elementLengths was renamed -> elementNROWS in S4Vectors (new name ref…

…lects 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

@@ -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 <[email protected]>

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,

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))),