Specify minimal version dependencies + add action

[pawelru]

Overview of verdepcheck

Workflow:

• Determines versions of packages to install according to strategy
• Dowload and installs each package
• Performs R CMD check with the packages that were installed
  • Builds vignettes
  • Runs examples
  • Runs tests
  • Notifies of API call being used that are not available (package version might be too old)

Strategies:

• min_isolated: dependencies resolved independently with different PPM snapshots
• min_cohort: dependencies installed from 1 PPM snapshot, the most "minimum" version that was last released
• release: installs latest release of all packages
• max: install all dependecies from Github repos

[tasks]: verdepcheck 📦

• Fixes and improvements for strategies verdepcheck#26
• Training verdepcheck#24

[tasks]: Github Actions:

• https://github.com/insightsengineering/idr-tasks/issues/492
• https://github.com/insightsengineering/idr-tasks/issues/513
• Supports new strategies min_isolated and min_cohort r-verdepcheck-action#16
• Update strategies on R min deps check workflow r.pkg.template#175

[tasks]: Repos to review (For the 🪹 CoreDev team)

• Please add your name at the end of the PR.
• Use the checklist below as a guideline on how to review the PRs
• note that base packages don't need a Config/Needs/verdepcheck entry (stats, utils, grDevices, methods, ...)

📑 Checklist for PR review:

(each PR has the checklist)

Repos (please add your name at the end)

• CI: ✅ https://github.com/insightsengineering/citril/pull/313 @m7pr
• CI: ✅ https://github.com/insightsengineering/citril.metadata/pull/72
• CI: ✅ Adds min package version dunlin#111 @donyunardi
• CI: ✅ Adds min package version formatters#182 @vedhav
• CI: ✅ Adds min package version nestcolor#59
• CI: ✅ Adds min package version random.cdisc.data#286
• CI: ✅ Adds min package version rlistings#139
• CI: ✅ Adds min package version rtables#693 @m7pr
• CI: ✅ Adds min package version teal.code#123 @chlebowa
• CI: ✅ Adds min package version teal.data#158 @chlebowa
• CI: ✅ Adds min package version teal.modules.general#538
  • (doesn't fail as {tmc} because it has {teal.data} in dependencies
• CI: ✅ Adds min package version teal.reporter#194 @kartikeyakirar
• CI: ✅ Adds min package version teal.transform#150 @chlebowa
• CI: ✅ Adds min package version teal.widgets#168 @vedhav

---

Repos (only max is failing)

• CI: 🟠 Adds min package version teal#912
  • max: {teal.logger} repo problem
• CI: 🟠 (test fails max) Adds min package version teal.logger#49
  • max: Conflict with max as test/example fails
• CI: 🟠 Adds min package version teal.slice#405
  • max: Vignettes fail with 'con' is not a connection

Repos (failing)

• CI: 🔴 Adds min package version chevron#582
  • min_cohort, min_isolated: Can't install {tern} 0.9.9013 no tag exists!
• CI: 🔴 Adds min package version teal.goshawk#229
  • all: Secondary GH deps (from teal)
• CI: 🔴 Adds min package version teal.modules.clinical#797
  • all: Secondary GH deps (from {teal.slice} needs {teal.data})
• CI: 🔴 Adds min package version teal.osprey#222
  • all: Secondary GH deps (from {teal} needs {teal.slice})
• CI: 🟠 Adds min package version tern#1012
  • all: fails to build {vdiffr} from CRAN & GH repo
• CI: 🔴 Adds min package version tern.rbmi#57 @kartikeyakirar
  • max & min_isolated
  • CI image using using g++17
  • {rbmi} requires {TMB} version that is failing with this g++ version (g++12 works fine)

(there are more repos but I have only included those which has integration tests at the moment of doing this task)

Repos (PRs to be closed and superseded by section above):

Click to see abandoned PRs

• verdepcheck r.pkg.template#158
• verdepcheck random.cdisc.data#278
• specify minimal dependency version nestcolor#54
• https://github.com/insightsengineering/citril.metadata/pull/66
• specify min deps dunlin#96
• min deps chevron#517
• https://github.com/insightsengineering/citril/pull/250
• vbump deps formatters#163
• specify min deps rtables#650
• specify min deps rlistings#130
• specify minimal version of dependencies tern#957
• verdepcheck tern.rbmi#54
• verdepcheck teal#844
• verdepcheck teal.data#148
• specify min deps teal.code#104
• verdepcheck teal.logger#45
• verdepcheck teal.reporter#189
• verdepcheck teal.slice#332
• verdepcheck teal.transform#137
• verdepcheck teal.widgets#159
• verdepcheck goshawk#195
• verdepcheck osprey#118
• verdepcheck teal.goshawk#218
• verdepcheck teal.modules.clinical#780
• verdepcheck teal.modules.general#527
• verdepcheck teal.osprey#206

[averissimo]

Non-exaustive list of motives behind some of the minimum versions that are required:

Rcpp versions below v1.0.0 don't compile in R (>= 4) :

• purrr use purrr (>= 0.3.0)
• tidyr tidyr (>= 0.8.3)
• tibble use tibble (>= 2.0.0)
• rmarkdown use rmarkdown (>= 1.11)
• knitr use knitr (>= 1.34)

Compilation errors (header files changed)

• styler use styler (>= 1.2.0)
• stringr use stringr (>= 1.4.1)
  • stringi has problem compiling up to 1.7.3 with isNull not declared in scope, stringr from 2021 is needed
• checkmate use checkmate (>= 2.1.0)
  • 2.1.0 :: Removed deprecated S macro DOUBLE_EPS from C source
• testhat use testhat (>= 3.0.4)
  • error: size of array ‘altStackMem’ is not an integral constant-expression until 3.0.3

Due to some functions not being exported

• dplyr use dplyr (>= 1.1.0)
  • where re-export from tidyselect
• yaml use yaml (>= 2.1.15)
  • adds function read_yaml write_yaml
• r2rtf use r2rtf (>= 0.3.2)
  • adds render_safe in 0.3.0, but errors appear until 0.3.2

[averissimo]

Current status:

Short term:

4 PRs to go, blocked by {rmarkdown} discussion: insightsengineering/teal.logger#49 (comment)

teal, teal.logger & tern & tern.rbmi

• (with some strategies failing, as they're supposed to)
• probable action: add rmarkdown (>= 2.19), to suggests and rstudio/rmarkdown to Config/Needs/verdepcheck
• alternative: Core dev or IDR needs to understand why R CMD check it's failing for some packages and not others in CI (local docker image runs without issues in all cases)
  • important: it's the R CMD check that is the problem not really the verdepcheck

Medium/long term (will be resolved once all teal packages are on CRAN)

Discussion on insightsengineering/verdepcheck#38