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commit e033b3a8c660156d7126e133b833596655369553 Author: Andreas Tille <[email protected]> Date: Fri Nov 6 15:19:14 2015 +0100 Imported Upstream version 2.12.0 --- DESCRIPTION | 4 ++-- R/database-setup.R | 6 +++--- build/vignette.rds | Bin 302 -> 303 bytes inst/doc/cummeRbund-example-workflow.pdf | Bin 198279 -> 169400 bytes inst/doc/cummeRbund-manual.pdf | Bin 1563785 -> 1360978 bytes 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a23cacf..cef6e7d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: cummeRbund Title: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. -Version: 2.10.0 +Version: 2.12.0 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. @@ -22,4 +22,4 @@ biocViews: HighThroughputSequencing, HighThroughputSequencingData, Infrastructure, DataImport, DataRepresentation, Visualization, Bioinformatics, Clustering, MultipleComparisons, QualityControl NeedsCompilation: no -Packaged: 2015-04-17 03:36:01 UTC; biocbuild +Packaged: 2015-10-14 02:08:17 UTC; biocbuild diff --git a/R/database-setup.R b/R/database-setup.R index 8f9cd36..c150d39 100644 --- a/R/database-setup.R +++ b/R/database-setup.R @@ -1950,7 +1950,7 @@ readCufflinks<-function(dir = getwd(), stop("Must provide a dbConn connection") write("Reading GTF file",stderr()) - gr<-import(gtfFile,asRangedData=FALSE) + gr<-import(gtfFile) gr<-as(gr,"data.frame") #gr$genome<-genomebuild colnames(gr)[grepl('^transcript_id$',colnames(gr))]<-'isoform_id' @@ -1981,7 +1981,7 @@ readCufflinks<-function(dir = getwd(), requiredAttribs <- c("gene_id", "transcript_id", "exon_number") if (verbose) message("Importing ", gtfFile) - tmp <- import(gtfFile, asRangedData=FALSE) + tmp <- import(gtfFile) #dispose of unspliced unstranded transcripts #tmp <- tmp[ which(strand(tmp) %in% c('+','-')) ] @@ -2033,7 +2033,7 @@ readCufflinks<-function(dir = getwd(), #create the db if (verbose) message("Creating TranscriptDb") - tmpdb <- makeTranscriptDb(transcripts, splicings, genes=genes) + tmpdb <- makeTxDb(transcripts, splicings, genes=genes) if (verbose) message("Use saveFeatures() to save the database to a file") return(tmpdb) diff --git a/build/vignette.rds b/build/vignette.rds index 69addd8..e5d65a0 100644 Binary files a/build/vignette.rds and b/build/vignette.rds differ diff --git a/inst/doc/cummeRbund-example-workflow.pdf b/inst/doc/cummeRbund-example-workflow.pdf index c2ac74f..04e524c 100644 Binary files a/inst/doc/cummeRbund-example-workflow.pdf and b/inst/doc/cummeRbund-example-workflow.pdf differ diff --git a/inst/doc/cummeRbund-manual.pdf b/inst/doc/cummeRbund-manual.pdf index 72154c9..5d89d2c 100644 Binary files a/inst/doc/cummeRbund-manual.pdf and b/inst/doc/cummeRbund-manual.pdf differ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-cummerbund.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
