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bug fix: expr to relab from resolved conflict #142

bug fix: expr to relab from resolved conflict

bug fix: expr to relab from resolved conflict #142

Workflow file for this run

name: build
on:
push:
branches:
- devel
jobs:
build:
runs-on: ubuntu-latest
container: bioconductor/bioconductor_docker:latest
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: Checkout Repository
uses: actions/checkout@v3
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v2
with:
path: /usr/local/lib/R/site-library
key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-r-1-
# This lets us augment with additional dependencies
- name: Install system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
- name: Install dependencies
run: |
options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))
remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install(c("rcmdcheck", "pkgdown"), ask = FALSE, update = TRUE)
shell: Rscript {0}
- name: Check
env:
_R_CHECK_CRAN_INCOMING_REMOTE_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
- name: generate codecov report
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
run: |
Rscript -e "suppressMessages(x <- covr::codecov())"
- name: Build pkgdown
run: |
PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'
# deploy needs rsync? Seems so.
- name: Install deploy dependencies
run: |
apt-get update
apt-get -y install rsync git
- name: Deploy 🚀
uses: JamesIves/github-pages-deploy-action@v4
with:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
BRANCH: gh-pages # The branch the action should deploy to.
FOLDER: docs # The folder the action should deploy.