Testing R package with GitLab CI (with code coverage)

.gitlab-ci.yml

variables:
  CODECOV_TOKEN: "CODECOV_TOKEN_STRING"
  _R_CHECK_CRAN_INCOMING_: "false"
  _R_CHECK_FORCE_SUGGESTS_: "true"
  APT_PKGS: "libcurl4-openssl-dev libssh2-1-dev libssl-dev libxml2-dev zlib1g-dev git"

before_script:
  - apt-get update
  - apt-get install -y --no-install-recommends ${APT_PKGS}
  - apt-get install -y --no-install-recommends qpdf pandoc pandoc-citeproc
  - export PATH="/usr/local/lib/R/site-library/littler/examples/:${PATH}"
  - echo "options(Ncpus = $(nproc --all))" >> /usr/local/lib/R/etc/Rprofile.site
  - install2.r devtools
  - r -e 'devtools::install_dev_deps()'

r-release:
  stage: test
  tags:
    - docker
  image: rocker/r-ver:latest
  script:
    - r -e 'devtools::check(check_dir = ".")'
  artifacts:
    paths:
      - "*.Rcheck"
    name: logs
    when: always

r-devel:
  stage: test
  tags:
    - docker
  image: rocker/r-ver:devel
  script:
    - r -e 'devtools::check(check_dir = ".")'
  artifacts:
    paths:
      - "*.Rcheck"
    name: logs
    when: always

coverage:
  stage: deploy
  tags:
    - docker
  image: rocker/r-ver:latest
  when: on_success
  only:
    - master
  script:
    - install2.r covr
    - r -e 'devtools::install()'
    - r -e 'covr::codecov(type = c("tests", "examples"), quiet = FALSE)'

pages:
  stage: deploy
  tags:
    - docker
  image: rocker/tidyverse:latest
  script:
    - install2.r pkgdown drat
    - r -e 'devtools::install()'
    - r -e 'pkgdown::build_site(override = list(destination = "public"))'
    - mkdir -p public/drat
    - r -e 'devtools::build(path = ".")'
    - r -e 'drat::insertPackage(argv, "public/drat")' $(ls -1t *.tar.gz | head -n 1)
  artifacts:
    paths:
      - public

littler doesn't work well with commandArgs, so the line that inserts the package into the pages using drat fails because it doesn't pick up the tarball as an argument. For example:

$ r -e 'print(commandArgs(TRUE))' $(ls)
character(0)

you can instead use argv or R.utils::commandArgs:

$ r -e 'print(argv)' $(ls L*)
[1] "LICENSE"  "LICENSE~"

$ r -e 'print(R.utils::commandArgs(TRUE))' $(ls L*)
[1] "LICENSE"  "LICENSE~"