@@ -11,10 +11,11 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

         it provides methods to tally alignment results on a

         per-nucleotide basis using the bam_tally tool.

 Version: 1.7.3

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

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

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

-        tools, Biobase, BSgenome, GenomicAlignments

+Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),

+        GenomicRanges (>= 1.17.12)

+Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),

+        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.4),

+        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9)

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

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

         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,

@@ -1,18 +1,18 @@

 useDynLib(gmapR, .registration = TRUE)

-importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,

-           BamSampler)

+import(methods)

 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,

            list_files_with_exts)

+importFrom(utils, packageVersion)

+

+importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,

+           BamSampler)

 importFrom(Biobase, createPackage)

 import(S4Vectors)

 import(IRanges)

-import(methods)

+import(GenomeInfoDb)

 import(GenomicRanges)

-importFrom(utils, packageVersion)

 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)

-importFrom(GenomicRanges, genome, seqinfo)

-importMethodsFrom(GenomicRanges, seqnames, strand)

 importMethodsFrom(Rsamtools, asBam)

 importClassesFrom(GenomicFeatures, TranscriptDb)

 importFrom(GenomicFeatures, transcripts, exons)