Repository navigation
asan: make Additional_repositories reach the dependency install - #6
Merged
Merged
Conversation
"Configure additional repositories" set options(repos) inside its own
Rscript step, so the setting died with that process and the later
pak::local_install_deps() / pak::pkg_install() never saw DESCRIPTION's
Additional_repositories or the extra-repositories input. Packages
hosted only there failed the solve ("Can't find package called
TreeDistData" on ms609/TreeDist's vignettes leg), forcing callers to
pre-install them.
Append the repositories to the site profile instead, which every later
R process reads. Reading DESCRIPTION with read.dcf() also picks up a
multi-line Additional_repositories field, which the grep missed.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Collaborator
Author
|
Validated on ms609/TreeDist#206 in gcc-ASAN run 35575870744, vignettes leg, which pins
The tests and examples legs also pass on this branch. Once this merges, ms609/TreeDist#206 will switch back to |
ms609
pushed a commit
to ms609/TreeDist
that referenced
this pull request
Sep 21, 2026
ms609/actions#6 (Additional_repositories now reach the dependency install) is merged, so drop the validation pin. Validated on run 35575870744: TreeDistData resolved from the ms609 repo and all nine articles built under ASan/UBSan with no reports. Each leg runs for up to an hour, and on pull requests every push re-triggers all three. Per-leg concurrency cancels the stale runs. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
ms609-agent
added a commit
to ms609/TreeDist
that referenced
this pull request
Sep 21, 2026
Adopt the ms609/actions CI model used by Coreset, TreeTools, ConsTree and TreeSearch, and fix gcc-ASAN, which had failed on every main commit since 2026-09-11 and so ran no sanitizer check in that time. - gcc-ASAN: ms609/actions/asan@main in the r-hub gcc-asan container, with per-leg concurrency. Rogue is excluded (Rfast source build). Tests, examples and vignettes all run clean under ASan/UBSan. Needed ms609/actions#6 so Additional_repositories reach the install. - R-CMD-check: Coreset's waves. codemeta (update-codemeta, replacing codemeta.yml) -> arm sense-check -> core (Windows + codecov, R 4.1, devel) and benchmark -> full (ubuntu release, macOS x2) and a per-dependency-type revdepcheck. Per-leg concurrency, job timeouts and apt timeouts. Push triggers are limited to main/master. - Benchmark: four alternating passes with Coreset's _compare_results.R, installed from the PR checkout. DESCRIPTION gains Config/Needs/benchmark. - macOS: dependencies are installed without pak, because pak cannot extract CRAN's zstd binaries. The install pins CRAN because P3M's macOS TreeDist binaries are built with OpenMP but don't link libomp. - Least-privilege permissions on every workflow. Arm runners for memcheck, update-csl and copilot-setup-steps. pkgdown gets a dev/ redirect after release. RcppDeepState uses checkout@v6 and also runs on PRs. - test-tree_distance_spr.R no longer requires TBRDist, which is in Suggests only. - codemeta.json is regenerated with the update-codemeta generator. Co-authored-by: ms609-agent <313734811+ms609-agent@users.noreply.github.com> Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
asan's "Configure additional repositories" step calledoptions(repos = ...)inside its ownRscript {0}step. The setting ended when that R process exited, so the laterpak::local_install_deps()andpak::pkg_install()calls never saw DESCRIPTION'sAdditional_repositoriesor theextra-repositoriesinput.It surfaced on ms609/TreeDist#206: the vignettes leg failed its solve with
Can't find package called TreeDistData, a package hosted at https://ms609.github.io/packages/. ConsTree's "pre-install TreeSearch" step works around the same gap.Fix: append the repositories to the site profile (
$R_PROFILE, elseR_HOME/etc/Rprofile.site). Every later R process reads it, including pak's install subprocesses. A new "Report repositories" step prints the result. Reading DESCRIPTION withread.dcf()also picks up a multi-lineAdditional_repositoriesfield, which the oldgrepmissed.memcheck is unaffected: it passes the repos to
setup-r, which already persists them.Validation: ms609/TreeDist#206 temporarily pins
ms609/actions/asan@asan-persist-reposwith the TreeDistData workaround removed. I'll mark this ready once that vignettes leg passes the dependency install.🤖 Generated with Claude Code