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R_CMD_check_Hades.yml
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# 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:
fail-fast: false
matrix:
config:
- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: windows-latest, r: '4.2.3'}
- {os: macOS-latest, r: '4.2.3'}
- {os: ubuntu-20.04, r: '4.2.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
env:
GITHUB_PAT: ${{ secrets.GH_TOKEN }}
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }}
WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }}
WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }}
WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }}
steps:
- uses: actions/checkout@v3
- 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: Install system requirements
if: runner.os == 'Linux'
run: |
sudo apt-get install -y libssh-dev
Rscript -e 'install.packages("remotes")'
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
needs: check
- uses: r-lib/actions/check-r-package@v2
with:
args: 'c("--no-manual", "--as-cran")'
build_args: 'c("--compact-vignettes=both")'
error-on: '"warning"'
check-dir: '"check"'
- name: Upload source package
if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main' && matrix.config.r == 'release'
uses: actions/upload-artifact@v2
with:
name: package_tarball
path: check/*.tar.gz
- name: Install covr
if: runner.os == 'macOS' && matrix.config.r == 'release'
run: |
install.packages("covr")
shell: Rscript {0}
- name: Test coverage
if: runner.os == 'macOS' && matrix.config.r == 'release'
run: covr::codecov()
shell: Rscript {0}
Release:
needs: R-CMD-Check
runs-on: macOS-latest
env:
GH_TOKEN: ${{ secrets.GH_TOKEN }}
if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }}
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Check if version has increased
run: |
echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV
- name: Display new version number
if: ${{ env.new_version != '' }}
run: |
echo "${{ env.new_version }}"
- name: Create release
if: ${{ env.new_version != '' }}
uses: actions/create-release@v1
env:
GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
with:
tag_name: ${{ env.new_version }}
release_name: Release ${{ env.new_version }}
body: |
See NEWS.md for release notes.
draft: false
prerelease: false
- uses: r-lib/actions/setup-r@v2
if: ${{ env.new_version != '' }}
- name: Install drat
if: ${{ env.new_version != '' }}
run: |
install.packages('drat')
shell: Rscript {0}
- name: Remove any tarballs that already exists
if: ${{ env.new_version != '' }}
run: |
rm -f *.tar.gz
- name: Download package tarball
if: ${{ env.new_version != '' }}
uses: actions/download-artifact@v2
with:
name: package_tarball
- name: Push to drat
if: ${{ env.new_version != '' }}
run: |
bash deploy.sh
- name: Push to BroadSea
if: ${{ env.new_version != '' }}
run: |
curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/