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Merge branch 'devel' into annot_from_TxDB
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‎.github/workflows/check-bioc.yml

+118-50
Original file line numberDiff line numberDiff line change
@@ -39,6 +39,7 @@ env:
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run_pkgdown: 'false'
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has_RUnit: 'false'
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cache-version: 'cache-v1'
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run_docker: 'false'
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jobs:
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build-check:
@@ -51,9 +52,11 @@ jobs:
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fail-fast: false
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matrix:
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config:
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- { os: ubuntu-latest, r: '4.0', bioc: '3.12', cont: "bioconductor/bioconductor_docker:RELEASE_3_12", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
55-
- { os: macOS-latest, r: '4.0', bioc: '3.12'}
56-
- { os: windows-latest, r: '4.0', bioc: '3.12'}
55+
- { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
56+
- { os: macOS-latest, r: '4.4', bioc: '3.20'}
57+
- { os: windows-latest, r: '4.4', bioc: '3.20'}
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## Check https://github.com/r-lib/actions/tree/master/examples
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## for examples using the http-user-agent
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
@@ -76,48 +79,49 @@ jobs:
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## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
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## If they update their steps, we will also need to update ours.
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- name: Checkout Repository
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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## R is already included in the Bioconductor docker images
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- name: Setup R from r-lib
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if: runner.os != 'Linux'
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uses: r-lib/actions/setup-r@master
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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## pandoc is already included in the Bioconductor docker images
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- name: Setup pandoc from r-lib
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if: runner.os != 'Linux'
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uses: r-lib/actions/setup-pandoc@master
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uses: r-lib/actions/setup-pandoc@v2
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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shell: Rscript {0}
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- name: Cache R packages
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- name: Restore R package cache
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if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
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uses: actions/cache@v2
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uses: actions/cache@v3
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
108+
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-
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- name: Cache R packages on Linux
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if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
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uses: actions/cache@v2
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uses: actions/cache@v3
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with:
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path: /home/runner/work/_temp/Library
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
116+
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }}
117+
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-
114118

115-
- name: Install Linux system dependencies
116-
if: runner.os == 'Linux'
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run: |
118-
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 = " "))')
119-
echo $sysreqs
120-
sudo -s eval "$sysreqs"
119+
# - name: Install Linux system dependencies
120+
# if: runner.os == 'Linux'
121+
# run: |
122+
# 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 = " "))')
123+
# echo $sysreqs
124+
# sudo -s eval "$sysreqs"
121125

122126
- name: Install macOS system dependencies
123127
if: matrix.config.os == 'macOS-latest'
@@ -133,8 +137,11 @@ jobs:
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## For textshaping, required by ragg, and required by pkgdown
134138
brew install harfbuzz fribidi
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## Helps compile RCurl from source
137-
brew uninstall curl
140+
## For installing usethis's dependency gert
141+
brew install libgit2
142+
143+
## Required for tcltk
144+
brew install xquartz --cask
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- name: Install Windows system dependencies
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if: runner.os == 'Windows'
@@ -150,10 +157,10 @@ jobs:
150157

151158
- name: Set BiocVersion
152159
run: |
153-
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
160+
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
154161
shell: Rscript {0}
155162

156-
- name: Install dependencies
163+
- name: Install dependencies pass 1
157164
run: |
158165
## Try installing the package dependencies in steps. First the local
159166
## dependencies, then any remaining dependencies to avoid the
@@ -162,23 +169,21 @@ jobs:
162169
## https://github.com/r-lib/remotes/issues/296
163170
## Ideally, all dependencies should get installed in the first pass.
164171
165-
## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79
166-
remotes::install_github("ropensci/bibtex")
167-
remotes::install_github("ropensci/RefManageR")
168-
remotes::install_github("cboettig/knitcitations")
172+
## For running the checks
173+
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
174+
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
169175
170176
## Pass #1 at installing dependencies
171177
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
172-
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
178+
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
179+
continue-on-error: true
180+
shell: Rscript {0}
173181

182+
- name: Install dependencies pass 2
183+
run: |
174184
## Pass #2 at installing dependencies
175185
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
176-
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
177-
178-
## For running the checks
179-
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
180-
remotes::install_cran("rcmdcheck")
181-
BiocManager::install("BiocCheck")
186+
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
182187
shell: Rscript {0}
183188

184189
- name: Install BiocGenerics
@@ -189,15 +194,15 @@ jobs:
189194
shell: Rscript {0}
190195

191196
- name: Install covr
192-
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
197+
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
193198
run: |
194199
remotes::install_cran("covr")
195200
shell: Rscript {0}
196201

197202
- name: Install pkgdown
198-
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
203+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
199204
run: |
200-
remotes::install_cran("pkgdown")
205+
remotes::install_github("r-lib/pkgdown")
201206
shell: Rscript {0}
202207

203208
- name: Session info
@@ -210,10 +215,12 @@ jobs:
210215
- name: Run CMD check
211216
env:
212217
_R_CHECK_CRAN_INCOMING_: false
218+
DISPLAY: 99.0
213219
run: |
220+
options(crayon.enabled = TRUE)
214221
rcmdcheck::rcmdcheck(
215-
args = c("--no-build-vignettes", "--no-manual", "--timings"),
216-
build_args = c("--no-manual", "--no-resave-data"),
222+
args = c("--no-manual", "--no-vignettes", "--timings"),
223+
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
217224
error_on = "warning",
218225
check_dir = "check"
219226
)
@@ -231,6 +238,8 @@ jobs:
231238
shell: Rscript {0}
232239

233240
- name: Run BiocCheck
241+
env:
242+
DISPLAY: 99.0
234243
run: |
235244
BiocCheck::BiocCheck(
236245
dir('check', 'tar.gz$', full.names = TRUE),
@@ -241,30 +250,89 @@ jobs:
241250
shell: Rscript {0}
242251

243252
- name: Test coverage
244-
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
253+
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
245254
run: |
246-
covr::codecov()
255+
covr::codecov(coverage = covr::package_coverage(type = "all"))
247256
shell: Rscript {0}
248257

249258
- name: Install package
250-
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
259+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
251260
run: R CMD INSTALL .
252261

253-
- name: Deploy package
254-
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
255-
run: |
256-
git config --local user.email "actions@github.com"
257-
git config --local user.name "GitHub Actions"
258-
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
259-
shell: bash {0}
262+
- name: Build pkgdown site
263+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
264+
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
265+
shell: Rscript {0}
260266
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
261267
## at least one locally before this will work. This creates the gh-pages
262268
## branch (erasing anything you haven't version controlled!) and
263269
## makes the git history recognizable by pkgdown.
264270

271+
- name: Install deploy dependencies
272+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
273+
run: |
274+
apt-get update && apt-get -y install rsync
275+
276+
- name: Deploy pkgdown site to GitHub pages 🚀
277+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
278+
uses: JamesIves/github-pages-deploy-action@releases/v4
279+
with:
280+
clean: false
281+
branch: gh-pages
282+
folder: docs
283+
265284
- name: Upload check results
266285
if: failure()
267286
uses: actions/upload-artifact@master
268287
with:
269-
name: ${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-results
288+
name: ${{ runner.os }}-biocversion-devel-r-4.4-results
270289
path: check
290+
291+
292+
## Code adapted from
293+
## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
294+
docker-build-and-push:
295+
runs-on: ubuntu-latest
296+
needs: build-check
297+
steps:
298+
- name: Checkout Repository
299+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
300+
uses: actions/checkout@v3
301+
302+
- name: Register repo name
303+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
304+
id: reg_repo_name
305+
run: |
306+
echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
307+
308+
- name: Set up QEMU
309+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
310+
uses: docker/setup-qemu-action@v2
311+
312+
- name: Set up Docker Buildx
313+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
314+
uses: docker/setup-buildx-action@v2
315+
316+
- name: Login to Docker Hub
317+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
318+
uses: docker/login-action@v2
319+
with:
320+
username: ${{ secrets.DOCKERHUB_USERNAME }}
321+
password: ${{ secrets.DOCKERHUB_TOKEN }}
322+
## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
323+
## account, not your actual dockerhub account password. You can get it
324+
## from https://hub.docker.com/settings/security.
325+
## Check https://github.com/docker/build-push-action/tree/v4.0.0
326+
## for more details.
327+
## Alternatively, try checking
328+
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
329+
330+
- name: Build and Push Docker
331+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
332+
uses: docker/build-push-action@v4
333+
with:
334+
context: .
335+
push: true
336+
tags: >
337+
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
338+
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel

‎.gitignore

+1
Original file line numberDiff line numberDiff line change
@@ -3,3 +3,4 @@
33
.RData
44
.Ruserdata
55
.httr-oauth
6+
CAGEr.Rproj

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