.travis.yml

#----------------------------------------------------------------
# Travis-CI configuration for R packages
#
# REFERENCES:
# * Travis CI: https://travis-ci.org/
# * r-builder: https://github.com/metacran/r-builder
# * covr: https://github.com/jimhester/covr
# * Coveralls: https://coveralls.io/
#
# Validate your .travis.yml file at http://lint.travis-ci.org/
#----------------------------------------------------------------
language: c

env:
  global:
    - RENV="./pkg-build.sh"  ## r-builder
    - R_BUILD_ARGS="--no-manual"
    - R_CHECK_ARGS="--no-manual --as-cran"
    - _R_CHECK_FORCE_SUGGESTS_=false
    # Need LaTeX? (very time consuming!)
    - BOOTSTRAP_LATEX=""
    # time consuming because LaTeX needs to be installed
    - R_BUILD_ARGS="--no-build-vignettes ${R_BUILD_ARGS}"
    - R_CHECK_ARGS="--no-build-vignettes ${R_CHECK_ARGS}"
    - BIOC_USE_DEVEL="TRUE"

  # R versions r-builder should test on (ignored by r-travis)
  matrix:
#    - RVERSION=3.0.3
#    - RVERSION=3.1.2
    - RVERSION=devel


before_install:
  - echo RENV=$RENV
  - curl -OL https://raw.githubusercontent.com/HenrikBengtsson/r-builder/master/pkg-build.sh;
  - chmod 755 $RENV
  - $RENV bootstrap
  - if [ "BOOTSTRAP_LATEX" == "true" ]; then
      (cd /tmp && curl -OL http://mirrors.ctan.org/macros/latex/contrib/xcolor.zip && cd /usr/share/texmf/tex/latex && sudo unzip /tmp/xcolor.zip && cd xcolor && sudo latex xcolor.ins && sudo texhash);
    else
      export R_RSP_COMPILELATEX_FALLBACK="copy-force";
    fi

install:
  - $RENV install_r R.utils matrixStats R.cache digest future
  - $RENV install_bioc Biobase CGHbase CGHcall DNAcopy Rsamtools BSgenome GenomeInfoDb BiocStyle
## Less overhead when not using 'install_deps'
##  - $RENV install_deps

script:
  - $RENV run_build
  - $RENV run_check

after_success:
  - $RENV dump_logs_by_extension out
  - $RENV install_devtools
  - $RENV install_github HenrikBengtsson/R.methodsS3@develop
  - $RENV install_github HenrikBengtsson/covr
  - curl -OL https://raw.githubusercontent.com/HenrikBengtsson/covr-utils/master/covr-utils.R
  - $RENV run_script .coveralls.R

after_failure:
  - $RENV dump_logs

notifications:
  email:
    on_success: change
    on_failure: change

branches:
  except:
   - /-expt$/