v1.27.1 -- match bioc 1.3.6 and fix lcolladotor/derfinder#42

leekgroup · Aug 5, 2021 · 74530c8 · 74530c8
1 parent ccf6de5
commit 74530c8
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Showing 4 changed files with 48 additions and 27 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -39,6 +39,7 @@ env:
   run_pkgdown: 'true'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
+  run_docker: 'false'
 
 jobs:
   build-check:
@@ -51,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { 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" }
-          - { os: macOS-latest, r: '4.0', bioc: '3.12'}
-          - { os: windows-latest, r: '4.0', bioc: '3.12'}
+          - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:devel", 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'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -101,16 +102,16 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
 
       - 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_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -135,6 +136,9 @@ 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'
@@ -150,7 +154,7 @@ 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
@@ -162,28 +166,32 @@ jobs:
           ## https://github.com/r-lib/remotes/issues/296
           ## Ideally, all dependencies should get installed in the first pass.
 
-          ## For testing regionReport v1.25.3 that depends on derfinder 1.25.3
-          ## that I just updated due to an error on the BBS as noted at
-          ## https://github.com/lcolladotor/derfinder/commit/2a6d8ac1161d85dcf142551ebdb0ff5a07cf61fc
-          ## This will be temporary.
-          BiocManager::install("lcolladotor/derfinder")
+          ## 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") c("AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.14/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)
+          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)
-
-          ## For running the checks
-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          remotes::install_cran("rcmdcheck")
-          BiocManager::install("BiocCheck")
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install BiocGenerics
@@ -202,7 +210,7 @@ jobs:
       - name: Install pkgdown
         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          remotes::install_cran("pkgdown")
+          remotes::install_github("r-lib/pkgdown")
         shell: Rscript {0}
 
       - name: Session info
@@ -215,6 +223,7 @@ jobs:
       - name: Run CMD check
         env:
           _R_CHECK_CRAN_INCOMING_: false
+          DISPLAY: 99.0
         run: |
           rcmdcheck::rcmdcheck(
               args = c("--no-build-vignettes", "--no-manual", "--timings"),
@@ -236,6 +245,8 @@ jobs:
         shell: Rscript {0}
 
       - name: Run BiocCheck
+        env:
+          DISPLAY: 99.0
         run: |
           BiocCheck::BiocCheck(
               dir('check', 'tar.gz$', full.names = TRUE),
@@ -271,5 +282,15 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-results
+          name: ${{ runner.os }}-biocversion-devel-r-4.1-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: leekgroup/regionreport
+          tag_with_ref: true
+          tag_with_sha: true
+          tags: latest
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: regionReport
 Type: Package
 Title: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
-Version: 1.27.0
-Date: 2021-05-01
+Version: 1.27.1
+Date: 2021-08-05
 Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
     = "[email protected]", comment = c(ORCID = "0000-0003-2140-308X")),
     person(c("Andrew", "E."), "Jaffe", role = "aut",

diff --git a/README.Rmd b/README.Rmd
@@ -49,7 +49,7 @@ For more information about `derfinderPlot` check the vignettes [through Biocondu
 
 ## Installation instructions
 
-Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `regionReport` using from [Bioconductor](http://bioconductor.org/) the following code:
+Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `regionReport` from [Bioconductor](http://bioconductor.org/) using the following code:
 
 ```{r 'install', eval = FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE)) {

diff --git a/README.md b/README.md
@@ -54,8 +54,8 @@ Bioconductor](http://bioconductor.org/packages/regionReport) or at the
 ## Installation instructions
 
 Get the latest stable `R` release from
-[CRAN](http://cran.r-project.org/). Then install `regionReport` using
-from [Bioconductor](http://bioconductor.org/) the following code:
+[CRAN](http://cran.r-project.org/). Then install `regionReport` from
+[Bioconductor](http://bioconductor.org/) using the following code:
 
 ``` r
 if (!requireNamespace("BiocManager", quietly = TRUE)) {