# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # # https://gitlab.com/msberends/AMR # # # # LICENCE # # (c) 2018-2020 Berends MS, Luz CF et al. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # # to do a full CRAN check with R-Hub: # chck <- rhub::check(devtools::build(), platform = rhub::platforms()[!is.na(rhub::platforms()$`cran-name`), 'name']) stages: - test - check - lint - website - coverage image: rocker/r-base before_script: - apt-get update -qq --allow-releaseinfo-change # install dependencies for packages - apt-get install -y wget locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev > /dev/null # recent pandoc - wget --quiet https://github.com/jgm/pandoc/releases/download/2.9.2.1/pandoc-2.9.2.1-1-amd64.deb - dpkg -i pandoc*.deb - rm pandoc*.deb # set R system language - echo "LC_ALL=en_US.UTF-8" >> /etc/environment - echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen - echo "LANG=en_US.UTF-8" > /etc/locale.conf - locale-gen # cache R packages - mkdir -p installed_deps - echo 'R_LIBS="installed_deps"' > .Renviron - echo 'R_LIBS_USER="installed_deps"' >> .Renviron - echo 'R_LIBS_SITE="installed_deps"' >> .Renviron # set language - echo 'LANGUAGE="en_US.utf8"' >> .Renviron - echo 'LANG="en_US.utf8"' >> .Renviron - echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron # ---- TEST R-release: stage: test when: always allow_failure: false script: - Rscript -e 'sessionInfo()' # install missing and outdated packages - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)' - Rscript -e 'devtools::test(stop_on_failure = FALSE)' cache: key: release paths: - installed_deps/ R-devel: stage: test when: always image: rocker/r-devel allow_failure: false script: - Rscriptdevel -e 'sessionInfo()' # install missing and outdated packages - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)' - Rscriptdevel -e 'devtools::test(stop_on_failure = FALSE)' cache: key: devel paths: - installed_deps/ # ---- CHECK R-release: stage: check when: on_success allow_failure: true script: - Rscript -e 'sessionInfo()' # install missing and outdated packages - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)' # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file - rm -rf vignettes - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' # build package - R CMD build . --no-build-vignettes --no-manual - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1) - Rscript -e 'Sys.setenv(NOT_CRAN = "true")' - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran artifacts: when: always paths: - '*.Rcheck/*' expire_in: '1 month' cache: key: release paths: - installed_deps/ R-devel: stage: check when: on_success image: rocker/r-devel allow_failure: true script: - Rscriptdevel -e 'sessionInfo()' # install missing and outdated packages - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE)' # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file - rm -rf vignettes - Rscriptdevel -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' # build package - Rdevel CMD build . --no-build-vignettes --no-manual - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1) - Rscript -e 'Sys.setenv(NOT_CRAN = "true")' - Rdevel CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran artifacts: when: always paths: - '*.Rcheck/*' expire_in: '1 month' cache: key: devel paths: - installed_deps/ # ---- OTHER lintr: stage: lint allow_failure: true when: always only: - premaster - master script: # check all syntax with lintr - Rscript -e 'lintr::lint_package()' cache: key: release paths: - installed_deps/ policy: pull # no uploading after run pages: stage: website allow_failure: true when: always only: - master script: - mv docs public artifacts: paths: - public codecovr: stage: coverage allow_failure: true when: always only: - premaster - master script: - apt-get install --yes git # codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd # Sys.setenv(NOT_CRAN = 'true'), because otherwise skip_on_cran() will be applied on Covr too, resulting in extremely low coverage percentages - Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_history.R', 'R/mo_source.R', 'R/resistance_predict.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))" coverage: '/Code coverage: \d+\.\d+/' cache: key: release paths: - installed_deps/ policy: pull # no uploading after run