resync with latest changes in GenomicRanges/GenomeInfoDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPQC@89908 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ChIPQC
 Type: Package
 Title: Quality metrics for ChIPseq data
-Version: 1.1.1
+Version: 1.1.2
 Date: 2014-04-15
 Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark
 Maintainer: Tom Carroll <[email protected]>, Rory Stark <[email protected]>
@@ -10,9 +10,11 @@ biocViews: Sequencing, ChIPSeq, QualityControl, ReportWriting
 License: GPL (>= 3)
 LazyLoad: yes
 Depends: R (>= 3.0.0), ggplot2, DiffBind
-Imports: BiocGenerics (>= 0.8.0), Rsamtools (>= 1.14.2), GenomicRanges (>= 1.14.4),
-         chipseq (>= 1.12.0), GenomicAlignments (>= 0.99.2), 
-        gtools, BiocParallel, methods, IRanges, reshape2, Nozzle.R1, Biobase,grDevices, stats, utils
+Imports: methods, utils, grDevices, stats, BiocGenerics (>= 0.8.0), IRanges,
+        GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.17.11),
+        Rsamtools (>= 1.17.8), GenomicAlignments (>= 1.1.9),
+        Biobase, chipseq (>= 1.12.0), BiocParallel,
+        gtools, reshape2, Nozzle.R1
 Suggests: BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene,
           TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene,
           TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene 

NAMESPACE

@@ -1,8 +1,10 @@
-importClassesFrom(GenomicRanges, GRanges, Seqinfo)
+import(methods)
 
 importClassesFrom(IRanges, DataFrame, IRanges, Rle)
 
-importClassesFrom(methods, character, list, numeric, oldClass)
+import(GenomeInfoDb)
+
+importClassesFrom(GenomicRanges, GRanges)
 
 importMethodsFrom(BiocGenerics, as.data.frame, as.vector, cbind,
                   colnames, duplicated, lapply, ncol, nrow, order,
@@ -13,18 +15,13 @@ importMethodsFrom(BiocParallel, bplapply)
 
 importMethodsFrom(GenomicAlignments, readGAlignmentsFromBam)
 
-importMethodsFrom(GenomicRanges, seqlengths, "seqlengths<-",
-                  "seqlevels<-", seqnames)
-
 importMethodsFrom(IRanges, "%in%", as.list, as.matrix, "colnames<-",
                   countOverlaps, coverage, elementMetadata,
                   "elementMetadata<-", end, flank, gsub, mean, median,
                   merge, ranges, reduce, resize, "rownames<-",
                   runLength, runValue, sd, shiftApply, start, t,
                   viewMaxs, viewApply, Views, which, which.max, width)
 
-importMethodsFrom(methods, show)
-
 importMethodsFrom(Rsamtools, scanBamHeader, ScanBamParam)
 
 import(chipseq)
@@ -48,8 +45,6 @@ importFrom(gtools, running)
 
 importFrom(IRanges, "%over%", IRanges)
 
-importFrom(methods, as, new)
-
 importFrom(Nozzle.R1, addTo, asLink, asStrong, newCustomReport,
            newFigure, newList, newParagraph, newSection, newSubSection,
            newTable, writeReport)