Adding document GitHub action #58

[gregorgorjanc]

Fixed #58

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

📢 Thoughts on this report? Let us know!

[gregorgorjanc]

R universe GH failing https://github.com/HighlanderLab/RcppTskit/actions/runs/21780174441/job/62842916038 with

/usr/bin/docker run --name ghcrioruniverseorgbuildsource_fccb2d --label a7e461 --workdir /github/workspace --rm -e "UNIVERSE_NAME" -e "MY_UNIVERSE" -e "CRAN_VERSION" -e "GITHUB_PAT" -e "INPUT_URL" -e "INPUT_REF" -e "INPUT_SUBDIR" -e "INPUT_BRANCH" -e "INPUT_ARTICLES" -e "HOME" -e "GITHUB_JOB" -e "GITHUB_REF" -e "GITHUB_SHA" -e "GITHUB_REPOSITORY" -e "GITHUB_REPOSITORY_OWNER" -e "GITHUB_REPOSITORY_OWNER_ID" -e "GITHUB_RUN_ID" -e "GITHUB_RUN_NUMBER" -e "GITHUB_RETENTION_DAYS" -e "GITHUB_RUN_ATTEMPT" -e "GITHUB_ACTOR_ID" -e "GITHUB_ACTOR" -e "GITHUB_WORKFLOW" -e "GITHUB_HEAD_REF" -e "GITHUB_BASE_REF" -e "GITHUB_EVENT_NAME" -e "GITHUB_SERVER_URL" -e "GITHUB_API_URL" -e "GITHUB_GRAPHQL_URL" -e "GITHUB_REF_NAME" -e "GITHUB_REF_PROTECTED" -e "GITHUB_REF_TYPE" -e "GITHUB_WORKFLOW_REF" -e "GITHUB_WORKFLOW_SHA" -e "GITHUB_REPOSITORY_ID" -e "GITHUB_TRIGGERING_ACTOR" -e "GITHUB_WORKSPACE" -e "GITHUB_ACTION" -e "GITHUB_EVENT_PATH" -e "GITHUB_ACTION_REPOSITORY" -e "GITHUB_ACTION_REF" -e "GITHUB_PATH" -e "GITHUB_ENV" -e "GITHUB_STEP_SUMMARY" -e "GITHUB_STATE" -e "GITHUB_OUTPUT" -e "RUNNER_OS" -e "RUNNER_ARCH" -e "RUNNER_NAME" -e "RUNNER_ENVIRONMENT" -e "RUNNER_TOOL_CACHE" -e "RUNNER_TEMP" -e "RUNNER_WORKSPACE" -e "ACTIONS_RUNTIME_URL" -e "ACTIONS_RUNTIME_TOKEN" -e "ACTIONS_CACHE_URL" -e "ACTIONS_RESULTS_URL" -e "ACTIONS_ORCHESTRATION_ID" -e GITHUB_ACTIONS=true -e CI=true -v "/var/run/docker.sock":"/var/run/docker.sock" -v "/home/runner/work/_temp":"/github/runner_temp" -v "/home/runner/work/_temp/_github_home":"/github/home" -v "/home/runner/work/_temp/_github_workflow":"/github/workflow" -v "/home/runner/work/_temp/_runner_file_commands":"/github/file_commands" -v "/home/runner/work/RcppTskit/RcppTskit":"/github/workspace" ghcr.io/r-universe-org/build-source  "https://github.com/HighlanderLab/RcppTskit" "8960d27bd9e0c46fd02f192572db79023ddef2b0" "" "" ""
Building https://github.com/HighlanderLab/RcppTskit in /github/workspace
CommitRef: 8960d27bd9e0c46fd02f192572db79023ddef2b0
Subdir: 
Branch: 
Articles: 

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> .libPaths()
[1] "/github/workspace/pkglib"      "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"       "/usr/lib/R/library"           
> 
Cloning R package repository
  Cloning into 'RcppTskit'...
  Submodule 'extern/tskit' (https://github.com/tskit-dev/tskit) registered for path 'extern/tskit'
  Cloning into '/github/workspace/RcppTskit/extern/tskit'...
  Submodule path 'extern/tskit': checked out 'afacd4f21412c22dc036bc53b97d0ebdab5ae98b'
  Resetting to 8960d27bd9e0c46fd02f192572db79023ddef2b0
  From https://github.com/HighlanderLab/RcppTskit
   * branch            8960d27bd9e0c46fd02f192572db79023ddef2b0 -> FETCH_HEAD
  HEAD is now at 8960d27 Merge 9c1bec10e941220fc6c6e4ff2a7dbaa06594abe0 into 67a3a8eef7e2ba82fbbf4568386e5bb51e6d2d8d
Installing system dependencies
  This is pak 0.9.2.9000
  Error: 
  ! error in pak subprocess
  Caused by error: 
  ! Could not solve package dependencies:
  * local::.: ! pkgdepends resolution error for local::..
  Caused by error: 
  ! Could not find R package in `.` or its parent directories.
  ---
  Backtrace:
   1. buildtools::install_sysdeps("RcppTskit")
   2. base::tryCatch({ …
   3. base::tryCatchList(expr, classes, parentenv, handlers)
   4. base::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5. base::doTryCatch(return(expr), name, parentenv, handler)
   6. unix::eval_fork({ …
   7. unix:::eval_fork_internal(expr = clexpr, envir = clenv, tmp = tmp, timeout = time…
   8. pak::pkg_sysreqs(".", upgrade = FALSE)
   9. pak:::remote(function(...) { …
  10. err$throw(res$error)
  ---
  Subprocess backtrace:
  1. base::withCallingHandlers(cli_message = function(msg) { …
  2. get("pkg_sysreqs_internal", asNamespace("pak"))(...)
  3. pkgdepends::sysreqs_install_plan(pkg, upgrade = upgrade, config = config)
  4. prop$stop_for_solution_error()
  5. private$plan$stop_for_solve_error()
  6. pkgdepends:::pkgplan_stop_for_solve_error(self, private)
  7. base::throw(new_error("Could not solve package dependencies:\n", msg, …
  8. | base::signalCondition(cond)
  9. global (function (e) …
  <simpleError in {    options(pak.no_extra_messages = TRUE)    pak::pkg_sysreqs(".", upgrade = FALSE)}: child process has died>
  Problem looking for system requirements: child process has died

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> buildtools:::normalize_description('RcppTskit/DESCRIPTION')
> 
Error: contains a blank line
Execution halted

So, it seems we are failing because of the subdir!?

Aha, I have removed R universe from GH (because of this issue, but on the main branch, ups!) and rely on another setup - see https://github.com/HighlanderLab/highlanderlab.r-universe.dev.

Other GH actions pass.

Will close this and sort branches ...