Merge pull request #87 from gladkia/86-fix-bioc-builds-on-windows

86 fix bioc builds on windows
gladkia · Aug 25, 2024 · 188c455 · 188c455
2 parents 425cda0 + e3d93f4
commit 188c455
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Showing 5 changed files with 9 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: igvShiny
 Title: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive
     tool for visualization and exploration integrated genomic data)
-Version: 1.0.3
+Version: 1.0.4
 Date: 2024-08-25
 Authors@R: c(
     person("Paul","Shannon", role = c("aut"), 
@@ -29,7 +29,6 @@ Imports:
     httr,
     jsonlite,
     randomcoloR,
-    RCurl,
     utils
 Suggests: 
     BiocStyle,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+## igvShiny 1.0.4 - 2024-08-25
+* switch from Rcurl::url.exists to httr::http_error (Windows compatibility)
+
 ## igvShiny 1.0.3 - 2024-08-25
 * stop using Amazon S3 URLs by default
 

diff --git a/R/GWASTrack.R b/R/GWASTrack.R
@@ -127,7 +127,7 @@ GWASTrack <- function(trackName,
   }
 
   if (data.class == "character") {
-    if (!RCurl::url.exists(data)) {
+    if (httr::http_error(data)) {
       # was a legitimate url provided?
       error.message <-
         sprintf("error: putative gwas file url unreachable: '%s'",

diff --git a/R/genomeSpec.R b/R/genomeSpec.R
@@ -61,7 +61,7 @@ get_css_genomes <- function(test = FALSE) {
 
   current.genomes.file <- "https://igv.org/genomes/genomes.json"
 
-  if (!RCurl::url.exists(current.genomes.file))
+  if (httr::http_error(current.genomes.file))
     return(get_basic_genomes())
 
   current.genomes.raw <-
@@ -189,7 +189,9 @@ parseAndValidateGenomeSpec <- function(genomeName,
 
     exists.function <- switch(dataMode,
                               "localFiles" = file.exists,
-                              "http" = RCurl::url.exists)
+                              "http" = function(x, ...) {
+                                !(httr::http_error(x, ...))
+                              })
     stopifnot(exists.function(fasta))
     stopifnot(exists.function(fastaIndex))
     if (!is.na(genomeAnnotation))

diff --git a/R/packages.R b/R/packages.R
@@ -2,4 +2,3 @@
 # switch to namespace::function
 
 #' @importFrom checkmate assert_string
-#' @importFrom RCurl url.exists
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,4 +2,3 @@
		# switch to namespace::function

		#' @importFrom checkmate assert_string
		#' @importFrom RCurl url.exists