Merge pull request #56 from fishR-Core-Team/dev

Prepping v0.4.6

.github/workflows/pkgdown.yaml

@@ -15,8 +15,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -29,16 +31,13 @@ jobs:
           extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Install dependencies
-        run: Rscript -e 'install.packages(c("prettydoc","captioner"))'
-
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/[email protected].4
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -1,48 +1,50 @@
+# 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, dev]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master, dev]
 
 name: test-coverage
 
 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@v3
 
-      - 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
+          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")
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@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-
-
-      - name: Install dependencies
+      - 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@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -5,5 +5,5 @@
 # Temporary plots from running tests
 tests/testthat/Rplots*.*
 # RDS files for vignettes (can be re-made from code)
-vignettes/MeasureRadii/*.rds
-vignettes/MeasureRadii/zzzTempRdsFiles/
+vignettes/*.rds
+vignettes/zzzTempRdsFiles/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RFishBC
-Version: 0.2.5
-Date: 2023-8-25
+Version: 0.2.6
+Date: 2023-8-28
 Title: Back-Calculation of Fish Length
 Authors@R: person("Derek","Ogle",
     email="[email protected]",

NEWS.md

@@ -1,4 +1,11 @@
-# RFishBC 0.2.5 ongoing
+# RFishBC 0.2.5.9000
+* Updated `test-coverage.yaml` to [latest version](https://github.com/r-lib/actions/blob/v2/examples/test-coverage.yaml).
+* Updated `pkgdown.yaml` to [latest version](https://github.com/r-lib/actions/blob/v2/examples/pkgdown.yaml).
+* `listFiles()`: Corrected URL errors in documentation.
+* Fixed URL issues in `listFiles()` update (per CRAN request on 28-Aug-2023).
+* Corrected many (all?) internal URLs in vignettes.
+
+# RFishBC 0.2.5 25-Aug-2023
 * Updated sticker.
 * Updated `CITATION` file to meet CRAN requirements.
 * Added Code of Conduct

R/listFiles.R

@@ -10,7 +10,7 @@
 #' 
 #' @seealso \code{\link{digitizeRadii}} and \code{\link{combineData}}; and \code{\link{list.files}} in base R.
 #'
-#' @details An example of using this function is in \href{https://fishr-core-team.github.io/RFishBC/articles/MeasureRadii/collectRadiiData.html}{this vignette} and \href{https://fishr-core-team.github.io/RFishBC/articles/MeasureRadii/seeRadiiData.html}{this vignette} on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
+#' @details An example of using this function is in \href{https://fishr-core-team.github.io/RFishBC/articles/collectRadiiData.html}{this vignette} and \href{https://fishr-core-team.github.io/RFishBC/articles/seeRadiiData.html}{this vignette} on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
 #'
 #' @return Character vector.
 #' 

R/showDigitizedImage.R

@@ -20,9 +20,9 @@
 #' @param cex.ann See details in \code{\link{RFBCoptions}}.
 #' @param offset.ann See details in \code{\link{RFBCoptions}}.
 #'
-#' @return A list that contains the size of the window in \code{windowSize} and the pixel width to heigh ration in \code{pixW2H}. In addition, an image is plotted with, at least, the selected points.
+#' @return A list that contains the size of the window in \code{windowSize} and the pixel width to height ratio in \code{pixW2H}. In addition, an image is plotted with, at least, the selected points.
 #' 
-#' @details This function requires interaction from the user. A detailed description of its use is in \href{https://fishr-core-team.github.io/RFishBC/articles/MeasureRadii/seeRadiiData.html}{this vignette} on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
+#' @details This function requires interaction from the user. A detailed description of its use is in \href{https://fishr-core-team.github.io/RFishBC/articles/seeRadiiData.html}{this vignette} on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
 #'
 #' @seealso \code{\link{digitizeRadii}} and \code{\link{RFBCoptions}}.
 #' 

cran-comments/cran-comments-v0_2_6.md

@@ -0,0 +1,9 @@
+* This updates the existing RFishBC package on CRAN with minor fixes to URLs in documentation per e-mail from Uwe Liggest on 28-Aug-23.
+
+## Notes
+* If there is a note about "fishBC" being misspelled in the description, then note that this is not a misspelling.
+
+## Testing Environments
+* My Windows machine.
+* Win Builder -- old-release, release, and development.
+* GitHub Action (R-CMD-check.yaml)