doc example fixes

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

@@ -25,6 +25,7 @@ jobs:
           # check compatibility with older releases
           - {os: ubuntu-latest,   r: 'oldrel-1'}
           - {os: ubuntu-latest,   r: 'oldrel-2'}
+          - {os: ubuntu-latest,   r: 'oldrel-3'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

R/packageDevelopment.R

@@ -6,14 +6,14 @@
 #' This function retrieves keywords from all package documentation files located
 #' in the `/man` directory of the specified R package. It can return a unique list
 #' of keywords or a frequency distribution of these keywords as a `table` object,
-#' sorted by the keys. 
+#' sorted by the keys.
 #'
 #' Note that the "internal" keyword is ignored.
 #'
 #' @param pkg The path to the R package directory.
 #' @param asDistribution Logical; if FALSE, returns a character vector of unique keywords. If TRUE, returns a table with the frequency of each keyword.
 #'
-#' @return If \code{asDistribution} is FALSE, a character vector of unique keywords is returned.
+#' @return If \code{asDistribution} is FALSE, a sorted character vector of unique keywords is returned.
 #'         If \code{asDistribution} is TRUE, a table of keywords and their frequencies is returned.
 #'         If no keywords were detected, returns a character of length 0.
 #' @export
@@ -78,35 +78,20 @@ getPkgKeywords <- function(pkg = ".", asDistribution = FALSE) {
 #' specified sections in their Rd files. May be length 0 if all fulfill criteria.
 #' @export
 #' @keywords packageDevelopment
+#'
 #' @examples
-#' findMissingRdSections(c("examples", "example"), pkg = ".")
+#' try(
+#'   findMissingRdSections(c("examples", "example"), pkg = "."),
+#'   silent = TRUE
+#' )
 #'
 findMissingRdSections <- function(
     sectionName, pkg = ".", ignore = NULL, .ignore = "-package$"
 ) {
-
-    rdPath <- file.path(pkg, "man")
-    rdFiles <- list.files(rdPath, pattern = "\\.Rd$", full.names = TRUE)
-
-    missingFunctionNames <- character(0)
-
-    for (file in rdFiles) {
-
-        rdContent <- readLines(file)
-
-        sectionMissing <- sapply(paste("\\", sectionName, "{", sep = ""), function(section) {
-            all(grepl(section, rdContent, fixed = TRUE) == FALSE)
-        })
-
-        if (!any(sectionMissing)) next
-
-        missingFunctionNames <- c(
-            missingFunctionNames,
-            tools::file_path_sans_ext(basename(file))
-        )
-    }
-
-    Filter(function(x) !grepl(joinRegex(.ignore, ignore), x), missingFunctionNames)
+    paste("\\", sectionName, "{", sep = "") %>%
+        greplDir(file.path(pkg, "man")) %>%
+        (function(x) names(which(!x))) %>%
+        basename()
 }
 
 #' @rdname findMissingRdSections

R/regex.R

@@ -29,14 +29,15 @@ joinRegex <- function(...) {
 #' names of elements to be removed.
 #' @param silent A logical indicating whether to silence a warning if no names are
 #' detected.
-#' 
+#'
 #' @return The input object with elements removed based on the name regex.
 #' @export
 #' @keywords regex
-#' 
+#'
 #' @examples
 #' myList <- list(a = 1, b_test = 2, c = 3, d_test = 4)
 #' rmByName(myList, "_test")
+#'
 rmByName <- function(x, pattern, silent = FALSE) {
 
     assertthat::assert_that(is.character(pattern))
@@ -54,31 +55,38 @@ rmByName <- function(x, pattern, silent = FALSE) {
 
 #' Search for a Pattern in Files within a Directory
 #'
+#' @description
+#' `r lifecycle::badge("experimental")`
+#' 
 #' The `greplDir` function searches for a specified pattern in all files within a given directory.
 #' It allows for optional exclusion of files matching a specified regular expression.
 #' Note that all files are assumed to be a single string, with each line joined by the
 #' newline character `"\n"`.
 #'
-#' @param dirPath Character. The path to the directory containing files to be searched.
 #' @param fpattern Character. The pattern to search for within the files.
+#' @param dirPath Character. The path to the directory containing files to be searched.
 #' @param fIgnoreRegex Character. A regular expression to match file names that should be ignored (default is NULL).
 #' @param ... Additional arguments passed to [listFiles()], which are passed to [list.files()]
 #' 
 #' @return A named logical vector indicating which files contain the pattern.
 #' The names attribute contains the file names.
 #' @export
 #' @keywords regex
-#' 
+#'
 #' @examples
 #' \donttest{
-#' result <- greplDir(getwd(), "error", "\\.log$")
+#' result <- tryCatch(
+#'   greplDir("error", fIgnoreRegex = "\\.log$"),
+#'   warning = function(w) c(exFname = TRUE),
+#'   error = function(e) c(exFname = TRUE)
+#' )
 #' # its even more useful to use `base::which` on the result to
 #' # get matches and mismatches - this returns it with names
 #' # by default
 #' which(result)
 #' which(!result)
 #' }
-greplDir <- function(dirPath, fpattern, fIgnoreRegex = NULL, ...) {
+greplDir <- function(fpattern, dirPath = getwd(), fIgnoreRegex = NULL, ...) {
 
     allFiles <- listFiles(dirPath, ...)
 

R/testing.R

@@ -18,12 +18,13 @@
 #'
 #' @examples
 #' \donttest{
-#' # Initialize testthat files in the default directories
+#' try({
+#' 
 #' initTestthat()
-#' # Initialize testthat files in a custom R directory and test directory
 #' initTestthat(rDir = "src", testDir = "tests")
-#' # Initialize testthat files, ignoring additional patterns
 #' initTestthat(ignore = c("^foo", "-bar.R$"))
+#' 
+#' }, silent = TRUE)
 #' }
 #'
 initTestthat <- function(