Capr v2.0.6 release candidate. #179
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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'} # Does not appear to have Java 32-bit, hence the --no-multiarch | |
- {os: macOS-latest, r: 'release'} | |
- {os: ubuntu-20.04, r: 'release', 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 }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: r-lib/actions/setup-r@v2 | |
with: | |
r-version: ${{ matrix.config.r }} | |
use-public-rspm: true | |
- uses: r-lib/actions/setup-tinytex@v2 | |
- uses: r-lib/actions/setup-pandoc@v2 | |
- name: Query dependencies | |
run: | | |
install.packages('remotes') | |
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
shell: Rscript {0} | |
- name: Cache R packages | |
if: runner.os != 'Windows' | |
uses: actions/cache@v2 | |
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: | | |
install.packages("curl") | |
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/main' | |
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} | |
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/ |