@@ -144,13 +144,13 @@ makeCNEDensity <- function(x, outputDir=".",

   message("Making bedGraph files...")

   bedFirst <- reduce(bedFirst, ignore.strand=TRUE)

   covFirst <- coverage(bedFirst)

-  densityFirst <- runmean(covFirst, k=windowSizeFirst*1000, 

-                          endrule = "constant") * 100

+  densityFirst <- suppressWarnings(runmean(covFirst, k=windowSizeFirst*1000, 

+                          endrule = "constant") * 100)

   bedSecond <- reduce(bedSecond, ignore.strand=TRUE)

   covSecond <- coverage(bedSecond)

-  densitySecond <- runmean(covSecond, k=windowSizeSecond*1000,

-                           endrule = "constant") * 100

+  densitySecond <- suppressWarnings(runmean(covSecond, k=windowSizeSecond*1000,

+                           endrule = "constant") * 100)

   firstTrackLine <- new("GraphTrackLine",

                         name=paste(genomeFirst, "CNEs density", threshold),

@@ -37,7 +37,7 @@ makeGRBs <- function(x, winSize=NULL, genes=NULL, ratio=1,

     stop("The `genes` must be a `GRanges` object!")

   }

-  density <- runmean(cov, k=winSize,  endrule="constant")

+  density <- suppressWarnings(runmean(cov, k=winSize,  endrule="constant"))

   if(background == "genome"){

     # calculate the background percentage of coverage

     totalGenomeSize <- 

@@ -118,5 +118,4 @@ makeGRBs <- function(x, winSize=NULL, genes=NULL, ratio=1,

   clusterRanges <- clusterRanges[indexToKeep]

   return(clusterRanges)

-}

-

+}

\ No newline at end of file

@@ -49,7 +49,7 @@ CNEDensity <- function(dbName, tableName, chr, start, end,

   # Implement get_cne_ranges_in_region_partitioned_by_other_chr later!!!

   ranges <- reduce(ranges)

   covAll <- coverage(ranges, width=context_end)

-  runMeanAll <- runmean(covAll, k=windowSize, "constant")

+  runMeanAll <- suppressWarnings(runmean(covAll, k=windowSize, "constant"))

   ans <- as(runMeanAll, "GRanges")

   ans$score <- ans$score * 100

   return(ans)