Fixes to get CHECK to pass.

R/AllGenerics.R

@@ -40,7 +40,8 @@
 #' list.files(tmp, recursive=TRUE)
 #'
 #' @export
-#' @aliases stageObject,ANY-method
+#' @aliases 
+#' stageObject stageObject,ANY-method
 #' searchForMethods .searchForMethods
 #' @import methods
 #' @importFrom jsonlite fromJSON

R/altReadObject.R

@@ -46,17 +46,16 @@
 #' library(S4Vectors)
 #' df <- DataFrame(A=1:10, B=LETTERS[1:10])
 #' tmp <- tempfile()
-#' dir.create(tmp)
-#' out <- stageObject(df, tmp, path="coldata")
+#' saveObject(df, tmp)
 #'
 #' # And now reading it - this should print our message.
-#' altReadObject(out, tmp)
+#' altReadObject(tmp)
 #' 
 #' # Restoring the old reader:
 #' altReadObjectFunction(old)
 #'
 #' @export
-#' @aliases .altReadObject .readObject
+#' @aliases .altLoadObject .loadObject altLoadObject altLoadObjectFunction
 altReadObject <- function(...) {
     FUN <- altReadObjectFunction()
     if (is.null(FUN)) {

R/altSaveObject.R

@@ -50,9 +50,8 @@
 #' library(S4Vectors)
 #' df <- DataFrame(A=1:10, B=LETTERS[1:10])
 #' tmp <- tempfile()
-#' dir.create(tmp)
-#' out <- altSaveObject(df, tmp, path="coldata")
-#' 
+#' altSaveObject(df, tmp)
+#'
 #' # Restoring the old loader:
 #' altSaveObjectFunction(old)
 #'

R/listObjects.R

@@ -3,7 +3,7 @@
 #' List all objects in a directory, along with their types.
 #' 
 #' @param dir String containing a path to a staging directory.
-#' @param ignore.children Logical scalar indicating whether to ignore child objects.
+#' @param include.children Logical scalar indicating whether to include child objects.
 #' 
 #' @return \linkS4class{DataFrame} where each row corresponds to an object and contains;
 #' \itemize{
@@ -12,7 +12,7 @@
 #' \item \code{child}, whether or not the object is a child of another object.
 #' }
 #'
-#' If \code{ignore.children=TRUE}, metadata is only returned for non-child objects. 
+#' If \code{include.children=FALSE}, metadata is only returned for non-child objects. 
 #'
 #' @author Aaron Lun
 #'

R/readDataFrameFactor.R

@@ -22,7 +22,7 @@
 #' readDataFrameFactor(tmp)
 #'
 #' @export
-#' @aliases readDataFrameFactor
+#' @aliases loadDataFrameFactor
 #' @importFrom S4Vectors DataFrameFactor
 readDataFrameFactor <- function(path, ...) {
     fpath <- file.path(path, "contents.h5")

R/readObject.R

@@ -19,7 +19,7 @@
 #'
 #' @section Comments for extension developers:
 #' When writing alabaster extensions, developers may need to load child objects inside the loading functions for their classes. 
-#' In such cases, developers should use \code{\link{altRoadObject}} rather than calling \code{readObject} directly.
+#' In such cases, developers should use \code{\link{altReadObject}} rather than calling \code{readObject} directly.
 #' This ensures that any application-level overrides of the loading functions are respected. 
 #' Once in memory, the child objects can then be assembled into more complex objects by the developer's loading function.
 #'
@@ -39,16 +39,15 @@
 #'
 #' @author Aaron Lun
 #' @examples
-#' # Same example as stageObject, but reversed.
 #' library(S4Vectors)
 #' df <- DataFrame(A=1:10, B=LETTERS[1:10])
 #'
 #' tmp <- tempfile()
-
-#' readObject(out, tmp)
+#' saveObject(df, tmp)
+#' readObject(tmp)
 #' 
 #' @export
-#' @aliases loadObject schemaLocations customLoadObjectHelper .loadObjectInternal 
+#' @aliases loadObject schemaLocations customloadObjectHelper .loadObjectInternal 
 readObject <- function(path, type=NULL, ...) {
     if (is.null(type)) {
         type <- readLines(file.path(path, "OBJECT"))

R/saveAtomicVector.R

@@ -26,6 +26,7 @@
 #' stageObject,character-method
 #' stageObject,double-method
 #' stageObject,POSIXct-method
+#' stageObject,POSIXlt-method
 #' stageObject,Date-method
 NULL
 

R/saveBaseFactor.R

@@ -18,7 +18,9 @@
 #' 
 #' @export
 #' @name saveBaseFactor
-#' @aliases stageObject,factor-method
+#' @aliases 
+#' saveObject,factor-method
+#' stageObject,factor-method
 setMethod("saveObject", "factor", function(x, path, ...) {
     dir.create(path, showWarnings=FALSE)
 

R/saveBaseList.R

@@ -3,7 +3,7 @@
 #' Save a \link{list} or \linkS4class{List} to a JSON or HDF5 file, with extra files created for any of the more complex list elements (e.g., DataFrames, arrays). 
 #' This uses the \href{https://github.com/LTLA/uzuki2}{uzuki2} specification to ensure that appropriate types are declared.
 #'
-#' @param A list or \linkS4class{List}.
+#' @param x A list or \linkS4class{List}.
 #' @inheritParams saveObject
 #' @param list.format String specifying the format in which to save the list.
 #' @param ... Further arguments, passed to \code{\link{altSaveObject}} for complex child objects.
@@ -32,7 +32,11 @@
 #' list.files(tmp, recursive=TRUE)
 #' 
 #' @export
-#' @rdname saveBaseList
+#' @name saveBaseList
+#' @aliases 
+#' saveObject,list-method
+#' stageObject,list-method
+#' stageObject,List-method
 #' @importFrom jsonlite toJSON
 setMethod("saveObject", "list", function(x, path, list.format=saveBaseListFormat(), ...) {
     dir.create(path, showWarnings=FALSE)

R/saveDataFrame.R

@@ -28,9 +28,7 @@
 #' df <- DataFrame(A=1:10, B=LETTERS[1:10])
 #'
 #' tmp <- tempfile()
-#' dir.create(tmp)
 #' saveObject(df, tmp)
-#'
 #' list.files(tmp, recursive=TRUE)
 #' 
 #' @export