first stable installation - which is now again possible - then devel

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ribiosUtils
 Type: Package
 Title: Utilities from and Interface to the 'Bioinfo-C' ('BIOS') Library
-Version: 1.7.8
-Date: 2026-01-22
+Version: 1.7.9
+Date: 2026-03-17
 Authors@R:
   c(person(given = "Jitao David",
            family = "Zhang",

NAMESPACE

@@ -32,6 +32,7 @@ export(compTwoVecs)
 export(corByRownames)
 export(countTokens)
 export(createDir)
+export(createRmdTemplate)
 export(cumJaccardDistance)
 export(cumJaccardIndex)
 export(cumOverlapCoefficient)

R/createRmdTemplate.R

@@ -0,0 +1,48 @@
+#' Copy the skeleton RMarkdown file to a specified location
+#'
+#' This function copies the skeleton RMarkdown template shipped with
+#' \code{ribiosUtils} to the current working directory (or any specified path)
+#' under a user-given file name. When no file name is provided, a default name
+#' based on the current date is used.
+#'
+#' @param filename Character string, the name (or path) of the destination
+#'   file. If \code{NULL} (default), the file is named
+#'   \code{Report_[YYYY-DD-MM]-report.Rmd}, where the date components reflect
+#'   the current date.
+#' @param overwrite Logical, whether to overwrite an existing file. Default is
+#'   \code{FALSE}.
+#' @return The path of the copied file (invisible).
+#' @author Jitao David Zhang <jitao_david.zhang@@roche.com>
+#' @examples
+#' \dontrun{
+#' ## copy with default file name
+#' createRmdTemplate()
+#'
+#' ## copy with a custom file name
+#' createRmdTemplate("my_analysis.Rmd")
+#' }
+#'
+#' ## copy to a temporary directory
+#' dest <- createRmdTemplate(file.path(tempdir(), "test_report.Rmd"))
+#' file.exists(dest)
+#' unlink(dest)
+#'
+#' @export
+createRmdTemplate <- function(filename = NULL, overwrite = FALSE) {
+  if (is.null(filename)) {
+    filename <- format(Sys.time(), "Report_%Y-%d-%m-report.Rmd")
+  }
+  skeleton <- system.file("rmarkdown", "templates",
+    "ribios-rmarkdown-template", "skeleton", "skeleton.Rmd",
+    package = "ribiosUtils")
+  if (skeleton == "") {
+    stop("Skeleton file not found in ribiosUtils installation.")
+  }
+  if (file.exists(filename) && !overwrite) {
+    stop("File '", filename, "' already exists. ",
+      "Use overwrite=TRUE to overwrite.")
+  }
+  file.copy(skeleton, filename, overwrite = overwrite)
+  message("Skeleton file copied to '", filename, "'")
+  return(invisible(filename))
+}

README.md

@@ -11,21 +11,19 @@ distributed under the GPL-3 license.
 
 ## Installation
 
-### Install the devel version from GitHub
+### Install the stable version on CRAN
 
 Run following commands in the R console.
 
-```{R}
-library(devtools)
-devtools::install_github("bedapub/ribiosUtils")
+```r
+install.packages("ribiosUtils")
 ```
 
-### Install the stable version on CRAN
-
-*The CRAN version is temporarily not available due to pending changes*.
+### Install the devel version from GitHub
 
-```r
-install.packages("ribiosUtils")
+```{R}
+library(devtools)
+devtools::install_github("bedapub/ribiosUtils")
 ```
 
 ## History

tests/testthat/test_createRmdTemplate.R

@@ -0,0 +1,36 @@
+library(testthat)
+library(ribiosUtils)
+
+context("createRmdTemplate")
+
+test_that("createRmdTemplate copies the skeleton file with a custom name", {
+  dest <- file.path(tempdir(), "test_skeleton.Rmd")
+  on.exit(unlink(dest))
+  result <- createRmdTemplate(dest)
+  expect_true(file.exists(dest))
+  expect_equal(result, dest)
+})
+
+test_that("createRmdTemplate uses default filename when none given", {
+  old_wd <- setwd(tempdir())
+  on.exit(setwd(old_wd))
+  result <- createRmdTemplate()
+  on.exit(unlink(result), add = TRUE)
+  expect_true(file.exists(result))
+  expect_true(grepl("^Report_.*-report\\.Rmd$", basename(result)))
+})
+
+test_that("createRmdTemplate refuses to overwrite by default", {
+  dest <- file.path(tempdir(), "test_no_overwrite.Rmd")
+  on.exit(unlink(dest))
+  createRmdTemplate(dest)
+  expect_error(createRmdTemplate(dest), "already exists")
+})
+
+test_that("createRmdTemplate overwrites when overwrite=TRUE", {
+  dest <- file.path(tempdir(), "test_overwrite.Rmd")
+  on.exit(unlink(dest))
+  createRmdTemplate(dest)
+  expect_message(createRmdTemplate(dest, overwrite = TRUE), "Skeleton file copied")
+  expect_true(file.exists(dest))
+})