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Update github action to Bioc 3.15 #234

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Merged
merged 2 commits into from
May 28, 2022
Merged

Update github action to Bioc 3.15 #234

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d35f7a1
Update github action to Bioc 3.15
mblue9 May 27, 2022
4a110fa
Edit to action
mblue9 May 28, 2022
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44 changes: 13 additions & 31 deletions .github/workflows/check-bioc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,6 @@ env:
run_pkgdown: 'true'
has_RUnit: 'false'
cache-version: 'cache-v1'
run_docker: 'false'

jobs:
build-check:
Expand All @@ -52,9 +51,9 @@ 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: '4.2', bioc: '3.15', cont: "bioconductor/bioconductor_docker:RELEASE_3_15", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
- { os: macOS-latest, r: '4.2', bioc: '3.15'}
- { os: windows-latest, r: '4.2', bioc: '3.15'}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
Expand Down Expand Up @@ -102,16 +101,16 @@ jobs:
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-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-

- 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-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-

- name: Install Linux system dependencies
if: runner.os == 'Linux'
Expand Down Expand Up @@ -157,13 +156,6 @@ jobs:
run: |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
shell: Rscript {0}

## 12th April 2021 No Seurat binary available for Mac currently so install from source
- name: Install Seurat for macOS-latest
if: matrix.config.os == 'macOS-latest'
run: |
BiocManager::install("Seurat", type="source")
shell: Rscript {0}

- name: Install dependencies pass 1
run: |
Expand All @@ -173,9 +165,6 @@ jobs:
## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.

## To fix preprocessCore error https://github.com/stemangiola/tidybulk/issues/145
BiocManager::install("preprocessCore", configure.args="--disable-threading")

## Pass #1 at installing dependencies
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
Expand All @@ -188,7 +177,7 @@ jobs:
## 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 = TRUE, upgrade = TRUE)

## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
Expand All @@ -211,7 +200,7 @@ jobs:
- name: Install pkgdown
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
remotes::install_github("r-lib/pkgdown")
remotes::install_cran("pkgdown")
shell: Rscript {0}

- name: Session info
Expand Down Expand Up @@ -269,6 +258,9 @@ jobs:
- 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 "actions@github.com"
git config --local user.name "GitHub Actions"
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
Expand All @@ -282,15 +274,5 @@ jobs:
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-results
name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-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: stemangiola/tidybulk
tag_with_ref: true
tag_with_sha: true
tags: latest