language: r r: #- bioc-devel - bioc-release # warnings_are_errors: true sudo: false fortran: true cache: packages services: - docker addons: apt: packages: - libprotobuf-dev - libapparmor-dev - protobuf-compiler - libcurl4-openssl-dev r_packages: - covr - data.table - ggplot2 - testthat - knitr - rmarkdown - httpuv - opencpu - protolite - Rook os: - linux - osx bioc_required: true bioc_packages: - BiocCheck #- GEOquery - limma - rhdf5 - BiocStyle before_install: - if [ ${TRAVIS_OS_NAME} = 'osx' ]; then brew unlink python; brew install protobuf; fi - R -e 'install.packages("devtools")' - R -e 'source("https://bioconductor.org/biocLite.R"); biocLite()' - R -e 'devtools::install_github("seandavi/geoquery")' script: - R CMD build . - FILE=$(ls -1t *.tar.gz | head -n 1) - R CMD check "$FILE" - bash inst/test_js.sh after_script: - FILE=$(ls -1t *.tar.gz | head -n 1) - Rscript -e "library(BiocCheck); BiocCheck(\"${FILE}\")" after_success: - Rscript -e 'covr::codecov()' - DOCKER_TAG="$TRAVIS_BRANCH-$TRAVIS_BUILD_NUMBER" - if [ "$TRAVIS_OS_NAME" == "linux" ] && [ "$TRAVIS_BRANCH" == "master" ]; then docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD"; docker build -t dzenkova/phantasus --build-arg PHANTASUS_BUILD=$DOCKER_TAG . ; docker tag dzenkova/phantasus dzenkova/phantasus:$DOCKER_TAG ; docker push dzenkova/phantasus; fi - if [ "$TRAVIS_OS_NAME" == "linux" ] && [ "$TRAVIS_BRANCH" == "develop" ]; then docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD"; docker build --build-arg PHANTASUS_BUILD=$DOCKER_TAG --build-arg GITHUB_PAT=$GITHUB_PAT -t dzenkova/phantasus:develop . ; docker tag dzenkova/phantasus:develop dzenkova/phantasus:$DOCKER_TAG ; docker push dzenkova/phantasus:develop; docker push dzenkova/phantasus:$DOCKER_TAG; fi notifications: slack: rooms: - sysbio1:Kt2QCRqnbzJpNE8TvOvgwEMz#phantasus