@@ -10,10 +10,10 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

         methods to work with GMAP and GSNAP from within R. In addition,

         it provides methods to tally alignment results on a

         per-nucleotide basis using the bam_tally tool.

-Version: 1.7.1

+Version: 1.7.2

 Depends: R (>= 2.15.0), methods, GenomicRanges

-Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),

-        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),

+Imports: S4Vectors, IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),

+        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.1),

         tools, Biobase, BSgenome, GenomicAlignments

 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,

         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,

@@ -5,6 +5,7 @@ importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,

 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,

            list_files_with_exts)

 importFrom(Biobase, createPackage)

+import(S4Vectors)

 import(IRanges)

 import(methods)

 import(GenomicRanges)

@@ -44,7 +44,7 @@ setMethod("path", "GmapBamReader", function(object) object@path)

 GmapBamReader <- function(path, which = NULL) {

   if (is(path, "BamFile"))

     path <- path(path)

-  if (!IRanges:::isSingleString(path))

+  if (!isSingleString(path))

     stop("'path' must be a single, non-NA string")

   path <- path.expand(path)

   obj <- new("GmapBamReader", .extptr = .Call(R_Bamread_new, path), path = path)