Fix vignette entry (#6)

* updated roxygen version * fixing the name of the index entry - displayed when rendered in the Bioc landing page * re-rendering manpages * update github action workflow to that of iSEE --------- Co-authored-by: Kevin Rue-Albrecht <[email protected]>
iSEE · Sep 4, 2024 · 82c7093 · 82c7093
1 parent 8ebd71b
commit 82c7093
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -6,3 +6,4 @@
 ^README\.Rmd$
 ^\.github$
 ^codecov\.yml$
+^iSEEhex\.Rproj$
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { 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'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.20'}
+          - { os: windows-latest, r: 'devel', bioc: '3.20'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -79,20 +79,20 @@ jobs:
       ## 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
+        uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         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
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -102,19 +102,19 @@ jobs:
 
       - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          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-
+          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
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          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-
+          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'
@@ -128,7 +128,7 @@ jobs:
         run: |
           ## Enable installing XML from source if needed
           brew install libxml2
-          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
+          echo "XML_CONFIG=/opt/homebrew/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
 
           ## Required to install magick as noted at
           ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
@@ -143,6 +143,21 @@ jobs:
           ## Required for tcltk
           brew install xquartz --cask
 
+          ## Required for terra
+          brew install gdal
+
+          ## Temporary fix for freetype (https://github.com/r-lib/ragg/issues/170; Sep 2024)
+          #brew install --cask https://raw.githubusercontent.com/Homebrew/homebrew-core/d28afc3bfdb5d24eab02157bfffcc9e17ed6666c/Formula/f/freetype.rb
+          brew unlink freetype
+          curl -L https://raw.githubusercontent.com/Homebrew/homebrew-core/3db6dc6c4baf5a75e345f380cc4e8224c1ae5ae0/Formula/f/freetype.rb > freetype.rb && brew install freetype.rb
+
+      - name: Install binary units for macOS
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+          ## temporary fix due to issue in udunits (Sep 2024)
+          install.packages('https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/units_0.8-5.tgz')
+        shell: Rscript {0}
+
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
         run: |
@@ -176,7 +191,7 @@ jobs:
           gha_repos <- if(
               .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
           ) c(
-              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.15/bioc",
+              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.20/bioc",
               BiocManager::repositories()
               ) else BiocManager::repositories()
 
@@ -210,13 +225,13 @@ jobs:
         shell: Rscript {0}
 
       - name: Install covr
-        if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Install pkgdown
-        if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("pkgdown")
         shell: Rscript {0}
@@ -237,7 +252,7 @@ jobs:
           rcmdcheck::rcmdcheck(
               args = c("--no-manual", "--no-vignettes", "--timings"),
               build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
-              error_on = "error",
+              error_on = "warning",
               check_dir = "check"
           )
         shell: Rscript {0}
@@ -259,28 +274,28 @@ jobs:
         run: |
           BiocCheck::BiocCheck(
               dir('check', 'tar.gz$', full.names = TRUE),
-              `quit-with-status` = TRUE,
+              `quit-with-status` = FALSE,
               `no-check-R-ver` = TRUE,
               `no-check-bioc-help` = TRUE
           )
         shell: Rscript {0}
 
       - name: Test coverage
-        if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           covr::codecov()
         shell: Rscript {0}
 
       - name: Install package
-        if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
       - name: Build and deploy pkgdown site
-        if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
           git config --global user.name "$GITHUB_ACTOR"
           git config --global user.email "[email protected]"
-          git config --global --add safe.directory /__w/iSEEhex/iSEEhex
+          git config --global --add safe.directory /__w/iSEE/iSEEhex
           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)
@@ -292,15 +307,15 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-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: iseedevelopers/iseehex
+          repository: isee/iseehex
           tag_with_ref: true
           tag_with_sha: true
           tags: latest
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -34,7 +34,7 @@ biocViews: Software,
     Infrastructure
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.3.2
 Depends:
     SummarizedExperiment,
     iSEE

diff --git a/man/iSEEhex-pkg.Rd b/man/iSEEhex-pkg.Rd
diff --git a/vignettes/iSEEhex.Rmd b/vignettes/iSEEhex.Rmd
@@ -22,7 +22,7 @@ date: "`r BiocStyle::doc_date()`"
 package: iSEEhex
 output: BiocStyle::html_document
 vignette: >
-  %\VignetteIndexEntry{Panel universe}
+  %\VignetteIndexEntry{The iSEEhex package}
   %\VignetteEncoding{UTF-8}  
   %\VignettePackage{iSEEhex}
   %\VignetteKeywords{GeneExpression, RNASeq, Sequencing, Visualization, QualityControl, GUI}