Switch from RCurl::url_exists() to !httr::http_error()

Recommended by @ChristopherWilks + discussed also with @nellore
LieberInstitute · May 6, 2023 · 4e217d7 · 4e217d7
1 parent 70efda3
commit 4e217d7
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Showing 5 changed files with 8 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -41,7 +41,7 @@ Imports:
     rtracklayer,
     S4Vectors,
     utils,
-    RCurl,
+    httr,
     data.table,
     R.utils,
     Matrix,

diff --git a/NAMESPACE b/NAMESPACE
@@ -29,7 +29,6 @@ importFrom(GenomicRanges,GRanges)
 importFrom(GenomicRanges,mcols)
 importFrom(Matrix,readMM)
 importFrom(R.utils,gunzip)
-importFrom(RCurl,url.exists)
 importFrom(S4Vectors,DataFrame)
 importFrom(SummarizedExperiment,"assayNames<-")
 importFrom(SummarizedExperiment,"colData<-")
@@ -39,6 +38,7 @@ importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(data.table,fread)
+importFrom(httr,http_error)
 importFrom(methods,is)
 importFrom(rtracklayer,import.gff)
 importFrom(sessioninfo,package_info)

diff --git a/R/file_retrieve.R b/R/file_retrieve.R
@@ -13,7 +13,7 @@
 #' @export
 #' @importFrom BiocFileCache bfcrpath
 #' @importFrom methods is
-#' @importFrom RCurl url.exists
+#' @importFrom httr http_error
 #'
 #' @family internal functions for accessing the recount3 data
 #' @examples
@@ -56,7 +56,7 @@ file_retrieve <-
         ## In case the url is a local file, there's no need to cache it then
         if (file.exists(url)) {
             return(url)
-        } else if (!url.exists(url)) {
+        } else if (http_error(url)) {
             if (!grepl("tcga\\.recount_pred|gtex\\.recount_pred", url)) {
                 warning("The 'url' <",
                     url,

diff --git a/R/project_homes.R b/R/project_homes.R
@@ -13,7 +13,7 @@
 #'
 #' @return A `character()` vector with the available `project_home` options.
 #'
-#' @importFrom RCurl url.exists
+#' @importFrom httr http_error
 #' @family internal functions for accessing the recount3 data
 #' @export
 #'
@@ -43,7 +43,7 @@ project_homes <-
         ## Construct the URL for the homes_index file
         homes_url <-
             paste(recount3_url, organism, "homes_index", sep = "/")
-        if (url.exists(homes_url)) {
+        if (!http_error(homes_url)) {
             homes_from_url <- readLines(homes_url)
 
             ## Cache the result for the resulting organism so we don't need

diff --git a/vignettes/recount3-quickstart.Rmd b/vignettes/recount3-quickstart.Rmd
@@ -66,7 +66,7 @@ bib <- c(
     interactiveDisplayBase = citation("interactiveDisplayBase")[1],
     rtracklayer = citation("rtracklayer")[1],
     S4Vectors = citation("S4Vectors")[1],
-    RCurl = citation("RCurl")[1],
+    httr = citation("httr")[1],
     data.table = citation("data.table")[1],
     R.utils = citation("R.utils")[1],
     Matrix = citation("Matrix")[1],
@@ -564,13 +564,13 @@ The `r Biocpkg('recount3')` package `r citep(bib[['recount3']])` was made possib
 * `r CRANpkg('covr')` `r citep(bib[['covr']])`
 * `r CRANpkg('data.table')` `r citep(bib[['data.table']])`
 * `r Biocpkg('GenomicRanges')` `r citep(bib[['GenomicRanges']])`
+* `r CRANpkg('httr')` `r citep(bib[['httr']])`
 * `r Biocpkg('interactiveDisplayBase')` `r citep(bib[['interactiveDisplayBase']])`
 * `r CRANpkg('knitcitations')` `r citep(bib[['knitcitations']])`
 * `r CRANpkg('knitr')` `r citep(bib[['knitr']])`
 * `r CRANpkg('Matrix')` `r citep(bib[['Matrix']])`
 * `r CRANpkg('pryr')` `r citep(bib[['pryr']])`
 * `r CRANpkg('RefManageR')` `r citep(bib[['RefManageR']])`
-* `r CRANpkg('RCurl')` `r citep(bib[['RCurl']])`
 * `r CRANpkg('rmarkdown')` `r citep(bib[['rmarkdown']])`
 * `r Biocpkg('rtracklayer')` `r citep(bib[['rtracklayer']])`
 * `r CRANpkg('R.utils')` `r citep(bib[['R.utils']])`