OMOP/.github/workflows/R_CMD_check.yaml

129 lines
4.7 KiB
YAML

# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
on:
push:
branches:
- '**'
pull_request:
branches:
- '**'
name: R-CMD-check
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
# Test create and drop tables in a database so they cannot be executed in parallel
max-parallel: 1
fail-fast: false
matrix:
config:
- {os: macOS-latest, r: 'release'}
- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: windows-latest, r: 'release'} # Does not appear to have Java 32-bit, hence the --no-multiarch
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
CDMDDLBASE_POSTGRESQL_USER: ${{ secrets.CDMDDLBASE_POSTGRESQL_USER }}
CDMDDLBASE_POSTGRESQL_PASSWORD: ${{ secrets.CDMDDLBASE_POSTGRESQL_PASSWORD }}
CDMDDLBASE_POSTGRESQL_SERVER: ${{ secrets.CDMDDLBASE_POSTGRESQL_SERVER }}
CDMDDLBASE_POSTGRESQL_SCHEMA: ${{ secrets.CDMDDLBASE_POSTGRESQL_SCHEMA }}
CDMDDLBASE_REDSHIFT_USER: ${{ secrets.CDMDDLBASE_REDSHIFT_USER }}
CDMDDLBASE_REDSHIFT_PASSWORD: ${{ secrets.CDMDDLBASE_REDSHIFT_PASSWORD }}
CDMDDLBASE_REDSHIFT_SERVER: ${{ secrets.CDMDDLBASE_REDSHIFT_SERVER }}
CDMDDLBASE_REDSHIFT_SCHEMA: ${{ secrets.CDMDDLBASE_REDSHIFT_SCHEMA }}
CDMDDLBASE_SQL_SERVER_USER: ${{ secrets.CDMDDLBASE_SQL_SERVER_USER }}
CDMDDLBASE_SQL_SERVER_PASSWORD: ${{ secrets.CDMDDLBASE_SQL_SERVER_PASSWORD }}
CDMDDLBASE_SQL_SERVER_SERVER: ${{ secrets.CDMDDLBASE_SQL_SERVER_SERVER }}
CDMDDLBASE_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_SQL_SERVER_CDM_SCHEMA }}
CDMDDLBASE_ORACLE_USER: ${{ secrets.CDMDDLBASE_ORACLE_USER }}
CDMDDLBASE_ORACLE_PASSWORD: ${{ secrets.CDMDDLBASE_ORACLE_PASSWORD }}
CDMDDLBASE_ORACLE_SERVER: ${{ secrets.CDMDDLBASE_ORACLE_SERVER }}
CDMDDLBASE_ORACLE_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_ORACLE_CDM_SCHEMA }}
steps:
- uses: actions/checkout@v4
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-tinytex@v2
- uses: r-lib/actions/setup-pandoc@v2
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v3.3.1
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
- name: Install system dependencies
if: runner.os == 'Linux'
run: |
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
- name: Install libssh
if: runner.os == 'Linux'
run: |
sudo apt-get install libssh-dev
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
remotes::install_cran("rcmdcheck")
shell: Rscript {0}
- name: Install covr
if: runner.os == 'macOS'
run: |
remotes::install_cran("covr")
shell: Rscript {0}
- name: Remove check folder if exists
if: runner.os == 'macOS'
run: unlink("check", recursive = TRUE)
shell: Rscript {0}
- name: Check
env:
_R_CHECK_CRAN_INCOMING_REMOTE_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
- name: Upload check results
if: failure()
uses: actions/upload-artifact@v2
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
- name: Upload source package
if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/master'
uses: actions/upload-artifact@v2
with:
name: package_tarball
path: check/*.tar.gz
- name: Test coverage
if: runner.os == 'macOS'
run: covr::codecov()
shell: Rscript {0}