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‎.github/workflows/rhub.yaml‎

Lines changed: 157 additions & 108 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,22 @@
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name: Minimal Sanitizer Checks
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# R-hub's sanitizer checks with custom test integration
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# Skips vignette building to avoid pandoc-citeproc issues
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name: R-hub Sanitizer Checks
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run-name: "${{ github.event.inputs.id || 'Sanitizer checks' }}: ${{ github.event.inputs.name || github.event.head_commit.message || github.event.pull_request.title || format('triggered by {0}', github.triggering_actor) }}"
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on:
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workflow_dispatch:
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inputs:
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config:
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description: 'Sanitizer configurations'
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type: string
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default: 'clang-asan,clang-ubsan,valgrind'
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name:
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description: 'Custom run name'
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type: string
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id:
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description: 'Custom run ID'
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type: string
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push:
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branches: [main]
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pull_request:
@@ -9,144 +25,177 @@ on:
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permissions: read-all
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jobs:
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setup:
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runs-on: ubuntu-latest
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outputs:
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containers: ${{ steps.rhub-setup.outputs.containers }}
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steps:
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- uses: r-hub/actions/setup@v1
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with:
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config: ${{ github.event.inputs.config || 'clang-asan,clang-ubsan,valgrind' }}
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id: rhub-setup
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sanitizer-checks:
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needs: setup
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if: ${{ needs.setup.outputs.containers != '[]' }}
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runs-on: ubuntu-latest
14-
name: "${{ matrix.config.name }}"
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name: "${{ matrix.config.label }}"
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strategy:
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fail-fast: false
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matrix:
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config:
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- {name: 'Clang-ASAN', container: 'ghcr.io/r-hub/containers/clang-asan:latest', check_args: '--no-manual --no-vignettes --no-build-vignettes'}
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- {name: 'Clang-UBSAN', container: 'ghcr.io/r-hub/containers/clang-ubsan:latest', check_args: '--no-manual --no-vignettes --no-build-vignettes'}
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config: ${{ fromJson(needs.setup.outputs.containers) }}
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container:
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image: ${{ matrix.config.container }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
29-
_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_FORCE_SUGGESTS_: false
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R_BUILD_ARGS: "--no-manual --no-vignettes"
32-
R_CHECK_ARGS: "${{ matrix.config.check_args }}"
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_R_CHECK_CRAN_INCOMING_: false
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# Skip vignettes
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R_BUILD_ARGS: "--no-manual --no-build-vignettes"
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R_CHECK_ARGS: "--no-manual --no-vignettes --no-build-vignettes"
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steps:
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- uses: actions/checkout@v4
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- uses: r-hub/actions/checkout@v1
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37-
- name: Install system dependencies
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- uses: r-hub/actions/platform-info@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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# Setup dependencies but skip vignette-related packages
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- uses: r-hub/actions/setup-deps@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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extra-packages: |
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any::testthat
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any::pak
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needs: |
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testthat
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- name: Remove vignettes to prevent build issues
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run: |
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# Update package list
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apt-get update || true
41-
42-
# Install minimal dependencies needed for R packages
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apt-get install -y --no-install-recommends \
44-
libcurl4-openssl-dev \
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libssl-dev \
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libxml2-dev \
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libgit2-dev || true
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# Remove vignettes directory to ensure they're not built
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if [ -d "vignettes" ]; then
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echo "Removing vignettes directory"
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rm -rf vignettes
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fi
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if [ -d "cpp11armadillotest/vignettes" ]; then
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echo "Removing cpp11armadillotest/vignettes directory"
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rm -rf cpp11armadillotest/vignettes
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fi
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shell: bash
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- name: Install R dependencies
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- name: Install cpp11armadillotest with tests
5095
run: |
51-
# Install essential packages
52-
install.packages(c("remotes", "rcmdcheck", "testthat"))
53-
54-
# Install package dependencies
55-
remotes::install_deps(".", dependencies = TRUE, upgrade = "never")
56-
57-
# Install cpp11armadillotest dependencies if it exists
5896
if (dir.exists("cpp11armadillotest")) {
59-
remotes::install_deps("cpp11armadillotest", dependencies = TRUE, upgrade = "never")
97+
cat("Installing cpp11armadillotest dependencies\n")
98+
# Use pak which should be available from setup-deps
99+
if (requireNamespace("pak", quietly = TRUE)) {
100+
pak::local_install_deps("cpp11armadillotest", upgrade = FALSE)
101+
}
102+
103+
cat("Building and installing cpp11armadillotest with tests\n")
104+
# Build without vignettes
105+
system("R CMD build --no-build-vignettes --no-manual cpp11armadillotest")
106+
107+
# Find the built package
108+
tarball <- list.files(pattern = "^cpp11armadillotest.*\\.tar\\.gz$", full.names = TRUE)[1]
109+
if (!is.na(tarball) && file.exists(tarball)) {
110+
install.packages(tarball, repos = NULL, type = "source", INSTALL_opts = "--install-tests")
111+
cat("cpp11armadillotest installed successfully\n")
112+
} else {
113+
cat("Could not find cpp11armadillotest tarball\n")
114+
}
60115
}
61116
shell: Rscript {0}
62-
63-
- name: Build and install main package (no vignettes)
64-
run: |
65-
R CMD build --no-build-vignettes --no-manual .
66-
R CMD INSTALL *.tar.gz
67-
68-
- name: Build and install cpp11armadillotest (no vignettes)
69-
run: |
70-
if [ -d "cpp11armadillotest" ]; then
71-
R CMD build --no-build-vignettes --no-manual cpp11armadillotest
72-
R CMD INSTALL --install-tests cpp11armadillotest*.tar.gz
73-
fi
74-
75-
- name: Run R CMD check (no vignettes)
76-
run: |
77-
# Get the package tarball name
78-
PKG_TARBALL=$(ls -1 *.tar.gz | grep -v cpp11armadillotest | head -n 1)
79-
echo "Checking package: $PKG_TARBALL"
117+
118+
# Run check without vignettes
119+
- uses: r-hub/actions/run-check@v1
120+
with:
121+
token: ${{ secrets.RHUB_TOKEN }}
122+
job-config: ${{ matrix.config.job-config }}
123+
args: 'c("--no-manual", "--no-vignettes", "--no-build-vignettes")'
124+
build_args: 'c("--no-manual", "--no-build-vignettes")'
80125

81-
# Run R CMD check with sanitizers
82-
R CMD check ${{ matrix.config.check_args }} "$PKG_TARBALL"
83-
84126
- name: Run cpp11armadillotest tests with sanitizers
85127
if: always()
86128
run: |
87-
Rscript -e '
88-
if (dir.exists("cpp11armadillotest/tests") && requireNamespace("cpp11armadillotest", quietly = TRUE)) {
89-
cat("\n=== Running cpp11armadillotest tests with sanitizers ===\n")
90-
library(testthat)
91-
library(cpp11armadillotest)
92-
93-
# Set working directory
94-
old_wd <- getwd()
95-
setwd("cpp11armadillotest/tests")
96-
97-
# Run tests
98-
tryCatch({
99-
test_results <- test_check("cpp11armadillotest", reporter = "progress")
100-
print(test_results)
101-
102-
# Check for failures
103-
if (any(as.data.frame(test_results)$failed > 0)) {
104-
stop("Tests failed under sanitizers")
105-
}
106-
}, error = function(e) {
107-
cat("Error: ", conditionMessage(e), "\n")
108-
stop(e)
109-
}, finally = {
110-
setwd(old_wd)
111-
})
112-
} else {
113-
cat("cpp11armadillotest not found or not installed\n")
129+
cat("\n=== Running cpp11armadillotest tests ===\n")
130+
131+
# Check if package and tests exist
132+
if (!requireNamespace("cpp11armadillotest", quietly = TRUE)) {
133+
cat("cpp11armadillotest package not installed\n")
134+
quit(status = 0)
135+
}
136+
137+
if (!dir.exists("cpp11armadillotest/tests")) {
138+
cat("cpp11armadillotest/tests directory not found\n")
139+
quit(status = 0)
140+
}
141+
142+
# Load required packages
143+
library(testthat)
144+
library(cpp11armadillotest)
145+
146+
# Run tests
147+
old_wd <- getwd()
148+
setwd("cpp11armadillotest/tests")
149+
150+
test_results <- tryCatch({
151+
test_check("cpp11armadillotest", reporter = "progress")
152+
}, error = function(e) {
153+
cat("Error running tests: ", conditionMessage(e), "\n")
154+
NULL
155+
})
156+
157+
setwd(old_wd)
158+
159+
# Check results
160+
if (!is.null(test_results)) {
161+
print(test_results)
162+
failures <- sum(as.data.frame(test_results)$failed)
163+
if (failures > 0) {
164+
cat(sprintf("\n%d test(s) failed under %s\n", failures, "${{ matrix.config.label }}"))
165+
quit(status = 1)
114166
}
115-
'
167+
}
168+
shell: Rscript {0}
116169

117-
- name: Show sanitizer output
170+
- name: Show sanitizer results
118171
if: always()
119172
run: |
120-
# Find and display any sanitizer output
121-
echo "=== Looking for sanitizer output ==="
122-
find . -name "*.Rcheck" -type d -exec sh -c '
123-
echo "=== Check directory: {} ==="
124-
find {} -name "*.Rout" -o -name "*.Rout.fail" | while read f; do
125-
if grep -E "(AddressSanitizer|UndefinedBehaviorSanitizer|ERROR: LeakSanitizer|valgrind)" "$f" >/dev/null 2>&1; then
126-
echo "=== Sanitizer output in $f ==="
127-
cat "$f"
173+
echo "=== Searching for sanitizer output ==="
174+
175+
# Function to check files for sanitizer output
176+
check_sanitizer_output() {
177+
local file="$1"
178+
if [ -f "$file" ]; then
179+
if grep -E "(AddressSanitizer|UndefinedBehaviorSanitizer|ERROR: LeakSanitizer|==ERROR==|runtime error:|attempting free on address|memcheck)" "$file" >/dev/null 2>&1; then
180+
echo "=== Sanitizer output found in $file ==="
181+
grep -E "(AddressSanitizer|UndefinedBehaviorSanitizer|ERROR: LeakSanitizer|==ERROR==|runtime error:|attempting free on address|memcheck)" "$file" -A 5 -B 5
128182
fi
129-
done
130-
' \;
183+
fi
184+
}
131185
132-
# Also check test output
133-
if [ -f "cpp11armadillotest.Rcheck/tests/testthat.Rout" ]; then
134-
echo "=== Test output ==="
135-
cat "cpp11armadillotest.Rcheck/tests/testthat.Rout"
136-
fi
186+
# Check R CMD check output
187+
find . -name "*.Rcheck" -type d | while read checkdir; do
188+
echo "Checking $checkdir"
189+
find "$checkdir" -name "*.Rout" -o -name "*.Rout.fail" -o -name "*.log" | while read f; do
190+
check_sanitizer_output "$f"
191+
done
192+
done
137193
138-
# Check for core dumps
139-
if ls core* 1> /dev/null 2>&1; then
140-
echo "=== Core dumps found ==="
141-
ls -la core*
142-
fi
143-
144-
- name: Upload check results
145-
if: failure()
146-
uses: actions/upload-artifact@v4
147-
with:
148-
name: ${{ matrix.config.name }}-results
149-
path: |
150-
*.Rcheck/
151-
*.tar.gz
152-
194+
# Check test output specifically
195+
for f in cpp11armadillo.Rcheck/tests/testthat.Rout cpp11armadillotest.Rcheck/tests/testthat.Rout; do
196+
if [ -f "$f" ]; then
197+
echo "=== Test output from $f ==="
198+
cat "$f"
199+
fi
200+
done
201+

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