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Update GHA to bioc-devel
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Co-authored-by: Josh Stolz <[email protected]>
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@lcolladotor @joshstolz
lcolladotor and joshstolz committed Mar 23, 2022
1 parent 1b28ad3 commit 7bec550
Showing 1 changed file with 50 additions and 25 deletions.
75 changes: 50 additions & 25 deletions .github/workflows/check-bioc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@ name: R-CMD-check-bioc
## Note that you can always run a GHA test without the cache by using the word
## "/nocache" in the commit message.
env:
has_testthat: 'false'
run_covr: 'false'
has_testthat: 'true'
run_covr: 'true'
run_pkgdown: 'true'
has_RUnit: 'false'
cache-version: 'cache-v1'
Expand All @@ -52,9 +52,11 @@ jobs:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
- { os: macOS-latest, r: '4.1', bioc: '3.14'}
- { os: windows-latest, r: '4.1', bioc: '3.14'}
- { os: ubuntu-latest, r: 'devel', bioc: '3.15', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
- { os: macOS-latest, r: 'devel', bioc: '3.15'}
- { os: windows-latest, r: 'devel', bioc: '3.15'}
## 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 Down Expand Up @@ -85,6 +87,7 @@ jobs:
uses: r-lib/actions/setup-r@master
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 @@ -97,21 +100,21 @@ 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
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-

- name: Cache R packages on Linux
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
uses: actions/cache@v2
with:
path: /home/runner/work/_temp/Library
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-

- name: Install Linux system dependencies
if: runner.os == 'Linux'
Expand All @@ -137,6 +140,9 @@ jobs:
## For installing usethis's dependency gert
brew install libgit2
## Required for tcltk
brew install xquartz --cask
- name: Install Windows system dependencies
if: runner.os == 'Windows'
run: |
Expand All @@ -151,7 +157,7 @@ jobs:

- 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 @@ -163,22 +169,37 @@ jobs:
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Set the repos source depending on the OS
## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
## though based on https://bit.ly/bioc2021-package-binaries
## the Azure link will be the main one going forward.
gha_repos <- if(
.Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
) c(
"AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.15/bioc",
BiocManager::repositories()
) else BiocManager::repositories()
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
## Pass #1 at installing dependencies
## This pass uses AnVIL-powered fast binaries
## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
## The speed gains only apply to the docker builds.
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
continue-on-error: true
shell: Rscript {0}

- name: Install dependencies pass 2
run: |
## Pass #2 at installing dependencies
## This pass does not use AnVIL and will thus update any packages
## that have seen been updated in Bioconductor
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
BiocManager::install("BiocCheck")
shell: Rscript {0}

- name: Install BiocGenerics
Expand All @@ -197,7 +218,7 @@ jobs:
- name: Install pkgdown
if: github.ref == 'refs/heads/main' && 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 @@ -210,10 +231,12 @@ jobs:
- name: Run CMD check
env:
_R_CHECK_CRAN_INCOMING_: false
DISPLAY: 99.0
run: |
options(crayon.enabled = TRUE)
rcmdcheck::rcmdcheck(
args = c("--no-build-vignettes", "--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 @@ -231,6 +254,8 @@ jobs:
shell: Rscript {0}

- name: Run BiocCheck
env:
DISPLAY: 99.0
run: |
BiocCheck::BiocCheck(
dir('check', 'tar.gz$', full.names = TRUE),
Expand All @@ -250,11 +275,11 @@ jobs:
if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .

- name: Deploy package
- name: Build and deploy pkgdown site
if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
git config --local user.email "[email protected]"
git config --local user.name "GitHub Actions"
git config --local user.name "$GITHUB_ACTOR"
git config --local user.email "[email protected]"
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
shell: bash {0}
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
Expand All @@ -266,15 +291,15 @@ jobs:
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-results
name: ${{ runner.os }}-biocversion-devel-r-devel-results
path: check

- uses: docker/build-push-action@v1
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
repository: lieberinstitute/qsvaR
repository: lieberinstitute/qsvar
tag_with_ref: true
tag_with_sha: true
tags: latest

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