From c53f27048b309fa67fe9879702ab330525130d60 Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Thu, 13 Aug 2020 08:04:04 -0400
Subject: [PATCH] [ci-skip] Add donttest

---
 R/objects.R       | 4 ++++
 R/preprocessing.R | 2 ++
 R/utilities.R     | 2 ++
 R/visualization.R | 6 ++++++
 4 files changed, 14 insertions(+)

diff --git a/R/objects.R b/R/objects.R
index 2a16f9d6..bebb8136 100644
--- a/R/objects.R
+++ b/R/objects.R
@@ -1332,7 +1332,9 @@ setMethod(
 #' @export
 #' @concept assay
 #' @examples
+#' \donttest{
 #' Annotation(atac_small[["peaks"]])
+#' }
 Annotation.ChromatinAssay <- function(object, ...) {
   return(slot(object = object, name = "annotation"))
 }
@@ -1344,7 +1346,9 @@ Annotation.ChromatinAssay <- function(object, ...) {
 #' @export
 #' @concept assay
 #' @examples
+#' \donttest{
 #' Annotation(atac_small)
+#' }
 Annotation.Seurat <- function(object, ...) {
   assay <- DefaultAssay(object = object)
   return(Annotation(object = object[[assay]]))
diff --git a/R/preprocessing.R b/R/preprocessing.R
index 75e0872e..738e70b0 100644
--- a/R/preprocessing.R
+++ b/R/preprocessing.R
@@ -502,6 +502,7 @@ FRiP <- function(
 #' @concept utilities
 #' @return Returns a sparse matrix
 #' @examples
+#' \donttest{
 #' genome <- 780007
 #' names(genome) <- 'chr1'
 #' fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
@@ -511,6 +512,7 @@ FRiP <- function(
 #'   genome = genome,
 #'   binsize = 1000
 #' )
+#' }
 GenomeBinMatrix <- function(
   fragments,
   genome,
diff --git a/R/utilities.R b/R/utilities.R
index cb3055fe..8348265e 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -334,8 +334,10 @@ ConnectionsToLinks <- function(conns, ccans = NULL, threshold = 0) {
 #' @export
 #' @concept utilities
 #' @examples
+#' \donttest{
 #' fc <- FoldChange(object = atac_small, ident.1 = 0)
 #' head(fc)
+#' }
 FoldChange <- function(
   object,
   ident.1,
diff --git a/R/visualization.R b/R/visualization.R
index d906b7ff..60ecc377 100644
--- a/R/visualization.R
+++ b/R/visualization.R
@@ -796,9 +796,11 @@ TSSPlot <- function(
 #' @importFrom patchwork wrap_plots plot_layout guide_area
 #' @concept visualization
 #' @examples
+#' \donttest{
 #' p1 <- PeakPlot(atac_small, region = "chr1-29554-39554")
 #' p2 <- AnnotationPlot(atac_small, region = "chr1-29554-39554")
 #' CombineTracks(plotlist = list(p1, p2), heights = c(1, 1))
+#' }
 CombineTracks <- function(
   plotlist,
   expression.plot = NULL,
@@ -980,7 +982,9 @@ LinkPlot <- function(object, region) {
 #' @importFrom fastmatch fmatch
 #' @concept visualization
 #' @examples
+#' \donttest{
 #' AnnotationPlot(object = atac_small, region = c("chr1-29554-39554"))
+#' }
 AnnotationPlot <- function(object, region) {
   annotation <- Annotation(object = object)
   if (is.null(x = annotation)) {
@@ -1688,6 +1692,7 @@ VariantPlot <- function(
 #' @export
 #' @concept visualization
 #' @examples
+#' \donttest{
 #' fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
 #' fragments <- CreateFragmentObject(
 #'   path = fpath,
@@ -1696,6 +1701,7 @@ VariantPlot <- function(
 #' )
 #' Fragments(atac_small) <- fragments
 #' TilePlot(object = atac_small, region = c("chr1-713500-714500"))
+#' }
 TilePlot <- function(
   object,
   region,