@@ -1,6 +1,6 @@

 Package: CNEr 

-Version: 1.11.5

-Date: 2016-12-01

+Version: 1.11.7

+Date: 2017-02-23

 Title: CNE Detection and Visualization

 Description: Large-scale identification and advanced visualization 

              of sets of conserved noncoding elements.

@@ -14,7 +14,7 @@ Imports: Biostrings (>= 2.33.4),

          XVector (>= 0.5.4),

          GenomicAlignments (>= 1.1.9),

          methods,

-         S4Vectors (>= 0.9.25),

+         S4Vectors (>= 0.13.13),

          IRanges (>= 2.5.27),

          readr (>= 0.2.2),

          BiocGenerics,

@@ -5,7 +5,7 @@ import(BiocGenerics)

 ### Import S4 classes defined in other packages

 ###

 importClassesFrom(methods, ANY, character, integer, missing)

-importClassesFrom(S4Vectors, List, characterORNULL, DataFrame, Pairs)

+importClassesFrom(S4Vectors, List, character_OR_NULL, DataFrame, Pairs)

 importClassesFrom(GenomicRanges, GRanges)

 importClassesFrom(Biostrings, DNAStringSet)

@@ -89,7 +89,6 @@ exportMethods(

   syntenicDotplot,

   ## Axt-methods.R

-  #  mismatchSummary

   summary

 )

@@ -104,7 +103,6 @@ export(

   binRangesFromCoordRange,

   binRestrictionString,

   readCNERangesFromSQLite,

-  #queryAnnotationSQLite,

   fetchChromSizes,

   ## Axt-class.R

@@ -118,6 +116,7 @@ export(

   ## CNE-class.R

   CNE,

+  

   ## GRangePairs-class.R

   GRangePairs,

@@ -131,14 +130,7 @@ export(

   read.rmskFasta,

   ## ceScan.R

-  

   blatCNE,

-  #ceScanOneStep,

-

-  ## makeGeneDbFromUCSC.r

-  #supportedUCSCtables,

-  #queryrefGene, queryknownGene, queryensGene,

-  #makeGeneDbFromUCSC,

   ## WholeGenomeAlignment.R

   lastz,

@@ -40,8 +40,7 @@ axtMatchDistribution <- function(x, size=10000, title=NULL){

     ggtitle(ifelse(is.null(title), "Distribution of matched bases",

                   title)) +

     scale_fill_continuous(low="deepskyblue4", high="gold") +

-    geom_text(aes(fill=toPlot$percentage, 

-                  label=round(toPlot$percentage, 1)))

+    geom_text(aes(label=round(toPlot$percentage, 1)))

 }

 ### -----------------------------------------------------------------