Merge branch 'fix-check' into develop

.github/workflows/build.yml

@@ -11,7 +11,7 @@
 # ======================================================== #
 
 on: [push, pull_request]
-name: package-build
+name: R-CMD-check
 
 # ======================================================== #
 # Determine actions to take                                #
@@ -28,76 +28,32 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-latest, r: 'release'}
-          - {os: ubuntu-latest, r: 'devel'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
     steps:
-        - name: Retrieving current month
-          if: runner.os == 'Linux'
-          run: echo "CURRENT_MONTH=$(date +%m)" >> $GITHUB_ENV
-
-        # Checking out code -------------------------------------- #
         - name: Checking out the repository
-          uses: actions/checkout@v2
+          uses: actions/checkout@v3
+
+        - name: Setting up pandoc
+          uses: r-lib/actions/setup-pandoc@v2
 
-        # Setting up environment --------------------------------- #
         - name: Setting up R ${{ matrix.config.r }} on ${{ matrix.config.os }}
-          uses: r-lib/actions/setup-r@v1
+          uses: r-lib/actions/setup-r@v2
           with:
             r-version: ${{ matrix.config.r }}
+            http-user-agent: ${{ matrix.config.http-user-agent }}
+            use-public-rspm: true
 
-        # Installing Pandoc -------------------------------------- #
-        - name: Installing Pandoc
-          uses: r-lib/actions/setup-pandoc@v1
-
-        # Querying dependencies ---------------------------------- #
         - name: Querying dependencies
-          run: |
+          uses: r-lib/actions/setup-r-dependencies@v2
-            install.packages("remotes")
-            saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-            writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-          shell: Rscript {0}
-
-        # Restoring R package cache ------------------------------ #
-        - name: Restoring R package cache
-          uses: actions/cache@v2
           with:
-            path: ${{ env.R_LIBS_USER }}
+            extra-packages: any::rcmdcheck
-            key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+            needs: check
-            restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-        # Installing system dependencies ------------------------- #
-        - name: Installing system dependencies
-          if: runner.os == 'Linux'
-          run: |
-            sudo apt-get install libcurl4-openssl-dev
-            while read -r cmd
-            do
-              eval sudo $cmd
-            done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-        # Installing package dependencies ------------------------ #
-        - name: Installing package dependencies
-          if: ${{ env.CURRENT_MONTH < 4 || env.CURRENT_MONTH > 10 }}
-          run: |
-            remotes::install_cran(c("rcmdcheck", "BiocManager"))
-            BiocManager::install("GenomicRanges")
-            BiocManager::install("Rsamtools")
-            remotes::install_deps(dependencies = TRUE)
-          shell: Rscript {0}
-
-        # Checking package --------------------------------------- #
         - name: Checking package
-          if: ${{ env.CURRENT_MONTH < 4 || env.CURRENT_MONTH > 10 }}
+          uses: r-lib/actions/check-r-package@v2
-          env:
-            _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          run: |
-            options(crayon.enabled = TRUE)
-            rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-          shell: Rscript {0}
-
-        # Uploading check results -------------------------------- #
-        - name: Uploading check results
-          if: failure()
-          uses: actions/upload-artifact@main
           with:
-            name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+            upload-snapshots: true
-            path: check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rBAPS
 Title: Bayesian Analysis of Population Structure
-Version: 0.0.0.9010
+Version: 0.0.0.9011
 Date: 2020-11-09
 Authors@R:
     c(