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Discontinue use of ‘\donttest’ in examples

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gothub committed Jun 26, 2018
1 parent 37f5163 commit 738023276275ada080ac859c5ba93868629d6fce
@@ -240,7 +240,7 @@ setMethod("getFormat", signature("CNode"), function(x, formatId) {

#' @rdname getChecksum
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' pid <- "doi:10.5063/F1QN64NZ"
#' cn <- CNode()
#' pid <- "doi:10.5063/F1QN64NZ"
@@ -274,8 +274,7 @@ setMethod("getChecksum", signature("CNode"), function(x, pid, ...) {
#' @return the list of nodes in the DataONE CN environment
#' @seealso \code{\link[=CNode-class]{CNode}}{ class description.}
#' @export
#' @examples
#' \donttest{
#' @examples \dontrun{
#' cn <- CNode()
#' nodelist <- listNodes(cn)
#' nodeid <- nodelist[[2]]@identifier
@@ -481,7 +480,7 @@ setMethod("getObject", signature("CNode"), function(x, pid) {
#' @import datapack
#' @export
#' @rdname getSystemMetadata
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' cn <- CNode()
#' pid <- "aceasdata.3.2"
@@ -512,8 +511,7 @@ setMethod("getSystemMetadata", signature("CNode"), function(x, pid) {
#' @rdname resolve
#' @aliases resolve
#' @return A list of URLs that the object can be downloaded from, or NULL if the object is not found.
#' @examples
#' \donttest{
#' @examples \dontrun{
#' library(dataone)
#' cn <- CNode("STAGING")
#' id <- "doi:10.6073/pasta/9a27a1615e8e4c366ad09fefbfa2fced"
@@ -67,7 +67,7 @@ setClass("D1Client", slots = c(cn = "CNode", mn="MNode"))
#' @return the D1Client object representing the DataONE environment
#' @seealso \code{\link[=D1Client-class]{D1Client}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' cli <- D1Client("PROD", "urn:node:KNB")
#' cn <- CNode('STAGING2')
#' mn <- getMNode(cn,'urn:node:mnTestKNB')
@@ -115,7 +115,7 @@ setMethod("D1Client", signature("CNode", "MNode"), function(x, y, ...) {
#' @rdname D1Client-initialize
#' @aliases D1Client-initialize
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' d1c <- D1Client("PROD", "urn:node:KNB")
#' }
@@ -227,7 +227,7 @@ setMethod("getD1Object", "D1Client", function(x, identifier) {
#' @return A DataObject or NULL if the object was not found in DataONE
#' @seealso \code{\link[=D1Client-class]{D1Client}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' d1c <- D1Client("PROD", "urn:node:KNB")
#' pid <- "solson.5.1"
@@ -358,7 +358,7 @@ setMethod("getDataObject", "D1Client", function(x, identifier, lazyLoad=FALSE, l
#' @return A DataPackage or NULL if the package was not found in DataONE
#' @seealso \code{\link[=D1Client-class]{D1Client}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' d1c <- D1Client("PROD", "urn:node:KNB")
#' pid <- "solson.5.1"
@@ -698,7 +698,7 @@ setMethod("createDataPackage", signature("D1Client", "DataPackage"), function(x,
#' @aliases getEndpoint
#' @seealso \code{\link[=D1Client-class]{D1Client}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' cli <- D1Client("STAGING2", "urn:node:mnTestKNB")
#' cnUrl <- getEndpoint(cli)
#' }
@@ -720,7 +720,7 @@ setMethod("getEndpoint", "D1Client", function(x) {
#' @aliases getMNodeId
#' @seealso \code{\link[=D1Client-class]{D1Client}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' cli <- D1Client("STAGING2", "urn:node:mnTestKNB")
#' mn <- getMNodeId(cli)
#' }
@@ -1313,7 +1313,7 @@ setMethod("uploadDataObject", signature("D1Client"), function(x, do, replicate=
#' @aliases listMemberNodes
#' @seealso \code{\link[=D1Client-class]{D1Client}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' d1c <- D1Client("PROD")
#' nodelist <- listMemberNodes(d1c)
#' }
@@ -1543,7 +1543,7 @@ setMethod("getMetadataMember", signature("D1Client", "DataPackage"), function(x,
#' @return A path where the ouput file is written to.
#' @seealso \code{\link[=D1Client-class]{D1Client}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' d1c <- D1Client("PROD", "urn:node:KNB")
#' pid <- "solson.5.1"
@@ -140,7 +140,7 @@ setMethod("D1Node", signature("XMLInternalElementNode"), function(xml) {
#' @aliases archive
#' @seealso \code{\link[=D1Node-class]{D1Node}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' library(uuid)
#' library(digest)
@@ -205,7 +205,7 @@ setMethod("archive", signature("D1Node"), function(x, pid) {
#' @return the bytes of the object
#' @seealso \code{\link{D1Node-class}{D1Node}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' cn <- CNode()
#' mn <- getMNode(cn, "urn:node:KNB")
@@ -229,7 +229,7 @@ setGeneric("getObject", function(x, ...) {
#' @return character the checksum value, with the checksum algorithm as the attribute "algorithm"
#' @seealso \code{\link{D1Node-class}{D1Node}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' cn <- CNode()
#' mn <- getMNode(cn, "urn:node:KNB")
@@ -322,7 +322,7 @@ setMethod("getQueryEngineDescription", signature("D1Node"), function(x, queryEng
#' @return SystemMetadata for the object
#' @import datapack
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' cn <- CNode()
#' mn <- getMNode(cn, "urn:node:KNB")
@@ -345,7 +345,7 @@ setGeneric("getSystemMetadata", function(x, ...) {
#' @aliases describeObject
#' @return A list of header elements
#' @seealso \url{https://purl.dataone.org/architecture/apis/MN_APIs.html#MNRead.describe}
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' mn_uri <- "https://knb.ecoinformatics.org/knb/d1/mn/v1"
#' mn <- MNode(mn_uri)
@@ -564,7 +564,7 @@ setMethod("parseCapabilities", signature("D1Node"), function(x, xml) {
#' @aliases ping
#' @return logical A logical value set to TRUE if the node is up and FALSE if it is not
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' cn <- CNode()
#' mn <- getMNode(cn, "urn:node:KNB")
#' isAlive <- ping(mn)
@@ -700,7 +700,7 @@ setMethod("encodeSolr", signature(x="character"), function(x, ...) {
#' @aliases query
## Need plyr for rbind.fill in query()
#' @import plyr
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' cn <- CNode("PROD")
#' queryParams <- list(q="id:doi*", rows="5",
@@ -963,7 +963,7 @@ parseSolrField <- function(xNode, parse) {
#' @return a logical, TRUE if the action is authorized, false if not.
#' @seealso \code{\link[=CNode-class]{CNode}}{ class description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' # Send an authorization check to the D1 production CN.
#' cn <- CNode("PROD")
#' pid <- "doi:10.6073/pasta/7fcb8fea57843fae65f63094472f502d"
@@ -53,7 +53,7 @@
#' }
#' @seealso \code{\link{dataone}}{ package description.}
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' library(uuid)
#' library(digest)
@@ -189,7 +189,7 @@ setMethod("MNode", signature("D1Node"), function(x) {
#' @import XML
#' @import httr
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' library(dataone)
#' cn <- CNode()
#' mn <- getMNode(cn, "urn:node:KNB")
@@ -326,7 +326,7 @@ setMethod("getChecksum", signature("MNode"), function(x, pid, checksumAlgorithm=
#' @seealso \url{https://purl.dataone.org/architecture/apis/MN_APIs.html#MNStorage.create}
#' @import datapack
#' @export
#' @examples \donttest{
#' @examples \dontrun{
#' # Create an object in the DataONE "STAGING" environment
#' library(dataone)
#' library(uuid)
@@ -644,8 +644,7 @@ setMethod("generateIdentifier", signature("MNode"), function(x, scheme="UUID", f
#' @seealso \code{\link[=MNode-class]{MNode}}{ class description.}
#' @import uuid
#' @export
#' @examples
#' \donttest{
#' @examples \dontrun{
#' cn <- CNode()
#' mn <- getMNode(cn, "urn:node:KNB")
#' packageFileName <- getPackage(mn, id="resourceMap_Blandy.76.2")

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