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backends odbc

backends odbc #1642

Workflow file for this run

# Adapted from backends.yaml, with contents from odbc/db.yaml
on:
push:
branches:
- main
- master
pull_request:
branches:
- main
- master
schedule:
- cron: '0 8 * * *'
name: backends odbc
jobs:
matrix:
runs-on: ubuntu-latest
outputs:
matrix: ${{ steps.set-matrix.outputs.matrix }}
steps:
- uses: actions/checkout@v3
# https://github.blog/changelog/2020-04-15-github-actions-new-workflow-features/
- id: set-matrix
run: |
matrix=$((
echo '{ "include" : ['
sed -n "/^REVDEP *:= */ { s///; p }" revdep-dev/Makefile | sed 's/ /,\n/g' | grep odbc | sed -r 's/^odbc-([^,]*)(,?)$/{ "database": "\1", "package": "odbc" }\2/'
echo " ]}"
) | jq -c .)
echo $matrix
echo $matrix | jq .
echo "matrix=$matrix" >> $GITHUB_OUTPUT
check-matrix:
runs-on: ubuntu-latest
needs: matrix
steps:
- name: Install json2yaml
run: |
sudo npm install -g json2yaml
- name: Check matrix definition
run: |
matrix='${{ needs.matrix.outputs.matrix }}'
echo $matrix
echo $matrix | jq .
echo $matrix | json2yaml
backend:
needs: matrix
# Need Ubuntu 20.04 for remotes::system_requirements()
runs-on: ubuntu-20.04
services:
postgres:
image: postgres
ports:
- 5432:5432
env:
POSTGRES_USER: postgres
POSTGRES_PASSWORD: password
POSTGRES_DB: test
options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
sqlserver:
image: mcr.microsoft.com/mssql/server:2017-latest-ubuntu
ports:
- 1433:1433
env:
ACCEPT_EULA: Y
SA_PASSWORD: Password12
strategy:
fail-fast: false
matrix: ${{fromJson(needs.matrix.outputs.matrix)}}
name: ${{ matrix.database }}
env:
RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
ODBCSYSINI: ${{ github.workspace }}/.github/odbc
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: Check rate limits
run: |
curl -s --header "authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" https://api.github.com/rate_limit
shell: bash
- uses: actions/checkout@v3
- uses: ./.github/workflows/install
with:
install-r: false
cache-version: backends-${{ matrix.package }}
needs: check
extra-packages: "any::pkgbuild any::remotes decor ."
token: ${{ secrets.GITHUB_TOKEN }}
- name: Clone backend
run: |
make -C revdep-dev ${{ matrix.package }}
- name: Install system dependencies
if: runner.os == 'Linux'
# "22.04" fails here
run: |
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04", path = "revdep-dev/${{ matrix.package }}"))')
- name: Install package and dependencies
run: |
remotes::install_local("revdep-dev/${{ matrix.package }}", dependencies = TRUE, type = .Platform$pkgType)
remotes::install_local(".", type = .Platform$pkgType, force = TRUE)
shell: Rscript {0}
- name: Session info
run: |
options(width = 100)
if (!requireNamespace("sessioninfo", quietly = TRUE)) install.packages("sessioninfo")
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
# Begin custom: after install
- name: Setup MySQL
if: matrix.database == 'mysql'
run: |
sudo systemctl start mysql.service
mysql -uroot -h127.0.0.1 -proot -e 'CREATE DATABASE `test`;'
.github/odbc/install-mariadb-driver.sh
- name: Install SQLite Driver
if: matrix.database == 'sqlite'
run: |
sudo apt-get install -y libsqliteodbc
- name: Install PostgreSQL Driver
if: matrix.database == 'postgres'
run: |
sudo apt-get install -y unixodbc-dev odbc-postgresql devscripts
- name: Install SQL Server Driver
if: matrix.database == 'sql-server'
run: |
curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
curl https://packages.microsoft.com/config/ubuntu/20.04/prod.list > /etc/apt/sources.list.d/mssql-release.list
apt-get update
ACCEPT_EULA=Y apt-get install -y msodbcsql17
ln -s /opt/microsoft/msodbcsql17/lib64/libmsodbcsql-17.*.so.* /opt/microsoft/msodbcsql17/lib64/libmsodbcsql-17.so
shell: sudo bash {0}
- name: Install locally to avoid error with test_local()
run: |
R CMD INSTALL revdep-dev/${{ matrix.package }}
env:
LIB_DIR: /usr/lib/x86_64-linux-gnu/
INCLUDE_DIR: /usr/include
# End custom: after install
- name: Test backend
run: |
make -C revdep-dev test-${{ matrix.package }}-${{ matrix.database }}
- name: Upload check results
if: failure()
uses: actions/upload-artifact@main
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: revdep-dev/${{ matrix.package }}
- name: Check rate limits
if: always()
run: |
curl -s --header "authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" https://api.github.com/rate_limit
shell: bash