[med-svn] [r-bioc-cummerbund] 02/05: Imported Upstream version 2.12.0

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-cummerbund.

commit e033b3a8c660156d7126e133b833596655369553
Author: Andreas Tille <tille at debian.org>
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

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