diff --git a/.github/workflows/ASan.yml b/.github/workflows/ASan.yml
index 7c564c2f..507f46b9 100644
--- a/.github/workflows/ASan.yml
+++ b/.github/workflows/ASan.yml
@@ -1,4 +1,7 @@
# Address Sanitizer: Replicate CRAN's gcc-ASAN 'Additional Test'
+# Uses the r-hub gcc-asan container (R-devel built with ASAN/UBSAN).
+# Additional_repositories in DESCRIPTION (https://ms609.github.io/packages/) is
+# read automatically by ms609/actions/asan, so TreeDistData needs no extra input.
on:
workflow_dispatch:
push:
@@ -24,14 +27,24 @@ on:
name: gcc-ASAN
+permissions:
+ contents: read
+
jobs:
mem-check:
- runs-on: ubuntu-24.04 # Update RSPM when increasing
+ # The r-hub gcc-asan image has no arm64 variant: stay on x86.
+ runs-on: ubuntu-latest
+ timeout-minutes: 120
container:
- image: rocker/r-devel-san
+ image: ghcr.io/r-hub/containers/gcc-asan:latest
name: AddressSanitizer ${{ matrix.config.test }}
+ # Each leg runs for up to an hour: a superseding push cancels the stale one.
+ concurrency:
+ group: ${{ github.workflow }}-${{ matrix.config.test }}-${{ github.ref }}
+ cancel-in-progress: true
+
strategy:
fail-fast: false
matrix:
@@ -41,36 +54,14 @@ jobs:
- {test: 'vignettes'}
env:
- R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
- _R_CHECK_FORCE_SUGGESTS_: false
- RSPM: https://packagemanager.rstudio.com/cran/__linux__/noble/latest
- USING_ASAN: true
- STRINGI_DISABLE_PKG_CONFIG: true
- BIOCONDUCTOR_USE_CONTAINER_REPOSITORY: FALSE # For stringi
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
- FS_USE_BUNDLED_LIBUV: 1
- ASAN_OPTIONS: detect_container_overflow=1:verify_asan_link_order=0
steps:
- - uses: actions/checkout@v6
-
- - name: Install system dependencies
- run: |
- apt-get update && apt-get install -y --no-install-recommends \
- libxml2-dev \
- libssl-dev \
- libcurl4-openssl-dev
-
- - name: Install R package dependencies
- run: |
- Rscript -e 'options(repos = c(CRAN = "https://cloud.r-project.org", ms609 = "https://ms609.github.io/packages/"))' \
- -e 'install.packages(c("remotes", "testthat"))' \
- -e 'remotes::install_github("ms609/TreeDistData")' \
- -e 'remotes::install_deps(dependencies = TRUE)' \
- -e 'remotes::install_local(build_opts = c("--no-build-vignettes", "--no-manual", "--no-resave-data"))'
- -e 'remotes::install_local()'
-
- - name: ASAN - memcheck ${{ matrix.config.test }}
- run: |
- sudo sysctl -w vm.mmap_rnd_bits=16
- Rscript memcheck/${{ matrix.config.test }}.R
+ - uses: ms609/actions/asan@main
+ with:
+ test: ${{ matrix.config.test }}
+ token: ${{ secrets.GITHUB_TOKEN }}
+ # Rogue hard-imports Rfast, a ~30-min source build under ASAN that
+ # adds no coverage to TreeDist's own compiled code. Its only use (the
+ # compare-treesets vignette) is requireNamespace()-guarded.
+ exclude-packages: Rogue
diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index d31c33b1..002b0a85 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -5,7 +5,9 @@ on:
- cron: "24 06 * * 1"
workflow_dispatch:
push:
- branches: ["*"]
+ branches:
+ - main
+ - master
paths-ignore:
- "Meta**"
- "AGENT**"
@@ -25,7 +27,7 @@ on:
- "**.R[dD]ata"
- "**.Rpro*"
pull_request:
- branches: ["*"]
+ branches: ["**"]
paths-ignore:
- "Meta**"
- "AGENT**"
@@ -47,18 +49,70 @@ on:
name: R-CMD-check
+# NB: there is deliberately NO workflow-level `concurrency`. Workflow-level
+# cancel-in-progress would kill the whole run (sense-check included) on every
+# new push. Instead, each EXPENSIVE job carries its own per-leg concurrency
+# group so superseded Windows/macOS work is cancelled, while the cheap
+# `sense-check` job has no concurrency and therefore always runs to completion
+# -- giving a per-commit "did this build?" signal even under rapid iteration.
+
+# Waves:
+# codemeta -> PRs only, ~15 s; pushes a stale codemeta.json to the PR
+# branch and holds back later waves.
+# sense-check -> arm (cheapest), never cancelled. Fast signal. Skipped only
+# when codemeta pushed (the fresh run covers the new head).
+# core -> Windows (+codecov) / R 4.1 / R devel; only if sense-check passed.
+# benchmark -> PR-vs-base timings; also only if sense-check passed, and only
+# on pull_request / workflow_dispatch.
+# full -> macOS x2 + ubuntu-24.04 (release) backstop; only once core is green.
+# revdepcheck -> reverse-dependency checks; also gated on core being green.
+permissions:
+ contents: read
+ issues: write # scheduled-failure notifier comments on and reopens #164
+
jobs:
- check-release:
- runs-on: ubuntu-24.04
- name: ubuntu-24.04 (release)
+ # ---------------------------------------------------------------------------
+ # Wave 0 (PRs only): is codemeta.json current? If stale, pushes the
+ # regenerated file to the PR branch (as the codemeta-writer App, so the push
+ # starts a fresh run) and fails. See ms609/actions/update-codemeta.
+ # ---------------------------------------------------------------------------
+ codemeta:
+ if: github.event_name == 'pull_request'
+ runs-on: ubuntu-24.04-arm
+ timeout-minutes: 5 # healthy run is ~15 s
+ permissions:
+ contents: read
+ outputs:
+ pushed: ${{ steps.codemeta.outputs.pushed }}
+
+ steps:
+ - id: codemeta
+ uses: ms609/actions/update-codemeta@main
+ with:
+ client-id: ${{ vars.CODEMETA_APP_ID }}
+ private-key: ${{ secrets.CODEMETA_APP_KEY }}
+
+ # ---------------------------------------------------------------------------
+ # Wave 1: cheapest leg as a fail-fast sense-check. No concurrency group, so a
+ # rapid follow-up push does NOT cancel it -- each commit gets its own signal.
+ # Waits ~15 s for codemeta, and skips if codemeta pushed an update: the
+ # fresh run checks the new head. Still runs if codemeta failed otherwise.
+ # ---------------------------------------------------------------------------
+ sense-check:
+ needs: codemeta
+ if: ${{ !cancelled() && needs.codemeta.outputs.pushed != 'true' }}
+ runs-on: ubuntu-24.04-arm
+ timeout-minutes: 30 # healthy run is ~10 min
+ name: sense-check (ubuntu-24.04-arm, release)
env:
- _R_CHECK_CRAN_INCOMING_: true # Seemingly not set by --as-cran
+ _R_CHECK_CRAN_INCOMING_: ${{ github.event_name == 'pull_request' }}
_R_CHECK_FORCE_SUGGESTS_: false # CRAN settings
R_COMPILE_AND_INSTALL_PACKAGES: 'never'
_R_CHECK_THINGS_IN_CHECK_DIR_: false
R_REMOTES_STANDALONE: true
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+ _R_CHECK_CRAN_INCOMING_USE_ASPELL_: false
RSPM: "https://packagemanager.posit.co/cran/__linux__/noble/latest"
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -70,17 +124,34 @@ jobs:
run: |
old_version=$(grep "Version:" DESCRIPTION | awk '{print $2}')
if [[ $(echo "$old_version" | tr -cd '.' | wc -c) -eq 2 ]]; then
- new_version="${old_version}.8888"
- if [[ "$RUNNER_OS" == "macOS" ]]; then
- sed -i "" "s/Version: .*/Version: ${new_version}/" DESCRIPTION
- else
- sed -i "s/Version: .*/Version: ${new_version}/" DESCRIPTION
- fi
+ new_version="${old_version}.9999"
+ sed -i "s/Version: .*/Version: ${new_version}/" DESCRIPTION
fi
shell: bash
-
+
+ # setup-r's first act on Linux is an internal `apt-get update`, and apt
+ # applies no transfer timeout by default: when a mirror accepts the
+ # connection and then stalls, the fetch never returns and the step burns
+ # the job's entire 6-hour budget. Observed 2026-08-19, when
+ # azure.archive.ubuntu.com went dark and the archive.ubuntu.com fallback
+ # stalled part-way through the index fetch -- a step whose healthy cost is
+ # ~35 s sat at 75 minutes. Capping the timeout turns that into a retry.
+ - name: Make apt fail fast on a stalled mirror
+ shell: bash
+ run: |
+ sudo tee /etc/apt/apt.conf.d/99-ci-timeouts > /dev/null <<'EOF'
+ Acquire::Retries "3";
+ Acquire::http::Timeout "20";
+ Acquire::https::Timeout "20";
+ Acquire::ftp::Timeout "20";
+ EOF
+
- name: Set up R
uses: r-lib/actions/setup-r@v2
+ timeout-minutes: 15
+ with:
+ r-version: release
+ extra-repositories: https://ms609.github.io/packages/
- name: Set up R dependencies
uses: r-lib/actions/setup-r-dependencies@v2
@@ -94,20 +165,69 @@ jobs:
- name: Check package
uses: r-lib/actions/check-r-package@v2
+ - name: Notify on failure
+ if: failure() && github.event_name == 'schedule'
+ uses: actions/github-script@v7
+ with:
+ github-token: ${{ secrets.GITHUB_TOKEN }}
+ script: ¬ify |
+ const issue_number = 164;
- check-all:
+ const { data: comments } = await github.rest.issues.listComments({
+ owner: context.repo.owner,
+ repo: context.repo.repo,
+ issue_number: issue_number,
+ per_page: 3
+ });
+
+ const oneHourAgo = new Date(Date.now() - 60 * 60 * 1000);
+ const recentFailureNotified = comments.some(comment =>
+ new Date(comment.created_at) > oneHourAgo &&
+ comment.body.includes('Scheduled workflow has failed')
+ );
+
+ if (recentFailureNotified) {
+ console.log("Recently notified; don't bombard");
+ } else {
+ await github.rest.issues.createComment({
+ owner: context.repo.owner,
+ repo: context.repo.repo,
+ issue_number: issue_number,
+ body: 'Scheduled workflow has failed: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}'
+ });
+
+ await github.rest.issues.update({
+ owner: context.repo.owner,
+ repo: context.repo.repo,
+ issue_number: issue_number,
+ state: 'open'
+ });
+ }
+
+ # ---------------------------------------------------------------------------
+ # Wave 2: Windows (+codecov), R 4.1, R devel. Runs only if the sense-check
+ # passed and codemeta.json is current (or not checked, outside PRs).
+ # Per-leg concurrency so a superseding push cancels in-flight legs.
+ # ---------------------------------------------------------------------------
+ core:
+ needs: [sense-check, codemeta]
+ if: >-
+ !cancelled() && needs.sense-check.result == 'success' &&
+ contains(fromJSON('["success", "skipped"]'), needs.codemeta.result)
runs-on: ${{ matrix.config.os }}
+ timeout-minutes: 60 # healthy run is ~20 min (Windows, with coverage)
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+ concurrency:
+ group: ${{ github.workflow }}-core-${{ matrix.config.os }}-${{ matrix.config.r }}-${{ github.ref }}
+ cancel-in-progress: true
+
strategy:
fail-fast: false
matrix:
config:
- {os: windows-latest, r: "release"}
- - {os: macos-15-intel, r: "release"} # Until Intel architecture retired 2027-11
- - {os: macOS-latest, r: "release"}
- - {os: ubuntu-22.04, r: '4.1', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
- - {os: ubuntu-24.04-arm, r: "release", rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest"}
+ - {os: ubuntu-22.04, r: "4.1", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
- {os: ubuntu-24.04, r: "devel", rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest"}
env:
@@ -118,6 +238,7 @@ jobs:
R_REMOTES_STANDALONE: true
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
R_REALLY_FORCE_SYMBOLS: true # Until R4.3
+ _R_CHECK_CRAN_INCOMING_USE_ASPELL_: false # Set to true when can figure how to install aspell on Windows
RSPM: ${{ matrix.config.rspm }}
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -130,17 +251,28 @@ jobs:
run: |
old_version=$(grep "Version:" DESCRIPTION | awk '{print $2}')
if [[ $(echo "$old_version" | tr -cd '.' | wc -c) -eq 2 ]]; then
- new_version="${old_version}.8888"
- if [[ "$RUNNER_OS" == "macOS" ]]; then
- sed -i "" "s/Version: .*/Version: ${new_version}/" DESCRIPTION
- else
- sed -i "s/Version: .*/Version: ${new_version}/" DESCRIPTION
- fi
+ new_version="${old_version}.9999"
+ sed -i "s/Version: .*/Version: ${new_version}/" DESCRIPTION
fi
+ echo "Current package version is now: $(grep "Version:" DESCRIPTION | awk '{print $2}')"
shell: bash
-
+
+ # See sense-check: without a transfer timeout a stalled apt mirror burns
+ # the job's whole 6-hour budget.
+ - name: Make apt fail fast on a stalled mirror
+ if: runner.os == 'Linux'
+ shell: bash
+ run: |
+ sudo tee /etc/apt/apt.conf.d/99-ci-timeouts > /dev/null <<'EOF'
+ Acquire::Retries "3";
+ Acquire::http::Timeout "20";
+ Acquire::https::Timeout "20";
+ Acquire::ftp::Timeout "20";
+ EOF
+
- name: Set up R
uses: r-lib/actions/setup-r@v2
+ timeout-minutes: 15
with:
r-version: ${{ matrix.config.r }}
extra-repositories: https://ms609.github.io/packages/
@@ -155,7 +287,9 @@ jobs:
needs: |
check
coverage
-
+
+ # Suggests whose current CRAN releases need a newer R than the 4.1 leg
+ # offers are skipped there rather than pinned.
- name: Set up R dependencies (Non-Windows)
if: runner.os != 'Windows'
uses: r-lib/actions/setup-r-dependencies@v2
@@ -173,7 +307,7 @@ jobs:
uwot=?ignore-before-r=4.4.0
needs: |
check
-
+
- name: Check package
uses: r-lib/actions/check-r-package@v2
@@ -187,62 +321,35 @@ jobs:
uses: actions/github-script@v7
with:
github-token: ${{ secrets.GITHUB_TOKEN }}
- script: |
- const issue_number = 164;
-
- const { data: comments } = await github.rest.issues.listComments({
- owner: context.repo.owner,
- repo: context.repo.repo,
- issue_number: issue_number,
- per_page: 3
- });
-
- const oneHourAgo = new Date(Date.now() - 60 * 60 * 1000);
- const recentFailureNotified = comments.some(comment =>
- new Date(comment.created_at) > oneHourAgo &&
- comment.body.includes('Scheduled workflow has failed')
- );
-
- if (recentFailureNotified) {
- console.log("Recently notified; don't bombard");
- } else {
- await github.rest.issues.createComment({
- owner: context.repo.owner,
- repo: context.repo.repo,
- issue_number: issue_number,
- body: 'Scheduled workflow has failed: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}'
- });
-
- await github.rest.issues.update({
- owner: context.repo.owner,
- repo: context.repo.repo,
- issue_number: issue_number,
- state: 'open'
- });
- }
- rev-dep-check:
- runs-on: ubuntu-latest
- needs: check-release
-
- name: revdepcheck
-
- env:
- R_COMPILE_AND_INSTALL_PACKAGES: 'never'
- R_REMOTES_STANDALONE: true
- R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
- GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
- steps:
- - uses: ms609/actions/revdepcheck@main
- with:
- extra-packages: ms609/TreeDistData
-
+ script: *notify
+
+ # ---------------------------------------------------------------------------
+ # Also wave 2: the benchmark comparison, gated on sense-check for the same
+ # reason as `core` -- a tree that does not build cannot be timed, so four
+ # benchmark passes over a broken package only rediscover what the cheap leg
+ # already said. Never runs on push or schedule: outside a PR there is no base
+ # ref to compare against.
+ # ---------------------------------------------------------------------------
benchmark:
+ needs: [sense-check, codemeta]
+ if: >-
+ !cancelled() && needs.sense-check.result == 'success' &&
+ contains(fromJSON('["success", "skipped"]'), needs.codemeta.result) &&
+ (github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch')
runs-on: ubuntu-latest
- needs: check-release
- if: github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
+ # A hung setup or a wedged benchmark otherwise runs to the 6-hour default,
+ # holding a runner the whole time.
+ timeout-minutes: 45
name: benchmark
+ concurrency:
+ group: ${{ github.workflow }}-benchmark-${{ github.ref }}
+ cancel-in-progress: true
+
+ permissions:
+ contents: read
+ pull-requests: write
+
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
RSPM: "https://packagemanager.posit.co/cran/__linux__/noble/latest"
@@ -252,7 +359,7 @@ jobs:
R_REMOTES_STANDALONE: true
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
R_REALLY_FORCE_SYMBOLS: true
- PKG_CXXFLAGS: "-O3"
+ PKG_CXXFLAGS: "-O3" # release-grade optimisation for the compiled kernels
steps:
- name: Checkout PR branch
@@ -266,16 +373,35 @@ jobs:
ref: ${{ github.event.pull_request.base.ref || 'main' }}
path: main
+ # See sense-check: without a transfer timeout a stalled apt mirror burns
+ # the job's whole 6-hour budget.
+ - name: Make apt fail fast on a stalled mirror
+ shell: bash
+ run: |
+ sudo tee /etc/apt/apt.conf.d/99-ci-timeouts > /dev/null <<'EOF'
+ Acquire::Retries "3";
+ Acquire::http::Timeout "20";
+ Acquire::https::Timeout "20";
+ Acquire::ftp::Timeout "20";
+ EOF
+
- name: Set up R
uses: r-lib/actions/setup-r@v2
+ timeout-minutes: 15
with:
extra-repositories: https://ms609.github.io/packages/
+ # A cache of its own: the default key prefix is shared with every
+ # ubuntu/R-release job, so a partial restore can bring back a library
+ # where the package itself is installed, and benchmark-step then refuses
+ # to run.
- name: Install R dependencies
uses: r-lib/actions/setup-r-dependencies@v2
with:
+ working-directory: pr
dependencies: '"hard"'
needs: benchmark
+ cache-version: benchmark
- name: Benchmark PR
uses: ms609/actions/benchmark-step@main
@@ -295,6 +421,15 @@ jobs:
path: pr
output: pr2
+ # Both trees are measured twice, alternating, so the comparison can size
+ # its noise band from replicates of each: a single sample of the target
+ # cannot tell a real change from the runner's between-step drift.
+ - name: Benchmark target again
+ uses: ms609/actions/benchmark-step@main
+ with:
+ path: main
+ output: main2
+
- run: dir pr-benchmark-results
working-directory: pr
- run: dir main-benchmark-results
@@ -323,7 +458,7 @@ jobs:
- name: Comment on PR
if: always() && github.event_name == 'pull_request' && steps.compare_results.outputs.report != ''
- uses: actions/github-script@v7
+ uses: actions/github-script@v9
env:
BENCHMARK_MESSAGE: ${{ steps.compare_results.outputs.report }}
with:
@@ -390,3 +525,191 @@ jobs:
issue_number: context.issue.number,
body: newCommentBody
});
+
+ # ---------------------------------------------------------------------------
+ # Wave 3 (backstop): the expensive, mostly-duplicate-failure legs. Only runs
+ # once the core wave is green, which in practice is "about to merge".
+ # macOS is ~10x runner-minutes, so keeping it off every push is the big save.
+ # ---------------------------------------------------------------------------
+ full:
+ needs: core
+ runs-on: ${{ matrix.config.os }}
+ timeout-minutes: 60 # macOS legs are the slow ones
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ concurrency:
+ group: ${{ github.workflow }}-full-${{ matrix.config.os }}-${{ matrix.config.r }}-${{ github.ref }}
+ cancel-in-progress: true
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-24.04, r: "release", rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest"}
+ - {os: macos-15-intel, r: "release"} # Until Intel architecture retired 2027-11
+ - {os: macOS-latest, r: "release"}
+
+ env:
+ _R_CHECK_CRAN_INCOMING_: ${{ github.event_name == 'pull_request' }}
+ _R_CHECK_FORCE_SUGGESTS_: false # CRAN settings
+ R_COMPILE_AND_INSTALL_PACKAGES: 'never'
+ _R_CHECK_THINGS_IN_CHECK_DIR_: false
+ R_REMOTES_STANDALONE: true
+ R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+ _R_CHECK_CRAN_INCOMING_USE_ASPELL_: false
+ RSPM: ${{ matrix.config.rspm }}
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+ steps:
+ - name: Checkout git repo
+ uses: actions/checkout@v6
+
+ - name: Temporarily bump package version
+ run: |
+ old_version=$(grep "Version:" DESCRIPTION | awk '{print $2}')
+ if [[ $(echo "$old_version" | tr -cd '.' | wc -c) -eq 2 ]]; then
+ new_version="${old_version}.9999"
+ if [[ "$RUNNER_OS" == "macOS" ]]; then
+ sed -i "" "s/Version: .*/Version: ${new_version}/" DESCRIPTION
+ else
+ sed -i "s/Version: .*/Version: ${new_version}/" DESCRIPTION
+ fi
+ fi
+ echo "Current package version is now: $(grep "Version:" DESCRIPTION | awk '{print $2}')"
+ shell: bash
+
+ # See sense-check: without a transfer timeout a stalled apt mirror burns
+ # the job's whole 6-hour budget.
+ - name: Make apt fail fast on a stalled mirror
+ if: runner.os == 'Linux'
+ shell: bash
+ run: |
+ sudo tee /etc/apt/apt.conf.d/99-ci-timeouts > /dev/null <<'EOF'
+ Acquire::Retries "3";
+ Acquire::http::Timeout "20";
+ Acquire::https::Timeout "20";
+ Acquire::ftp::Timeout "20";
+ EOF
+
+ - name: Set up R
+ uses: r-lib/actions/setup-r@v2
+ timeout-minutes: 15
+ with:
+ r-version: ${{ matrix.config.r }}
+ extra-repositories: https://ms609.github.io/packages/
+
+ - name: Set up R dependencies
+ if: runner.os != 'macOS'
+ uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ cache-version: 2-${{ runner.arch }}
+ extra-packages: |
+ ms609/TreeDistData
+ needs: |
+ check
+
+ # Temporary: CRAN's macOS binaries are now partly zstd-compressed, which
+ # pak cannot extract ("unknown archive type"; r-lib/pkgdepends#485,
+ # r-lib/pak#915). Base R's untar() reads zstd, so install through
+ # install.packages() on macOS, and set up the pandoc that
+ # setup-r-dependencies would otherwise provide. Once pak supports zstd,
+ # delete both macOS steps and the `if` on the pak step above.
+ - name: Set up pandoc (macOS, without pak)
+ if: runner.os == 'macOS'
+ uses: r-lib/actions/setup-pandoc@v2
+
+ - name: Set up R dependencies (macOS, without pak)
+ if: runner.os == 'macOS'
+ run: |
+ lib <- Sys.getenv("R_LIBS_USER")
+ dir.create(lib, recursive = TRUE, showWarnings = FALSE)
+ .libPaths(c(lib, .libPaths()))
+
+ # CRAN's own binaries, not P3M's: P3M's macOS build of TreeDist
+ # (needed here by TreeDistData) references libomp's __kmpc_*
+ # symbols without linking libomp, so it fails to load ("symbol not
+ # found in flat namespace '___kmpc_dispatch_init_4'").
+ options(repos = c(CRAN = "https://cloud.r-project.org",
+ ms609 = "https://ms609.github.io/packages/"))
+
+ install.packages(c("remotes", "rcmdcheck"))
+ remotes::install_deps(dependencies = TRUE, upgrade = "never")
+ remotes::install_github("ms609/TreeDistData", upgrade = "never")
+
+ # install.packages() only warns on failure: fail the step instead.
+ deps <- remotes::local_package_deps(dependencies = TRUE)
+ wanted <- c(deps, "rcmdcheck", "TreeDistData")
+ missing <- setdiff(wanted, rownames(installed.packages()))
+ if (length(missing)) {
+ stop("Failed to install: ", paste(missing, collapse = ", "))
+ }
+ shell: Rscript {0}
+
+ - name: Check package
+ uses: r-lib/actions/check-r-package@v2
+
+ - name: Notify on failure
+ if: failure() && github.event_name == 'schedule'
+ uses: actions/github-script@v7
+ with:
+ github-token: ${{ secrets.GITHUB_TOKEN }}
+ script: *notify
+
+ # ---------------------------------------------------------------------------
+ # Reverse-dependency checks: also a wave-3 backstop, gated on core being green.
+ # One leg per dependency type, so a slow Suggests sweep neither blocks nor
+ # masks the hard-dependency results.
+ # ---------------------------------------------------------------------------
+ rev-dep-check:
+ needs: core
+ runs-on: ubuntu-latest
+ timeout-minutes: 120 # revdepchecks are genuinely long
+
+ name: revdepcheck (${{ matrix.config.deps }})
+
+ concurrency:
+ group: ${{ github.workflow }}-revdep-${{ matrix.config.deps }}-${{ github.ref }}
+ cancel-in-progress: true
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {deps: '"Depends"'}
+ - {deps: '"Suggests"'}
+ - {deps: '"Imports"'}
+ - {deps: '"LinkingTo"'}
+
+ env:
+ _R_CHECK_CRAN_INCOMING_: false
+ _R_CHECK_FORCE_SUGGESTS_: false # CRAN settings
+ R_COMPILE_AND_INSTALL_PACKAGES: 'never'
+ _R_CHECK_THINGS_IN_CHECK_DIR_: false
+ R_REMOTES_STANDALONE: true
+ R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+ steps:
+ # See sense-check: without a transfer timeout a stalled apt mirror burns
+ # the job's whole 6-hour budget.
+ - name: Make apt fail fast on a stalled mirror
+ shell: bash
+ run: |
+ sudo tee /etc/apt/apt.conf.d/99-ci-timeouts > /dev/null <<'EOF'
+ Acquire::Retries "3";
+ Acquire::http::Timeout "20";
+ Acquire::https::Timeout "20";
+ Acquire::ftp::Timeout "20";
+ EOF
+
+ - uses: ms609/actions/revdepcheck@main
+ with:
+ deps: ${{ matrix.config.deps }}
+ extra-packages: ms609/TreeDistData
+
+ - name: Notify on failure
+ if: failure() && github.event_name == 'schedule'
+ uses: actions/github-script@v7
+ with:
+ github-token: ${{ secrets.GITHUB_TOKEN }}
+ script: *notify
diff --git a/.github/workflows/RcppDeepState.yml b/.github/workflows/RcppDeepState.yml
index a15b6a79..1e1f354c 100644
--- a/.github/workflows/RcppDeepState.yml
+++ b/.github/workflows/RcppDeepState.yml
@@ -11,8 +11,23 @@ on:
- 'memcheck/**'
- 'tests/testthat/**.R'
- 'vignettes/**.Rmd'
+ pull_request:
+ branches:
+ - main
+ - master
+ paths:
+ - '.github/workflows/RcppDeepState.yml'
+ - 'src/**'
+ - 'inst/include/**'
+ - 'memcheck/**'
+ - 'tests/testthat/**.R'
+ - 'vignettes/**.Rmd'
name: 'RcppDeepState analysis'
+permissions:
+ contents: read
+ pull-requests: write # comment: true posts results to the PR
+
jobs:
RcppDeepState:
runs-on: ubuntu-latest
@@ -21,7 +36,7 @@ jobs:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v6
- uses: FabrizioSandri/RcppDeepState-action@main
with:
diff --git a/.github/workflows/codemeta.yml b/.github/workflows/codemeta.yml
deleted file mode 100644
index 161215cd..00000000
--- a/.github/workflows/codemeta.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-on:
- push:
- branches:
- - main
- - master
- paths:
- - 'DESCRIPTION'
- - '**codemeta.yml'
-
-name: codemeta
-
-jobs:
- codemeta:
- runs-on: ubuntu-latest
- env:
- GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
- steps:
- - uses: ms609/actions/codemeta@main
diff --git a/.github/workflows/copilot-setup-steps.yml b/.github/workflows/copilot-setup-steps.yml
index de903b35..24b421ae 100644
--- a/.github/workflows/copilot-setup-steps.yml
+++ b/.github/workflows/copilot-setup-steps.yml
@@ -14,7 +14,7 @@ on:
jobs:
# The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
copilot-setup-steps:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-24.04-arm
# Set the permissions to the lowest permissions possible needed for your steps.
# Copilot will be given its own token for its operations.
diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml
index dbf58e22..44932b0a 100644
--- a/.github/workflows/memcheck.yml
+++ b/.github/workflows/memcheck.yml
@@ -28,9 +28,13 @@ on:
name: mem-check
+permissions:
+ contents: read
+
jobs:
mem-check:
- runs-on: ubuntu-24.04
+ runs-on: ubuntu-24.04-arm
+ timeout-minutes: 180
name: valgrind ${{ matrix.config.test }}
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
index 85e25ffa..454197e3 100644
--- a/.github/workflows/pkgdown.yml
+++ b/.github/workflows/pkgdown.yml
@@ -22,6 +22,10 @@ name: pkgdown
jobs:
pkgdown:
runs-on: ubuntu-latest
+ timeout-minutes: 60
+
+ permissions:
+ contents: write
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -156,3 +160,60 @@ jobs:
folder: docs
branch: gh-pages
clean: false
+
+ # ── Point /dev/ at the release site once a release is deployed ──
+ - name: Check if release version
+ id: version-check
+ run: |
+ VERSION=$(grep '^Version:' DESCRIPTION | sed 's/Version: *//')
+ # Release = exactly 3 numeric components (e.g. 2.2.0)
+ # Dev = 4+ components (e.g. 2.2.0.9001)
+ if echo "$VERSION" | grep -qE '^[0-9]+\.[0-9]+[.\-][0-9]+$'; then
+ echo "is_release=true" >> "$GITHUB_OUTPUT"
+ echo "Release version: $VERSION"
+ else
+ echo "is_release=false" >> "$GITHUB_OUTPUT"
+ echo "Dev version: $VERSION"
+ fi
+ shell: bash
+
+ - name: Replace dev docs with redirects
+ if: steps.version-check.outputs.is_release == 'true'
+ run: |
+ TMPDIR=$(mktemp -d)
+ git clone --single-branch --branch gh-pages \
+ "https://x-access-token:${GITHUB_PAT}@github.com/${GITHUB_REPOSITORY}.git" \
+ "$TMPDIR"
+ cd "$TMPDIR"
+
+ git config user.email "actions@github.com"
+ git config user.name "GitHub Actions"
+
+ # Remove old dev docs from git
+ git rm -rf dev || true
+
+ # Redirect template: strips /dev/ from the current URL
+ cat > /tmp/redirect.html << 'EOF'
+
+
+
+
+ Redirecting to release documentation…
+
+
+ EOF
+
+ # Create a redirect stub for every HTML page in the release site
+ find . -name '*.html' -not -path './dev/*' -not -path './.git/*' \
+ | while read -r f; do
+ rel="${f#./}"
+ mkdir -p "dev/$(dirname "$rel")"
+ cp /tmp/redirect.html "dev/$rel"
+ done
+
+ git add dev/
+ git commit -m "Replace dev/ docs with redirects to release" || true
+ git push origin gh-pages
+
+ rm -rf "$TMPDIR"
+ shell: bash
diff --git a/.github/workflows/revdepcheck.yml b/.github/workflows/revdepcheck.yml
index 53a46a38..4e9fdeb7 100644
--- a/.github/workflows/revdepcheck.yml
+++ b/.github/workflows/revdepcheck.yml
@@ -4,6 +4,9 @@ name: rev-dep-check
on:
workflow_dispatch:
+permissions:
+ contents: read
+
jobs:
mem-check:
runs-on: ubuntu-latest
diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
index e3fa9124..b10fe0af 100644
--- a/.github/workflows/rhub.yaml
+++ b/.github/workflows/rhub.yaml
@@ -25,6 +25,9 @@ on:
description: 'Run name (optional)'
type: string
+permissions:
+ contents: read
+
jobs:
setup:
diff --git a/.github/workflows/update-csl.yml b/.github/workflows/update-csl.yml
index baac81b6..24e8878b 100644
--- a/.github/workflows/update-csl.yml
+++ b/.github/workflows/update-csl.yml
@@ -9,9 +9,12 @@ on:
paths:
- '.github/workflows/update-csl.yml'
+permissions:
+ contents: write # pushes the refreshed CSL file
+
jobs:
update-csl:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-24.04-arm
steps:
- uses: actions/checkout@v6
diff --git a/.github/workflows/wasm-build.yml b/.github/workflows/wasm-build.yml
index 76a6f441..d0d73691 100644
--- a/.github/workflows/wasm-build.yml
+++ b/.github/workflows/wasm-build.yml
@@ -29,6 +29,9 @@ on:
description: "Comma-separated packages to build (deps resolved automatically)"
default: "fastmatch"
+permissions:
+ contents: read
+
jobs:
build:
runs-on: ubuntu-latest
diff --git a/DESCRIPTION b/DESCRIPTION
index c23b529c..a69a6da9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -83,6 +83,7 @@ LinkingTo:
RdMacros: Rdpack
VignetteBuilder: knitr
Config/Needs/app/optional: uwot
+Config/Needs/benchmark: bench, phangorn, testthat
Config/Needs/check: rcmdcheck
Config/Needs/coverage: covr
Config/Needs/memcheck: pkgdown, testthat
diff --git a/benchmark/_compare_results.R b/benchmark/_compare_results.R
index 21e0b736..2cb48c10 100644
--- a/benchmark/_compare_results.R
+++ b/benchmark/_compare_results.R
@@ -5,7 +5,7 @@ output <- paste0(
"report< min_meaningful_diff &&
+ median_pr < median_main - 2 * noise
+
is_slower <- matched &&
- median_pr > median_main + 2 * mad_main &&
- median_pr > noise_range[[2]]
+ abs_diff > min_meaningful_diff &&
+ median_pr > median_main + 2 * noise
report[[fn_name]] <- list(
matched = matched,
@@ -66,6 +86,8 @@ for (pr_file in pr_files) {
median_pr = median(pr1_times),
median_cf = median(pr2_times),
median_main = median_main,
+ median_main1 = median(main1_times),
+ median_main2 = median(main2_times),
change = percentage_change
)
}
@@ -73,25 +95,28 @@ for (pr_file in pr_files) {
# Create a markdown-formatted message
has_significant_regression <- FALSE
- for (fn_name in names(report)) {
- res <- report[[fn_name]]
- status <- if (res$matched) {
+ for (i in seq_along(report)) {
+ fn_name <- names(report)[[i]]
+ res <- report[[i]]
+ if (is.null(res) || is.null(res$matched)) next
+
+ status <- if (isTRUE(res$matched)) {
if (res$slower) {
- if (abs(percentage_change) > threshold_percent) {
+ if (abs(res$change) > threshold_percent) {
has_significant_regression <- TRUE
"\U1F7E0 Slower \U1F641"
} else {
"\U1F7E3 ~same"
}
} else if (res$faster) {
- if (abs(percentage_change) > threshold_percent) {
+ if (abs(res$change) > threshold_percent) {
"\U1F7E2 Faster!"
} else {
"\U1F7E3 ~same"
}
} else {
"\U26AA NSD"
- }
+ }
} else {
"\U1F7E4 ?Mismatch"
}
@@ -100,19 +125,20 @@ for (pr_file in pr_files) {
message <- paste0(
"| `", fn_name, "` | ", status, " | ",
- bold, round(res$change, 2), "%", bold, " | ",
- signif(res$median_main * 1e3, 3), " \u2192
",
+ bold, round(res$change, 2), "%", bold, " | ",
+ signif(res$median_main1 * 1e3, 3), ", ",
+ signif(res$median_main2 * 1e3, 3), " \u2192
",
signif(res$median_pr * 1e3, 3), ", ",
signif(res$median_cf * 1e3, 3), " |\n"
)
+
+ cat(message)
+ output <- paste0(output, message)
}
if (has_significant_regression) {
regressions <- TRUE
}
-
- cat(message)
- output <- paste0(output, message)
}
cat(paste0(output, "\nEOF"), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
diff --git a/codemeta.json b/codemeta.json
index 2c7972c7..5af80745 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -14,7 +14,6 @@
"name": "R",
"url": "https://r-project.org"
},
- "runtimePlatform": "R version 4.6.1 (2026-06-24)",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
@@ -397,19 +396,19 @@
"sameAs": "https://CRAN.R-project.org/package=withr"
}
],
- "softwareRequirements": {
- "1": {
+ "softwareRequirements": [
+ {
"@type": "SoftwareApplication",
"identifier": "R",
"name": "R",
"version": ">= 4.0"
},
- "2": {
+ {
"@type": "SoftwareApplication",
"identifier": "stats",
"name": "stats"
},
- "3": {
+ {
"@type": "SoftwareApplication",
"identifier": "ape",
"name": "ape",
@@ -422,7 +421,7 @@
},
"sameAs": "https://CRAN.R-project.org/package=ape"
},
- "4": {
+ {
"@type": "SoftwareApplication",
"identifier": "cli",
"name": "cli",
@@ -435,7 +434,7 @@
},
"sameAs": "https://CRAN.R-project.org/package=cli"
},
- "5": {
+ {
"@type": "SoftwareApplication",
"identifier": "Rdpack",
"name": "Rdpack",
@@ -448,7 +447,7 @@
},
"sameAs": "https://CRAN.R-project.org/package=Rdpack"
},
- "6": {
+ {
"@type": "SoftwareApplication",
"identifier": "shiny",
"name": "shiny",
@@ -460,7 +459,7 @@
},
"sameAs": "https://CRAN.R-project.org/package=shiny"
},
- "7": {
+ {
"@type": "SoftwareApplication",
"identifier": "shinyjs",
"name": "shinyjs",
@@ -472,7 +471,7 @@
},
"sameAs": "https://CRAN.R-project.org/package=shinyjs"
},
- "8": {
+ {
"@type": "SoftwareApplication",
"identifier": "TreeTools",
"name": "TreeTools",
@@ -485,10 +484,12 @@
},
"sameAs": "https://CRAN.R-project.org/package=TreeTools"
},
- "SystemRequirements": "C++17, pandoc-citeproc"
- },
- "keywords": ["phylogenetics", "tree-distance"],
- "fileSize": "2086.252KB",
+ "C++17, pandoc-citeproc"
+ ],
+ "keywords": [
+ "phylogenetics",
+ "tree-distance"
+ ],
"citation": [
{
"@type": "ScholarlyArticle",
@@ -496,7 +497,10 @@
"author": [
{
"@type": "Person",
- "givenName": ["Martin", "R."],
+ "givenName": [
+ "Martin",
+ "R."
+ ],
"familyName": "Smith",
"email": "martin.smith@durham.ac.uk"
}
@@ -511,7 +515,10 @@
"issueNumber": "20",
"datePublished": "2020",
"isPartOf": {
- "@type": ["PublicationVolume", "Periodical"],
+ "@type": [
+ "PublicationVolume",
+ "Periodical"
+ ],
"volumeNumber": "36",
"name": "Bioinformatics"
}
@@ -523,7 +530,10 @@
"author": [
{
"@type": "Person",
- "givenName": ["Martin", "R."],
+ "givenName": [
+ "Martin",
+ "R."
+ ],
"familyName": "Smith",
"email": "martin.smith@durham.ac.uk"
}
@@ -538,7 +548,10 @@
"issueNumber": "5",
"datePublished": "2022",
"isPartOf": {
- "@type": ["PublicationVolume", "Periodical"],
+ "@type": [
+ "PublicationVolume",
+ "Periodical"
+ ],
"volumeNumber": "71",
"name": "Systematic Biology"
}
@@ -550,7 +563,10 @@
"author": [
{
"@type": "Person",
- "givenName": ["Martin", "R."],
+ "givenName": [
+ "Martin",
+ "R."
+ ],
"familyName": "Smith",
"email": "martin.smith@durham.ac.uk"
}
@@ -563,7 +579,10 @@
"@type": "PublicationIssue",
"datePublished": "2020",
"isPartOf": {
- "@type": ["PublicationVolume", "Periodical"],
+ "@type": [
+ "PublicationVolume",
+ "Periodical"
+ ],
"name": "Comprehensive R Archive Network"
}
}
diff --git a/tests/testthat/test-tree_distance_spr.R b/tests/testthat/test-tree_distance_spr.R
index ff0a3ee8..1a2ffc9d 100644
--- a/tests/testthat/test-tree_distance_spr.R
+++ b/tests/testthat/test-tree_distance_spr.R
@@ -177,7 +177,13 @@ test_that("SPR shortcuts okay - larger trees", {
test_that("SPR calculated correctly", {
library("TreeTools", quietly = TRUE)
+ # Compares against TBRDist's exact uSPR distance, when available (Suggests);
+ # the fixed-value expectations below run regardless.
+ haveTBRDist <- requireNamespace("TBRDist", quietly = TRUE)
expect_exact <- function(x, y, method = "rogue") {
+ if (!haveTBRDist) {
+ return(invisible())
+ }
if (is.character(x)) x <- Tree(x)
if (is.character(y)) y <- Tree(y)
expect_equal(
@@ -204,9 +210,11 @@ test_that("SPR calculated correctly", {
expect_exact("(a,(d,(b,(c,X))));", "(a,((b,c),(X,d)));", "rogue") # distance = 1
expect_exact("((((b,c),d),e),a);", "(a,(b,((e,c),d)));", "rogue")
- expect_failure(
- expect_exact("((((b,c),d),e),a);", "(a,(b,((e,c),d)));", "deo")
- )
+ if (haveTBRDist) {
+ expect_failure(
+ expect_exact("((((b,c),d),e),a);", "(a,(b,((e,c),d)));", "deo")
+ )
+ }
# Passes with ami, joint, vi
# Fails with viNorm - should tiebreaker be non-normalized?