Correct errors reported by CRAN

- Set `rf` parameter in `td_env` function call to FALSE in features.Rmd, overview.Rmd and README.Rmd files. It was causing problems with CRAN checks [#2] - Delete old check-standard.yaml file. Replace it with R-CMD-check.yaml - Update lint.yaml and test-coverage.yaml files to latest version - Run lintr on the project. Implement the recommendations of the tool - Update badges in README.Rmd so they have the correct url - Correct error in codecov badge link in README.md
pakjiddat · Oct 8, 2024 · de9f818 · de9f818
1 parent a642b2e
commit de9f818
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,3 +14,5 @@
 ^CRAN-RELEASE$
 ^codecov\.yml$
 ^CRAN-SUBMISSION$
+^NEWS.html$
+^revdep$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -1,49 +1,33 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
 
-name: lint
+name: lint.yaml
+
+permissions: read-all
 
 jobs:
   lint:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: actions/checkout@v4
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("lintr")
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
 
       - name: Lint
         run: lintr::lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,48 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         run: |
-          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")
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: codecov/codecov-action@v4
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,4 @@
 vignettes/features_cache
 vignettes/overview_cache
 README_cache
+revdep
diff --git a/.lintr b/.lintr
@@ -1,4 +1,9 @@
-linters: with_defaults(
+linters: linters_with_defaults(
     object_name_linter(styles = c("CamelCase", "snake_case")),
     cyclocomp_linter(complexity_limit = 35),
-    paren_brace_linter = NULL)
+    indentation_linter=NULL,
+    T_and_F_symbol_linter=NULL,
+    commented_code_linter=NULL,
+    object_usage_linter=NULL
+    ) # see vignette("lintr")
+encoding: "UTF-8"
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.0.3
-Date: 2022-01-03 10:44:59 UTC
-SHA: e08f755a59570f644a442d01647e672e6a1a73f1
+Version: 0.0.4
+Date: 2024-10-07 17:05:32 UTC
+SHA: f4eaa36fe102b1ae43cd2ee729ce6139d46c7102
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: wordpredictor
 Title: Develop Text Prediction Models Based on N-Grams
-Version: 0.0.3
+Version: 0.0.5
 URL: https://github.com/pakjiddat/word-predictor, https://pakjiddat.github.io/word-predictor/
 BugReports: https://github.com/pakjiddat/word-predictor/issues
 Authors@R: 
@@ -13,14 +13,14 @@ Description: A framework for developing n-gram models for text prediction.
     It provides data cleaning, data sampling, extracting tokens from text,
     model generation, model evaluation and word prediction. For information on how n-gram models 
     work we referred to: "Speech and Language Processing"
-    <https://web.stanford.edu/~jurafsky/slp3/3.pdf>. For optimizing R code and
+    <https://web.archive.org/web/20240919222934/https%3A%2F%2Fweb.stanford.edu%2F~jurafsky%2Fslp3%2F3.pdf>. For optimizing R code and
     using R6 classes we referred to "Advanced R" 
     <https://adv-r.hadley.nz/r6.html>. For writing R extensions we referred to 
     "R Packages", <https://r-pkgs.org/index.html>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Imports: digest, ggplot2, patchwork, stringr, dplyr, SnowballC
 Suggests: 
     testthat,

diff --git a/NEWS.html b/NEWS.html
diff --git a/NEWS.md b/NEWS.md
@@ -1,20 +1,27 @@
+# wordpredictor 0.0.5
+
+## Bug fixes
+
+-   Set `rf` parameter in `td_env` function call to FALSE in features.Rmd, overview.Rmd and README.Rmd files.
+    It was causing problems with CRAN checks [#2](https://github.com/pakjiddat/word-predictor/issues/2).
+
 # wordpredictor 0.0.3
 
 ## Bug fixes
 
-  * Disabled caching in R Markdown files, because it was causing problems with CRAN checks.
-  
+-   Disabled caching in R Markdown files, because it was causing problems with CRAN checks.
+
 # wordpredictor 0.0.2
 
 ## Bug fixes
 
-  * Fixed small bugs that were causing problems with GitHub actions and CRAN checks.
-  * Removed custom `.Rprofile` file as it was causing problems with GitHub actions.
-  * Updated sample code in `features.Rmd` vignette so it does not cause issues with R CMD Check on MacOs.
-  * Removed `inst/extdata folder` from `.gitignore` since it was causing problems with check-standard workflow on GitHub.
-  * Removed non-standard characters from example in data-cleaner.R file as they were causing problems with CRAN check on "Debian Linux, R-devel, clang".
-  * Issues related to the bug fixes: [#318](https://github.com/r-lib/actions/issues/318), [#319](https://github.com/r-lib/actions/issues/319), [#320](https://github.com/r-lib/actions/issues/320)
- 
+-   Fixed small bugs that were causing problems with GitHub actions and CRAN checks.
+-   Removed custom `.Rprofile` file as it was causing problems with GitHub actions.
+-   Updated sample code in `features.Rmd` vignette so it does not cause issues with R CMD Check on MacOs.
+-   Removed `inst/extdata folder` from `.gitignore` since it was causing problems with check-standard workflow on GitHub.
+-   Removed non-standard characters from example in data-cleaner.R file as they were causing problems with CRAN check on "Debian Linux, R-devel, clang".
+-   Issues related to the bug fixes: [#318](https://github.com/r-lib/actions/issues/318), [#319](https://github.com/r-lib/actions/issues/319), [#320](https://github.com/r-lib/actions/issues/320).
+
 # wordpredictor 0.0.1
 
-  * Initial Release.
+-   Initial Release.