.gitlab-ci.yml

# This file is a template, and might need editing before it works on your project.
# This is a sample GitLab CI/CD configuration file that should run without any modifications.
# It demonstrates a basic 3 stage CI/CD pipeline. Instead of real tests or scripts,
# it uses echo commands to simulate the pipeline execution.
#
# A pipeline is composed of independent jobs that run scripts, grouped into stages.
# Stages run in sequential order, but jobs within stages run in parallel.
#
# For more information, see: https://docs.gitlab.com/ee/ci/yaml/index.html#stages
#
# You can copy and paste this template into a new `.gitlab-ci.yml` file.
# You should not add this template to an existing `.gitlab-ci.yml` file by using the `include:` keyword.
#
# To contribute improvements to CI/CD templates, please follow the Development guide at:
# https://docs.gitlab.com/ee/development/cicd/templates.html
# This specific template is located at:
# https://gitlab.com/gitlab-org/gitlab/-/blob/master/lib/gitlab/ci/templates/Getting-Started.gitlab-ci.yml
# 
# stages:          # List of stages for jobs, and their order of execution
#   - build
#   - test
#   - deploy
# 
# build-job:       # This job runs in the build stage, which runs first.
#   stage: build
#   script:
#     - echo "Compiling the code..."
#     - echo "Compile complete."
# 
# unit-test-job:   # This job runs in the test stage.
#   stage: test    # It only starts when the job in the build stage completes successfully.
#   script:
#     - echo "Running unit tests... This will take about 60 seconds."
#     - sleep 60
#     - echo "Code coverage is 90%"
# 
# lint-test-job:   # This job also runs in the test stage.
#   stage: test    # It can run at the same time as unit-test-job (in parallel).
#   script:
#     - echo "Linting code... This will take about 10 seconds."
#     - sleep 10
#     - echo "No lint issues found."
# 
# deploy-job:      # This job runs in the deploy stage.
#   stage: deploy  # It only runs when *both* jobs in the test stage complete successfully.
#   environment: production
#   script:
#     - echo "Deploying application..."
#     - echo "Application successfully deployed."
stages:
  - test2
  
image: registry-gitlab.pasteur.fr/bernd/utechscb-schnapps  

test2:
  stage: test2
  script:
    - set
    - echo $GITHUB_PAT
    - R -e "sessionInfo()"
    - R -e "installed.packages()"
    - export GITHUB_PAT=${R_PAT_TOKEN};R -e "devtools::update_packages(dependencies = T, upgrade='always')"    
    - R -e "devtools::install_gitlab(host='https://gitlab.pasteur.fr', repo = 'bernd/UTechSCB-SCHNAPPs', dependencies = TRUE)"
  only:
    - master