.gitlab-ci.yml

variables:
  PKGNAME:     "FraseR"
  PKGDIR:      "./"
  RVER:        "3.6.0-Bioc3.9"
  TEXVER:      "2016"
  R_LIBS_U:    "tmp_libs"

before_script:
  - module load "i12g/R/$RVER"
  - module load "i12g/texlive/$TEXVER"
  - R --vanilla CMD build --no-build-vignettes --no-manual $PKGDIR
  - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)

stages:
  - RCheck
  - BiocCheck
  - CovR
  - Vignette

before_script:
  - module load "i12g/R/$RVER"
  - module load "i12g/texlive/$TEXVER"
  - R --vanilla CMD build --no-build-vignettes --no-manual $PKGDIR
  - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
  - mkdir $R_LIBS_U/$CI_JOB_ID -p
  - R_LIBS_USER=$R_LIBS_U/$CI_JOB_ID Rscript --vanilla -e "install.packages('${PKG_FILE_NAME}', lib='$R_LIBS_U/$CI_JOB_ID', repo=NULL)"

R-check:
  stage: RCheck
  when: always
  tags: [shell]
  script:
    # TODO remove no-tests
    - R_LIBS_USER=$R_LIBS_U/$CI_JOB_ID R --vanilla CMD check --no-tests --no-vignettes --timings "${PKG_FILE_NAME}"

R-BiocCheck:
  stage: BiocCheck
  when: always
  tags: [shell]
  script:
    # TODO remove no-tests
    - R_LIBS_USER=$R_LIBS_U/$CI_JOB_ID R --vanilla CMD BiocCheck --new-package --no-tests --no-check-vignettes "${PKG_FILE_NAME}"

R-check_vignettes:
  stage: Vignette
  when: always
  tags: [shell]
  script:
    - echo "TRUE"
  #  - R_LIBS_USER=$R_LIBS_U/$CI_JOB_ID R --vanilla CMD Sweave --engine=knitr::knitr --pdf "$PKGDIR/vignettes/$PKGNAME.Rnw"

R-coverage:
  stage: CovR
  when: always
  tags: [shell]
  script:
    - R_LIBS_USER=$R_LIBS_U/$CI_JOB_ID Rscript --vanilla -e "covr::package_coverage('$PKGDIR')"