From 459d0b4b2930a283b90263bd74c69ee6c8f832d8 Mon Sep 17 00:00:00 2001
From: JP Flores <jpflores@JPs-MacBook-Pro-9.local>
Date: Fri, 12 Jun 2026 11:39:41 -0400
Subject: [PATCH] Wrap large mcool download in \dontrun to prevent example
 timeout on CI

---
 R/readCool.R    | 8 +++++---
 man/readCool.Rd | 6 ++++--
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/R/readCool.R b/R/readCool.R
index b76884ce..f73350fe 100755
--- a/R/readCool.R
+++ b/R/readCool.R
@@ -521,7 +521,8 @@ readCoolChroms <- function(file, resolution = NULL){
 #'                      chromend = 22000000,
 #'                      resolution = 1000000)
 #' 
-#' ## .mcool file
+#' ## .mcool file (large download, skipped in automated checks)
+#' \dontrun{
 #' mcoolFile <- file.path(tempdir(), "LEUK_HEK_PJA27_inter_30.mcool")
 #' download.file(url = "https://zenodo.org/records/10906240/files/LEUK_HEK_PJA27_inter_30.mcool?download=1",
 #'     destfile = mcoolFile, mode = "wb")
@@ -530,10 +531,11 @@ readCoolChroms <- function(file, resolution = NULL){
 #' mcoolData_100Kb <- readCool(file = mcoolFile, chrom = "2",
 #'                             chromstart = 1000000, chromend = 5000000,
 #'                             resolution = 100000)
-#' 
-#' ## Read in data for chr2 at 2500Kb resolution 
+#'
+#' ## Read in data for chr2 at 2500Kb resolution
 #' mcoolData_2500Kb <- readCool(file = mcoolFile, chrom = "2",
 #'                              resolution = 2500000)
+#' }
 #' @seealso \link[plotgardener]{readHic}
 #'
 #' @importFrom rlang inform warn
diff --git a/man/readCool.Rd b/man/readCool.Rd
index e962a685..76973c51 100644
--- a/man/readCool.Rd
+++ b/man/readCool.Rd
@@ -79,7 +79,8 @@ coolData <- readCool(file = coolFile, chrom = "chr2", chromstart = 10000000,
                      chromend = 22000000,
                      resolution = 1000000)
 
-## .mcool file
+## .mcool file (large download, skipped in automated checks)
+\dontrun{
 mcoolFile <- file.path(tempdir(), "LEUK_HEK_PJA27_inter_30.mcool")
 download.file(url = "https://zenodo.org/records/10906240/files/LEUK_HEK_PJA27_inter_30.mcool?download=1",
     destfile = mcoolFile, mode = "wb")
@@ -89,10 +90,11 @@ mcoolData_100Kb <- readCool(file = mcoolFile, chrom = "2",
                             chromstart = 1000000, chromend = 5000000,
                             resolution = 100000)
 
-## Read in data for chr2 at 2500Kb resolution 
+## Read in data for chr2 at 2500Kb resolution
 mcoolData_2500Kb <- readCool(file = mcoolFile, chrom = "2",
                              resolution = 2500000)
 }
+}
 \seealso{
 \link[plotgardener]{readHic}
 }