fix: dont run failing ideogram example check

Author: m-jahn

NAMESPACE

@@ -131,7 +131,13 @@ importFrom(methods,extends)
 importFrom(patchwork,wrap_plots)
 importFrom(rlang,.data)
 importFrom(rlang,as_label)
+importFrom(rtracklayer,GRangesForUCSCGenome)
+importFrom(rtracklayer,browserSession)
+importFrom(rtracklayer,getTable)
 importFrom(rtracklayer,import)
+importFrom(rtracklayer,tableName)
+importFrom(rtracklayer,ucscGenomes)
+importFrom(rtracklayer,ucscTableQuery)
 importFrom(scales,comma)
 importFrom(scales,rescale)
 importFrom(scales,scientific)

R/geom_ideogram.R

@@ -21,18 +21,21 @@
 #'
 #' @return Plot.
 #' @importFrom dplyr %>%
-#' @importFrom GenomicRanges GRanges makeGRangesFromDataFrame
+#' @importFrom GenomicRanges GRanges makeGRangesFromDataFrame trim
 #' @importFrom IRanges IRanges subsetByOverlaps
-#' @importFrom ggplot2 ggplot_add ggplot geom_rect aes_string geom_polygon theme_classic theme element_blank
-#' scale_x_continuous scale_y_continuous margin
+#' @importFrom ggplot2 ggplot_add ggplot geom_rect aes_string geom_polygon
+#'   theme_classic theme element_blank scale_x_continuous scale_y_continuous
+#'   margin
 #' @importFrom patchwork wrap_plots
 #' @importFrom methods extends
 #' @importFrom utils menu
+#' @importFrom rtracklayer ucscGenomes ucscTableQuery tableName getTable
+#'   GRangesForUCSCGenome browserSession
 #' @importFrom GenomeInfoDb seqlengths seqlengths<- seqnames
-#' @importFrom GenomicRanges trim GRanges
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' library(ggbio)
 #'
 #' # load metadata
@@ -68,6 +71,7 @@
 #' basic_coverage +
 #'   geom_gene(gtf.gr = gtf_gr) +
 #'   geom_ideogram(genome = "hg19", plot.space = 0)
+#' }
 #'
 geom_ideogram <- function(genome = "hg19", mark.color = "red", mark.alpha = 0.7, mark.line.size = 1,
                           add.shadow = TRUE, shadow.color = "grey", shadow.alpha = 0.7, shadow.line.size = 1,

R/utils.R

@@ -275,7 +275,7 @@ getIdeogram <- function(genome, subchr = NULL, cytobands = TRUE) {
         suppressWarnings(GenomeInfoDb::seqlengths(gr) <- new.seqlength)
         gr <- GenomicRanges::trim(gr)
       } else {
-        message("cytoBand informatin is not available, only get ranges.")
+        message("cytoBand information is not available, only getting ranges.")
         message("Loading ranges...")
         gr <- rtracklayer::GRangesForUCSCGenome(genome)
         message("Done")