Merge branch 'main' into chore-parallel-testing

.Rbuildignore

@@ -23,9 +23,11 @@
 ^bench$
 ^tests/testthat/dummy_packages/package/[.]Rbuildignore$
 ^tests/testthat/dummy_packages/cp1252/[.]Rbuildignore$
+testthat-problems[.]rds$
 ^_pkgdown\.yaml$
 ^docs$
 ^pkgdown$
 ^vignettes/[^-]+.gif$
 ^CRAN-SUBMISSION$
 ^CODE_OF_CONDUCT\.md$
+^paper$

.github/CONTRIBUTING.md

@@ -0,0 +1,39 @@
+# Contributing to `{lintr}`
+
+This outlines how to propose a change to `{lintr}`. For a detailed discussion on contributing to this, r-lib, and other tidyverse packages, please see the [development contributing guide](https://rstd.io/tidy-contrib) and our [code review principles](https://code-review.tidyverse.org/).
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file.  You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. If you’ve found a bug, please file an issue that illustrates the bug with a minimal [reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed). See the tidyverse guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
+
+### Adding a new linter
+
+If you wish to contribute a new linter, the [Creating new linters](https://lintr.r-lib.org/articles/creating_linters.html) article serves as a comprehensive guide.
+
+### Pull request process
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("r-lib/lintr", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`. At a minimum, please avoid submitting PRs from your fork's `main` branch` as this can make the review process more complicated.
+
+*   Make your changes, commit them to Git, and create a PR using `usethis::pr_push()`. Follow the prompts in your browser to complete the process. Use a concise title for your PR that summarizes the change, and include `Fixes #issue-number` in the PR _description_. Doing so will automatically close the linked issue when the PR is merged. For complicated changes, add a textual overview of what your PR does in the description. Consider breaking up large PRs into a chain of more digestible+focused smaller PRs.
+
+*  For user-facing changes, add a bullet appropriately in the top section of `NEWS.md` (i.e. below the first header). Follow the style described in <https://style.tidyverse.org/news.html>. Most importantly, your audience for NEWS items is a package user, i.e., _not_ a package developer.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles.
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. Contributions with test cases included are easier to accept.
+
+## Code of Conduct
+
+Please note that the lintr project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project you agree to abide by its terms.

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

@@ -48,6 +48,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          install-quarto: false
           pak-version: devel
           dependencies: '"hard"'
           cache: false

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

@@ -70,6 +70,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          install-quarto: false
           extra-packages: |
             any::rcmdcheck
           needs: check

.github/workflows/draft-pdf.yml

@@ -0,0 +1,30 @@
+# TODO: delete this file once the paper is published
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

.github/workflows/pkgdown.yaml

@@ -39,7 +39,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.6.1
+        uses: JamesIves/github-pages-deploy-action@v4.7.1
         with:
           clean: false
           branch: gh-pages

.lintr

@@ -17,7 +17,8 @@ linters: all_linters(
       options = NULL,
       message = "use cli::cli_inform()",
       warning = "use cli::cli_warn()",
-      stop = "use cli::cli_abort()"
+      stop = "use cli::cli_abort()",
+      normalizePath = "use normalize_path()"
     )),
     undesirable_operator_linter(modify_defaults(
       defaults = default_undesirable_operators,
@@ -28,6 +29,8 @@ linters: all_linters(
     absolute_path_linter = NULL,
     library_call_linter = NULL,
     nonportable_path_linter = NULL,
+    # We now require R>=4.0.0
+    strings_as_factors_linter = NULL,
     todo_comment_linter = NULL,
     # TODO(#2327): Enable this.
     unreachable_code_linter = NULL

DESCRIPTION

@@ -21,7 +21,7 @@ License: MIT + file LICENSE
 URL: https://lintr.r-lib.org, https://github.com/r-lib/lintr
 BugReports: https://github.com/r-lib/lintr/issues
 Depends:
-    R (>= 3.6)
+    R (>= 4.0)
 Imports:
     backports (>= 1.1.7),
     cli (>= 3.4.0),
@@ -56,7 +56,7 @@ Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate:
     'make_linter_from_xpath.R'
     'xp_utils.R'

NAMESPACE

@@ -1,11 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-
-if (getRversion() >= "4.0.0") {
-  importFrom(tools, R_user_dir)
-} else {
-  importFrom(backports, R_user_dir)
-}
 S3method("[",lints)
 S3method(as.data.frame,lints)
 S3method(format,lint)
@@ -182,7 +176,9 @@ importFrom(rex,re_matches)
 importFrom(rex,re_substitutes)
 importFrom(rex,regex)
 importFrom(rex,rex)
+importFrom(stats,complete.cases)
 importFrom(stats,na.omit)
+importFrom(tools,R_user_dir)
 importFrom(utils,capture.output)
 importFrom(utils,getParseData)
 importFrom(utils,getTxtProgressBar)

NEWS.md

@@ -17,6 +17,9 @@
 * Drop support for posting GitHub comments from inside GitHub comment bot, Travis, Wercker, and Jenkins CI tools (spurred by #2148, @MichaelChirico). We rely on GitHub Actions for linting in CI, and don't see any active users relying on these alternatives. We welcome and encourage community contributions to get support for different CI system going again.
 * `cyclocomp_linter()` is no longer part of the default linters (#2555, @IndrajeetPatil) because the tidyverse style guide doesn't contain any guidelines on meeting certain complexity requirements. Note that users with `cyclocomp_linter()` in their configs may now need to install {cyclocomp} intentionally, in particular in CI/CD pipelines.
 * `scalar_in_linter` is now configurable to allow other `%in%` like operators to be linted. The data.table operator `%chin%` is no longer linted by default; use `in_operators = "%chin%"` to continue linting it. (@F-Noelle)
+* `lint()` and friends now normalize paths to forward slashes on Windows (@olivroy, #2613).
+* `undesirable_function_linter()`, `undesirable_operator_linter()`, and `list_comparison_linter()` were removed from the tag `efficiency` (@IndrajeetPatil, #2655). If you use `linters_with_tags("efficiency")` to include these linters, you'll need to adjust your config to keep linting your code against them. We did not find any such users on GitHub.
+
 
 ## Bug fixes
 
@@ -26,6 +29,7 @@
 * `.lintr` configs set by option `lintr.linter_file` or environment variable `R_LINTR_LINTER_FILE` can point to subdirectories (#2512, @MichaelChirico).
 * `indentation_linter()` returns `ranges[1L]==1L` when the offending line has 0 spaces (#2550, @MichaelChirico).
 * `literal_coercion_linter()` doesn't surface a warning about NAs during coercion for code like `as.integer("a")` (#2566, @MichaelChirico).
+* `commented_code_linter()` can detect commented code that ends with a pipe (#2671, @jcken95)
 
 ## Changes to default linters
 
@@ -57,6 +61,7 @@
 * `make_linter_from_xpath()` errors up front when `lint_message` is missing (instead of delaying this error until the linter is used, #2541, @MichaelChirico).
 * `paste_linter()` is extended to recommend using `paste()` instead of `paste0()` for simply aggregating a character vector with `collapse=`, i.e., when `sep=` is irrelevant (#1108, @MichaelChirico).
 * `expect_no_lint()` was added as new function to cover the typical use case of expecting no lint message, akin to the recent {testthat} functions like `expect_no_warning()` (#2580, @F-Noelle).
+* `lint()` and friends emit a message if no lints are found (#2643, @IndrajeetPatil).
 
 ### New linters
 
@@ -82,10 +87,14 @@
 ### Lint accuracy fixes: removing false positives
 
 * `object_name_linter()` and `object_length_linter()` ignore {rlang} name injection like `x |> mutate("{new_name}" := foo(col))` (#1926, @MichaelChirico). No checking is applied in such cases. {data.table} in-place assignments like `DT[, "sPoNGeBob" := "friend"]` are still eligible for lints.
+* `object_usage_linter()` finds global variables assigned with `=` or `->`, which avoids some issues around "undefined global variables" in scripts (#2654, @MichaelChirico).
 
 ## Notes
 
 * All user-facing messages are now prepared using the `{cli}` package (#2418, @IndrajeetPatil). All messages have been reviewed and updated to be more informative and consistent.
+* File locations in lints and error messages contain clickable hyperlinks to improve code navigation (#2645, #2588, @olivroy).
+* {lintr} now depends on R version 4.0.0. It already does so implicitly due to recursive upstream dependencies requiring this version; we've simply made that dependency explicit and up-front (#2569, @MichaelChirico).
+* Some code with parameters accepting regular expressions is less strict about whether there are capture groups  (#2678, @MichaelChirico). In particular, this affects `unreachable_code_linter(allow_comment_regex=)` and `expect_lint(checks=)`.
 
 # lintr 3.1.2
 

R/absolute_path_linter.R

@@ -8,9 +8,7 @@
 #' * contain at least two path elements, with one having at least two characters and
 #' * contain only alphanumeric chars (including UTF-8), spaces, and win32-allowed punctuation
 #'
-#' @examplesIf getRversion() >= "4.0"
-#' # Following examples use raw character constant syntax introduced in R 4.0.
-#'
+#' @examples
 #' # will produce lints
 #' lint(
 #'   text = 'R"--[/blah/file.txt]--"',

R/actions.R

@@ -2,6 +2,10 @@ in_github_actions <- function() {
   identical(Sys.getenv("GITHUB_ACTIONS"), "true")
 }
 
+in_pkgdown <- function() {
+  identical(Sys.getenv("IN_PKGDOWN"), "true")
+}
+
 # Output logging commands for any lints found
 github_actions_log_lints <- function(lints, project_dir = "") {
   for (x in lints) {

R/cache.R

@@ -53,10 +53,10 @@ load_cache <- function(file, path = NULL) {
         invokeRestart("muffleWarning")
       },
       error = function(e) {
-        cli_warn(c(
-          x = "Could not load cache file {.file {file}}:",
-          i = conditionMessage(e)
-        ))
+        cli_warn(
+          "Could not load cache file {.file {file}}:",
+          parent = e
+        )
       }
     )
   } # else nothing to do for source file that has no cache

R/class_equals_linter.R

@@ -48,9 +48,10 @@ class_equals_linter <- function() {
     bad_expr <- xml_find_all(xml_calls, xpath)
 
     operator <- xml_find_chr(bad_expr, "string(*[2])")
-    lint_message <- sprintf(
-      "Use inherits(x, 'class-name'), is.<class> or is(x, 'class') instead of comparing class(x) with %s.",
-      operator
+    lint_message <- paste0(
+      "Use inherits(x, 'class-name'), is.<class> for S3 classes, ",
+      "or is(x, 'S4Class') for S4 classes, ",
+      "instead of comparing class(x) with ", operator, "."
     )
     xml_nodes_to_lints(
       bad_expr,

R/commented_code_linter.R

@@ -83,9 +83,10 @@ commented_code_linter <- function() {
     all_comments <- xml_text(all_comment_nodes)
     code_candidates <- re_matches(all_comments, code_candidate_regex, global = FALSE, locations = TRUE)
     extracted_code <- code_candidates[, "code"]
-    # ignore trailing ',' when testing for parsability
-    extracted_code <- re_substitutes(extracted_code, rex(",", any_spaces, end), "")
+    # ignore trailing ',' or pipes ('|>', '%>%') when testing for parsability
+    extracted_code <- re_substitutes(extracted_code, rex(or(",", "|>", "%>%"), any_spaces, end), "")
     extracted_code <- re_substitutes(extracted_code, rex(start, any_spaces, ","), "")
+
     is_parsable <- which(vapply(extracted_code, parsable, logical(1L)))
 
     lint_list <- xml_nodes_to_lints(

R/exclude.R

@@ -326,7 +326,7 @@ normalize_exclusions <- function(x, normalize_path = TRUE,
     paths[rel_path] <- file.path(root, paths[rel_path])
     names(x) <- paths
     x <- x[file.exists(paths)] # remove exclusions for non-existing files
-    names(x) <- normalizePath(names(x)) # get full path for remaining files
+    names(x) <- normalize_path(names(x)) # get full path for remaining files
   }
 
   remove_line_duplicates(

R/expect_lint.R

@@ -105,16 +105,10 @@ expect_lint <- function(content, checks, ..., file = NULL, language = "en") {
           )
           # deparse ensures that NULL, list(), etc are handled gracefully
           ok <- if (field == "message") {
-            re_matches(value, check)
+            re_matches_logical(value, check)
           } else {
             isTRUE(all.equal(value, check))
           }
-          if (!is.logical(ok)) {
-            cli_abort(c(
-              x = "Invalid regex result. Did you mistakenly have a capture group in the regex?",
-              i = "You can match parentheses with a character class, i.e. inside `[]`."
-            ))
-          }
           testthat::expect(ok, msg)
         })
       },

R/extract.R

@@ -9,7 +9,7 @@ extract_r_source <- function(filename, lines, error = identity) {
   output <- rep.int(NA_character_, length(lines))
 
   chunks <- tryCatch(get_chunk_positions(pattern = pattern, lines = lines), error = error)
-  if (inherits(chunks, "error") || inherits(chunks, "lint")) {
+  if (is_error(chunks) || is_lint(chunks)) {
     assign("e", chunks, envir = parent.frame())
     # error, so return empty code
     return(output)

R/get_source_expressions.R

@@ -86,7 +86,7 @@ get_source_expressions <- function(filename, lines = NULL) {
   source_expression$content <- get_content(source_expression$lines)
   parsed_content <- get_source_expression(source_expression, error = function(e) lint_parse_error(e, source_expression))
 
-  if (inherits(e, "lint") && (is.na(e$line) || !nzchar(e$line) || e$message == "unexpected end of input")) {
+  if (is_lint(e) && (is.na(e$line) || !nzchar(e$line) || e$message == "unexpected end of input")) {
     # Don't create expression list if it's unreliable (invalid encoding or unhandled parse error)
     expressions <- list()
   } else {
@@ -502,7 +502,7 @@ get_source_expression <- function(source_expression, error = identity) {
     error = error
   )
 
-  if (inherits(parsed_content, c("error", "lint"))) {
+  if (is_error(parsed_content) || is_lint(parsed_content)) {
     assign("e", parsed_content, envir = parent.frame())
     parse_error <- TRUE
   }
@@ -513,7 +513,7 @@ get_source_expression <- function(source_expression, error = identity) {
     error = error
   )
 
-  if (inherits(parsed_content, c("error", "lint"))) {
+  if (is_error(parsed_content) || is_lint(parsed_content)) {
     # Let parse errors take precedence over encoding problems
     if (!parse_error) assign("e", parsed_content, envir = parent.frame())
     return() # parsed_content is unreliable if encoding is invalid
@@ -636,8 +636,7 @@ fix_eq_assigns <- function(pc) {
     parent = integer(n_expr),
     token = character(n_expr),
     terminal = logical(n_expr),
-    text = character(n_expr),
-    stringsAsFactors = FALSE
+    text = character(n_expr)
   )
 
   for (i in seq_len(n_expr)) {