@@ -1,7 +1,7 @@

 Package: SplicingGraphs

 Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads

 	to them

-Version: 1.16.0

+Version: 1.16.1

 Encoding: UTF-8

 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pagès

 License: Artistic-2.0

@@ -185,13 +185,13 @@

             ans_d <- c(ans_d, bubble_d)

             ## Format the bubble partitions.

             bubble_partitions <- bubble_variants[ , "partition"]

-            bubble_partitions <- sapply(bubble_partitions, paste, collapse=",")

+            bubble_partitions <- sapply(bubble_partitions, base::paste, collapse=",")

             bubble_partitions <- paste0("{", bubble_partitions, "}")

             ans_partitions <- c(ans_partitions,

                                 CharacterList(bubble_partitions))

             ## Format the bubble paths.

             bubble_paths <- bubble_variants[ , "path"]

-            bubble_paths <- sapply(bubble_paths, paste, collapse=",")

+            bubble_paths <- sapply(bubble_paths, base::paste, collapse=",")

             bubble_paths <- paste0("{", bubble_paths, "}")

             ans_paths <- c(ans_paths, CharacterList(bubble_paths))

             ## Format the bubble AScode.

@@ -106,7 +106,7 @@ setOldClass("igraph")

         stop("'tx_id.as.edge.label' must be TRUE or FALSE")

     d <- .precook_igraph_edges_from_sgedges(sgedges)

     if (tx_id.as.edge.label)

-        d$label <- sapply(d$tx_id, paste, collapse=",")

+        d$label <- sapply(d$tx_id, base::paste, collapse=",")

     d$tx_id <- NULL

     ## Turning 'd' into an ordinary data.frame. (Looks like 'as.data.frame()'

     ## on a DataFrame ignores the 'stringsAsFactors' arg so we use