@@ -99,7 +99,10 @@ makeCNEDensity <- function(x, outputDir=".",

   if(seqlengthsNA(x)){

     stop("seqlengths must be provided in `x`!")

   }

-  

+  if(length(x) == 0L){

+    warning("No CNEs in `x`!")

+    return(FALSE)

+  }

   ## make the bed files

   message("Making bed files...")

   bedFirst <- first(x)

@@ -219,6 +222,7 @@ makeAncoraFiles <- function(cne, outputDir=".",

                       mcols(cne)$score,

                       mcols(cne)$cigar)

   }

+  dir.create(outputDir, showWarnings=FALSE, recursive=TRUE)

   write.table(ans, file=file.path(outputDir, fileName), 

               sep="\t", quote=FALSE, row.names=FALSE,

               col.names=FALSE)

@@ -21,7 +21,7 @@

   }

   \item{outputDir}{

     \code{character}(1): the output directory of 

-    \sQuote{Bed} and \sQuote{BigWig} files.

+    \sQuote{Bed}, \sQuote{bedGraph} and \sQuote{BigWig} files.

   }

   \item{genomeFirst,genomeSecond}{

     \code{character}(1): the genome name of the first and second species.