.travis.yml

# Use container-based Travis with caching

languague: c
sudo: false

addons:
  apt:
    sources:
    - r-packages-trusty
    packages:
    - r-base-dev
    - r-recommended
    - texinfo
    - qpdf

cache:
  directories:
    - ~/Rlib     # R libraries
    - ~/texlive  # LaTex
    - ~/bin      # pandoc

# install dependencies
install:
  # Save R packages in Rlib
  - mkdir -p ~/Rlib
  - echo 'R_LIBS=~/Rlib' > .Renviron
  - echo 'options(repos = "http://cran.rstudio.com")' > .Rprofile
  - mkdir -p ~/.R
  - grep '\-g'  /etc/R/Makeconf | sed 's/-g//g' > ~/.R/Makevars # Turn off debug symbols
  # Build LaTex and pandoc
  - mkdir -p ~/bin
  - wget -q -O - https://github.com/yihui/crandalf/raw/master/inst/scripts/install-texlive | bash
  - wget -q -O - https://github.com/yihui/crandalf/raw/master/inst/scripts/install-pandoc | bash
  - PATH=$HOME/texlive/bin/x86_64-linux:$PATH
  # Install R packages
  - Rscript -e "if (!require('devtools')) install.packages('devtools')"
  - Rscript -e "if (!require('covr')) devtools::install_github('jimhester/covr')"
  - Rscript -e "if (!require('rmarkdown')) install.packages('rmarkdown')"
  - Rscript -e "if (!require('knitr')) install.packages('knitr')"
  - Rscript -e "if (!require('drat')) install.packages('drat')"
  - Rscript -e "if (!require('Rcpp')) install.packages('Rcpp')"
  - Rscript -e "if (!require('RcppParallel')) install.packages('RcppParallel')"
  - Rscript -e "if (!require('BH')) install.packages('BH')"
  - Rscript -e "if (!require('testthat')) install.packages('testthat')"
  - Rscript -e "if (!require('matrixStats')) install.packages('matrixStats')"
  - Rscript -e "if (!require('ggplot2')) install.packages('ggplot2')"
  - Rscript -e "if (!require('graph')) { source('http://bioconductor.org/biocLite.R'); biocLite('graph') }"
  - Rscript -e "if (!require('Rgraphviz')) { source('http://bioconductor.org/biocLite.R'); biocLite('Rgraphviz') }"
  - Rscript -e "if (!require('MCMCpack')) install.packages('MCMCpack')"
  - Rscript -e "if (!require('plotrix')) install.packages('plotrix')"

before_script:
  - export PKG_NAME=$(Rscript -e 'cat(paste0(devtools::as.package(".")$package))')
  - export PKG_TARBALL=$(Rscript -e 'pkg <- devtools::as.package("."); cat(paste0(pkg$package,"_",pkg$version,".tar.gz"))')

# Build and check package
script:
  - R CMD build . --no-build-vignettes
  - _R_CHECK_CRAN_INCOMING_=FALSE R CMD check "${PKG_TARBALL}" --as-cran --no-build-vignettes
  - cat ${PKG_NAME}.Rcheck/00install.out # Print out install / compile log

after_success:
  # - Rscript -e 'covr::codecov()'
  # Rebuild drat repo
#  - test $TRAVIS_PULL_REQUEST == "false" && test $TRAVIS_BRANCH == "master" && bash deploy.sh

notifications:
  recipients:
    - msuchard@gmail.com
    - lamho86@gmail.com
  email:
    on_success: change
    on_failure: change

env:
  global:
#     - R_BUILD_ARGS=" "
#     - R_CHECK_ARGS="--as-cran"
#    secure: clBIB1ryoj28wttYw5YQClr4wTNw/s2rqs0OzjnvdnD3NAONxMz+8CXR7cmHow5nQ211J/zKP/+wnd8x0oCId2cJT2a8Kp99bjAMs6q0hvjAUBxmYQgQAJ3VQ8PNTXB4WglDimXPSJfYdExo3mqbQozWnqx9pu7Z+029/M7+h+M=