of every `.validate_*` helper. These guards are part of the security contract (the argument is interpolated into a generated Dockerfile directive) but were only exercised via the format-regex branch. Package coverage is back to 99.65% (`R/utils.R` 99.10%, was 80.18%); `cran-comments.md` updated with the real figure. Full test suite: 0 failures. R CMD check --as-cran: 0/0/0 (one transient "unable to verify current time" host NOTE, unrelated).

VincentGuyader · 2026-05-12T07:24:53Z

Force-pushed 437c48a: addressed pr-reviewer's nit — rmarkdown's smart-typography was turning -- into a U+2013 en-dash in the rendered README.md (and one slipped into cran-comments.md). Rephrased the parentheticals in README.Rmd / vignettes/dockerfiler.Rmd to use ; instead, re-knit README.md, fixed the cran-comments.md one. No en/em-dashes anywhere in source now. pr-reviewer verdict was APPROVE; local R CMD check (--no-manual --no-vignettes): 0/0/0 (one transient host NOTE). Re-triggered Copilot.

VincentGuyader · 2026-05-12T07:24:54Z

/copilot review

Copilot

Pull request overview

Pre-CRAN cleanup for the dockerfiler 0.3.0 release, including maintainer metadata alignment and documentation/test polishing. It also changes dock_from_desc()’s default CRAN repository configuration to Posit Public Package Manager (PPM) and wires in the PPM Rprofile rewrite so generated Dockerfiles pull Linux binaries by default.

Changes:

Revert maintainer role swap (keep Colin Fay as cre) and update CRAN submission notes accordingly.
Flip dock_from_desc() default repos to https://p3m.dev/cran/latest and apply the PPM Rprofile rewrite logic.
Documentation refresh (README, vignette, roxygen/Rd) plus additional validator-guard and dock_from_desc() regression tests.

Reviewed changes

Copilot reviewed 12 out of 16 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
vignettes/dockerfiler.Rmd	Vignette updates: clarify defaults, add `dock_from_renv()` / `parse_dockerfile()` sections, fix `repos=` usage.
tests/testthat/test-utils.R	New direct tests for `.validate_*` guard branches (type/length/NA/format).
tests/testthat/test-dock_from_desc.R	Tests asserting new `dock_from_desc()` default `repos` and PPM rewrite emission.
README.Rmd	README source updates: clarify generator defaults, add `parse_dockerfile()` section, link to vignette.
README.md	Regenerated README output reflecting README.Rmd changes.
R/rthis.R	Roxygen improvements for `r()` and example param fix (`repos=`).
R/get_sysreqs.R	Add roxygen examples (dontrun).
R/dockerfile.R	Roxygen clarification for `Dockerfile$new()` params and `ENV()` docs.
R/dock_from_desc.R	Default `repos` flipped to PPM + call into `.patch_rprofile_for_ppm()`; expanded parameter docs/examples.
NEWS.md	Release notes reorganized; document `repos` default flip for both generators.
man/r.Rd	Regenerated Rd for `r()` documentation updates.
man/get_sysreqs.Rd	Regenerated Rd with examples.
man/dockerfiles.Rd	Regenerated Rd reflecting `dock_from_desc()` default `repos` + details/examples.
man/Dockerfile.Rd	Regenerated Rd reflecting roxygen clarifications for `FROM`/`AS` and `ENV()`.
DESCRIPTION	Maintainer role reverted; RoxygenNote bumped.
cran-comments.md	Remove “Maintainer change” section; update coverage note.

Files not reviewed (4)

man/Dockerfile.Rd: Language not supported
man/dockerfiles.Rd: Language not supported
man/get_sysreqs.Rd: Language not supported
man/r.Rd: Language not supported

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+(`https://p3m.dev/cran/latest`). Pass `FROM = "rocker/r-base"` or
+`repos = c(CRAN = "https://cran.rstudio.com/")` to opt out.
+
+## Create a Dockerfile from an renv.lock


 #' @examples
 #' r(print("yeay"))
-#' r(install.packages("plumber", repo = "http://cran.irsn.fr/"))
+#' r(install.packages("plumber", repos = "http://cran.irsn.fr/"))



 ```{r}
-my_dock$RUN(r(install.packages("attempt", repo = "http://cran.irsn.fr/")))
+my_dock$RUN(r(install.packages("attempt", repos = "http://cran.irsn.fr/")))


VincentGuyader · 2026-05-12T07:46:22Z

Force-pushed 2dcdc73: one more doc nit — the vignette's \VignetteIndexEntry{getting_started} differed from its YAML title:, which triggers a rmarkdown title-mismatch warning. Aligned the index entry to Getting started with dockerfiler. Vignette renders clean. pkgdown::check_pkgdown(): no problems. Re-triggered Copilot.

VincentGuyader · 2026-05-12T07:46:23Z

/copilot review

…Entry (#116) #115 was merged from commit 437c48a, before the 2dcdc73 force-push that fixed the vignette index entry, so that fix was lost; this restores it. Plus the three Copilot inline comments on #115: - `vignettes/dockerfiler.Rmd`: section heading "Create a Dockerfile from an renv.lock" -> "... from a renv.lock" (article). - `R/rthis.R` `@examples`, `vignettes/dockerfiler.Rmd` "Basic workflow" chunk, `README.Rmd`: the illustrative `install.packages(..., repos = "http://cran.irsn.fr/")` now uses the canonical HTTPS CRAN mirror `https://cloud.r-project.org` instead of a plaintext-HTTP regional mirror. - restored `%\VignetteIndexEntry{Getting started with dockerfiler}` so it matches the vignette's YAML `title:` (silences the rmarkdown title-mismatch warning). regenerated `man/r.Rd`; re-knit `README.md`. No code-logic change. `devtools::test()` on the touched test file: 0 failures. Vignette renders clean. No en/em-dashes in source.

VincentGuyader mentioned this pull request May 12, 2026

chore: keep Colin Fay as the package maintainer #114

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VincentGuyader force-pushed the docs/pre-cran-polish-0.3.0 branch from 04480f1 to 437c48a Compare May 12, 2026 07:24

VincentGuyader requested a review from Copilot May 12, 2026 07:30

Copilot started reviewing on behalf of VincentGuyader May 12, 2026 07:31 View session

Copilot AI reviewed May 12, 2026

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VincentGuyader merged commit 581d38a into master May 12, 2026
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VincentGuyader mentioned this pull request May 12, 2026

docs: fold in Copilot's #115 review nits + restore lost VignetteIndexEntry #116

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Pre-CRAN polish for 0.3.0 (+ keep Colin as maintainer)#115

Pre-CRAN polish for 0.3.0 (+ keep Colin as maintainer)#115
VincentGuyader merged 2 commits into
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VincentGuyader commented May 12, 2026

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