fix unruly URL issues #36
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on: | |
push: | |
branches: [main, devel] | |
pull_request: | |
branches: [devel] | |
name: Build-Check | |
jobs: | |
R-CMD-check: | |
runs-on: ${{ matrix.config.os }} | |
name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- {os: macOS-latest, r: 'release'} | |
- {os: windows-latest, r: 'release'} | |
# - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} # bioconductor not ready | |
- {os: ubuntu-latest, r: 'release'} | |
- {os: ubuntu-latest, r: 'oldrel-1'} | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
R_KEEP_PKG_SOURCE: yes | |
_R_CHECK_CRAN_INCOMING_REMOTE_: false | |
steps: | |
- uses: actions/checkout@v2 | |
- uses: r-lib/actions/setup-pandoc@v2 | |
- uses: r-lib/actions/setup-r@v2 | |
with: | |
r-version: ${{ matrix.config.r }} | |
http-user-agent: ${{ matrix.config.http-user-agent }} | |
use-public-rspm: true | |
- uses: r-lib/actions/setup-tinytex@v2 | |
- run: | | |
tlmgr --version | |
tlmgr install colortbl | |
tlmgr install parskip | |
tlmgr install ae | |
tlmgr install upquote | |
- name: Install Bioconductor dependencies | |
run: | | |
# need to install some pkgs from Bioconductor | |
if (!requireNamespace("BiocManager", quietly = TRUE)) | |
install.packages("BiocManager") | |
BiocManager::install("MassSpecWavelet") | |
BiocManager::install("impute") | |
BiocManager::install("mixOmics") | |
shell: Rscript {0} | |
- name: Install other dependencies | |
run: | | |
install.packages("remotes") # needed here! | |
install.packages("roxygen2") | |
install.packages("rcmdcheck") # apparently assumed by check-r-package below | |
remotes::install_deps(dependencies = TRUE) # all others | |
shell: Rscript {0} | |
- name: Roxygenize | |
run: | | |
roxygen2::roxygenize() | |
shell: Rscript {0} | |
- name: Build and Check | |
# env: | |
# _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
uses: r-lib/actions/check-r-package@v2 | |
with: | |
upload-snapshots: true |