Remove renv and use cran latest (#176)

* add vignettes * add doc * use cran latest * temp comments * use tmp branch * fix * fix * fix * add supp packages * fix typo * update docker images * add needs * fix im name * update workflow to use latest im * fix * delete rprofile * fix deps name * add old release * add old release check * fix typo * fix release artifacts * update install deps script & lintr * fix link * fix link * rename latest image into release * Update push-docker-image.yml * install suggest deps * add step to install deps - r cmd check * add other r cmd check job * fix indent * fix * try p3m cran repo for devel * try another cran repo devel * update boilerplate steps with new deps, upload deps artifacts * add r_version to artifact * fix artifact name * trigger checks only on dispatch, generate renv.lock on artifacts * fix * fix * fix * fix * fix artifacts multiple paths * fix path * fix * retry * fix renv artifact names --------- Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: cicdguy <[email protected]>
pharmaverse · Jan 16, 2024 · a25b02b · a25b02b
1 parent f7617ba
commit a25b02b
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diff --git a/.Rprofile b/.Rprofile
diff --git a/.github/workflows/check-r-tags.yml b/.github/workflows/check-r-tags.yml
@@ -0,0 +1,31 @@
+---
+name: Check R tags
+
+on:
+  workflow_dispatch: # give possibility to run it manually
+  schedule:
+    - cron: '0 0 * * Sun' # Run every sunday at midnight UTC
+
+permissions: write-all
+env:
+  REGISTRY: ghcr.io
+  R_REPOS: "https://cran.r-project.org"
+  OLD_RELEASE: "4.3"
+
+concurrency:
+  group: check-r-tags-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-r-release:
+    runs-on: ubuntu-latest
+    steps:
+      - name: List rocker/rstudio tags
+        run: |
+          versions=$(curl -s "https://registry.hub.docker.com/v2/repositories/rocker/rstudio/tags/" | grep -o '"name": *"[^"]*' | grep -o '[^"]*$')
+          r_version=$(echo "$versions" | grep -oE '^[0-9]+\.[0-9]+$' | sort -r | head -n 1)
+          if [ $r_version != "${{ env.OLD_RELEASE }}" ]
+          then
+            echo "NEW RELEASE DETECTED - please update OLD_RELEASE env variable to $r_version in the workflows (this one and push-docker-image)"
+            exit 1
+          fi
diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
@@ -3,18 +3,17 @@ on:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: choice
         options:
-          - '4.1'
-          - '4.2'
-          - '4.3'
+          - devel
+          - latest
   workflow_call:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: string
 
@@ -111,6 +110,12 @@ jobs:
           renv-restore: false
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        run: |
+          devtools::install(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
+
       ##################### END boilerplate steps #####################
 
       - name: Install package

diff --git a/.github/workflows/code-coverage.yml b/.github/workflows/code-coverage.yml
@@ -3,13 +3,12 @@ on:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: choice
         options:
-          - '4.1'
-          - '4.2'
-          - '4.3'
+          - devel
+          - latest
       skip-coverage-badges:
         description: 'Skip code coverage badge creation'
         default: false
@@ -19,7 +18,7 @@ on:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: string
       skip-coverage-badges:
@@ -95,6 +94,11 @@ jobs:
           enable-check: false
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        run: |
+          devtools::install(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
       ##################### END boilerplate steps #####################
 
       - name: Run coverage 👟

diff --git a/.github/workflows/lintr.yml b/.github/workflows/lintr.yml
@@ -3,13 +3,12 @@ on:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: choice
         options:
-          - '4.1'
-          - '4.2'
-          - '4.3'
+          - devel
+          - latest
       lint-all-files:
         description: 'Lint all files every time'
         default: 'false'
@@ -29,7 +28,7 @@ on:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: string
       lint-all-files:

diff --git a/.github/workflows/man-pages.yml b/.github/workflows/man-pages.yml
@@ -3,18 +3,17 @@ on:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: choice
         options:
-          - '4.1'
-          - '4.2'
-          - '4.3'
+          - devel
+          - latest
   workflow_call:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: string
 
@@ -80,6 +79,12 @@ jobs:
           enable-check: false
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        run: |
+          devtools::install(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
+
       ##################### END boilerplate steps #####################
 
       - name: Generate man pages

diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
@@ -3,13 +3,12 @@ on:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: choice
         options:
-          - '4.1'
-          - '4.2'
-          - '4.3'
+          - devel
+          - latest
       skip-multiversion-docs:
         description: 'Skip creation of multi-version docs'
         default: false
@@ -38,7 +37,7 @@ on:
     inputs:
       r-version:
         description: 'The version of R to use'
-        default: '4.1'
+        default: 'release'
         required: false
         type: string
       skip-multiversion-docs:
@@ -148,6 +147,12 @@ jobs:
           enable-check: false
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        run: |
+          devtools::install(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
+
       ##################### END boilerplate steps #####################
 
       - name: Install package