.travis.yml

language: r
r: bioc-devel
cache:
  packages: true
sudo: required
warnings_are_errors: false
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
      - texlive-latex-recommended
      - texlive-fonts-extra

# Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
# this was causing mzR installation to fail
# see https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17189
# workaround stolen from https://github.com/hadley/devtools/blob/1ce84b04568ff7846c3da754f28e7e22a23c8737/.travis.yml#L23-L26
# before_install:
#   - if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi

jobs:
  include:
    - stage: "Build"
      r_packages:
        - covr
        - testthat
        - knitr
        - roxygen2
      before_install:
        - mkdir -p ~/.R
        - echo -e 'MAKEFLAGS = -j2' > ~/.R/Makevars
        - echo 'options(Ncpus = 2)' > ~/.Rprofile
        - echo 'options(repos = c(CRAN = "https://cran.rstudio.com"))' > ~/.Rprofile
        - echo 'utils::chooseCRANmirror(ind = 1)' > ~/.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"
    - install: skip
      script:
        - travis_wait 10 R CMD build --no-build-vignettes --no-manual .
        - travis_wait 40 R CMD check --as-cran --no-build-vignettes --no-vignettes --no-manual --no-codoc --no-examples xcms*tar.gz
      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: "CodeCov"
      install: skip
      script:
        - R CMD INSTALL .
        - travis_wait 40 Rscript -e 'covr::codecov()'
      name: "codecov"
      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:
    on_failure: johannes.rainer@eurac.edu