update action and dockerfile

Author: jtanevski

.Rbuildignore

@@ -5,8 +5,7 @@
 ^Meta$
 (^|/)\.misty\.temp$
 (^|/)results$
-^vignettes/mistySeurat.Rmd$
-^vignettes/mistySpatialExperiment.Rmd$
+^vignettes/mistyDataFormats.Rmd$
 ^LICENSE$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.github/workflows/check-bioc.yml

@@ -4,14 +4,7 @@ on:
       - master
       - devel
 
-name: check-bioc3.16
-
-## If you need to clear the cache of packages, update the number inside
-## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
-## Note that you can always run a GHA test without the cache by using the word
-## "/nocache" in the commit message.
-env:
-  cache-version: 'cache-v1'
+name: check-bioc
 
 jobs:
   build-check:
@@ -23,9 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-20.04, r: '4.2', bioc: '3.16', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          # - { os: macOS-latest, r: '4.2', bioc: '3.16'}
-          # - { os: windows-latest, r: '4.2', bioc: '3.16'}
+          - { os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -47,60 +38,22 @@ jobs:
         uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-
-
-      - name: Cache R packages on Linux
-        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
         run: |
+          Rscript -e 'install.packages("remotes")'
           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 = " "))')
           echo $sysreqs
           sudo -s eval "$sysreqs"
           
           # SpatialExperiment (magick) dependency
           sudo apt-get install -y libmagick++-dev  
 
-      - name: Install macOS system dependencies
-        if: matrix.config.os == 'macOS-latest'
-        run: |
-          ## Enable installing XML from source if needed
-          brew install libxml2
-          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
-
-          ## Required to install magick as noted at
-          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
-          brew install imagemagick@6
-
-          ## For textshaping, required by ragg, and required by pkgdown
-          brew install harfbuzz fribidi
-
-          ## For installing usethis's dependency gert
-          brew install libgit2
-      
-      - name: Install Windows system dependencies
-        if: runner.os == 'Windows'
-        run: |
-          # Nothing needed 
-        shell: Rscript {0}
-
       - name: Install BiocManager
         run: |
           message(paste('****', Sys.time(), 'installing BiocManager ****'))
@@ -109,7 +62,7 @@ jobs:
 
       - name: Set BiocVersion
         run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+          BiocManager::install(ask = FALSE)
         shell: Rscript {0}
 
       - name: Install dependencies pass 1
@@ -140,8 +93,7 @@ jobs:
           tinytex::tlmgr_install("pdfcrop")
 
           ## For running the checks
-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          remotes::install_cran("rcmdcheck")
+          message(paste('****', Sys.time(), 'installing BiocCheck ****'))
           BiocManager::install("BiocCheck")
         shell: Rscript {0}
 
@@ -153,25 +105,13 @@ jobs:
         shell: Rscript {0}
 
       - name: Run CMD check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: |
-          rcmdcheck::rcmdcheck(
-              args = c("--no-build-vignettes", "--no-manual", "--timings"),
-              build_args = c("--no-manual", "--no-resave-data"),
-              error_on = "warning",
-              check_dir = "check"
-          )
-        shell: Rscript {0}
-
-      ## Might need an to add this to the if:  && runner.os == 'Linux'
-      - name: Reveal testthat details
-        run: find . -name testthat.Rout -exec cat '{}' ';'
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          error-on: '"error"'
 
       - name: Run BiocCheck
         run: |
           BiocCheck::BiocCheck(
-              dir('check', 'tar.gz$', full.names = TRUE),
               `quit-with-status` = TRUE,
               `no-check-R-ver` = TRUE,
               `no-check-bioc-help` = TRUE
@@ -193,16 +133,14 @@ jobs:
         run: |
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"
-          # For Seurat only
-          sudo apt-get install -y libhdf5-dev libgeos++-dev libgeos-3.8.0 libgeos-c1v5 libgeos-dev libgeos-doc
         shell: bash {0}
 
       ## Changing package deployment to make the necessary changes to the vignette files
       - name: Deploy package
         if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
         run: |
-          remotes::install_cran(c("pkgdown", "Seurat", "hdf5r"), upgrade = TRUE)
-          BiocManager::install(c("progeny", "SpatialExperiment"), ask = FALSE)
+          remotes::install_cran(c("pkgdown"), upgrade = TRUE)
+          BiocManager::install(c("decoupleR", "SpatialExperiment"), ask = FALSE)
 
           ## modified from pkgdown::deploy_to_branch
           deploy_to_branch_mod <- function(pkg = ".", commit_message = pkgdown:::construct_commit_message(pkg), 
@@ -285,10 +223,3 @@ jobs:
           push: true
           tags: tanevski/mistyr:devel
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
-        with:
-          name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-results
-          path: check
-

Dockerfile

@@ -10,9 +10,9 @@ RUN apt-get install -y curl
 RUN Rscript -e 'install.packages("remotes")'
 RUN $(Rscript -e 'cat("apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04"))))')
 RUN apt-get install -y ghostscript libmagick++-dev libhdf5-dev libgeos-c1v5
-RUN Rscript -e 'remotes::install_cran("BiocManager", ask = FALSE); BiocManager::install(version = "3.16", ask = FALSE)'
+RUN Rscript -e 'remotes::install_cran("BiocManager", ask = FALSE); BiocManager::install(ask = FALSE)'
 RUN Rscript -e 'remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), upgrade = "always")'
-RUN Rscript -e 'remotes::install_cran(c("Seurat", "rhdf5", "tinytex"), ask = FALSE)'
+RUN Rscript -e 'remotes::install_cran("tinytex", ask = FALSE)'
 RUN Rscript -e 'tinytex::install_tinytex(); tinytex::tlmgr_update(); tinytex::tlmgr_install("pdfcrop")'
 
 RUN Rscript -e 'remotes::install_local(build_vignettes = TRUE)'

vignettes/mistyDataFormats.Rmd

@@ -95,7 +95,7 @@ spe.vs <- readRDS("visium_spe.rds")
 expression <- counts(spe.vs)
 
 # deal with duplicate names
-symbols <- rowData(spe)$symbol
+symbols <- rowData(spe.vs)$symbol
 d.index <- which(duplicated(symbols))
 symbols[d.index] <- paste0(symbols[d.index],".1")
 rownames(expression) <- symbols