From 04b0028094343d6b9646450a2a6e94629067f332 Mon Sep 17 00:00:00 2001 From: Herve Pages Date: Wed, 7 May 2014 18:44:49 +0000 Subject: [PATCH] Resync again with latest changes in S4vectors, IRanges, GenomeInfoDb, and GenomicRanges. [Note to the developpers: Please make sure you use 'svn merge' when you synchronize with release version so you don't overwrite these changes. Don't hesitate to ask on the Bioc-devel mailing list for questions or concerns about this. Thanks!] git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPQC@90048 bc3139a8-67e5-0310-9ffc-ced21a209358 --- DESCRIPTION | 10 ++++++---- NAMESPACE | 24 +++++++++--------------- 2 files changed, 15 insertions(+), 19 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index de526d8..7bdda15 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: ChIPQC Type: Package Title: Quality metrics for ChIPseq data -Version: 1.1.2 +Version: 1.1.3 Date: 2014-05-06 Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll , Rory Stark @@ -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, 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 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 diff --git a/NAMESPACE b/NAMESPACE index f465a1c..7162cd3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,30 +1,26 @@ -importClassesFrom(GenomicRanges, GRanges, Seqinfo) +import(methods) +import(BiocGenerics) +import(S4Vectors) importClassesFrom(IRanges, DataFrame, IRanges, Rle) -importClassesFrom(methods, character, list, numeric, oldClass) +importClassesFrom(GenomeInfoDb, Seqinfo) -importMethodsFrom(BiocGenerics, as.data.frame, as.vector, cbind, - colnames, duplicated, lapply, ncol, nrow, order, - paste, rbind, rownames, sapply, strand, table, - unique, unlist, xtabs) +importClassesFrom(GenomicRanges, GRanges) importMethodsFrom(BiocParallel, bplapply) importMethodsFrom(GenomicAlignments, readGAlignmentsFromBam) -importMethodsFrom(GenomicRanges, seqlengths, "seqlengths<-", +importMethodsFrom(GenomeInfoDb, 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<-", +importMethodsFrom(IRanges, countOverlaps, coverage, + end, flank, gsub, mean, median, + merge, ranges, reduce, resize, runLength, runValue, sd, shiftApply, start, t, viewMaxs, viewApply, Views, which, which.max, width) -importMethodsFrom(methods, show) - importMethodsFrom(Rsamtools, scanBamHeader, ScanBamParam) import(chipseq) @@ -48,8 +44,6 @@ 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)