remove browser() calls; sync DESCRIPTION and NAMESPACE

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPQC@90196 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

@@ -1,20 +1,18 @@
 Package: ChIPQC
 Type: Package
 Title: Quality metrics for ChIPseq data
-Version: 1.1.3
-Date: 2014-05-06
+Version: 1.1.4
+Date: 2014-05-12
 Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark
 Maintainer: Tom Carroll <[email protected]>, Rory Stark <[email protected]>
 Description: Quality metrics for ChIPseq data
 biocViews: Sequencing, ChIPSeq, QualityControl, ReportWriting
 License: GPL (>= 3)
 LazyLoad: yes
 Depends: R (>= 3.0.0), ggplot2, DiffBind
-Imports: methods, BiocGenerics (>= 0.8.0), S4Vectors, IRanges,
-         GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.17.11),
-         Rsamtools (>= 1.17.8), GenomicAlignments (>= 1.1.9),
-         chipseq (>= 1.12.0), gtools, BiocParallel, Biobase,
-         reshape2, Nozzle.R1, grDevices, stats, utils
+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
 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

@@ -1,26 +1,30 @@
-import(methods)
-import(BiocGenerics)
-import(S4Vectors)
+importClassesFrom(GenomicRanges, GRanges, Seqinfo)
 
 importClassesFrom(IRanges, DataFrame, IRanges, Rle)
 
-importClassesFrom(GenomeInfoDb, Seqinfo)
+importClassesFrom(methods, character, list, numeric, oldClass)
 
-importClassesFrom(GenomicRanges, GRanges)
+importMethodsFrom(BiocGenerics, as.data.frame, as.vector, cbind,
+                  colnames, duplicated, lapply, ncol, nrow, order,
+                  paste, rbind, rownames, sapply, strand, table,
+                  unique, unlist, xtabs)
 
 importMethodsFrom(BiocParallel, bplapply)
 
 importMethodsFrom(GenomicAlignments, readGAlignmentsFromBam)
 
-importMethodsFrom(GenomeInfoDb, seqlengths, "seqlengths<-",
+importMethodsFrom(GenomicRanges, seqlengths, "seqlengths<-",
                   "seqlevels<-", seqnames)
 
-importMethodsFrom(IRanges, countOverlaps, coverage,
-                  end, flank, gsub, mean, median,
-                  merge, ranges, reduce, resize,
+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)
@@ -44,6 +48,8 @@ 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)

R/plots.r

@@ -456,7 +456,6 @@ setGeneric("plotRegi", function(object="ChIPQCexperiment",facet=TRUE,
 setMethod("plotRegi", "ChIPQCexperiment", function(object,facet=TRUE,
                                                    facetBy=c("Tissue","Factor"),
                                                    addMetaData=NULL){
-  browser()
   regiScores <- regi(object)
   hasna = apply(is.na(regiScores),2,sum)>0
   if(sum(hasna)==length(hasna)) {
@@ -495,7 +494,6 @@ setMethod("plotRegi", "ChIPQCexperiment", function(object,facet=TRUE,
 
 setMethod("plotRegi", "ChIPQCsample", function(object){
   ### PlaceHolder!
-  browser()
   regiScores <- regi(object)
   if(sum(is.na(regiScores))>0) {
     warning('No genomic annotation computed')