Base packages attached by default

DESCRIPTION

@@ -49,7 +49,6 @@ Depends: R (>= 3.5.0)
 Imports:
     digest,
     knitr,
-    utils,
     rmarkdown,
     desc,
     yaml,

NAMESPACE

@@ -57,8 +57,6 @@ importFrom(rmarkdown,render)
 importFrom(roxygen2,roxygenise)
 importFrom(roxygen2,roxygenize)
 importFrom(rprojroot,is_r_package)
-importFrom(stats,runif)
-importFrom(stats,setNames)
 importFrom(stringr,str_trim)
 importFrom(usethis,create_package)
 importFrom(usethis,proj_get)
@@ -67,14 +65,6 @@ importFrom(usethis,use_build_ignore)
 importFrom(usethis,use_data_raw)
 importFrom(usethis,use_directory)
 importFrom(usethis,use_rstudio)
-importFrom(utils,capture.output)
-importFrom(utils,file_test)
-importFrom(utils,getSrcref)
-importFrom(utils,install.packages)
-importFrom(utils,modifyList)
-importFrom(utils,package.skeleton)
-importFrom(utils,packageDescription)
-importFrom(utils,packageVersion)
 importFrom(withr,with_options)
 importFrom(yaml,as.yaml)
 importFrom(yaml,read_yaml)

R/build.R

@@ -16,7 +16,6 @@
 #' @importFrom usethis use_build_ignore use_rstudio proj_set use_directory
 #' @importFrom rprojroot is_r_package
 #' @importFrom rmarkdown pandoc_available
-#' @importFrom utils install.packages
 #' @importFrom yaml read_yaml
 #' @importFrom futile.logger flog.logger flog.trace appender.file flog.debug flog.info flog.warn flog.error flog.fatal flog.appender flog.threshold INFO TRACE appender.console appender.tee
 #' @importFrom knitr knit spin
@@ -112,7 +111,7 @@ package_build <- function(packageName = NULL,
   )
   # try to install and then reload the package in the current session
   if (install) {
-    install.packages(location, repos = NULL, type = "source", ...)
+    utils::install.packages(location, repos = NULL, type = "source", ...)
   }
   .next_steps()
   return(location)

R/dataversion.R

@@ -10,7 +10,6 @@
 #' @rdname data_version
 #' @returns Object of class 'package_version' and 'numeric_version' specifying the DataVersion of the package
 #' @note \code{dataVersion()} has been renamed to \code{data_version()}
-#' @importFrom utils capture.output file_test package.skeleton packageDescription
 #' @export
 #' @examples
 #' if(rmarkdown::pandoc_available()){

R/parseDocumentation.R

@@ -1,6 +1,6 @@
 .doc_parse <- function(all_r_files) {
   sources <- lapply(all_r_files, function(x) parse(x, keep.source = TRUE))
-  docs <- lapply(sources, function(x) try(comments(getSrcref(x))))
+  docs <- lapply(sources, function(x) try(comments(utils::getSrcref(x))))
   docs <- lapply(docs, function(x) lapply(x, as.character))
   indx <- lapply(
     lapply(

R/processData.R

@@ -28,7 +28,6 @@
 #' @return logical TRUE if successful, FALSE, if not.
 #' @importFrom desc desc
 #' @importFrom rmarkdown render
-#' @importFrom utils getSrcref modifyList
 #' @importFrom usethis proj_set proj_get
 DataPackageR <- function(arg = NULL, deps = TRUE) {
   if (! getOption('DataPackageR_verbose', TRUE)){
@@ -775,7 +774,7 @@ document <- function(path = ".", install = FALSE, ...) {
   )
   # try to install and then reload the package in the current session
   if (install) {
-    install.packages(location, repos = NULL, type = "source", ...)
+    utils::install.packages(location, repos = NULL, type = "source", ...)
   }
   return(TRUE)
 }

R/roxygen2_functions.R

@@ -17,7 +17,6 @@ comments <- function(refs) {
   com
 }
 
-#' @importFrom stats setNames
 #' @importFrom stringr str_trim
 read.description <- function(file) {
   dcf <- read.dcf(file, keep.white = "Authors@R")

R/use.R

@@ -8,7 +8,6 @@
 #'
 #' @return invisibly returns TRUE for success. Stops on failure.
 #' @importFrom usethis proj_get proj_set create_package use_data_raw
-#' @importFrom utils file_test
 #' @export
 #'
 #' @examples
@@ -77,7 +76,6 @@ use_raw_dataset <- function(path = NULL, ignore = FALSE) {
 #'
 #' @return invisibly returns TRUE for success. Stops on failure.
 #' @importFrom usethis proj_get proj_set create_package use_data_raw
-#' @importFrom utils file_test packageVersion
 #' @export
 #'
 #' @examples
@@ -353,7 +351,7 @@ use_data_object <- function(object_name = NULL) {
 
 .yaml_load_utf8 <- function(string, ...) {
   string <- paste(string, collapse = "\n")
-  if (packageVersion("yaml") >= "2.1.14") {
+  if (utils::packageVersion("yaml") >= "2.1.14") {
     yaml::yaml.load(string, ...)
   }
   else {

R/yamlR.R

@@ -6,7 +6,6 @@
 #' @description Edit a yaml configuration file via an API.
 #' @details Add, remove files and objects, enable or disable parsing of specific files,  list objects or files in a yaml config, or write a config back to a package.
 #' @importFrom yaml yaml.load_file as.yaml write_yaml
-#' @importFrom stats runif
 #' @importFrom withr with_options
 #' @export
 #'

tests/testthat/test-datapackager-object-read.R

@@ -10,7 +10,7 @@ test_that("data objects can be read across scripts", {
   #   force = TRUE,
   #   r_object_names = "cars_over_20"
   # )
-  # 
+  #
   ENVS <- new.env()
   dataenv <- new.env()
   assign("foo", 100, ENVS)
@@ -47,7 +47,7 @@ test_that("data objects are saved incrementally in render_root", {
   package_build(
     file.path(tempdir(), "subsetCars")
   )
-  expect_true(file_test("-f",file.path(tempdir(),DataPackageR::yml_find(file.path(tempdir(),"subsetCars"))[["configuration"]][["render_root"]][["tmp"]],"cars_over_20.rds")))
+  expect_true(utils::file_test("-f",file.path(tempdir(),DataPackageR::yml_find(file.path(tempdir(),"subsetCars"))[["configuration"]][["render_root"]][["tmp"]],"cars_over_20.rds")))
 })
 
 
@@ -65,20 +65,20 @@ test_that("data objects can be read from render_root or the data dir", {
   package_build(
     file.path(tempdir(), "subsetCars")
   )
-  
+
   #create object that doesn't exist in temporary file, so datapackager_object_read is forced to look in the data dir
   file.copy(file.path(tempdir(),"subsetCars","data","cars_over_20.rda"),
             file.path(tempdir(), "subsetCars","data","cars_over_20_2.rda"))
-  
+
   original<-readRDS(file.path(tempdir(),DataPackageR::yml_find(file.path(tempdir(),"subsetCars"))[["configuration"]][["render_root"]][["tmp"]],"cars_over_20.rds"))
-  
+
   expect_identical(suppressMessages(datapackager_object_read("cars_over_20")),original)
   expect_identical(datapackager_object_read("cars_over_20_2"),original)
-  
+
   #check if the reading will try to read from the ENV
   options("DataPackageR_packagebuilding" = TRUE)
   on.exit({options("DataPackageR_packagebuilding" = FALSE)})
-  
+
   expect_error(datapackager_object_read("cars_over_20"))
-  
+
 })

tests/testthat/test-edge-cases.R

@@ -58,7 +58,7 @@ test_that("package built in different edge cases", {
   )
   test_env <- new.env()
   assign('test_obj', pi, envir = test_env)
-  package.skeleton("foo", path = tempdir(), environment = test_env)
+  utils::package.skeleton("foo", path = tempdir(), environment = test_env)
   suppressWarnings(expect_error(
     DataPackageR:::DataPackageR(
       file.path(tempdir(), "foo")
@@ -89,7 +89,7 @@ test_that("package built in different edge cases", {
   )
 
 
-  package.skeleton("foo", path = tempdir(), environment = test_env, force = TRUE)
+  utils::package.skeleton("foo", path = tempdir(), environment = test_env, force = TRUE)
   expect_error(yml_find(file.path(tempdir(), "foo")))
   dir.create(file.path(tempdir(), "foo", "data-raw"))
   unlink(file.path(tempdir(), "foo", "DESCRIPTION"))
@@ -169,7 +169,7 @@ test_that("package built in different edge cases", {
     force = TRUE,
     recursive = TRUE
   )
-  package.skeleton("foo", path = tempdir(), environment = test_env, force = TRUE)
+  utils::package.skeleton("foo", path = tempdir(), environment = test_env, force = TRUE)
   DataPackageR:::.multilog_setup(file.path(tempdir(),"test.log"))
   DataPackageR:::.multilog_thresold(INFO, TRACE)
 
@@ -297,7 +297,7 @@ test_that("package built in different edge cases", {
     force = TRUE,
     recursive = TRUE
   )
-  package.skeleton("foo", path = tempdir(), environment = test_env, force = TRUE)
+  utils::package.skeleton("foo", path = tempdir(), environment = test_env, force = TRUE)
   dir.create(file.path(tempdir(), "foo", "data-raw"))
   suppressWarnings(
     expect_error(

tests/testthat/test-logger.R

@@ -8,7 +8,7 @@ withr::with_options(list(DataPackageR_verbose = TRUE),{
   })
   test_that(".multilog_info", {
     expect_output(DataPackageR:::.multilog_info("message"), "INFO .* message")
-    expect_true(file_test("-f", file.path(tempdir(), "test.log")))
+    expect_true(utils::file_test("-f", file.path(tempdir(), "test.log")))
   })
   test_that(".multilog_error", {
     expect_output(DataPackageR:::.multilog_error("message"), "ERROR .* message")

tests/testthat/test-r-processing.R

@@ -30,7 +30,7 @@ test_that("R file processing works and creates vignettes", {
     v <- vignette(package = "rfiletest", lib.loc = temp_libpath)
 
     expect_equal(v$results[, "Item"], "rfileTest")
-    expect_true(file_test("-f", file.path(tempdir,"rfiletest","inst","doc","rfileTest.pdf")))
+    expect_true(utils::file_test("-f", file.path(tempdir,"rfiletest","inst","doc","rfileTest.pdf")))
     unlink(file.path(tempdir, "rfiletest"),
            recursive = TRUE,
            force = TRUE

tests/testthat/test-use_raw_data.R

@@ -37,7 +37,7 @@ test_that("use_raw_data works as expected", {
   )
   expect_true(use_raw_dataset(myfile))
   expect_true(use_raw_dataset(myfile, ignore = TRUE))
-  expect_true(file_test(
+  expect_true(utils::file_test(
     "-f",
     file.path(
       tempdir(),
@@ -74,14 +74,14 @@ test_that("use_processing_script works as expected", {
   expect_false(any(grepl("foo",readLines(normalizePath(file.path(tempdir(),"subsetCars20","data-raw","newScript.Rmd"), winslash = "/")))))
   expect_true(use_processing_script("newScript.Rmd", title = "foo", overwrite = TRUE))
   expect_true(any(grepl("foo",readLines(normalizePath(file.path(tempdir(),"subsetCars20","data-raw","newScript.Rmd"), winslash = "/")))))
-  
-  expect_true(use_processing_script("newScript.Rmd", 
+
+  expect_true(use_processing_script("newScript.Rmd",
                                     title = "foo", author = "bar", overwrite = TRUE))
   expect_true(use_processing_script("newScript.Rmd", author = "bar", overwrite = TRUE))
 
   expect_true(use_processing_script("newScript.R", overwrite = TRUE))
   expect_true(use_processing_script("newScript.R", title = "foo", overwrite = TRUE))
-  expect_true(use_processing_script("newScript.R", 
+  expect_true(use_processing_script("newScript.R",
                                     title = "foo", author = "bar", overwrite = TRUE))
   expect_true(use_processing_script("newScript.R", author = "bar", overwrite = TRUE))
   expect_equal(readLines(
@@ -144,8 +144,8 @@ test_that(".update_header", {
   )
 
   con <- file(file.path(tempdir(), "foo.Rmd"), open = "wt")
-  writeLines(text = 
-               c("---", "title: My Title", "author: My Name", "---"), 
+  writeLines(text =
+               c("---", "title: My Title", "author: My Name", "---"),
              con = con)
   close(con)
   DataPackageR:::.update_header(
@@ -188,12 +188,12 @@ test_that(".partition_r_front_matter", {
     DataPackageR:::.partition_r_front_matter(test_string2)$front_matter,
     NULL
   )
-  
+
   expect_equal(DataPackageR:::.partition_r_front_matter(
     c("#' ---","author:Greg Finak","#' ---","body")),
     list(front_matter = c("#' ---","author:Greg Finak","#' ---"),
          body = "body"))
-  
+
   expect_equal(
     is.null(
       DataPackageR:::.partition_r_front_matter(test_string3)$body
@@ -273,12 +273,12 @@ test_that(".partition_rmd_front_matter", {
     DataPackageR:::.partition_rmd_front_matter(test_string4)$front_matter,
     NULL
   )
-  
+
   expect_equal(DataPackageR:::.partition_rmd_front_matter(
     c("---","author:Greg Finak","---","body")),
     list(front_matter = c("---","author:Greg Finak","---"),
          body = "body"))
-  
+
   expect_equal(
     is.null(
       DataPackageR:::.partition_rmd_front_matter(test_string5)$front_matter