Remove warning msgs on summary extractors (been >1yr since last relea…

…se with older esummary object)

NAMESPACE

@@ -1,8 +1,5 @@
 # Generated by roxygen2 (4.1.1): do not edit by hand
 
-S3method("$",esummary)
-S3method("[",esummary)
-S3method("[[",esummary)
 S3method(as.data.frame,eInfoList)
 S3method(print,eInfoEntry)
 S3method(print,eInfoLink)

R/entrez_summary.r

@@ -150,59 +150,6 @@ parse_esumm_list <- function(node){
 }
 
 
-
-#' @export
-`[[.esummary` <- function(x, name, ...){
-    res <- NextMethod("[[") 
-    if(is.null(res)){
-        msg <- paste0("Esummary object '", deparse(substitute(x)), "' has no object",
-                     " named '", name, "' \b.\nIf you were expecting values from a ",
-                     " 'version 1.0' esummary record, try setting 'version' to ",
-                     " '1.0' in entrez_summary (see documentation for more)\n")
-        warning(msg)
-     }
-    res
-}
-
-
-#' @export
-`[.esummary` <- function(x, ...){
-    res <- NextMethod("[") 
-    if(any(vapply(res, is.null, TRUE))){
-        msg <- paste("Some values missing from Esumamry object. If you were",
-                     "expecting a 'Version 1.0' esummary record, try setting",
-                     "'version' to '1.0' in entrez_summary()")
-       warning(msg) 
-     }
-    res
-}
-
-
-
-#' @export
-`$.esummary` <- function(x, name){
-    suppressWarnings(
-        res <- x[[name]]
-    )
-    if(!is.null(res)){
-        return(res)
-    }
-    suppressWarnings(res <- x[[name, exact=FALSE]])
-    if(!is.null(res) &&  getOption("warnPartialMatchDollar", default=FALSE)){
-        warning("Returning partial match")
-        return(res)
-    }
-    if(is.null(res)){
-         msg <- paste0("Esummary object '", deparse(substitute(x)), "' has no object",
-                     " named '", name, "' \b.\nIf you were expecting values from a ",
-                     " 'versoin 1.0' esummary record, try setting 'version' to ",
-                     " '1.0' in entrez_summary (see documentation for more)\n")
-        warning(msg)
-    }
-    res
-}
-
-
 #' @export 
 print.esummary <- function(x, ...){
     len <- length(x)

man/entrez_link.Rd

@@ -12,7 +12,7 @@ entrez_link(dbfrom, web_history = NULL, id = NULL, db = NULL,
 
 \item{web_history}{a web_history object}
 
-\item{id}{vector with unique ID(s) for reacods in database \code{db}.}
+\item{id}{vector with unique ID(s) for records in database \code{db}.}
 
 \item{db}{character Name of the database to search for links (or use "all" to
 search all databases available for \code{db}. \code{entrez_db_links} allows you
@@ -35,13 +35,19 @@ to discover databases that might have linked information (see examples).}
   each ID.
 }}
 
+\item{by_id}{logial If FALSE (default) return a single
+\code{elink} objects containing links for all of the provided \code{id}s.
+Alternatively, if TRUE return a list of \code{elink} objects, one for each
+ID in \code{id}.}
+
 \item{config}{vector configuration options passed to httr::GET}
 
 \item{\dots}{character Additional terms to add to the request, see NCBI
 documentation linked to in referenes for a complete list}
 }
 \value{
 An elink object containing the data defined by the \code{cmd} argument
+(if by_id=FALSE) or a list of such object (if by_id=TRUE).
 
 file XMLInternalDocument xml file resulting from search, parsed with
 \code{\link{xmlTreeParse}}