@@ -11,7 +11,7 @@ biocViews: Genetics, Annotation, DataRepresentation, Visualization,

 	ImmunoOncology

 URL: https://bioconductor.org/packages/SplicingGraphs

 BugReports: https://github.com/Bioconductor/SplicingGraphs/issues

-Version: 1.43.0

+Version: 1.43.1

 License: Artistic-2.0

 Encoding: UTF-8

 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pagès

@@ -20,9 +20,8 @@ Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),

 	 Rgraphviz (>= 2.3.7)

 Imports: methods, utils, graphics, igraph, BiocGenerics,

 	 S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2),

-	 GenomeInfoDb, GenomicRanges (>= 1.23.21), GenomicFeatures, Rsamtools,

-	 GenomicAlignments, graph, Rgraphviz

-Suggests: igraph, Gviz,

+	 GenomeInfoDb, GenomicRanges (>= 1.23.21), Rsamtools, graph

+Suggests: igraph, Gviz, txdbmaker,

 	 TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14,

 	 RUnit

 Collate: utils.R

@@ -1,5 +1,5 @@

 import(methods)

-import(utils)

+importFrom(utils, read.table)

 importFrom(graphics, plot)

 importFrom(igraph, vcount, vertex_attr, ecount, edge_attr, as_edgelist,

@@ -4,7 +4,7 @@

 .make_toy_sg <- function()

 {

-     library(GenomicFeatures)

+     library(txdbmaker)

      suppressWarnings(

        toy_genes_txdb <- makeTxDbFromGFF(toy_genes_gff())

      )

@@ -240,7 +240,7 @@ SplicingGraphs(x, grouping=NULL, min.ntx=2, max.ntx=NA, check.introns=TRUE)

 ## 1. Load a toy gene model as a TxDb object

 ## ---------------------------------------------------------------------

-library(GenomicFeatures)

+library(txdbmaker)

 suppressWarnings(

   toy_genes_txdb <- makeTxDbFromGFF(toy_genes_gff())

 )

@@ -40,8 +40,10 @@ toy_overlaps()

           \link[GenomicAlignments]{GAlignmentPairs} classes defined

           in the \pkg{GenomicAlignments} package.

-    \item The \code{\link[GenomicFeatures]{makeTxDbFromGFF}}

-          function and the \link[GenomicFeatures]{TxDb} class

+    \item The \code{\link[txdbmaker]{makeTxDbFromGFF}}

+          function in the \pkg{txdbmaker} package.

+

+    \item The \link[GenomicFeatures]{TxDb} class

           defined in the \pkg{GenomicFeatures} package.

   }

 }

@@ -55,7 +57,7 @@ toy_genes_gff()

 ## Note that you can display the content of the file with:

 cat(readLines(toy_genes_gff()), sep="\n")

-library(GenomicFeatures)

+library(txdbmaker)

 suppressWarnings(

   txdb <- makeTxDbFromGFF(toy_genes_gff())

 )