.travis.yml

# use containers
sudo: false

os:
  - linux
  - osx

osx_image: xcode8.2

language: r
r:
  - release
#  - devel # stringi dependency makes this fail

matrix:
   allow_failures:
    - os: osx
#    - r: devel

cran: http://cran.rstudio.com

r_packages:
  - covr
  - wesanderson
  - magrittr
  - mFilter
  - igraph
  - magic
  - randomForest

r_binary_packages:
  - magrittr
  - devtools
  - testthat
  - ggplot2
  - Rcpp
  - dplyr
  - knitr
  - rmarkdown
  - randomForest
  - dplyr
  - psych
  - pracma

# cache local R libraries directory:
cache: packages

before_install:
  - basedir=${PWD}
  - cd ..
  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then cmake --version; wget --no-check-certificate https://cmake.org/files/v3.4/cmake-3.4.0-rc1-Linux-x86_64.sh; sh cmake-3.4.0-rc1-Linux-x86_64.sh --skip-license --prefix=${HOME}; export PATH=$HOME/bin/:$PATH; fi
  - export PATH=$HOME/bin/:$PATH
  - cd $basedir

install:
  - mkdir -p ~/.R
  - export CC=clang
  - export CXX=clang++
  - echo "CC=clang" >  ~/.R/Makevars
  - echo "CXX=clang++" >> ~/.R/Makevars
  - echo "CXX1X=clang++" >> ~/.R/Makevars
  - echo "CXX1XSTD=-std=c++11" >> ~/.R/Makevars
  - source ~/.R/Makevars
  - echo 'options(repos = "http://cran.rstudio.com")' > .Rprofile
  - echo '.travis.yml' > .Rbuildignore
#  - Rscript -e 'if(!"devtools" %in% rownames(installed.packages())) { install.packages("devtools") }'
#  - Rscript -e 'if(!"stringi" %in% rownames(installed.packages())) { devtools::install_github("gagolews/stringi", dependencies = TRUE) }'
  - Rscript -e 'install.packages("Rcpp", dependencies = TRUE)'
  - Rscript -e 'if(!"magrittr" %in% rownames(installed.packages())) { install.packages("magrittr", dependencies = TRUE) }'
  - Rscript -e 'if(!"tools" %in% rownames(installed.packages())) { install.packages("tools", dependencies = TRUE) }'
  - Rscript -e 'if(!"knitr" %in% rownames(installed.packages())) { install.packages("knitr", dependencies = TRUE) }'
#  - Rscript -e 'if(!"ggplot2" %in% rownames(installed.packages())) { install.packages("ggplot2", dependencies = TRUE) }'
  - Rscript -e 'if(!"igraph" %in% rownames(installed.packages())) { install.packages("igraph", dependencies = TRUE) }'
  - Rscript -e 'if(!"pracma" %in% rownames(installed.packages())) { install.packages("pracma", dependencies = TRUE) }'
  - Rscript -e 'if(!"dplyr" %in% rownames(installed.packages())) { install.packages("dplyr", dependencies = TRUE) }'
  - Rscript -e 'if(!"mFilter" %in% rownames(installed.packages())) { install.packages("mFilter", dependencies = TRUE) }'
  - Rscript -e 'if(!"rmarkdown" %in% rownames(installed.packages())) { install.packages("rmarkdown", dependencies = TRUE) }'
  - Rscript -e 'if(!"testthat" %in% rownames(installed.packages())) { install.packages("testthat", dependencies = TRUE) }'
  - Rscript -e 'if(!"randomForest" %in% rownames(installed.packages())) { install.packages("randomForest", dependencies = TRUE) }'
  - Rscript -e 'if(!"psych" %in% rownames(installed.packages())) { install.packages("psych", dependencies = TRUE) }'
#  - Rscript -e 'if(!"plyr" %in% rownames(installed.packages())) { install.packages("plyr", dependencies = TRUE) }'
#  - Rscript -e 'if(!"magic" %in% rownames(installed.packages())) { install.packages("magic", dependencies = TRUE) }'
  - Rscript -e 'if(!"covr" %in% rownames(installed.packages())) { install.packages("covr", dependencies = TRUE) }'
#  - Rscript -e 'update.packages( ask = FALSE )'
  - cd ~/
  - itkrrel=0.0.1
  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then wget https://github.com/stnava/ITKR/releases/download/latest/ITKR_${itkrrel}_R_x86_64-pc-linux-gnu.tar.gz; R CMD INSTALL ITKR_${itkrrel}_R_x86_64-pc-linux-gnu.tar.gz; fi
  - if [ "$TRAVIS_OS_NAME" == "osx" ]; then wget http://github.com/stnava/ITKR/releases/download/latest/ITKR_${itkrrel}.tgz; R CMD INSTALL ITKR_${itkrrel}.tgz; fi
  - ANTsRCorerel=0.0.0
  - reldir=untagged-a878f5e1fd9cffd7bb04
  - reldir=latest
  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then wget https://github.com/stnava/ANTsRCore/releases/download/${reldir}/ANTsRCore_${ANTsRCorerel}_R_x86_64-pc-linux-gnu.tar.gz; R CMD INSTALL ANTsRCore_${ANTsRCorerel}_R_x86_64-pc-linux-gnu.tar.gz; fi
  - if [ "$TRAVIS_OS_NAME" == "osx" ]; then wget http://github.com/stnava/ANTsRCore/releases/download/${reldir}/ANTsRCore_${ANTsRCorerel}.tgz; R CMD INSTALL ANTsRCore_${ANTsRCorerel}.tgz; fi
  - cd ${basedir}

# Build and check package
script:
  - source ~/.R/Makevars
  - export CXX=clang++
  - export CC=clang
  - cd ..
  - travis_wait 100 R CMD build ANTsR --no-build-vignettes --no-manual
  - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
  - if [[ ${#TRAVIS_TAG} -eq 0 ]]; then travis_wait 100 R CMD check "${PKG_FILE_NAME}" --no-manual; fi # --as-cran
  - mydir=${PWD}
  - if [[ ${#TRAVIS_TAG} -gt 0 ]]; then travis_wait 100  R CMD INSTALL --build ANTsR; PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1); if [ "$TRAVIS_OS_NAME" == "osx" ];  then  PKG_FILE_NAME=$(ls -1t *.tgz | head -n  1);  fi; fi


# report coverage rate to coveralls
after_success:
  - cd $mydir
#  - cd ANTsR
#  - travis_wait 100 Rscript -e 'covr::coveralls( type = "examples" )'
# takes too long, should add to matrix

after_failure:
  - cat ~/build/stnava/ANTsR.Rcheck/00install.out
  - cat ~/build/stnava/ANTsR.Rcheck/00check.log

# send e-mails if stuff changes
notifications:
  email:
    recipients:
    - stnava@gmail.com
    - arman.eshaghi@gmail.com
    - jeff.duda@gmail.com
    on_success: change
    on_failure: always

env:
  global:
  - R_BUILD_ARGS=" "
  - R_CHECK_ARGS=" --timings"
  - R_CHECK_TIME="TRUE"
  - R_CHECK_TESTS="TRUE"
  - _R_CHECK_TIMINGS_="0"
  - _R_CHECK_FORCE_SUGGESTS_="0"
  - BOOTSTRAP_LATEX=1
  - WARNINGS_ARE_ERRORS=0

deploy:
  provider: releases
  api_key:
    secure: VevZHK5WDwd2mFSrF3+b2jTRzImb6juOgewcOvZ8LJ2S70khn64Kx4+JGUvk5miKWVbKnHIhPxOJY50muO9sT15ApP+HFZYpiVpx4l/hEypk9zmJD+f+ERuN7j8elCzUZqet3v77XD+pBcYMxFARew4gGDkG2LO5casij0YNiyQ=
  file: ${PKG_FILE_NAME}
  skip_cleanup: true
  overwrite: true
  on:
    repo: stnava/ANTsR
    tags: true
    all_branches: true