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feat: full whitelist#88

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jonthegeek merged 2 commits into
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fix-87-whitelist
Apr 15, 2026
Merged

feat: full whitelist#88
jonthegeek merged 2 commits into
mainfrom
fix-87-whitelist

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@jonthegeek jonthegeek commented Apr 15, 2026

Compiled the full allowlist from my various packages and repos.

Also unified the @param overwrite definition and updated all impacted .Rd docs.

@jonthegeek
feat: full whitelist
08b32b2 
Compiled the full allowlist from my various packages and repos.

Also unified the `@param overwrite` definition and updated all impacted `.Rd` docs.

- Closes #87
@jonthegeek jonthegeek requested a review from Copilot April 15, 2026 11:49
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{qcthat} Report: User Acceptance

No issues are awaiting UAT.

This report was generated by this GitHub Actions run.

Last updated: 2026-04-15 12:07:10 UTC

Session Info ─ Session info ───────────────────────────────────────────────────────────────

setting value

version R version 4.5.3 (2026-03-11)

os Ubuntu 24.04.4 LTS

system x86_64, linux-gnu

ui X11

language (EN)

collate en_US.UTF-8

ctype en_US.UTF-8

tz UTC

date 2026-04-15

pandoc 3.1.3 @ /usr/bin/pandoc

quarto NA

─ Packages ───────────────────────────────────────────────────────────────────

package * version date (UTC) lib source

askpass 1.2.1 2024-10-04 [1] RSPM

astgrepr 0.1.1 2025-06-07 [1] RSPM

backports 1.5.1 2026-04-03 [1] RSPM

base * 4.5.3 2026-03-28 [2] local

base64enc 0.1-6 2026-02-02 [1] RSPM

boot 1.3-32 2025-08-29 [2] CRAN (R 4.5.3)

brew 1.0-10 2023-12-16 [1] RSPM

brio 1.1.5 2024-04-24 [1] RSPM

bslib 0.10.0 2026-01-26 [1] RSPM

cachem 1.1.0 2024-05-16 [1] RSPM

callr 3.7.6 2024-03-25 [1] RSPM

checkmate 2.3.4 2026-02-03 [1] RSPM

class 7.3-23 2025-01-01 [2] CRAN (R 4.5.3)

cli 3.6.6 2026-04-09 [1] RSPM

clipr 0.8.0 2022-02-22 [1] RSPM

cluster 2.1.8.2 2026-02-05 [2] CRAN (R 4.5.3)

codetools 0.2-20 2024-03-31 [2] CRAN (R 4.5.3)

commonmark 2.0.0 2025-07-07 [1] RSPM

compiler 4.5.3 2026-03-28 [2] local

covr 3.6.5 2025-11-09 [1] RSPM

crayon 1.5.3 2024-06-20 [1] RSPM

credentials 2.0.3 2025-09-12 [1] RSPM

curl 7.0.0 2025-08-19 [1] RSPM

datasets * 4.5.3 2026-03-28 [2] local

desc 1.4.3 2023-12-10 [1] RSPM

devtools 2.5.0 2026-03-14 [1] RSPM

diffobj 0.3.6 2025-04-21 [1] RSPM

digest 0.6.39 2025-11-19 [1] RSPM

docopt 0.7.2 2025-03-25 [1] RSPM (R 4.5.3)

downlit 0.4.5 2025-11-14 [1] RSPM

dplyr 1.2.1 2026-04-03 [1] RSPM

ellipsis 0.3.3 2026-04-04 [1] RSPM

emoji 16.0.0 2024-10-28 [1] RSPM

evaluate 1.0.5 2025-08-27 [1] RSPM

fansi 1.0.7 2025-11-19 [1] RSPM

fastmap 1.2.0 2024-05-15 [1] RSPM

fontawesome 0.5.3 2024-11-16 [1] RSPM

foreign 0.8-91 2026-01-29 [2] CRAN (R 4.5.3)

fs 2.0.1 2026-03-24 [1] RSPM

generics 0.1.4 2025-05-09 [1] RSPM

gert 2.3.1 2026-01-11 [1] RSPM

gh 1.5.0 2025-05-26 [1] RSPM

git2r 0.36.2 2025-03-29 [1] RSPM

gitcreds 0.1.2 2022-09-08 [1] RSPM

glue 1.8.0 2024-09-30 [1] RSPM

graphics * 4.5.3 2026-03-28 [2] local

grDevices * 4.5.3 2026-03-28 [2] local

grid 4.5.3 2026-03-28 [2] local

highr 0.12 2026-03-06 [1] RSPM

htmltools 0.5.9 2025-12-04 [1] RSPM

htmlwidgets 1.6.4 2023-12-06 [1] RSPM

httpuv 1.6.17 2026-03-18 [1] RSPM

httr 1.4.8 2026-02-13 [1] RSPM

httr2 1.2.2 2025-12-08 [1] RSPM

ini 0.3.1 2018-05-20 [1] RSPM

jquerylib 0.1.4 2021-04-26 [1] RSPM

jsonlite 2.0.0 2025-03-27 [1] RSPM

KernSmooth 2.23-26 2025-01-01 [2] CRAN (R 4.5.3)

knitr 1.51 2025-12-20 [1] RSPM

later 1.4.8 2026-03-05 [1] RSPM

lattice 0.22-9 2026-02-09 [2] CRAN (R 4.5.3)

lifecycle 1.0.5 2026-01-08 [1] RSPM

littler 0.3.22 2026-02-04 [1] RSPM (R 4.5.3)

magick 2.9.1 2026-02-28 [1] RSPM

magrittr 2.0.5 2026-04-04 [1] RSPM

MASS 7.3-65 2025-02-28 [2] CRAN (R 4.5.3)

Matrix 1.7-4 2025-08-28 [2] CRAN (R 4.5.3)

memoise 2.0.1 2021-11-26 [1] RSPM

methods * 4.5.3 2026-03-28 [2] local

mgcv 1.9-4 2025-11-07 [2] CRAN (R 4.5.3)

mime 0.13 2025-03-17 [1] RSPM

miniUI 0.1.2 2025-04-17 [1] RSPM

nlme 3.1-168 2025-03-31 [2] CRAN (R 4.5.3)

nnet 7.3-20 2025-01-01 [2] CRAN (R 4.5.3)

openssl 2.3.5 2026-02-26 [1] RSPM

otel 0.2.0 2025-08-29 [1] RSPM

pak 0.9.3 2026-04-09 [1] RSPM (R 4.5.0)

parallel 4.5.3 2026-03-28 [2] local

pillar 1.11.1 2025-09-17 [1] RSPM

pkgbuild 1.4.8 2025-05-26 [1] RSPM

pkgconfig 2.0.3 2019-09-22 [1] RSPM

pkgdown 2.2.0 2025-11-06 [1] RSPM

pkgload 1.5.1 2026-04-01 [1] RSPM

pkgskills 0.0.0.9000 2026-04-15 [1] local

praise 1.0.0 2015-08-11 [1] RSPM

prettyunits 1.2.0 2023-09-24 [1] RSPM

processx 3.8.7 2026-04-01 [1] RSPM

profvis 0.4.0 2024-09-20 [1] RSPM

promises 1.5.0 2025-11-01 [1] RSPM

ps 1.9.2 2026-03-31 [1] RSPM

purrr 1.2.2 2026-04-10 [1] RSPM

qcthat 1.1.2 2026-04-15 [1] Github (Gilead-BioStats/qcthat@d0958dc)

R6 2.6.1 2025-02-15 [1] RSPM

ragg 1.5.2 2026-03-23 [1] RSPM

rappdirs 0.3.4 2026-01-17 [1] RSPM

rcmdcheck 1.4.0 2021-09-27 [1] RSPM

Rcpp 1.1.1 2026-01-10 [1] RSPM

rex 1.2.2 2026-03-28 [1] RSPM

rlang 1.2.0 2026-04-06 [1] RSPM

rmarkdown 2.31 2026-03-26 [1] RSPM

roxygen2 7.3.3 2025-09-03 [1] RSPM

rpart 4.1.24 2025-01-07 [2] CRAN (R 4.5.3)

rprojroot 2.1.1 2025-08-26 [1] RSPM

rrapply 1.2.8 2025-11-25 [1] RSPM

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shiny 1.13.0 2026-02-20 [1] RSPM

sourcetools 0.1.7-2 2026-03-28 [1] RSPM

spatial 7.3-18 2025-01-01 [2] CRAN (R 4.5.3)

splines 4.5.3 2026-03-28 [2] local

stats * 4.5.3 2026-03-28 [2] local

stats4 4.5.3 2026-03-28 [2] local

stbl 0.3.0 2026-04-04 [1] RSPM

stringi 1.8.7 2025-03-27 [1] RSPM

stringr 1.6.0 2025-11-04 [1] RSPM

survival 3.8-6 2026-01-16 [2] CRAN (R 4.5.3)

sys 3.4.3 2024-10-04 [1] RSPM

systemfonts 1.3.2 2026-03-05 [1] RSPM

tcltk 4.5.3 2026-03-28 [2] local

testthat 3.3.2 2026-01-11 [1] RSPM

textshaping 1.0.5 2026-03-06 [1] RSPM

tibble 3.3.1 2026-01-11 [1] RSPM

tidyr 1.3.2 2025-12-19 [1] RSPM

tidyselect 1.2.1 2024-03-11 [1] RSPM

tinytex 0.59 2026-03-28 [1] RSPM

tools 4.5.3 2026-03-28 [2] local

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utf8 1.2.6 2025-06-08 [1] RSPM

utils * 4.5.3 2026-03-28 [2] local

vctrs 0.7.3 2026-04-11 [1] RSPM

waldo 0.6.2 2025-07-11 [1] RSPM

whisker 0.4.1 2022-12-05 [1] RSPM

withr 3.0.2 2024-10-28 [1] RSPM

xfun 0.57 2026-03-20 [1] RSPM

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xtable 1.8-8 2026-02-22 [1] RSPM

yaml 2.3.12 2025-12-10 [1] RSPM

zip 2.3.3 2025-05-13 [1] RSPM

[1] /usr/local/lib/R/site-library

[2] /usr/local/lib/R/library

[3] /__w/_temp/Library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

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{qcthat} Reports

PR-Associated Issues

█ A qcthat issue test matrix with 0 milestones, 0 issues, and 0 tests 
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
🙈 1 issue with label "qcthat-nocov" was ignored

Completed Issues

✅ A qcthat issue test matrix with 1 milestone, 21 issues, and 95 tests 
└─█─Milestone: v0.1.0 (21 issues, 95 tests)
  ├─☑️─Task 84: feat: hosted actions
  │ ├─✅─use_github_copilot() installs copilot-setup-steps.yml (#25, #84)
  │ └─✅─use_github_copilot() overwrites files when overwrite = TRUE (#25, #84)
  ├─☑️─Task 36: chore: standardize overwrite argument
  │ ├─✅─use_agent() errors if AGENTS.md exists and overwrite = FALSE (#36)
  │ └─✅─use_agent() overwrites AGENTS.md when overwrite = TRUE (#36)
  ├─☑️─Feature 28: feat: use_ai()
  │ ├─✅─use_ai() returns invisibly (#28)
  │ ├─✅─use_ai() returns a named list with all function names (#28)
  │ ├─✅─use_ai() installs only selected skills (#28)
  │ ├─✅─use_ai() errors on invalid skill name (#28)
  │ ├─✅─use_ai() creates AGENTS.md and copilot workflow (#28)
  │ ├─✅─use_ai() creates selected skill files (#28)
  │ ├─✅─use_ai() respects save_agent_as (#28)
  │ ├─✅─use_ai() respects target_skills_dir (#28)
  │ └─✅─use_ai() passes gh_token to use_skill_create_issue() (#28)
  ├─☑️─Feature 25: feat: use_github_copilot()
  │ ├─✅─use_github_copilot() installs copilot-setup-steps.yml (#25, #84)
  │ ├─✅─use_github_copilot() returns path to copilot-setup-steps.yml invisibly (#25)
  │ ├─✅─use_github_copilot() errors if copilot-setup-steps.yml exists and overwrite = FALSE (#25)
  │ └─✅─use_github_copilot() overwrites files when overwrite = TRUE (#25, #84)
  ├─☑️─Feature 20: feat: use_skill_search_code()
  │ ├─✅─use_skill_search_code() installs skill at correct path (#20)
  │ ├─✅─use_skill_search_code() returns path invisibly (#20)
  │ ├─✅─use_skill_search_code() adds astgrepr to Suggests when absent (#20)
  │ ├─✅─use_skill_search_code() does not modify DESCRIPTION when astgrepr already in Suggests (#20)
  │ └─✅─use_skill_search_code() does not modify DESCRIPTION when astgrepr already in Imports (#20)
  ├─☑️─Feature 19: feat: use_skill_r_code()
  │ ├─✅─use_skill_r_code() installs skill at correct path (#19)
  │ ├─✅─use_skill_r_code() returns path invisibly (#19)
  │ └─✅─use_skill_r_code() emits install message (#19)
  ├─☑️─Feature 18: feat: use_skill_implement_issue()
  │ ├─✅─use_skill_implement_issue() installs skill at correct path (#18)
  │ └─✅─use_skill_implement_issue() returns path invisibly (#18)
  ├─☑️─Feature 17: feat: use_skill_github()
  │ ├─✅─use_skill_github() installs skill at correct path (#17)
  │ └─✅─use_skill_github() returns path invisibly (#17)
  ├─☑️─Feature 15: feat: default `.use_skill()` `data` argument to `list()`
  │ └─✅─.use_skill() uses empty list as default data (#15)
  ├─☑️─Feature 11: feat: use_skill_tdd_workflow()
  │ ├─✅─use_skill_tdd_workflow() creates skill file at correct path (#11)
  │ ├─✅─use_skill_tdd_workflow() returns path invisibly (#11)
  │ ├─✅─use_skill_tdd_workflow() renders package name into skill file (#11)
  │ ├─✅─use_skill_tdd_workflow() emits inform message (#11, #52)
  │ └─✅─use_skill_tdd_workflow() errors when Package field is absent (#11)
  ├─☑️─Feature 9: feat: use_skill_document()
  │ ├─✅─use_skill_document() installs skill at correct path (#9)
  │ ├─✅─use_skill_document() returns path invisibly (#9)
  │ ├─✅─use_skill_document() creates R/aaa-shared_params.R when absent (#9)
  │ ├─✅─use_skill_document() does not overwrite existing R/aaa-shared_params.R (#9)
  │ ├─✅─use_skill_document() emits message when aaa-shared_params.R is created (#9)
  │ └─✅─use_skill_document() does not emit shared_params message when file exists (#9)
  ├─☑️─Bug 82: `use_ai()` fails without a Bugreports in DESCRIPTION
  │ ├─✅─.bug_reports_from_remote() falls back to origin GitHub remote (#82)
  │ ├─✅─.bug_reports_from_remote() prefers upstream over origin (#82)
  │ ├─✅─.bug_reports_from_remote() ignores non-GitHub remotes (#82)
  │ └─✅─.bug_reports_from_remote() works with SSH remote URL (#82)
  ├─☑️─Feature 6: feat: use_skill_create_issue()
  │ ├─✅─use_skill_create_issue() errors on non-scalar target_dir (#6)
  │ ├─✅─use_skill_create_issue() errors on non-logical overwrite (#6)
  │ ├─✅─use_skill_create_issue() errors when BugReports is absent (#6)
  │ ├─✅─use_skill_create_issue() errors when BugReports is not a GitHub URL (#6)
  │ ├─✅─use_skill_create_issue() passes correct data to .use_skill() (#6)
  │ ├─✅─use_skill_create_issue() returns path invisibly (#6)
  │ ├─✅─.use_skill() returns path invisibly (#6)
  │ ├─✅─.use_skill() creates file at correct path with use_skills_subdir = TRUE (#6)
  │ ├─✅─.use_skill() creates file at correct path with use_skills_subdir = FALSE (#6)
  │ ├─✅─.use_skill() renders template variables into skill file (#6)
  │ ├─✅─.use_skill() emits a cli_inform message (#6)
  │ ├─✅─.use_skill() upserts into AGENTS.md when it exists (#6)
  │ ├─✅─.use_skill() creates ## Skills section in AGENTS.md if missing (#6)
  │ ├─✅─.use_skill() updates trigger for existing row in AGENTS.md (#6)
  │ ├─✅─.use_skill() does not touch AGENTS.md when it does not exist (#6)
  │ ├─✅─.use_skill() errors when overwrite = FALSE and file exists (#6)
  │ ├─✅─.use_skill() overwrites file when overwrite = TRUE and file exists (#6)
  │ ├─✅─.use_skill() errors on non-scalar skill (#6)
  │ ├─✅─.use_skill() errors on non-logical use_skills_subdir (#6)
  │ ├─✅─.use_skill() errors on non-logical overwrite (#6)
  │ ├─✅─.read_skill_trigger() errors when template file not found (#6)
  │ ├─✅─.read_skill_trigger() errors when front matter is missing (#6)
  │ ├─✅─.read_skill_trigger() errors when trigger field is absent (#6)
  │ ├─✅─.upsert_agents_skill() creates table when ## Skills has no table (#6)
  │ ├─✅─.upsert_agents_skill() appends row after non-terminal table (#6)
  │ └─✅─.upsert_agents_skill() returns NULL invisibly when AGENTS.md absent (#6)
  ├─☑️─Feature 2: feat: use_agent()
  │ ├─✅─use_agent() writes AGENTS.md and returns the path invisibly (#2)
  │ ├─✅─use_agent() substitutes Package and Title into the template (#2, #59)
  │ ├─✅─use_agent() does not insert 'NA' when Description or URL is absent (#2, #59)
  │ ├─✅─use_agent() emits an informational message after writing (#2)
  │ ├─✅─use_agent() errors on non-scalar save_as (#2)
  │ ├─✅─use_agent() errors on NULL save_as (#2)
  │ ├─✅─use_agent() respects a custom save_as path (#2)
  │ ├─✅─.use_template() errors on non-logical open (#2)
  │ └─✅─.use_template() creates the file with default data and open args (#2)
  ├─☑️─Feature 79: Add github copilot whitelist
  │ ├─✅─use_github_copilot_whitelist() warns and informs user (#79)
  │ ├─✅─use_github_copilot_whitelist() message contains allowlist URL (#79)
  │ ├─✅─use_github_copilot_whitelist() message contains allowlist entries (#79)
  │ ├─✅─use_github_copilot_whitelist() returns NULL invisibly (#79)
  │ ├─✅─use_github_copilot_whitelist() aborts with bad_endpoint subclass (#79)
  │ └─✅─use_github_copilot_whitelist() errors if no BugReports in DESCRIPTION (#79)
  ├─☑️─Bug 76: Add `AGENTS.md` to .Rbuildignore
  │ ├─✅─use_agent() adds AGENTS.md to .Rbuildignore (#76)
  │ └─✅─use_agent() adds custom save_as path to .Rbuildignore (#76)
  ├─☑️─Documentation 59: docs: reconcile AGENT.md
  │ ├─✅─use_agent() substitutes Package and Title into the template (#2, #59)
  │ └─✅─use_agent() does not insert 'NA' when Description or URL is absent (#2, #59)
  ├─☑️─Feature 52: feat: use_skill_tdd_workflow() no longer installs helper-expectations.R
  │ └─✅─use_skill_tdd_workflow() emits inform message (#11, #52)
  ├─☑️─Feature 48: Install minimal `R/aaa-conditions.R` with `use_skill_r_code()`
  │ ├─✅─use_skill_r_code() creates R/aaa-conditions.R when absent (#48)
  │ ├─✅─use_skill_r_code() substitutes Package into aaa-conditions.R (#48)
  │ ├─✅─use_skill_r_code() does not overwrite existing R/aaa-conditions.R (#48)
  │ └─✅─use_skill_r_code() does not emit conditions message when file exists (#48)
  ├─☑️─Bug 44: fix: `use_github_copilot()` corrupts `${{ }}` GitHub Actions expressions
  │ ├─✅─use_github_copilot() preserves ${{ }} in copilot-setup-steps.yml (#44)
  │ ├─✅─.use_template_as_is() errors on non-logical open (#44)
  │ ├─✅─.use_template_as_is() writes template content verbatim (#44)
  │ └─✅─.use_template_as_is() calls edit_file when open = TRUE (#44)
  └─☑️─Bug 42: fix: use_ai() fails when called via pkgskills::use_ai() without library(pkgskills)
    └─✅─pkgskills::use_ai() works without library(pkgskills) (#42)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
✅ All tests passed

🟢 All issues have at least one test

🙈 10 issues with label "qcthat-nocov" were ignored

This report was generated by this GitHub Actions run.

Last updated: 2026-04-15 12:07:11 UTC

Session Info ─ Session info ───────────────────────────────────────────────────────────────

setting value

version R version 4.5.3 (2026-03-11)

os Ubuntu 24.04.4 LTS

system x86_64, linux-gnu

ui X11

language (EN)

collate en_US.UTF-8

ctype en_US.UTF-8

tz UTC

date 2026-04-15

pandoc 3.1.3 @ /usr/bin/pandoc

quarto NA

─ Packages ───────────────────────────────────────────────────────────────────

package * version date (UTC) lib source

askpass 1.2.1 2024-10-04 [1] RSPM

astgrepr 0.1.1 2025-06-07 [1] RSPM

backports 1.5.1 2026-04-03 [1] RSPM

base * 4.5.3 2026-03-28 [2] local

base64enc 0.1-6 2026-02-02 [1] RSPM

boot 1.3-32 2025-08-29 [2] CRAN (R 4.5.3)

brew 1.0-10 2023-12-16 [1] RSPM

brio 1.1.5 2024-04-24 [1] RSPM

bslib 0.10.0 2026-01-26 [1] RSPM

cachem 1.1.0 2024-05-16 [1] RSPM

callr 3.7.6 2024-03-25 [1] RSPM

checkmate 2.3.4 2026-02-03 [1] RSPM

class 7.3-23 2025-01-01 [2] CRAN (R 4.5.3)

cli 3.6.6 2026-04-09 [1] RSPM

clipr 0.8.0 2022-02-22 [1] RSPM

cluster 2.1.8.2 2026-02-05 [2] CRAN (R 4.5.3)

codetools 0.2-20 2024-03-31 [2] CRAN (R 4.5.3)

commonmark 2.0.0 2025-07-07 [1] RSPM

compiler 4.5.3 2026-03-28 [2] local

covr 3.6.5 2025-11-09 [1] RSPM

crayon 1.5.3 2024-06-20 [1] RSPM

credentials 2.0.3 2025-09-12 [1] RSPM

curl 7.0.0 2025-08-19 [1] RSPM

datasets * 4.5.3 2026-03-28 [2] local

desc 1.4.3 2023-12-10 [1] RSPM

devtools 2.5.0 2026-03-14 [1] RSPM

diffobj 0.3.6 2025-04-21 [1] RSPM

digest 0.6.39 2025-11-19 [1] RSPM

docopt 0.7.2 2025-03-25 [1] RSPM (R 4.5.3)

downlit 0.4.5 2025-11-14 [1] RSPM

dplyr 1.2.1 2026-04-03 [1] RSPM

ellipsis 0.3.3 2026-04-04 [1] RSPM

emoji 16.0.0 2024-10-28 [1] RSPM

evaluate 1.0.5 2025-08-27 [1] RSPM

fansi 1.0.7 2025-11-19 [1] RSPM

fastmap 1.2.0 2024-05-15 [1] RSPM

fontawesome 0.5.3 2024-11-16 [1] RSPM

foreign 0.8-91 2026-01-29 [2] CRAN (R 4.5.3)

fs 2.0.1 2026-03-24 [1] RSPM

generics 0.1.4 2025-05-09 [1] RSPM

gert 2.3.1 2026-01-11 [1] RSPM

gh 1.5.0 2025-05-26 [1] RSPM

git2r 0.36.2 2025-03-29 [1] RSPM

gitcreds 0.1.2 2022-09-08 [1] RSPM

glue 1.8.0 2024-09-30 [1] RSPM

graphics * 4.5.3 2026-03-28 [2] local

grDevices * 4.5.3 2026-03-28 [2] local

grid 4.5.3 2026-03-28 [2] local

highr 0.12 2026-03-06 [1] RSPM

htmltools 0.5.9 2025-12-04 [1] RSPM

htmlwidgets 1.6.4 2023-12-06 [1] RSPM

httpuv 1.6.17 2026-03-18 [1] RSPM

httr 1.4.8 2026-02-13 [1] RSPM

httr2 1.2.2 2025-12-08 [1] RSPM

ini 0.3.1 2018-05-20 [1] RSPM

jquerylib 0.1.4 2021-04-26 [1] RSPM

jsonlite 2.0.0 2025-03-27 [1] RSPM

KernSmooth 2.23-26 2025-01-01 [2] CRAN (R 4.5.3)

knitr 1.51 2025-12-20 [1] RSPM

later 1.4.8 2026-03-05 [1] RSPM

lattice 0.22-9 2026-02-09 [2] CRAN (R 4.5.3)

lifecycle 1.0.5 2026-01-08 [1] RSPM

littler 0.3.22 2026-02-04 [1] RSPM (R 4.5.3)

magick 2.9.1 2026-02-28 [1] RSPM

magrittr 2.0.5 2026-04-04 [1] RSPM

MASS 7.3-65 2025-02-28 [2] CRAN (R 4.5.3)

Matrix 1.7-4 2025-08-28 [2] CRAN (R 4.5.3)

memoise 2.0.1 2021-11-26 [1] RSPM

methods * 4.5.3 2026-03-28 [2] local

mgcv 1.9-4 2025-11-07 [2] CRAN (R 4.5.3)

mime 0.13 2025-03-17 [1] RSPM

miniUI 0.1.2 2025-04-17 [1] RSPM

nlme 3.1-168 2025-03-31 [2] CRAN (R 4.5.3)

nnet 7.3-20 2025-01-01 [2] CRAN (R 4.5.3)

openssl 2.3.5 2026-02-26 [1] RSPM

otel 0.2.0 2025-08-29 [1] RSPM

pak 0.9.3 2026-04-09 [1] RSPM (R 4.5.0)

parallel 4.5.3 2026-03-28 [2] local

pillar 1.11.1 2025-09-17 [1] RSPM

pkgbuild 1.4.8 2025-05-26 [1] RSPM

pkgconfig 2.0.3 2019-09-22 [1] RSPM

pkgdown 2.2.0 2025-11-06 [1] RSPM

pkgload 1.5.1 2026-04-01 [1] RSPM

pkgskills 0.0.0.9000 2026-04-15 [1] local

praise 1.0.0 2015-08-11 [1] RSPM

prettyunits 1.2.0 2023-09-24 [1] RSPM

processx 3.8.7 2026-04-01 [1] RSPM

profvis 0.4.0 2024-09-20 [1] RSPM

promises 1.5.0 2025-11-01 [1] RSPM

ps 1.9.2 2026-03-31 [1] RSPM

purrr 1.2.2 2026-04-10 [1] RSPM

qcthat 1.1.2 2026-04-15 [1] Github (Gilead-BioStats/qcthat@d0958dc)

R6 2.6.1 2025-02-15 [1] RSPM

ragg 1.5.2 2026-03-23 [1] RSPM

rappdirs 0.3.4 2026-01-17 [1] RSPM

rcmdcheck 1.4.0 2021-09-27 [1] RSPM

Rcpp 1.1.1 2026-01-10 [1] RSPM

rex 1.2.2 2026-03-28 [1] RSPM

rlang 1.2.0 2026-04-06 [1] RSPM

rmarkdown 2.31 2026-03-26 [1] RSPM

roxygen2 7.3.3 2025-09-03 [1] RSPM

rpart 4.1.24 2025-01-07 [2] CRAN (R 4.5.3)

rprojroot 2.1.1 2025-08-26 [1] RSPM

rrapply 1.2.8 2025-11-25 [1] RSPM

rstudioapi 0.18.0 2026-01-16 [1] RSPM

rversions 3.0.0 2025-10-09 [1] RSPM

sass 0.4.10 2025-04-11 [1] RSPM

sessioninfo 1.2.3 2025-02-05 [1] RSPM

shiny 1.13.0 2026-02-20 [1] RSPM

sourcetools 0.1.7-2 2026-03-28 [1] RSPM

spatial 7.3-18 2025-01-01 [2] CRAN (R 4.5.3)

splines 4.5.3 2026-03-28 [2] local

stats * 4.5.3 2026-03-28 [2] local

stats4 4.5.3 2026-03-28 [2] local

stbl 0.3.0 2026-04-04 [1] RSPM

stringi 1.8.7 2025-03-27 [1] RSPM

stringr 1.6.0 2025-11-04 [1] RSPM

survival 3.8-6 2026-01-16 [2] CRAN (R 4.5.3)

sys 3.4.3 2024-10-04 [1] RSPM

systemfonts 1.3.2 2026-03-05 [1] RSPM

tcltk 4.5.3 2026-03-28 [2] local

testthat 3.3.2 2026-01-11 [1] RSPM

textshaping 1.0.5 2026-03-06 [1] RSPM

tibble 3.3.1 2026-01-11 [1] RSPM

tidyr 1.3.2 2025-12-19 [1] RSPM

tidyselect 1.2.1 2024-03-11 [1] RSPM

tinytex 0.59 2026-03-28 [1] RSPM

tools 4.5.3 2026-03-28 [2] local

urlchecker 1.0.1 2021-11-30 [1] RSPM

usethis 3.2.1 2025-09-06 [1] RSPM

utf8 1.2.6 2025-06-08 [1] RSPM

utils * 4.5.3 2026-03-28 [2] local

vctrs 0.7.3 2026-04-11 [1] RSPM

waldo 0.6.2 2025-07-11 [1] RSPM

whisker 0.4.1 2022-12-05 [1] RSPM

withr 3.0.2 2024-10-28 [1] RSPM

xfun 0.57 2026-03-20 [1] RSPM

xml2 1.5.2 2026-01-17 [1] RSPM

xopen 1.0.1 2024-04-25 [1] RSPM

xtable 1.8-8 2026-02-22 [1] RSPM

yaml 2.3.12 2025-12-10 [1] RSPM

zip 2.3.3 2025-05-13 [1] RSPM

[1] /usr/local/lib/R/site-library

[2] /usr/local/lib/R/library

[3] /__w/_temp/Library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

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🌐 PR pkgdown deployed

This report was generated by this GitHub Actions run.

Last updated: 2026-04-15 12:07:21 UTC

Session Info ─ Session info ───────────────────────────────────────────────────────────────

setting value

version R version 4.5.3 (2026-03-11)

os Ubuntu 24.04.4 LTS

system x86_64, linux-gnu

ui X11

language (EN)

collate en_US.UTF-8

ctype en_US.UTF-8

tz UTC

date 2026-04-15

pandoc 3.1.3 @ /usr/bin/pandoc

quarto NA

─ Packages ───────────────────────────────────────────────────────────────────

package * version date (UTC) lib source

askpass 1.2.1 2024-10-04 [1] RSPM

astgrepr 0.1.1 2025-06-07 [1] RSPM

backports 1.5.1 2026-04-03 [1] RSPM

base * 4.5.3 2026-03-28 [2] local

base64enc 0.1-6 2026-02-02 [1] RSPM

boot 1.3-32 2025-08-29 [2] CRAN (R 4.5.3)

brew 1.0-10 2023-12-16 [1] RSPM

brio 1.1.5 2024-04-24 [1] RSPM

bslib 0.10.0 2026-01-26 [1] RSPM

cachem 1.1.0 2024-05-16 [1] RSPM

callr 3.7.6 2024-03-25 [1] RSPM

checkmate 2.3.4 2026-02-03 [1] RSPM

class 7.3-23 2025-01-01 [2] CRAN (R 4.5.3)

cli 3.6.6 2026-04-09 [1] RSPM

clipr 0.8.0 2022-02-22 [1] RSPM

cluster 2.1.8.2 2026-02-05 [2] CRAN (R 4.5.3)

codetools 0.2-20 2024-03-31 [2] CRAN (R 4.5.3)

commonmark 2.0.0 2025-07-07 [1] RSPM

compiler 4.5.3 2026-03-28 [2] local

covr 3.6.5 2025-11-09 [1] RSPM

crayon 1.5.3 2024-06-20 [1] RSPM

credentials 2.0.3 2025-09-12 [1] RSPM

curl 7.0.0 2025-08-19 [1] RSPM

datasets * 4.5.3 2026-03-28 [2] local

desc 1.4.3 2023-12-10 [1] RSPM

devtools 2.5.0 2026-03-14 [1] RSPM

diffobj 0.3.6 2025-04-21 [1] RSPM

digest 0.6.39 2025-11-19 [1] RSPM

docopt 0.7.2 2025-03-25 [1] RSPM (R 4.5.3)

downlit 0.4.5 2025-11-14 [1] RSPM

dplyr 1.2.1 2026-04-03 [1] RSPM

ellipsis 0.3.3 2026-04-04 [1] RSPM

emoji 16.0.0 2024-10-28 [1] RSPM

evaluate 1.0.5 2025-08-27 [1] RSPM

fansi 1.0.7 2025-11-19 [1] RSPM

fastmap 1.2.0 2024-05-15 [1] RSPM

fontawesome 0.5.3 2024-11-16 [1] RSPM

foreign 0.8-91 2026-01-29 [2] CRAN (R 4.5.3)

fs 2.0.1 2026-03-24 [1] RSPM

generics 0.1.4 2025-05-09 [1] RSPM

gert 2.3.1 2026-01-11 [1] RSPM

gh 1.5.0 2025-05-26 [1] RSPM

git2r 0.36.2 2025-03-29 [1] RSPM

gitcreds 0.1.2 2022-09-08 [1] RSPM

glue 1.8.0 2024-09-30 [1] RSPM

graphics * 4.5.3 2026-03-28 [2] local

grDevices * 4.5.3 2026-03-28 [2] local

grid 4.5.3 2026-03-28 [2] local

highr 0.12 2026-03-06 [1] RSPM

htmltools 0.5.9 2025-12-04 [1] RSPM

htmlwidgets 1.6.4 2023-12-06 [1] RSPM

httpuv 1.6.17 2026-03-18 [1] RSPM

httr 1.4.8 2026-02-13 [1] RSPM

httr2 1.2.2 2025-12-08 [1] RSPM

ini 0.3.1 2018-05-20 [1] RSPM

jquerylib 0.1.4 2021-04-26 [1] RSPM

jsonlite 2.0.0 2025-03-27 [1] RSPM

KernSmooth 2.23-26 2025-01-01 [2] CRAN (R 4.5.3)

knitr 1.51 2025-12-20 [1] RSPM

later 1.4.8 2026-03-05 [1] RSPM

lattice 0.22-9 2026-02-09 [2] CRAN (R 4.5.3)

lifecycle 1.0.5 2026-01-08 [1] RSPM

littler 0.3.22 2026-02-04 [1] RSPM (R 4.5.3)

magick 2.9.1 2026-02-28 [1] RSPM

magrittr 2.0.5 2026-04-04 [1] RSPM

MASS 7.3-65 2025-02-28 [2] CRAN (R 4.5.3)

Matrix 1.7-4 2025-08-28 [2] CRAN (R 4.5.3)

memoise 2.0.1 2021-11-26 [1] RSPM

methods * 4.5.3 2026-03-28 [2] local

mgcv 1.9-4 2025-11-07 [2] CRAN (R 4.5.3)

mime 0.13 2025-03-17 [1] RSPM

miniUI 0.1.2 2025-04-17 [1] RSPM

nlme 3.1-168 2025-03-31 [2] CRAN (R 4.5.3)

nnet 7.3-20 2025-01-01 [2] CRAN (R 4.5.3)

openssl 2.3.5 2026-02-26 [1] RSPM

otel 0.2.0 2025-08-29 [1] RSPM

pak 0.9.3 2026-04-09 [1] RSPM (R 4.5.0)

parallel 4.5.3 2026-03-28 [2] local

pillar 1.11.1 2025-09-17 [1] RSPM

pkgbuild 1.4.8 2025-05-26 [1] RSPM

pkgconfig 2.0.3 2019-09-22 [1] RSPM

pkgdown 2.2.0 2025-11-06 [1] RSPM

pkgload 1.5.1 2026-04-01 [1] RSPM

pkgskills 0.0.0.9000 2026-04-15 [1] local

praise 1.0.0 2015-08-11 [1] RSPM

prettyunits 1.2.0 2023-09-24 [1] RSPM

processx 3.8.7 2026-04-01 [1] RSPM

profvis 0.4.0 2024-09-20 [1] RSPM

promises 1.5.0 2025-11-01 [1] RSPM

ps 1.9.2 2026-03-31 [1] RSPM

purrr 1.2.2 2026-04-10 [1] RSPM

qcthat 1.1.2.9000 2026-04-15 [1] Github (Gilead-BioStats/qcthat@eec991d)

quarto 1.5.1 2025-09-04 [1] RSPM

R6 2.6.1 2025-02-15 [1] RSPM

ragg 1.5.2 2026-03-23 [1] RSPM

rappdirs 0.3.4 2026-01-17 [1] RSPM

rcmdcheck 1.4.0 2021-09-27 [1] RSPM

Rcpp 1.1.1 2026-01-10 [1] RSPM

rex 1.2.2 2026-03-28 [1] RSPM

rlang 1.2.0 2026-04-06 [1] RSPM

rmarkdown 2.31 2026-03-26 [1] RSPM

roxygen2 7.3.3 2025-09-03 [1] RSPM

rpart 4.1.24 2025-01-07 [2] CRAN (R 4.5.3)

rprojroot 2.1.1 2025-08-26 [1] RSPM

rrapply 1.2.8 2025-11-25 [1] RSPM

rstudioapi 0.18.0 2026-01-16 [1] RSPM

rversions 3.0.0 2025-10-09 [1] RSPM

sass 0.4.10 2025-04-11 [1] RSPM

sessioninfo 1.2.3 2025-02-05 [1] RSPM

shiny 1.13.0 2026-02-20 [1] RSPM

sourcetools 0.1.7-2 2026-03-28 [1] RSPM

spatial 7.3-18 2025-01-01 [2] CRAN (R 4.5.3)

splines 4.5.3 2026-03-28 [2] local

stats * 4.5.3 2026-03-28 [2] local

stats4 4.5.3 2026-03-28 [2] local

stbl 0.3.0 2026-04-04 [1] RSPM

stringi 1.8.7 2025-03-27 [1] RSPM

stringr 1.6.0 2025-11-04 [1] RSPM

survival 3.8-6 2026-01-16 [2] CRAN (R 4.5.3)

sys 3.4.3 2024-10-04 [1] RSPM

systemfonts 1.3.2 2026-03-05 [1] RSPM

tcltk 4.5.3 2026-03-28 [2] local

testthat 3.3.2 2026-01-11 [1] RSPM

textshaping 1.0.5 2026-03-06 [1] RSPM

tibble 3.3.1 2026-01-11 [1] RSPM

tidyr 1.3.2 2025-12-19 [1] RSPM

tidyselect 1.2.1 2024-03-11 [1] RSPM

tinytex 0.59 2026-03-28 [1] RSPM

tools 4.5.3 2026-03-28 [2] local

urlchecker 1.0.1 2021-11-30 [1] RSPM

usethis 3.2.1 2025-09-06 [1] RSPM

utf8 1.2.6 2025-06-08 [1] RSPM

utils * 4.5.3 2026-03-28 [2] local

vctrs 0.7.3 2026-04-11 [1] RSPM

waldo 0.6.2 2025-07-11 [1] RSPM

whisker 0.4.1 2022-12-05 [1] RSPM

withr 3.0.2 2024-10-28 [1] RSPM

xfun 0.57 2026-03-20 [1] RSPM

xml2 1.5.2 2026-01-17 [1] RSPM

xopen 1.0.1 2024-04-25 [1] RSPM

xtable 1.8-8 2026-02-22 [1] RSPM

yaml 2.3.12 2025-12-10 [1] RSPM

zip 2.3.3 2025-05-13 [1] RSPM

[1] /usr/local/lib/R/site-library

[2] /usr/local/lib/R/library

[3] /__w/_temp/Library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

Copilot AI reviewed Apr 15, 2026
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Pull request overview

Expands the default GitHub Copilot coding agent firewall allowlist and standardizes the overwrite parameter documentation across the package’s exported helpers and internal utilities, aligning behavior/docs for the Copilot setup workflow.

Changes:

  • Expanded the default allowlist domains used by use_github_copilot() / use_github_copilot_whitelist().
  • Unified the overwrite parameter wording in shared params and regenerated impacted .Rd docs.
  • Updated use_github_copilot() documentation wording to reflect current installation behavior.

Reviewed changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated 3 comments.

Show a summary per file
File Description
man/use_skill_tdd_workflow.Rd Regenerated overwrite param docs with unified wording.
man/use_skill_search_code.Rd Regenerated overwrite param docs with unified wording.
man/use_skill_r_code.Rd Regenerated overwrite param docs with unified wording.
man/use_skill_implement_issue.Rd Regenerated overwrite param docs with unified wording.
man/use_skill_github.Rd Regenerated overwrite param docs with unified wording.
man/use_skill_document.Rd Regenerated overwrite param docs with unified wording.
man/use_skill_create_issue.Rd Regenerated overwrite param docs with unified wording.
man/use_github_copilot_whitelist.Rd Updated usage signature to reflect expanded allowlist default.
man/use_github_copilot.Rd Updated usage signature for expanded allowlist + clarified description text.
man/use_ai.Rd Regenerated overwrite param docs with unified wording.
man/use_agent.Rd Regenerated overwrite param docs with unified wording.
man/dot-use_template_as_is.Rd Regenerated overwrite param docs with unified wording.
man/dot-use_skill.Rd Regenerated overwrite param docs with unified wording.
man/dot-shared-params.Rd Regenerated shared overwrite docs with unified wording.
man/dot-path_proj_save_as.Rd Regenerated overwrite param docs with unified wording.
man/dot-check_path_writable.Rd Regenerated overwrite param docs with unified wording.
R/use_github_copilot_whitelist.R Expanded the default allowlist vector used for firewall instructions.
R/use_github_copilot.R Expanded the default allowlist vector and relied on inherited shared params for overwrite.
R/aaa-shared_params.R Updated canonical shared overwrite parameter documentation text.

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Comment thread R/use_github_copilot.R Outdated
Comment thread R/aaa-shared_params.R Outdated
Comment thread man/dot-check_path_writable.Rd Outdated
@jonthegeek jonthegeek enabled auto-merge (squash) April 15, 2026 12:05
@jonthegeek jonthegeek merged commit eddff56 into main Apr 15, 2026
10 checks passed
@jonthegeek jonthegeek deleted the fix-87-whitelist branch April 15, 2026 12:08
github-actions Bot pushed a commit that referenced this pull request Apr 15, 2026
@jonthegeek
Remove preview for PR #88
f988c9d
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Reconcile whitelist

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@jonthegeek