Merge branch 'main' into md-in-family

.github/workflows/R-CMD-check.yaml

@@ -12,6 +12,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -25,24 +27,22 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
           # use 4.1 to check with rtools40's older compiler
           - {os: windows-latest, r: '4.1'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -60,3 +60,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/pr-commands.yaml

@@ -6,6 +6,8 @@ on:
 
 name: Commands
 
+permissions: read-all
+
 jobs:
   document:
     if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
@@ -14,7 +16,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,7 +53,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -8,43 +8,54 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          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}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          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: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: roxygen2
 Title: In-Line Documentation for R
-Version: 7.3.1.9000
+Version: 7.3.2.9000
 Authors@R: c(
     person("Hadley", "Wickham", , "[email protected]", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0003-4757-117X")),
@@ -53,4 +53,4 @@ Config/testthat/parallel: TRUE
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE, load = "installed")
-RoxygenNote: 7.3.0.9000
+RoxygenNote: 7.3.1.9000

NEWS.md

@@ -3,6 +3,10 @@
 * Custom [`@family`
   titles](https://roxygen2.r-lib.org/articles/index-crossref.html) now support
   Markdown syntax (#1608, @salim-b).
+# roxygen2 7.3.2
+
+* `@includeRmd` now additionally sets `options(cli.hyperlink = FALSE)` to make
+  code run in included `.Rmd`s even more consistent across sessions (#1620).
 
 # roxygen2 7.3.1
 

R/block.R

@@ -4,7 +4,7 @@
 #' A `roxy_block` represents a single roxygen2 block.
 #'
 #' The `block_*` functions provide a few helpers for common operations:
-#' * `block_has_tag(blocks, tags)`: does `block` contain any of these `tags`?
+#' * `block_has_tags(blocks, tags)`: does `block` contain any of these `tags`?
 #' * `block_get_tags(block, tags)`: get all instances of `tags`
 #' * `block_get_tag(block, tag)`: get single tag. Returns `NULL` if 0,
 #'    throws warning if more than 1.

R/rd-eval.R

@@ -17,6 +17,7 @@ local_reproducible_output <- function(.envir = parent.frame()) {
     crayon.enabled = FALSE,
     cli.unicode = FALSE,
     cli.dynamic = FALSE,
+    cli.hyperlink = FALSE,
     rlang_interactive = FALSE,
     width = 80,
     .local_envir = .envir

R/rd.R

@@ -60,14 +60,14 @@ roclet_output.roclet_rd <- function(x, results, base_path, ..., is_first = FALSE
 
   names <- unname(map_chr(results, ~ .$get_name()[[1]]))
   if (length(names) > 0) {
-    hrefs <- paste0("ide:run:pkgload::dev_help('", names, "')")
+    commands <- paste0("pkgload::dev_help('", names, "')")
   } else {
-    hrefs <- character()
+    commands <- character()
   }
 
   # Always check for roxygen2 header before overwriting NAMESPACE (#436),
   # even when running for the first time
-  mapply(write_if_different, paths, contents, href = hrefs)
+  mapply(write_if_different, paths, contents, command = commands)
 
   if (!is_first) {
     # Automatically delete any files in man directory that were generated

R/utils.R

@@ -61,7 +61,7 @@ nice_name <- function(x) {
   x
 }
 
-write_if_different <- function(path, contents, href = NULL, check = TRUE) {
+write_if_different <- function(path, contents, command = NULL, check = TRUE) {
   if (!file.exists(dirname(path))) {
     dir.create(dirname(path), showWarnings = FALSE)
   }
@@ -87,8 +87,10 @@ write_if_different <- function(path, contents, href = NULL, check = TRUE) {
     ))
     FALSE
   } else {
-    if (!is.null(href)) {
-      name <- cli::style_hyperlink(name, href)
+    if (!is.null(command)) {
+      scheme <- "x-r-run"
+      url <- paste0(scheme, ":", command)
+      name <- cli::style_hyperlink(name, url)
     }
     cli::cli_inform("Writing {.path {name}}")
 

cran-comments.md

@@ -1,5 +1,8 @@
 ## R CMD check results
-There were no ERRORs, WARNINGs or NOTEs.
+
+There was one note:  Found non-API calls to R: 'SETLENGTH', 'SET_GROWABLE_BIT', 'SET_TRUELENGTH'.
+
+These come from the upstream cpp11, and we're working to fix them there.
 
 ## revdepcheck results
 

tests/testthat/_snaps/rd-include-rmd.md

@@ -16,11 +16,13 @@
 
     Code
       . <- roc_proc_text(rd_roclet(), text)
+    Output
+      
     Message
       
       Quitting from lines 2-3 [unnamed-chunk-2] (<temp-path.Rmd>)
       
-      Quitting from lines 2-3 [unnamed-chunk-1] (<temp-path.Rmd>)
+      Quitting from lines 2-2 [unnamed-chunk-1] (<another-temp-path.Rmd>)
       x <text>:3: @includeRmd failed to evaluate '<temp-path.Rmd>'.
       Caused by error:
       ! Error

tests/testthat/_snaps/utils.md

@@ -27,3 +27,12 @@
     Output
       [1] FALSE
 
+# write_if_different produces correct command hyperlink
+
+    Code
+      write_if_different(path, "a <- 2", command = "rlang::inform('hi')")
+    Message
+      Writing ']8;;x-r-run:rlang::inform('hi')test.R]8;;'
+    Output
+      [1] TRUE
+

tests/testthat/test-rd-include-rmd.R

@@ -291,7 +291,11 @@ test_that("useful warnings", {
   )
   expect_snapshot(
     . <- roc_proc_text(rd_roclet(), text),
-    transform = function(x) gsub(path, "<temp-path.Rmd>", x, fixed =TRUE)
+    transform = function(x) {
+      x <- gsub(path, "<temp-path.Rmd>", x, fixed = TRUE)
+      x <- gsub("file.*\\.Rmd", "<another-temp-path.Rmd>", x)
+      x
+    }
   )
 })
 

tests/testthat/test-utils.R

@@ -68,3 +68,13 @@ test_that("write_if_different and end of line", {
   expect_message(write_if_different(tmp, cnt_mix, check = FALSE), "Writing ")
   expect_identical(readBin(tmp, "raw", 100), readBin(tmp_win, "raw", 100))
 })
+
+test_that("write_if_different produces correct command hyperlink", {
+  testthat::local_reproducible_output(hyperlinks = TRUE)
+
+  dir <- withr::local_tempdir()
+  path <- file.path(dir, "test.R")
+
+  write_lines(made_by("#"), path)
+  expect_snapshot(write_if_different(path, "a <- 2", command = "rlang::inform('hi')"))
+})