Merge pull request #117 from ropensci/cran_edits

Cran edits

R/build.R

@@ -10,6 +10,7 @@
 #' @param deps \code{logical} should we pass data objects into subsequent scripts? Default TRUE
 #' @param install \code{logical} automatically install and load the package after building. Default FALSE
 #' @param ... additional arguments passed to \code{install.packages} when \code{install=TRUE}.
+#' @returns Character vector. File path of the built package.
 #' @importFrom roxygen2 roxygenise roxygenize
 #' @importFrom devtools build_vignettes build parse_deps reload
 #' @importFrom usethis use_build_ignore use_rstudio proj_set use_directory
@@ -132,6 +133,7 @@ package_build <- function(packageName = NULL,
 #' @name keepDataObjects-defunct
 #' @aliases  keepDataObjects
 #' @param ... arguments
+#' @returns Defunct. No return value.
 #' @rdname keepDataObjects-defunct
 #' @export
 keepDataObjects <- function(...) {

R/dataversion.R

@@ -8,6 +8,7 @@
 #' @param lib.loc \code{character} path to library location.
 #' @seealso \code{\link[utils]{packageVersion}}
 #' @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

R/digests.R

@@ -4,13 +4,13 @@
 
 .check_dataversion_string <- function(old_data_digest, new_data_digest) {
   oldwarn <- options("warn")$warn
-  options(warn = -1)
-  oldv <- strsplit(old_data_digest[["DataVersion"]], "\\.")
-  newv <- strsplit(new_data_digest[["DataVersion"]], "\\.")
-  oldv <- lapply(oldv, as.numeric)[[1]]
-  newv <- lapply(newv, as.numeric)[[1]]
+  suppressWarnings({
+    oldv <- strsplit(old_data_digest[["DataVersion"]], "\\.")
+    newv <- strsplit(new_data_digest[["DataVersion"]], "\\.")
+    oldv <- lapply(oldv, as.numeric)[[1]]
+    newv <- lapply(newv, as.numeric)[[1]]
+  })
   if (any(is.na(oldv)) | any(is.na(newv))) {
-    options(warn = oldwarn)
     .multilog_fatal(paste0(
       "Invalid DataVersion string found ",
       old_data_digest[["DataVersion"]],
@@ -36,10 +36,10 @@
   existed <- names(new_digest)[names(new_digest) %in% names(old_digest)]
   added <- setdiff(names(new_digest), existed)
   removed <- names(old_digest)[!names(old_digest) %in% names(new_digest)]
-  existed <- existed[existed != "DataVersion"]  
+  existed <- existed[existed != "DataVersion"]
 
   if(length(existed) > 0){
-    changed <- names(new_digest)[ unlist(new_digest[existed]) != unlist(old_digest[existed]) ] 
+    changed <- names(new_digest)[ unlist(new_digest[existed]) != unlist(old_digest[existed]) ]
     if(length(changed) > 0){
       for(name in changed){
         .multilog_warn(paste(name, "has changed."))
@@ -53,15 +53,15 @@
     .multilog_debug(paste(name, "was removed."))
     return(FALSE)
   }
-  
+
   for(name in added){
     .multilog_debug(paste(name, "was added."))
     return(FALSE)
   }
 
   return(TRUE)
 };
-  
+
 .combine_digests <- function(new, old) {
   intersection <- intersect(names(new), names(old))
   difference <- setdiff(names(new), names(old))

R/environments.R

@@ -11,7 +11,7 @@
 #' @return An R object.
 #' @export
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if(rmarkdown::pandoc_available()){
 #' ENVS <- new.env() # ENVS would be in the environment
 #'                   # where the data processing is run. It is
@@ -25,43 +25,43 @@
 #' }
 #' }
 datapackager_object_read <- function(name) {
-  
+
   # get(name, get("ENVS", parent.frame()))
-  
+
   #when the datapackage is being build, it will only read the object from the environment. when
-  # in interactive mode, it should be try to load the objects reviously generated. 
+  # in interactive mode, it should be try to load the objects reviously generated.
   # It will preferentially read the object from the the temporary folder, but if that does not exist, it will read the
   # object from the the data folder
   buildingPackage<-getOption("DataPackageR_packagebuilding",TRUE)
-  
-  
+
+
   object<-try(get(name, get("ENVS", parent.frame(),inherits=FALSE),inherits=FALSE),silent=TRUE)
-  
+
   if( !buildingPackage && inherits(object,"try-error")){
     #if the package is not being build and the object is not found in the "ENVS" environment
     temp_folder_path<-file.path(tempdir(),yml_find(usethis::proj_get())[["configuration"]][["render_root"]]$tmp)
-    
+
     if(file.exists(objectPath<-file.path(temp_folder_path,paste0(name,".rds")))){
       message('loading ',name,' from temporary folder from previous build attempt.')
       object<-readRDS(objectPath)
-      
+
     }else if(file.exists(objectPath<-file.path(project_data_path(),paste0(name,".rda")))){
       message('loading ',name,' from data directory.')
       print(objectPath)
       load_env<-new.env()
       load(objectPath,envir = load_env)
       object<-load_env[[ls(load_env)[1]]]
-      
+
     }else{
       stop(paste(name,'not found!'))
-      
+
     }
   }else if(inherits(object,"try-error")){
     #if the package is being build and the object is not found in the "ENVS" environment,
     # pass on the original error warning
     stop(object[1])
-    
+
   }
-  
+
   return(object)
 }

R/processData.R

@@ -718,6 +718,7 @@ project_data_path <- function(file = NULL) {
 #' @param path \code{character} the path to the data package source root.
 #' @param install \code{logical} install and reload the package. (default TRUE)
 #' @param ... additional arguments to \code{install}
+#' @returns Called for side effects. Returns TRUE on successful exit.
 #' @export
 #' @examples
 #' # A simple Rmd file that creates one data object
@@ -728,7 +729,7 @@ project_data_path <- function(file = NULL) {
 #' con <- file(f)
 #' writeLines("```{r}\n tbl = data.frame(1:10) \n```\n",con=con)
 #' close(con)
-#' \dontrun{
+#' \donttest{
 #' # construct a data package skeleton named "MyDataPackage" and pass
 #' # in the Rmd file name with full path, and the name of the object(s) it
 #' # creates.

R/skeleton.R

@@ -28,6 +28,7 @@
 #' @param r_object_names \code{vector} of quoted r object names , tables, etc. created when the files in \code{code_files} are run.
 #' @param raw_data_dir \code{character} pointing to a raw data directory. Will be moved with all its subdirectories to "inst/extdata"
 #' @param dependencies \code{vector} of \code{character}, paths to R files that will be moved to "data-raw" but not included in the yaml config file. e.g., dependency scripts.
+#' @returns No return value, called for side effects
 #' @note renamed \code{datapackage.skeleton()} to \code{datapackage_skeleton()}.
 #' @importFrom crayon bold green
 #' @export