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Update check-bioc.yml
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@stemangiola
stemangiola authored Oct 16, 2023
1 parent 3671b81 commit 2148006
Showing 1 changed file with 113 additions and 60 deletions.
173 changes: 113 additions & 60 deletions .github/workflows/check-bioc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,8 @@ env:
run_covr: 'false'
run_pkgdown: 'true'
has_RUnit: 'false'
cache-version: 'cache-v2'
cache-version: 'cache-v1'
run_docker: 'false'

jobs:
build-check:
Expand All @@ -48,12 +49,14 @@ jobs:
## Environment variables unique to this job.

strategy:
fail-fast: true
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
- { os: macOS-latest, r: '4.2', bioc: '3.16'}
- { os: windows-latest, r: '4.2', bioc: '3.16'}
- { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: '4.3', bioc: '3.18'}
- { os: windows-latest, r: '4.3', bioc: '3.18'}
## Check https://github.com/r-lib/actions/tree/master/examples
## for examples using the http-user-agent
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
Expand All @@ -76,14 +79,15 @@ jobs:
## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
## If they update their steps, we will also need to update ours.
- name: Checkout Repository
uses: actions/checkout@v2
uses: actions/checkout@v3

## R is already included in the Bioconductor docker images
- name: Setup R from r-lib
if: runner.os != 'Linux'
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}

## pandoc is already included in the Bioconductor docker images
- name: Setup pandoc from r-lib
Expand All @@ -96,26 +100,28 @@ jobs:
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}

- name: Cache R packages
- name: Restore R package cache
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ${{ env.R_LIBS_USER }}
key: "${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}r-{{ matrix.config.r }}"
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-

- name: Cache R packages on Linux
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: /home/runner/work/_temp/Library
key: "${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_${{ matrix.config.bioc }}r-{{ matrix.config.r }}"
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-

- name: Install Linux system dependencies
if: runner.os == 'Linux'
run: |
sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
echo $sysreqs
sudo -s eval "$sysreqs"
# - name: Install Linux system dependencies
# if: runner.os == 'Linux'
# run: |
# sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
# echo $sysreqs
# sudo -s eval "$sysreqs"

- name: Install macOS system dependencies
if: matrix.config.os == 'macOS-latest'
Expand All @@ -133,10 +139,9 @@ jobs:
## For installing usethis's dependency gert
brew install libgit2
## To fix x11/cairo error with tidyHeatmap/Complexheatmap here https://github.com/stemangiola/tidybulk/runs/1388237421?check_suite_focus=true#step:14:2134
## Suggested here https://stackoverflow.com/questions/63648591/how-to-install-x11-before-testing-with-github-actions-for-macos
brew install --cask xquartz
## Required for tcltk
brew install xquartz --cask
- name: Install Windows system dependencies
if: runner.os == 'Windows'
Expand All @@ -147,12 +152,12 @@ jobs:
- name: Install BiocManager
run: |
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_github("Bioconductor/BiocManager")
remotes::install_cran("BiocManager")
shell: Rscript {0}

- name: Set BiocVersion
run: |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
shell: Rscript {0}

- name: Install dependencies pass 1
Expand All @@ -164,6 +169,10 @@ jobs:
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
## Pass #1 at installing dependencies
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
Expand All @@ -174,21 +183,7 @@ jobs:
run: |
## Pass #2 at installing dependencies
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
BiocManager::install("BiocCheck")
shell: Rscript {0}

# This is a hack to fix this bug: https://stackoverflow.com/q/73700130/2148718
# Basically the Seurat and SeuratObject binary packages are compiled against an
# older version of Matrix, which causes an error we can fix by re-compiling from source
- name: Fix Matrix on MacOS.
if: matrix.config.os == 'macOS-latest'
run: |
install.packages(c("Seurat", "SeuratObject"), type="source")
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
shell: Rscript {0}

- name: Install BiocGenerics
Expand All @@ -199,15 +194,15 @@ jobs:
shell: Rscript {0}

- name: Install covr
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("covr")
shell: Rscript {0}

- name: Install pkgdown
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("pkgdown")
remotes::install_github("r-lib/pkgdown")
shell: Rscript {0}

- name: Session info
Expand All @@ -220,10 +215,12 @@ jobs:
- name: Run CMD check
env:
_R_CHECK_CRAN_INCOMING_: false
DISPLAY: 99.0
run: |
options(crayon.enabled = TRUE)
rcmdcheck::rcmdcheck(
args = c("--no-manual", "--timings"),
build_args = c("--no-manual", "--no-resave-data"),
args = c("--no-manual", "--no-vignettes", "--timings"),
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
error_on = "warning",
check_dir = "check"
)
Expand All @@ -241,45 +238,101 @@ jobs:
shell: Rscript {0}

- name: Run BiocCheck
env:
DISPLAY: 99.0
run: |
BiocCheck::BiocCheck(
dir('check', 'tar.gz$', full.names = TRUE),
`quit-with-status` = TRUE,
`no-check-R-ver` = TRUE,
`no-check-bioc-help` = TRUE,
`new-package` = TRUE
`no-check-bioc-help` = TRUE
)
shell: Rscript {0}

- name: Test coverage
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
covr::codecov()
shell: Rscript {0}

- name: Install package
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .

- name: Deploy package
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
## Temporary workaround for https://github.com/actions/checkout/issues/766
git config --global --add safe.directory "$GITHUB_WORKSPACE"
git config --local user.email "[email protected]"
git config --local user.name "GitHub Actions"
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
shell: bash {0}
- name: Build pkgdown site
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
shell: Rscript {0}
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
## at least one locally before this will work. This creates the gh-pages
## branch (erasing anything you haven't version controlled!) and
## makes the git history recognizable by pkgdown.

- name: Install deploy dependencies
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
apt-get update && apt-get -y install rsync
- name: Deploy pkgdown site to GitHub pages 🚀
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
uses: JamesIves/github-pages-deploy-action@releases/v4
with:
clean: false
branch: gh-pages
folder: docs

- name: Upload check results
if: failure()
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results
name: ${{ runner.os }}-biocversion-devel-r-4.3-results
path: check



## Code adapted from
## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
docker-build-and-push:
runs-on: ubuntu-latest
needs: build-check
steps:
- name: Checkout Repository
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: actions/checkout@v3

- name: Register repo name
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
id: reg_repo_name
run: |
echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
- name: Set up QEMU
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: docker/setup-qemu-action@v2

- name: Set up Docker Buildx
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: docker/setup-buildx-action@v2

- name: Login to Docker Hub
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: docker/login-action@v2
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
## account, not your actual dockerhub account password. You can get it
## from https://hub.docker.com/settings/security.
## Check https://github.com/docker/build-push-action/tree/v4.0.0
## for more details.
## Alternatively, try checking
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.

- name: Build and Push Docker
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
uses: docker/build-push-action@v4
with:
context: .
push: true
tags: >
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel

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