Merge pull request #363 from Olink-Proteomics/ci_fix_v2

Ci fix v2
Olink-Proteomics · May 24, 2024 · 6932023 · 6932023
2 parents e0cac06 + 1e63a5d
commit 6932023
Show file tree

Hide file tree

Showing 48 changed files with 2,504 additions and 8,857 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -19,15 +19,15 @@ jobs:
           inputFile: '.github/workflows/matrix_config_check.json' 
           filter: '[?runOn==`${{ github.event_name }}` || runOn==`always`]'
           # addInclude: true
-
+      
   R-CMD-check:
     needs: matrix_prep
-    strategy:      
-      fail-fast: false    
-      matrix: ${{fromJson(needs.matrix_prep.outputs.matrix)}}  
+    strategy:
+      fail-fast: false
+      matrix: ${{fromJson(needs.matrix_prep.outputs.matrix)}}
 
     runs-on: ${{ matrix.os }}
-    timeout-minutes: 120       
+    timeout-minutes: 120
 
     name: ${{ matrix.os }} (${{ matrix.r }})
 
@@ -42,7 +42,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.r }}
-          use-public-rspm: true            
+          use-public-rspm: true
 
       - uses: r-lib/actions/setup-pandoc@v2
         with:
@@ -54,100 +54,18 @@ jobs:
           forenv <- paste("R_BIOC_VERSION=", as.character(remotes::bioc_version()), sep = "")
           write(forenv, file = Sys.getenv("GITHUB_ENV"), append = TRUE) # Store current value to ENV          
         shell: Rscript {0}
-
-
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           working-directory: OlinkAnalyze
           extra-packages: any::rcmdcheck, pillar
 
-      - name: Install Matrix from source
+      - name: Install arrow from r-universe
+        if: matrix.os == 'macOS-latest'
         run: |
-          install.packages("Matrix", type="source", repos='http://cran.us.r-project.org')
+          install.packages('arrow', repos = c('https://apache.r-universe.dev'))
         shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          working-directory: OlinkAnalyze     
-
-
-  R-CMD-check-renv:
-    needs: matrix_prep
-    strategy:      
-      fail-fast: false
-      matrix:
-        config:
-          - {os: ubuntu-22.04,   r: '4.1.3'}
-
-
-    runs-on: ${{ matrix.config.os }}
-    timeout-minutes: 120       
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      _R_CHECK_FORCE_SUGGESTS_: false
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Install package
-        run: |
-          sudo apt update
-          sudo apt-get -y install libglpk-dev texlive-latex-base \
-             texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-          use-public-rspm: true            
-
-      - uses: r-lib/actions/setup-pandoc@v2
-        with:
-          pandoc-version: '2.18'
-
-      - name: Set RENV_PATHS_ROOT
-        shell: bash
-        run: |
-          echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV
-          
-      - name: Install and activate renv
-        run: |
-          install.packages("remotes")
-          remotes::install_version("renv", "0.16.0")
-          renv::activate(profile = "r413")
-        shell: Rscript {0}
-
-      - name: Get R and OS version
-        id: get-version
-        run: |
-          cat("os-version=", sessionInfo()$running, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
-          cat("r-version=", R.Version()$version.string, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
-        shell: Rscript {0}
-
-      - name: Restore Renv package cache
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.RENV_PATHS_ROOT }}
-          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-${{ hashFiles('renv.lock') }}
-          restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-
-
-      - name: Install renv dependencies
-        run: renv::restore()
-        shell: Rscript {0}
-
-      - name: Check package
-        run: |                             
-          check_results <- rcmdcheck::rcmdcheck(error_on = "error",
-                                                path = "OlinkAnalyze", 
-                                                check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure() 
-        uses: actions/upload-artifact@v3
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: "check"
+          working-directory: OlinkAnalyze
diff --git a/.github/workflows/matrix_config_check.json b/.github/workflows/matrix_config_check.json
@@ -12,16 +12,16 @@
    {
       "os": "ubuntu-20.04",
       "r": "release",
-      "runOn": "always"
+      "runOn": "pull_request"
    },
    {
-      "os": "ubuntu-20.04",
-      "r": "devel",
-      "runOn": "pull_request"
+      "os": "ubuntu-22.04",
+      "r": "release",
+      "runOn": "always"
    },
    {
-      "os": "ubuntu-20.04",
-      "r": "4.2.0",
+      "os": "ubuntu-22.04",
+      "r": "devel",
       "runOn": "pull_request"
    }
 ]
diff --git a/.github/workflows/r-cmd-check-docker.yaml b/.github/workflows/r-cmd-check-docker.yaml
@@ -0,0 +1,40 @@
+on: [pull_request]
+
+name: R-CMD-check-docker
+
+jobs:
+  R-CMD-check-docker:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        r_version: ["4.1.3", "4.2.3", "4.3.3", "4.4.0"]
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v3
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      -
+        name: Build docker image
+        uses: docker/build-push-action@v4
+        with:
+          push: false
+          tags: oa:latest
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          file: docker/Dockerfile_for_tests
+          load: true
+          build-args: R_VERSION=${{matrix.r_version}}
+      -
+        name: Run rcmdcheck
+        run: |
+          echo "rcmdcheck::rcmdcheck(path = '/OA', check_dir = '/check', error_on = 'warning')" | docker run -i -v "$(pwd)/OlinkAnalyze":/OA -v "$(pwd)/check":/check oa:latest
+      -
+        name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: docker-r${{ matrix.config.r }}-check-results
+          path: check
diff --git a/OlinkAnalyze/DESCRIPTION b/OlinkAnalyze/DESCRIPTION
@@ -111,5 +111,5 @@ VignetteBuilder:
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://olink.com/ https://github.com/Olink-Proteomics/OlinkRPackage 
diff --git a/OlinkAnalyze/NAMESPACE b/OlinkAnalyze/NAMESPACE
@@ -16,6 +16,7 @@ export(olink_heatmap_plot)
 export(olink_lmer)
 export(olink_lmer_plot)
 export(olink_lmer_posthoc)
+export(olink_lod)
 export(olink_normalization)
 export(olink_normalization_bridge)
 export(olink_normalization_n)

diff --git a/OlinkAnalyze/R/globals.R b/OlinkAnalyze/R/globals.R
@@ -17,5 +17,6 @@ utils::globalVariables(unique(c(
   "umapX_low", "umapY_high", "umapY_low", "LX", "LY", "PCX", "PCY", "rowname", "Normalization", "Quantified_value", "v1",
   "v2", "v", "v_name", "duplicateID", "SampleID_df1", "name", "data", "normalize_to", "PlateID1", "QC_Warning1", "V1", "V2",
   "cols", "ID", "AssayQC", "AssayType", "Block", "DataAnalysisRefID", "ExploreVersion", "ExtNPX", "PCNormalizedNPX", "SampleQC", "SampleType", "WellID",
-  "Max LOD", "Plate LOD", "Plate_LOD", "Normalization_df1", "Normalization_df2",   "Max_LOD", "maxLOD", "plateLOD"
+  "Max LOD", "Plate LOD", "Plate_LOD", "Normalization_df1", "Normalization_df2",   "Max_LOD", "maxLOD", "plateLOD",
+  ".env", ".data"
 )))