.travis.yml

# full script at https://github.com/travis-ci/travis-build/blob/master/lib/travis/build/script/r.rb
language: r
r: bioc-devel
cache:
  packages: true
  directories:
    - ~/.AnnotationHub
sudo: required
warnings_are_errors: true
dist: trusty

# unfortunately apt packages are not cached
# we could use these build dependencies just in the "Build" stage and
# install their runtime libraries counter parts in "Check" but that would make
# the script more complicated and saves just a few seconds
addons:
  apt:
    packages:
      - libnetcdf-dev
      - netcdf-bin # libnetcdf-dev doesn't contain nc-config in ubuntu 12.04 (in 16.04 [xerus] it is part of libnetcdf-dev)
      - libhdf5-dev
      - libgit2-dev # git2r

jobs:
  include:
    - stage: "Build"
      r_packages:
        - covr
        - pkgdown
        - testthat
        - knitr
        - roxygen2
      before_install:
        - mkdir -p ~/.R
        - echo -e 'MAKEFLAGS = -j2' > ~/.R/Makevars
        - echo 'options(Ncpus = 2)' > ~/.Rprofile
      script: true
      name: "Build dependencies and cache"
    - stage: "Check"
      r_build_args: --no-build-vignettes --no-manual
      r_check_args: --as-cran --no-build-vignettes --no-vignettes --no-manual --no-tests
      before_script: rm -rf vignettes
      install: skip
      name: "examples"
    - r_build_args: --no-build-vignettes --no-manual
      r_check_args: --as-cran --no-build-vignettes --no-vignettes --no-manual --no-codoc --no-examples
      install: skip
      before_script: rm -rf vignettes
      name: "tests"
    - r_build_args:
      r_check_args: --as-cran --no-build-vignettes --no-codoc --no-examples --no-tests
      install: skip
      name: "vignettes"
    - stage: "Deploy"
      install: skip
      script:
        - travis_wait 20 Rscript -e 'covr::codecov()'
      name: "codecov and pkgdown (on master)"
      before_deploy:
        - R CMD INSTALL .
        - travis_wait 20 Rscript -e 'pkgdown::build_site()'
      deploy:
        provider: pages
        skip-cleanup: true
        github-token: $GITHUB_PAT
        keep-history: true
        local-dir: docs
        on:
          branch: master

# In general the r-travis script automatically dump the logs after failure but
# because of a bug in travis the output is often truncated. See
# https://github.com/travis-ci/travis-ci/issues/6018
after_failure: sleep 10

notifications:
  email:
    recipients: lg390@cam.ac.uk
    on_failure: change
    on_success: change