[r/ci] Controlled downgrade for TileDB-R 0.23 [WIP]

single-cell-data · Feb 20, 2024 · abc68b8 · abc68b8
1 parent 3c658a0
commit abc68b8
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Showing 2 changed files with 39 additions and 11 deletions.
diff --git a/.github/workflows/r-ci.yml b/.github/workflows/r-ci.yml
@@ -55,16 +55,12 @@ jobs:
       - name: Install BioConductor package SingleCellExperiment
         run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment
 
-      # Uncomment these next two stanzas as needed whenever we've just released a new tiledb-r for
-      # which source is available but CRAN releases (and hence update r2u binaries) are not yet:
-
-      - name: Install r-universe build of tiledb-r (macOS)
-        if: ${{ matrix.os == 'macOS-latest' }}
-        run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev', 'https://cloud.r-project.org'))"
-
-      - name: Install r-universe build of tiledb-r (linux)
-        if: ${{ matrix.os != 'macOS-latest' }}
-        run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))"
+      - name: Install 0.23 build of tiledb-r with core 2.19
+        run: |
+          cd apis/r
+          wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.23.0.tar.gz
+          Rscript -e 'remotes::install_deps("0.23.0.tar.gz")'
+          R CMD INSTALL 0.23.0.tar.gz    # as 0.23.0 is needed by TileDB-SOMA 1.7
 
       - name: Install r-universe build of SeuratObject (macOS)
         if: ${{ matrix.os == 'macOS-latest' }}
@@ -93,6 +89,13 @@ jobs:
       - name: Update Packages
         run: Rscript -e 'update.packages(ask=FALSE)'
 
+      - name: Re-install 0.23 build of tiledb-r with core 2.19
+        run: |
+          cd apis/r
+          wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.23.0.tar.gz
+          Rscript -e 'remotes::install_deps("0.23.0.tar.gz")'
+          R CMD INSTALL 0.23.0.tar.gz    # as 0.23.0 is needed by TileDB-SOMA 1.7
+
       # - name: Build Package
       #   run: cd apis/r && R CMD build --no-build-vignettes --no-manual .
 

diff --git a/.github/workflows/r-python-interop-testing.yml b/.github/workflows/r-python-interop-testing.yml
@@ -41,6 +41,13 @@ jobs:
       - name: MkVars
         run: mkdir ~/.R && echo "CXX17FLAGS=-Wno-deprecated-declarations -Wno-deprecated" > ~/.R/Makevars
 
+      - name: Install 0.23 build of tiledb-r with core 2.19
+        run: |
+          cd apis/r
+          wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.23.0.tar.gz
+          Rscript -e 'remotes::install_deps("0.23.0.tar.gz")'
+          R CMD INSTALL 0.23.0.tar.gz    # as 0.23.0 is needed by TileDB-SOMA 1.7
+
       - name: Install r-universe build of tiledb-r (macOS)
         if: ${{ matrix.os == 'macOS-latest' }}
         run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev', 'https://cloud.r-project.org'))"
@@ -75,13 +82,31 @@ jobs:
       - name: Install tiledbsoma
         run: python -m pip -v install -e apis/python
 
-      - name: Show Python package versions
+      - name: Show package versions
         run: |
           python -c 'import tiledbsoma; tiledbsoma.show_package_versions()'
+          echo
           python scripts/show-versions.py
+          echo
+          Rscript -e 'tiledbsoma::show_package_versions()'
 
       - name: Update Packages
         run: Rscript -e 'update.packages(ask=FALSE)'
 
+      - name: Re-install 0.23 build of tiledb-r with core 2.19
+        run: |
+          cd apis/r
+          wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.23.0.tar.gz
+          Rscript -e 'remotes::install_deps("0.23.0.tar.gz")'
+          R CMD INSTALL 0.23.0.tar.gz    # as 0.23.0 is needed by SOMA 1.7
+
+      - name: Show package versions
+        run: |
+          python -c 'import tiledbsoma; tiledbsoma.show_package_versions()'
+          echo
+          python scripts/show-versions.py
+          echo
+          Rscript -e 'tiledbsoma::show_package_versions()'
+
       - name: Interop Tests
         run: python -m pytest apis/system/tests/