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R_CMD_check_Hades.yaml
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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: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
# - {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
# - {os: ubuntu-20.04, r: 'release', rtools: '', 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_CDM54_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_CDM54_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_CDM54_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_CDM54_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 }}
#
# 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
# 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")'
# error-on: '"warning"'
# check-dir: '"check"'
#
# - name: Upload source package
# if: success() && runner.os == 'Windows' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
# uses: actions/upload-artifact@v4
# with:
# name: package_tarball
# path: check/*.tar.gz
#
# - name: Install covr
# if: runner.os == 'Linux'
# run: |
# install.packages("covr")
# shell: Rscript {0}
#
# - name: Test coverage
# if: runner.os == 'Linux'
# run: covr::codecov()
# shell: Rscript {0}
#
# Release:
# needs: R-CMD-Check
#
# runs-on: macOS-latest
#
# env:
# GH_TOKEN: ${{ secrets.GH_TOKEN }}
#
# if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }}
#
# steps:
#
# - uses: actions/checkout@v2
# with:
# fetch-depth: 0
#
# - name: Check if version has increased
# run: |
# echo "new_version="$(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
#
# # AGS: Commenting out until Strategus is in HADES
# # - 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@v4
# # 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/
# #