Merge pull request #39 from HectorRDB/Fix_16

Fix # 16
HectorRDB · Dec 3, 2024 · ccf9736 · ccf9736
2 parents 483ec15 + a8b5dea
commit ccf9736
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/.github/workflows/Devel.yaml b/.github/workflows/Devel.yaml
@@ -25,9 +25,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: windows-latest, r: 'release', bioc: '3.13'}
-          - { os: macOS-latest, r: 'release', bioc: '3.13'}
-          - { os: ubuntu-20.04, r: 'release', bioc: '3.13', cran: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - { os: windows-latest, r: 'release', bioc: '3.20'}
+          - { os: macOS-latest, r: 'release', bioc: '3.20'}
+          - { os: ubuntu-20.04, r: 'release', bioc: '3.20', cran: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - { os: ubuntu-latest, r: 'release', image: 'bioconductor/bioconductor_docker:devel'}
 
     env:
@@ -41,13 +41,13 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Set up R
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         if: matrix.config.image == null
         with:
           r-version: ${{ matrix.config.r }}
 
       - name: Set up pandoc
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
         if: matrix.config.image == null
 
       - name: Install remotes
@@ -127,7 +127,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-results
           path: check

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -36,13 +36,13 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Set up R
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         if: matrix.config.image == null
         with:
           r-version: ${{ matrix.config.r }}
 
       - name: Set up pandoc
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
         if: matrix.config.image == null
 
       - name: Install remotes
@@ -122,7 +122,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-results
           path: check

diff --git a/R/topologyTest.R b/R/topologyTest.R
@@ -214,10 +214,10 @@
   order <- rownames(sds)
   if (is.null(order)) order <- rownames(reducedDim(sds))
   permutations <- lapply(permutations, function(perm){
-    lapply(perm, function(dat) dat[order, ]) %>% return()
+    lapply(perm, function(dat) dat[order, , drop = FALSE]) %>% return()
   })
   og <- lapply(og, function(dat){
-    return(dat[order, ])
+    return(dat[order, , drop = FALSE])
   })
 
   return(list("og" = og, "permutations" = permutations))