.travis.yml

# Neuroconductor Template no ANTs
language: r
cache: packages
warnings_are_errors: true
use_bioc: true
bioc_required: true
cran: http://cran.rstudio.com
dist: trusty


addons:
  apt:
    packages:
    - libfftw3-dev
r:
- release
- devel

matrix:
  allow_failures:
    - r: devel

env:
  global: 
    - RGL_USE_NULL=TRUE
    - PROJECT_NAME=neuroconductor
    - DISPLAY=:99.0
    - R_REMOTES_NO_ERRORS_FROM_WARNINGS=true
r_check_args: --as-cran --install-args=--build
# r_check_args: "--as-cran --install-args=--build"

before_install:
  - ulimit -n 2048
  - export PROJ_DIR=`basename $PWD`    
  - fname=travis_helpers.sh
  - wget -O ${fname} http://bit.ly/travis_helpers
  - cat ${fname}; source ${fname}; rm ${fname}  
  - tlmgr install filecontents ;
  - cat DESCRIPTION
  - start_xvfb ;
  - export rver=`r_version`; echo $rver ;
  - if [ "$TRAVIS_OS_NAME" = "osx" ];
    then
      no_open_mp ; 
    fi
  - jags_install ;  
  - v8_install ;
  - dcmtk_install ;
  - remove_neuroc_packages ;
  - cat DESCRIPTION
  - install_remotes_no_dep
  - cat DESCRIPTION
  - export PACKAGE_NAME=`package_name`
  - echo "Package Name is $PACKAGE_NAME"
  - if [[ "${PACKAGE_NAME}" == "waveslim" ]]; 
    then
      fftw_install ;
    fi
  - gsl_install_source;
  - echo $LD_LIBRARY_PATH ;
  - gsl-config --prefix; gsl-config --version ; gsl-config  --cflags; gsl-config  --libs
  - if [[ "${PACKAGE_NAME}" == "ROpenCVLite" || "${PACKAGE_NAME}" == "Rvision" ]]; 
    then
      shopt -s expand_aliases ;
      x=`Rscript -e "cat(Sys.which('R'))"` ;
      echo "reset R" ;
      alias R="travis_wait 100 ${x}" ;
    fi
  - install_python_requirements ;    
  - R CMD javareconf ;  
  - pwd;
  - cat DESCRIPTION; 
  # - ralias; R -e "cat('test')"; ls travis_*.log

after_success:
  - dump_logs

after_failure:
  - dump_logs

# need this explicitly
# for naming convention
before_deploy:
  # - travis_wait 100 R CMD INSTALL --build ${PKG_TARBALL}
  # so no overwrite of linux build
  - if [ "$TRAVIS_OS_NAME" = "osx" ];
    then 
      PKG_TARBALL=$(ls -1t *.tgz | head -n 1); 
      PKG_TARBALL_WITH_R=`echo $PKG_TARBALL | sed 's/.tgz/_'"R${rver}"'.tgz/'` ;
      mv ${PKG_TARBALL} ${PKG_TARBALL_WITH_R} ;
      echo "Built tarball is ${PKG_TARBALL_WITH_R}" ;
    fi   
  - if [ "$TRAVIS_OS_NAME" = "linux" ];
    then 
      PKG_TARBALL=$(ls -1t *.tar.gz | head -n 1); 
      PKG_TARBALL_WITH_R=`echo $PKG_TARBALL | sed 's/.tar.gz/_'"R${rver}"'.tar.gz/'` ;
      mv ${PKG_TARBALL} ${PKG_TARBALL_WITH_R} ;
      echo "Built tarball is ${PKG_TARBALL_WITH_R}" ;
    fi       
  - if [[ "${TRAVIS_OS_NAME}" = "osx" ]];
    then
      rm -f *.tar.gz;
    fi 


after_deploy:
  # travis_wait 100 Rscript -e 'covr::coveralls(type = "all")' ;
  - if [[ "${TRAVIS_OS_NAME}" == "linux" && ${TRAVIS_R_VERSION_STRING} = "release" ]]; 
    then
      echo 'covr::coveralls(type = "all", quiet = FALSE)' > neuroc_covr.R ;
      travis_wait 100 Rscript neuroc_covr.R ;
      rm neuroc_covr.R ;
    fi



# r:
#   - release
#   - devel

# matrix:
#   allow_failures:
#   - r: devel