replaced rcurl with httr, no longer an import

ropensci · Oct 14, 2015 · 544cd8b · 544cd8b
1 parent b019495
commit 544cd8b
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Showing 6 changed files with 10 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -20,7 +20,6 @@ Imports:
     plyr,
     stringr,
     httr,
-    RCurl,
     XML,
     jsonlite
 Suggests:

diff --git a/NAMESPACE b/NAMESPACE
@@ -19,7 +19,6 @@ export(split_to_df)
 export(swap)
 export(tryget)
 export(users)
-importFrom(RCurl,getURL)
 importFrom(XML,xmlInternalTreeParse)
 importFrom(XML,xmlToList)
 importFrom(httr,GET)

diff --git a/R/LDSearch.R b/R/LDSearch.R
@@ -48,6 +48,7 @@
 #' GeneCruiser for each SNP. This can slow the query down substantially.
 #' @param quiet boolean; if \code{TRUE} progress updates are written to the
 #' console.
+#' @param ... Curl options passed on to \code{\link[httr]{GET}}
 #' @return A list of data frames, one for each SNP queried, containing
 #' information about the SNPs found to be in LD with that SNP. A description
 #' of the columns follows:
@@ -109,7 +110,7 @@ LDSearch <- function(SNPs,
                       RSquaredLimit=0.8,
                       distanceLimit=500,
                       GeneCruiser=TRUE,
-                      quiet=FALSE ) {
+                      quiet=FALSE, ...) {
 
   ## error checking
 
@@ -171,7 +172,10 @@ LDSearch <- function(SNPs,
   query <- paste( sep = "", query_start, query_end )
 
   if ( !quiet ) cat("Querying SNAP...\n")
-  dat <- getURL( query )
+  # dat <- getURL( query )
+  dat_tmp <- GET(query, ...)
+  stop_for_status(dat_tmp)
+  dat <- content(dat_tmp)
 
   ## check for validation error
   if ( length( grep( "validation error", dat ) ) > 0 ) {

diff --git a/R/rsnps-package.R b/R/rsnps-package.R
@@ -7,7 +7,6 @@
 #' @importFrom httr GET content stop_for_status
 #' @importFrom plyr ldply llply laply compact
 #' @importFrom stringr str_split str_replace_all str_trim
-#' @importFrom RCurl getURL
 #' @importFrom XML xmlInternalTreeParse xmlToList 
 #' @importFrom jsonlite fromJSON
 #' @name rsnps-package

diff --git a/man/LDSearch.Rd b/man/LDSearch.Rd
@@ -5,7 +5,7 @@
 \title{Search for SNPs in Linkage Disequilibrium with a set of SNPs}
 \usage{
 LDSearch(SNPs, dataset = "onekgpilot", panel = "CEU", RSquaredLimit = 0.8,
-  distanceLimit = 500, GeneCruiser = TRUE, quiet = FALSE)
+  distanceLimit = 500, GeneCruiser = TRUE, quiet = FALSE, ...)
 }
 \arguments{
 \item{SNPs}{A vector of SNPs (rs numbers).}
@@ -48,6 +48,8 @@ GeneCruiser for each SNP. This can slow the query down substantially.}
 
 \item{quiet}{boolean; if \code{TRUE} progress updates are written to the
 console.}
+
+\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
 }
 \value{
 A list of data frames, one for each SNP queried, containing

diff --git a/man/rsnpsCache.Rd b/man/rsnpsCache.Rd
@@ -4,7 +4,7 @@
 \name{rsnpsCache}
 \alias{rsnpsCache}
 \title{rsnps environment}
-\format{\preformatted{<environment: 0x109d70f08> 
+\format{\preformatted{<environment: 0x1096d8558> 
 }}
 \usage{
 rsnpsCache