IndrajeetPatil · IndrajeetPatil · May 12, 2024 · May 12, 2024 · May 12, 2024 · May 12, 2024
diff --git a/.github/workflows/R-CMD-check-devel.yaml b/.github/workflows/R-CMD-check-devel.yaml
@@ -31,7 +31,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           needs: check
           extra-packages: |
             any::rcmdcheck

diff --git a/.github/workflows/R-CMD-check-hard.yaml b/.github/workflows/R-CMD-check-hard.yaml
@@ -36,7 +36,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           dependencies: '"hard"'
           cache: false
           extra-packages: |

diff --git a/.github/workflows/R-CMD-check-strict.yaml b/.github/workflows/R-CMD-check-strict.yaml
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -8,6 +8,10 @@ on:
 
 name: R-CMD-check
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -18,20 +22,28 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          # Checks are not run on R-devel because they are already run in
-          # `R-CMD-check-strict` workflow
-
-          #- { os: macos-latest,   r: "devel" }
-          - { os: macos-latest, r: "release" }
-          - { os: macos-latest, r: "oldrel-1" }
+          #- {os: macOS-latest, r: 'devel'}
+          - { os: macOS-latest, r: "release" }
+          - { os: macOS-latest, r: "oldrel" }
+          #- {os: macOS-latest, r: 'oldrel-2'}
+          #- {os: macOS-latest, r: 'oldrel-3'}
 
-          #- { os: windows-latest, r: "devel" }
+          #- { os: windows-latest, r: "next" }
+          - { os: windows-latest, r: "devel" }
           - { os: windows-latest, r: "release" }
-          - { os: windows-latest, r: "oldrel-1" }
+          - { os: windows-latest, r: "oldrel" }
+          #- {os: windows-latest, r: 'oldrel-2'}
+          #- {os: windows-latest, r: 'oldrel-3'}
 
-          #- { os: ubuntu-latest, r: "devel" }
-          #- { os: ubuntu-latest, r: "release" }
-          #- { os: ubuntu-latest, r: "oldrel-1" }
+          # use 4.1 to check with rtools40's older compiler
+          #- { os: windows-latest, r: "4.1" }
+
+          #- { os: ubuntu-latest, r: "next" }
+          - { os: ubuntu-latest, r: "devel" }
+          - { os: ubuntu-latest, r: "release" }
+          - { os: ubuntu-latest, r: "oldrel" }
+          # - { os: ubuntu-latest, r: "oldrel-2" }
+          # - { os: ubuntu-latest, r: "oldrel-3" }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -52,11 +64,27 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
+          cache-version: 10
           upgrade: 'TRUE'
           extra-packages: |
             any::rcmdcheck
+            Matrix=?ignore-before-r=100.0.0
+            lme4=?ignore-before-r=100.0.0
+            TMB=?ignore-before-r=100.0.0
           needs: check
 
+      - name: Install packages from source
+        run: |
+          utils::install.packages(c("Matrix", "lme4", "TMB"), type = "source")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          upload-results: true
+          error-on: 'ifelse(getRversion() > "4.3", "note", "warning")'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+          _R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_: true
diff --git a/.github/workflows/check-all-examples.yaml b/.github/workflows/check-all-examples.yaml
@@ -36,7 +36,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             any::devtools
             local::.

diff --git a/.github/workflows/check-link-rot.yaml b/.github/workflows/check-link-rot.yaml
@@ -31,7 +31,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           dependencies: '"hard"'
           extra-packages: |
             any::rcmdcheck

diff --git a/.github/workflows/check-random-test-order.yaml b/.github/workflows/check-random-test-order.yaml
@@ -24,7 +24,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             local::.
 

diff --git a/.github/workflows/check-readme.yaml b/.github/workflows/check-readme.yaml
@@ -41,7 +41,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             local::.
             any::gghalves

diff --git a/.github/workflows/check-spelling.yaml b/.github/workflows/check-spelling.yaml
@@ -30,7 +30,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           dependencies: '"hard"'
           extra-packages: |
             any::rcmdcheck

diff --git a/.github/workflows/check-styling.yaml b/.github/workflows/check-styling.yaml
@@ -26,7 +26,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           dependencies: '"hard"'
           extra-packages: |
             local::.

diff --git a/.github/workflows/check-test-warnings.yaml b/.github/workflows/check-test-warnings.yaml
@@ -28,7 +28,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             local::.
             any::devtools

diff --git a/.github/workflows/check-vignette-warnings.yaml b/.github/workflows/check-vignette-warnings.yaml
@@ -32,7 +32,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             local::.
 

diff --git a/.github/workflows/html-5-check.yaml b/.github/workflows/html-5-check.yaml
@@ -25,7 +25,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             any::rcmdcheck
             any::V8

diff --git a/.github/workflows/lint-changed-files.yaml b/.github/workflows/lint-changed-files.yaml
@@ -37,12 +37,11 @@ jobs:
           changed_files <- purrr::map_chr(files, "filename")
           all_files <- list.files(recursive = TRUE)
           exclusions_list <- as.list(setdiff(all_files, changed_files))
-          lint_package(linters = linters_with_defaults(
+          lint_package(linters = all_linters(
             absolute_path_linter = NULL,
             assignment_linter = NULL,
             commented_code_linter = NULL,
             cyclocomp_linter(25L),
-            extraction_operator_linter = NULL,
             if_not_else_linter(exceptions = character(0L)),
             implicit_integer_linter = NULL,
             library_call_linter = NULL,
@@ -58,8 +57,7 @@ jobs:
             undesirable_function_linter = NULL,
             undesirable_operator_linter = NULL,
             unnecessary_concatenation_linter(allow_single_expression = FALSE),
-            unused_import_linter = NULL,
-            defaults = linters_with_tags(tags = NULL)
+            unused_import_linter = NULL
           ), exclusions = exclusions_list)
         shell: Rscript {0}
         env:

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -27,7 +27,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             r-lib/lintr
             local::.
@@ -39,13 +39,11 @@ jobs:
         run: |
           options(crayon.enabled = TRUE)
           library(lintr)
-          lint_package(linters = linters_with_tags(
-            tags = NULL,
+          lint_package(linters = all_linters(
             absolute_path_linter = NULL,
             assignment_linter = NULL,
             commented_code_linter = NULL,
             cyclocomp_linter(25L),
-            extraction_operator_linter = NULL,
             if_not_else_linter(exceptions = character(0L)),
             implicit_integer_linter = NULL,
             library_call_linter = NULL,

diff --git a/.github/workflows/pkgdown-no-suggests.yaml b/.github/workflows/pkgdown-no-suggests.yaml
@@ -34,7 +34,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           dependencies: '"hard"'
           cache: false
           extra-packages: |

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -34,7 +34,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             r-lib/pkgdown
             local::.

diff --git a/.github/workflows/styler.yaml b/.github/workflows/styler.yaml
@@ -24,7 +24,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           dependencies: '"hard"'
           extra-packages: |
             local::.

diff --git a/.github/workflows/test-coverage-examples.yaml b/.github/workflows/test-coverage-examples.yaml
@@ -26,7 +26,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             any::covr
             local::.

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -25,7 +25,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           pak-version: devel
-          upgrade: 'TRUE'
+          upgrade: "TRUE"
           extra-packages: |
             any::covr
           needs: coverage

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,15 +6,15 @@ default_language_version:
 
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9003
+    rev: v0.4.2
     hooks:
       - id: no-browser-statement
       - id: no-debug-statement
       - id: parsable-R
       - id: deps-in-desc
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-json
@@ -30,7 +30,7 @@ repos:
           )$
 
   - repo: https://github.com/lorenzwalthert/gitignore-tidy
-    rev: "475bf5d96927a1887ce2863ff3075b1d7240bc51"
+    rev: "0.1.2"
     hooks:
       - id: tidy-gitignore