.travis.yml

# language: r
# r: bioc-devel
# sudo: required
# r_packages:
#   - knitr
#   - XML
#   - plyr
#   - doParallel
#   - foreach
#   - iterators
# bioc_packages: 
#   - xcms 
#   - Rgraphviz
# apt_packages:
#   - texlive-latex-extra
#   - texlive-fonts-extra
#   - texlive-latex-recommended
#   - libnetcdf-dev
#   - netcdf-bin
#   - libhdf5-dev

# # Set CXX1X for R-devel, as R-devel does not detect CXX1X support for gcc 4.6.3,
# # Thanks to jimhester pointing this out!
# before_install:
#   - if [[ "$TRAVIS_R_VERSION_STRING" = 'bioc-devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi


language: r
r: bioc-devel
cache: packages
sudo: false       # use container based build system
warnings_are_errors: true
dist: trusty

# 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

addons:
  apt:
    packages:
      - libnetcdf-dev
      - netcdf-bin # libnetcdf-dev doesn't contain nc-config in ubuntu 12.04 (in 16.04 it is part of libnetcdf-dev)
      - libhdf5-dev
      - texlive-latex-recommended
      - texlive-fonts-extra

r_packages:
  - covr

# before_script:
#   - echo "BiocParallel::register(BiocParallel::SerialParam())" > ~/.Rprofile
  
script: 
  - | 
    R CMD build .
    travis_wait 40 R CMD check --no-build-vignettes --no-vignettes xcms*tar.gz

after_failure:
  find *Rcheck -name '*.fail' -print -exec cat '{}' \;
  
after_success:
  - travis_wait 20 Rscript -e 'covr::codecov()'

# # print timings (of examples) and sysinfo
# after_script:
#   - dump_logs_by_extension "timings"
#   - dump_sysinfo