From ab084cc06a5146dfca2e626962a11ca7e1941d18 Mon Sep 17 00:00:00 2001 From: "hpages@fhcrc.org" Date: Fri, 29 Jan 2016 01:22:03 +0000 Subject: [PATCH] elementLengths was renamed -> elementNROWS in S4Vectors (new name reflects TRUE semantic, old name will be deprecated soon) git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cummeRbund@113044 bc3139a8-67e5-0310-9ffc-ced21a209358 --- DESCRIPTION | 4 ++-- NAMESPACE | 4 ++-- R/database-setup.R | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4491102..616530c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,10 @@ Package: cummeRbund Title: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. -Version: 2.13.0 +Version: 2.13.1 Date: 2013-04-22 Author: L. Goff, C. Trapnell, D. Kelley Description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. -Imports: methods, plyr, BiocGenerics, Biobase +Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson Maintainer: Loyal A. Goff diff --git a/NAMESPACE b/NAMESPACE index 78c96b2..e17ff94 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,9 +1,9 @@ -importFrom(BiocGenerics, annotation) - import(methods) #importFrom(graphics, plot) importFrom(plyr, defaults) +importFrom(BiocGenerics, annotation) +import(S4Vectors) importFrom(Biobase, featureNames) exportClasses(CuffSet, diff --git a/R/database-setup.R b/R/database-setup.R index c150d39..8bc7917 100644 --- a/R/database-setup.R +++ b/R/database-setup.R @@ -2014,7 +2014,7 @@ readCufflinks<-function(dir = getwd(), tmpS <- split(tmp, values(tmp)$transcript_id) if(verbose) message('Attempting to create the splicings data.frame') splicings <- data.frame( - tx_id=rep(1:length(tmpS), elementLengths(tmpS)), + tx_id=rep(1:length(tmpS), elementNROWS(tmpS)), exon_rank=as.integer(values(unlist(tmpS))$exon_number), exon_chrom=as.character(seqnames(unlist(tmpS))), exon_strand=as.character(strand(unlist(tmpS))),