From af333e45a81ed03a44152b2a3d918e6a0bb16a74 Mon Sep 17 00:00:00 2001
From: jahn <jahn@mpusp.mpg.de>
Date: Thu, 16 Jan 2025 13:18:23 +0100
Subject: [PATCH] fix: example run time exceeded for 2 geoms

---
 R/geom_cnv.R     |  2 +-
 R/geom_gc.R      |  2 +-
 cran-comments.md | 18 ++++++++++++++----
 man/geom_cnv.Rd  |  2 +-
 man/geom_gc.Rd   |  2 +-
 5 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/R/geom_cnv.R b/R/geom_cnv.R
index 4042d0c..15bd853 100644
--- a/R/geom_cnv.R
+++ b/R/geom_cnv.R
@@ -22,7 +22,7 @@
 #' @export
 #'
 #' @examples
-#' if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) {
+#' \dontrun{
 #'   library("BSgenome.Hsapiens.UCSC.hg19")
 #'
 #'   # load track data
diff --git a/R/geom_gc.R b/R/geom_gc.R
index 80fa337..3f7383b 100644
--- a/R/geom_gc.R
+++ b/R/geom_gc.R
@@ -20,7 +20,7 @@
 #' @export
 #'
 #' @examples
-#' if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) {
+#' \dontrun{
 #'   library("BSgenome.Hsapiens.UCSC.hg19")
 #'
 #'   # load track data
diff --git a/cran-comments.md b/cran-comments.md
index 3b314d6..4576a09 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,9 +1,19 @@
 # Resubmission
 
-Update for current submission: We have substantially removed the size of test
-files for the examples, reducing overall package size from ~30 Mb to only ~6 Mb.
-A further reduction was not possible as the package contains examples for 
-many different NGS file types.
+Update for current submission: 
+
+- We have substantially removed the size of test files for the examples,
+reducing overall package size from ~30 Mb to only ~6 Mb. A further reduction
+was not possible as the package contains examples for many different NGS file
+types.
+
+- Examples were reduced to run in shorter time or excluded from running at all.
+Please note that the 5 sec threshold feels very arbitrary and heavily depends
+on the test environment -- this package never exceeds the threshold when
+tested locally on a 3 year old average laptop, or in 3 different github actions 
+workflows, but regularly fails on the CRAN server.
+
+Background information:
 
 This package has been submitted previously (2023, v0.7.1) and was removed from
 CRAN due to several issues. In the mean time many functions were re-factored,
diff --git a/man/geom_cnv.Rd b/man/geom_cnv.Rd
index 1767123..ddde347 100644
--- a/man/geom_cnv.Rd
+++ b/man/geom_cnv.Rd
@@ -46,7 +46,7 @@ Plot.
 Add CNV Annotation to Coverage Plot.
 }
 \examples{
-if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) {
+\dontrun{
   library("BSgenome.Hsapiens.UCSC.hg19")
 
   # load track data
diff --git a/man/geom_gc.Rd b/man/geom_gc.Rd
index 708e4a4..45b264c 100644
--- a/man/geom_gc.Rd
+++ b/man/geom_gc.Rd
@@ -42,7 +42,7 @@ Plot.
 Add GC Content Annotation to Coverage Plot.
 }
 \examples{
-if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) {
+\dontrun{
   library("BSgenome.Hsapiens.UCSC.hg19")
 
   # load track data