@@ -20,7 +20,7 @@ Description: Genomic data analyses requires integrated visualization

     package. This results in genomic information plotted together with

     your data.

 Depends:

-    R (>= 4.0),

+    R (>= 4.2),

     methods,

     S4Vectors (>= 0.9.25),

     IRanges (>= 1.99.18),

@@ -1877,7 +1877,7 @@ IdeogramTrack <- function(chromosome = NULL, genome, name = NULL, bands = NULL,

             })

             out <- getTable(query)

             if (all(c("chrom", "size") %in% colnames(out))) {

-                out <- data.frame(chrom = out$chrom, chromStart = 0, chromEnd = out$size, name = "", gieStain = "gneg", stringsAsFactors = F)

+                out <- data.frame(chrom = out$chrom, chromStart = 0, chromEnd = out$size, name = "", gieStain = "gneg", stringsAsFactors = FALSE)

             }

             out

         }), env, cenv)

@@ -2102,6 +2102,7 @@ setMethod("drawGD", signature("AnnotationTrack"), function(GdObject, minBase, ma

         }

         ## Plotting of the item labels

         if (.dpOrDefault(GdObject, "showFeatureId", FALSE)) {

+            #grid.text(str2expression(box$text), box$textX, box$textY,

             grid.text(box$text, box$textX, box$textY,

                 rot = rotation, gp = .fontGp(GdObject, subtype = "item"),

                 default.units = "native", just = c("center", "center")

@@ -2377,13 +2378,13 @@ setMethod("drawGD", signature("AlignmentsTrack"), function(GdObject, minBase, ma

             )

             ## print the number of reads together with the connecting lines (currently no scaling/resolution)

             if (sashNumbers) {

-                grid.rect(sash$x[c(F, T, F)], -sash$y[c(F, T, F)],

+                grid.rect(sash$x[c(FALSE, TRUE, FALSE)], -sash$y[c(FALSE, TRUE, FALSE)],

                     width = convertUnit(stringWidth(sash$score) * 1.5, "inches"),

                     height = convertUnit(stringHeight(sash$score) * 1.5, "inches"),

                     default.units = "native", gp = gpar(col = gp$col, fill = gp$fill)

                 )

                 grid.text(

-                    label = sash$score, sash$x[c(F, T, F)], -sash$y[c(F, T, F)],

+                    label = sash$score, sash$x[c(FALSE, TRUE, FALSE)], -sash$y[c(FALSE, TRUE, FALSE)],

                     default.units = "native", gp = gpar(col = gp$col)

                 )

             }