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Add warning for unset 'where' argument in toolGetMapping function #72

Add warning for unset 'where' argument in toolGetMapping function

Add warning for unset 'where' argument in toolGetMapping function #72

Workflow file for this run

# Run CI for R using https://eddelbuettel.github.io/r-ci/
name: check
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]
env:
USE_BSPM: "true"
_R_CHECK_FORCE_SUGGESTS_: "false"
NO_BINARY_INSTALL_R_PACKAGES: 'c("madrat", "magclass", "citation", "gms", "goxygen", "GDPuc", "roxygen2")'
jobs:
check:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Bootstrap
run: |
sudo chown runner -R .
sudo locale-gen en_US.UTF-8
sudo add-apt-repository -y ppa:ubuntugis/ppa
curl -OLs https://eddelbuettel.github.io/r-ci/run.sh
chmod 0755 run.sh
./run.sh bootstrap
rm -f bspm_*.tar.gz
- name: Enable r-universe repo, modify bspm integration
run: |
# install packages from https://pik-piam.r-universe.dev and CRAN
echo '
options(repos = c(universe = "https://pik-piam.r-universe.dev",
CRAN = "https://cloud.r-project.org"))
' >> .Rprofile
cat .Rprofile
# modify bspm integration to never install binary builds of PIK CRAN packages
sudo sed -i '/bspm::enable()/d' /etc/R/Rprofile.site
# need double % because of printf, %s is replaced with "$NO_BINARY_INSTALL_R_PACKAGES" (see "env:" above)
printf '
local({
expr <- quote({
if (!is.null(repos)) {
noBinaryInstallRPackages <- %s
pkgs <- c(bspm::install_sys(pkgs[!pkgs %%in%% noBinaryInstallRPackages]),
pkgs[pkgs %%in%% noBinaryInstallRPackages])
}
type <- "source"
})
trace(utils::install.packages, expr, print = FALSE)
})
' "$NO_BINARY_INSTALL_R_PACKAGES" | sudo tee --append /etc/R/Rprofile.site >/dev/null
cat /etc/R/Rprofile.site
- name: Set up Pandoc
uses: r-lib/actions/setup-pandoc@v2
- name: Set up Python 3.9
uses: actions/setup-python@v4
with:
python-version: 3.9
- name: Cache R libraries
if: ${{ !env.ACT }} # skip when running locally via nektos/act
uses: pat-s/always-upload-cache@v3
with:
path: /usr/local/lib/R/
key: 3-${{ runner.os }}-usr-local-lib-R-${{ hashFiles('DESCRIPTION') }}
restore-keys: |
3-${{ runner.os }}-usr-local-lib-R-
- name: Restore R library permissions
run: |
sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library
- name: Install dependencies
run: |
./run.sh install_aptget libhdf5-dev libharfbuzz-dev libfribidi-dev
./run.sh install_all
./run.sh install_r_binary covr rstudioapi
./run.sh install_r lucode2
- name: Install python dependencies if applicable
run: |
[ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
[ -f requirements.txt ] && pip install -r requirements.txt || true
- name: Remove bspm integration # to get rid of error when running install.packages
run: |
sudo sed -i '/ trace(utils::install.packages, expr, print = FALSE)/d' /etc/R/Rprofile.site
cat /etc/R/Rprofile.site
- name: Verify validation key
shell: Rscript {0}
run: lucode2:::validkey(stopIfInvalid = TRUE)
- name: Checks
shell: Rscript {0}
run: |
options(crayon.enabled = TRUE)
lucode2::check(runLinter = FALSE)
- name: Test coverage
shell: Rscript {0}
run: covr::codecov(quiet = FALSE)
env:
NOT_CRAN: "true"