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Check data for relative abundances and provide helper function (#28) #129

Check data for relative abundances and provide helper function (#28)

Check data for relative abundances and provide helper function (#28) #129

Workflow file for this run

name: build
'on': push
jobs:
build:
runs-on: ubuntu-18.04
container: bioconductor/bioconductor_docker:devel
steps:
- name: Checkout Repository
uses: actions/checkout@v1
- 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@v1
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 "$sysreqs"
- name: Install dependencies
run: |
local_deps <- remotes::local_package_deps(dependencies = TRUE)
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpus=2)
remotes::install_cran('rcmdcheck')
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
- name: Deploy 🚀
uses: JamesIves/github-pages-deploy-action@releases/v3
with:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
BRANCH: gh-pages # The branch the action should deploy to.
FOLDER: docs # The folder the action should deploy.