Update GHA

neurogenomics · May 3, 2022 · 741df36 · 741df36
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Showing 4 changed files with 57 additions and 49 deletions.
diff --git a/.github/workflows/check-bioc-docker.yml b/.github/workflows/check-bioc-docker.yml
@@ -43,7 +43,7 @@ env:
   cache-version: 'cache-v1'
   run_docker: 'true'
 
-jobs: 
+jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -67,14 +67,14 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
       GITHUB_PAT: ${{ secrets.PAT_GITHUB }}
       GITHUB_REPO: ${{ github.repository }}
-      RGL_USE_NULL: TRUE 
-      ## Can save variable as GitHub Secret, or manually enter DockerHub 
+      RGL_USE_NULL: TRUE
+      ## Can save variable as GitHub Secret, or manually enter DockerHub
       ## username here (e.g. "bschilder").
       DOCKER_USERNAME: "bschilder"
-      ## Can save variable as GitHub Secret, or manually enter DockerHub 
+      ## Can save variable as GitHub Secret, or manually enter DockerHub
       ## organization name (or simply username) here (e.g. "neurogenomicslab").
-      DOCKER_ORG: "neurogenomicslab" 
-      
+      DOCKER_ORG: "neurogenomicslab"
+
     steps:
       ## Set the R library to the directory matching the
       ## R packages cache step further below when running on Docker (Linux).
@@ -84,26 +84,26 @@ jobs:
           mkdir /__w/_temp/Library
           echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
 
-      ## Most of these steps are the same as the ones in  
+      ## Most of these steps are the same as the ones in
       ## 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
 
-      # R is already included in the Bioconductor docker image, 
+      # R is already included in the Bioconductor docker image,
       # which is only available with Linux as the OS.
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
         uses: r-lib/actions/setup-r@master
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}  
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master 
-        
+        uses: r-lib/actions/setup-pandoc@master
+
       - name: Query dependencies
         run: |
           install.packages('remotes')
@@ -153,7 +153,7 @@ jobs:
 
           ## Required for tcltk
           brew install xquartz --cask
-          
+
           ## Required for some ggplot2 functions
           # brew tap homebrew/cask
           # brew tap homebrew/cask-fonts
@@ -196,8 +196,8 @@ jobs:
           ## 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.  
-          
+          ## the Azure link will be the main one going forward.
+
           bioc_ver <- BiocManager::version()
           gha_repos <- if(
               .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
@@ -208,15 +208,15 @@ jobs:
 
           ## For running the checks
           ### hrbrthemes necessary to avoid ggplot2 errors on MacOS: https://stackoverflow.com/a/66423481/13214824
-          
+
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
           install.packages(c("rcmdcheck", "BiocCheck","rmarkdown"), 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.  
-          
+          ## 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 = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
         continue-on-error: true
@@ -231,13 +231,13 @@ jobs:
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         continue-on-error: true
         shell: Rscript {0}
-        
+
       - name: Install dependencies pass 3
         run: |
           ## Pass #3 at installing dependencies
           ## Install via binaries
           message(paste('****', Sys.time(), 'pass number 3 at installing dependencies: any remaining dependencies ****'))
-          remotes::install_local(type = "binary", dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
+          remotes::install_local(type = "binary", dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install BiocGenerics
@@ -302,7 +302,7 @@ jobs:
         env:
           DISPLAY: 99.0
         run: |
-          if(!require("BiocManager")) install.packages("BiocManager") 
+          if(!require("BiocManager")) install.packages("BiocManager")
           if(!require("BiocCheck")) BiocManager::install("BiocCheck")
           BiocCheck::BiocCheck(
               dir('check', 'tar.gz$', full.names = TRUE),
@@ -321,7 +321,21 @@ jobs:
       - name: Install package
         if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
-
+
+      - name: Get R package info
+        if: runner.os == 'Linux'
+        run: |
+          #### DockerHub repos must be lowercase (,,) ####
+          name=$(grep '^Package:' DESCRIPTION | cut -d\   -f2)
+          echo "packageName=${name,,}" >> $GITHUB_ENV
+          echo "packageNameOrig=${name}" >> $GITHUB_ENV
+          echo $name
+
+          version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
+          echo "packageVersion=${version}" >> $GITHUB_ENV
+          echo $version
+        shell: bash {0}
+
       - name: Render README
         if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && env.run_pkgdown == 'true' && runner.os == 'Linux'
         env:
@@ -332,13 +346,14 @@ jobs:
             rmarkdown::render("README.Rmd", output_format = rmarkdown::github_document(html_preview = FALSE));
           }
         shell: Rscript {0}
-
+        
       - name: Build and deploy pkgdown site
         if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
+          git config --global --add safe.directory /__w/${{env.packageNameOrig}}/${{env.packageNameOrig}} 
+          git config --local user.name "$GITHUB_ACTOR" 
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" 
+          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)
         ## at least one locally before this will work. This creates the gh-pages
@@ -350,32 +365,17 @@ jobs:
         uses: actions/upload-artifact@master
         with:
           name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-results
-          path: check 
-          
+          path: check
+
       # DockerHub steps
-      - name: Get R package info
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
-        run: |
-          #### DockerHub repos must be lowercase (,,) ####
-          name=$(grep '^Package:' DESCRIPTION | cut -d\   -f2)
-          echo "packageName=${name,,}" >> $GITHUB_ENV
-          echo "packageNameOrig=${name}" >> $GITHUB_ENV
-          echo $name
-          
-          version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
-          echo "packageVersion=${version}" >> $GITHUB_ENV
-          echo $version
-        shell: bash {0}
-
       - name: Build and push to DockerHub
         if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
-        uses: docker/build-push-action@v1 
+        uses: docker/build-push-action@v1
         with:
           username: ${{ env.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_TOKEN }}
           repository: ${{ env.DOCKER_ORG }}/${{ env.packageName }}
           tag_with_ref: true
           tag_with_sha: false
           tags: ${{ env.packageVersion }},latest
-          build_args: PKG=${{ env.packageNameOrig }},BIOC=${{ env.run_bioccheck }} 
-
+          build_args: PKG=${{ env.packageNameOrig }},BIOC=${{ env.run_bioccheck }}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MAGMA.Celltyping
 Type: Package
 Title: Find Causal Cell-Types Underlying Complex Trait Genetics
-Version: 2.0.3
+Version: 2.0.4
 Authors@R:
     c(person(given = "Brian",
            family = "Schilder",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+# MAGMA.Celltyping 2.0.4
+
+## Bug fixes
+
+* Fix GHA pkgdown building: 
+    - The newest version of [git introduced bugs when building pkgdown sites](https://github.com/actions/checkout/issues/760) 
+    from within Docker containers (e.g. via my Linux GHA workflow). 
+    Adjusting GHA to fix this. 
+
 # MAGMA.Celltyping 2.0.3
 
 ## Bug fixes

diff --git a/man/adjust_zstat_in_genesOut.Rd b/man/adjust_zstat_in_genesOut.Rd