@@ -1,14 +1,14 @@

 Package: CNEr 

-Version: 1.1.0

+Version: 1.1.1

 Date: 2014-03-12

 Title: CNE detection and visualization.

 Description: Large-scale identification and advanced visualization of sets of conserved noncoding elements.

 Author: Ge Tan <ge.tan09@imperial.ac.uk> 

 Maintainer: Ge Tan <ge.tan09@imperial.ac.uk>

-Imports: Biostrings(>= 2.26.3), RSQLite(>= 0.11.4), GenomicRanges(>= 1.12.5), rtracklayer(>= 1.20.4), XVector(>= 0.2.0), DBI(>= 0.2-7), GenomicAlignments(>= 0.99.17), methods, IRanges(>= 1.19.38)

+Imports: Biostrings(>= 2.33.3), RSQLite(>= 0.11.4), GenomicRanges(>= 1.17.7), rtracklayer(>= 1.25.2), XVector(>= 0.5.3), DBI(>= 0.2-7), GenomicAlignments(>= 1.1.4), methods, S4Vectors(>= 0.0.1), IRanges(>= 1.99.1)

 Depends: R (>= 3.0.2)

 Suggests: Gviz(>= 1.7.4), RUnit, BiocGenerics

-LinkingTo: IRanges, XVector

+LinkingTo: S4Vectors, IRanges, XVector

 System Requirements: blat

 License: GPL-2 | file LICENSE

 License_restricts_use: yes

@@ -3,6 +3,7 @@ useDynLib(CNEr, .registration = TRUE)

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

 ### Import

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

+import(S4Vectors)

 import(IRanges)

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

@@ -9,6 +9,7 @@

 #include "Rdefines.h"

 #include "Rinternals.h"

 #include <string.h>

+#include "S4Vectors_interface.h"

 #include "IRanges_interface.h"

 #include "ucsc/binRange.h"

 #include "XVector_interface.h"

@@ -1,5 +1,6 @@

 PKG_OBJECTS = \

-  IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o

+  S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o \

+  utils.o io.o ceScan.o

 UCSC_OBJECTS = \

   axt.o base64.o binRange.o bits.o chain.o \

new file mode 100644

@@ -0,0 +1 @@

+#include "_S4Vectors_stubs.c"