removed add_dependencies_to_description()

R/core_manage_dependencies.R

@@ -1,137 +1,14 @@
-#' Searches for external packages and adds them to the Imports field in the description
-#'
-#' Scans script files (.R, .Rmd, .Rnw, .Rpres, etc.) for external package dependencies indicated by
-#' \code{library()}, \code{require()} or \code{::} and adds those packages to the Imports field in
-#' the package DESCRIPTION.
-#'
-#' @param path location of individual file or directory where to search for scripts.
-#' @param description_file location of description file to be updated.
-#' @param just_packages just give back a character vector of the found packages.
-#'
-#' @export
-add_dependencies_to_description <- function(
-  path = getwd(),
-  description_file = "DESCRIPTION",
-  just_packages = FALSE
-) {
-
-  # check if directory or single file
-  if (utils::file_test("-d", path)) {
-    # if directory, search for all possible R or Rmd files
-    pattern <- "\\.[rR]$|\\.[rR]md$|\\.[rR]nw$|\\.[rR]pres$"
-    R_files <- list.files(
-      path,
-      pattern = pattern,
-      ignore.case = TRUE,
-      recursive = TRUE,
-      full.names = TRUE
-    )
-  } else if (utils::file_test("-f", path)) {
-    # if file, just copy it into the files list
-    R_files <- path
-  } else {
-    # stop if path doesn't exist at all
-    stop("File or directory doesn't exist.")
-  }
-
-  # loop over every file
-  pkgs <- lapply(
-    R_files,
-    function(y) {
-      # read files libe by line
-      current_file <- readLines(y)
-      # get libraries explicitly called via library()
-      library_lines <- grep(pattern = "library", x = current_file, value = TRUE)
-      l_libs <- strsplit(library_lines, split = "library\\(")
-      l_libs <- lapply(l_libs, function(x){strsplit(x[2], split = "\\)")})
-      l_libs <- unlist(l_libs)
-      # get libraries explicitly called via require()
-      require_lines <- grep(pattern = "require", x = current_file, value = TRUE)
-      r_libs <- strsplit(require_lines, split = "require\\(")
-      r_libs <- lapply(r_libs, function(x){strsplit(x[2], split = "\\)")})
-      r_libs <- unlist(r_libs)
-      # get libraries implicitly called via ::
-      point_lines <- grep(pattern = "::", x = current_file, value = TRUE)
-      # search for all collections of alphanumeric signs in between the
-      # line start/a non-alphanumeric sign and ::
-      p_libs <- regmatches(
-        point_lines,
-        gregexpr("(?<=^|[^a-zA-Z0-9])[a-zA-Z0-9]*?(?=::)", point_lines, perl = TRUE)
-      )
-      p_libs <- unlist(p_libs)
-      # merge results for current file
-      res <- c(l_libs, r_libs, p_libs)
-      return(unique(res))
-    }
-  )
-
-  # merge results of every file
-  pkgs <- unique(unlist(pkgs))
-  # remove NA and empty string
-  pkgs <- pkgs[pkgs != "" & !is.na(pkgs)]
-  # order alphabetically
-  pkgs <- sort(pkgs)
-
-  # remove packages that are not on CRAN
-  # TODO: keep an eye on that one: https://github.com/ropenscilabs/available
-  if (curl::has_internet()==TRUE & RCurl::url.exists("https://cran.r-project.org") ==TRUE ) {
-    pkgs <- pkgs[pkgs %in% utils::available.packages(repos = "https://cran.r-project.org")[,1]==TRUE]
-  }
-
-  # if the just_packages option is selected, just give back the list of packages
-  if (just_packages) {
-    return(pkgs)
-  }
-
-  # read DESCRIPTION file
-  tmp <- readLines(description_file)
-  # check, if Imports fields is available
-  if (length(grep("Imports", tmp)) == 0) {
-    # if no: add it
-    tmp[length(tmp)+1] <- "Imports:"
-  }
-  # get line where Imports starts
-  i_begin <- grep("Imports", tmp)
-  # get line where Imports ends (determination via search for next ":")
-  # if Imports is the last tag, set i_end to the last line
-  if((i_begin + 1) >= length(tmp)) {
-    i_end <- length(tmp)
-  } else {
-    i_end <- i_begin + grep(":", tmp[(i_begin + 1):length(tmp)])[1] - 1
-    if(is.na(i_end)) {
-      i_end <- length(tmp)
-    }
-  }
-  # check which packages are already present in DESCRIPTION
-  present <- unlist(lapply(
-    pkgs,
-    function(x) {
-      doublespace <- paste0(" ", x, " ")
-      space <- any(grep(doublespace, tmp))
-      spacecomma <- paste0(" ", x, ",")
-      comma <- any(grep(spacecomma, tmp))
-      spacelinebreak <- paste0(" ", x, "$")
-      linebreak <- any(grep(spacelinebreak, tmp))
-      return(space | comma | linebreak)
-    }
-  ))
-  # stop if all packages already in DESCRIPTION
-  if(all(present)) {
-    stop("All used packages are already in the DESCRIPTION somewhere (Imports, Suggests, Depends).")
-  }
-  # create string with missing packages and their version number in correct layout
-  to_add_version <- unlist(lapply(
-    pkgs[!present],
-    function(x) {
-      # check if package is installed
-      if(x %in% rownames(installed.packages())) {
-        paste0(x, " (>= ", utils::packageDescription(x)$Version, ")")
-      } else {x}
-    }
-  ))
-  to_add_final <- paste0("\n    ", paste0(to_add_version, collapse = ",\n    "))
-  # add newly created package string to last line of Imports
-  tmp[i_end] <- paste0(tmp[i_end], ",", to_add_final)
-  # write result back into DESCRIPTION file
-  writeLines(text = tmp, con = description_file)
-}
+#' add_dependencies_to_description() is deprecated
+#'
+#' Please use \code{attachment::att_to_description()} from https://cran.r-project.org/package=attachment.
+#'
+#' @param ... nothing
+#'
+#' @export
+add_dependencies_to_description <- function(
+  ...
+) {
+
+  message("This function is deprecated. Please use attachment::att_to_description().")
+
+}

README.Rmd

@@ -112,7 +112,7 @@ analysis/
 - the `references.bib` file has just one item to demonstrate the format. It is ready to insert more reference details.
 - you can replace the supplied `csl` file with a different citation style from <https://github.com/citation-style-language/>
 - we recommend using the [citr addin](https://github.com/crsh/citr) and [Zotero](https://www.zotero.org/) to efficiently insert citations while writing in an Rmd file
-- remember that the `Imports:` field in the `DESCRIPTION` file must include the names of all packages used in analysis documents (e.g. `paper.Rmd`). We have a helper function `rrtools::add_dependencies_to_description()` that will scan the Rmd file, identify libraries used in there, and add them to the `DESCRIPTION` file.
+- remember that the `Imports:` field in the `DESCRIPTION` file must include the names of all packages used in analysis documents (e.g. `paper.Rmd`). The [attachment](https://github.com/Thinkr-open/attachment) package provides some useful functions that scan R and Rmd files, identify libraries used in there, and add them to the `DESCRIPTION` file.
 - this function has an `data_in_git =` argument, which is `TRUE` by default. If set to `FALSE` you will exclude files in the `data/` directory from being tracked by git and prevent them from appearing on GitHub. You should set `data_in_git = FALSE` if your data files are large (>100 mb is the limit for GitHub) or you do not want to make the data files publicly accessible on GitHub.
   -   To load your custom code in the `paper.Rmd`, you have a few options. You can write all your R code in chunks in the Rmd, that's the simplest method. Or you can write R code in script files in `/R`, and include `devtools::load_all(".")` at the top of your `paper.Rmd`. Or you can write functions in `/R` and use `library(pkgname)` at the top of your `paper.Rmd`, or omit `library` and preface each function call with `pkgname::`. Up to you to choose whatever seems most natural to you. 
 

README.md

@@ -216,10 +216,10 @@ your project: they are meant to be once-off setup functions.
     citations while writing in an Rmd file
   - remember that the `Imports:` field in the `DESCRIPTION` file must
     include the names of all packages used in analysis documents
-    (e.g. `paper.Rmd`). We have a helper function
-    `rrtools::add_dependencies_to_description()` that will scan the Rmd
-    file, identify libraries used in there, and add them to the
-    `DESCRIPTION` file.
+    (e.g. `paper.Rmd`). The
+    [attachment](https://github.com/Thinkr-open/attachment) package
+    provides some useful functions that scan R and Rmd files, identify
+    libraries used in there, and add them to the `DESCRIPTION` file.
   - this function has an `data_in_git =` argument, which is `TRUE` by
     default. If set to `FALSE` you will exclude files in the `data/`
     directory from being tracked by git and prevent them from appearing