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version bump 1.29.4

version bump 1.29.4 #8

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: devel
name: test-coverage
jobs:
test-coverage:
runs-on: ubuntu-22.04
container: bioconductor/bioconductor_docker:devel
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: Checkout Repository
uses: actions/checkout@v3
- name: Query dependencies
run: |
BiocManager::install(c("remotes", "covr"))
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v1
with:
path: /usr/local/lib/R/site-library
key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-r-1-
- name: Install Dependencies
run: |
remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install("rcmdcheck", ask = FALSE, update = TRUE)
shell: Rscript {0}
- name: Check Package
env:
_R_CHECK_CRAN_INCOMING_REMOTE_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")
shell: Rscript {0}
- name: Test coverage
run: |
covr::codecov(
quiet = FALSE,
clean = FALSE,
install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
)
shell: Rscript {0}
- name: Show testthat output
if: always()
run: |
## --------------------------------------------------------------------
find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload test results
if: failure()
uses: actions/upload-artifact@v3
with:
name: coverage-test-failures
path: ${{ runner.temp }}/package