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commit a0babb9cd97ef245577a50a44366f2bd73cdaadf Author: Andreas Tille <[email protected]> Date: Sun Oct 22 19:24:52 2017 +0200 New upstream version 1.36.6 --- DESCRIPTION | 4 ++-- R/ucsc.R | 7 ++++--- build/vignette.rds | Bin 196 -> 196 bytes inst/doc/rtracklayer.pdf | Bin 311228 -> 311311 bytes 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c28f144..ab07c52 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: rtracklayer Title: R interface to genome browsers and their annotation tracks -Version: 1.36.4 +Version: 1.36.6 Author: Michael Lawrence, Vince Carey, Robert Gentleman Depends: R (>= 3.3), methods, GenomicRanges (>= 1.21.20) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.13.8), S4Vectors (>= @@ -27,4 +27,4 @@ Collate: io.R web.R ranges.R trackDb.R browser.R ucsc.R readGFF.R gff.R test_rtracklayer_package.R ncbi.R zzz.R biocViews: Annotation,Visualization,DataImport NeedsCompilation: yes -Packaged: 2017-07-12 22:31:13 UTC; biocbuild +Packaged: 2017-10-11 22:33:17 UTC; biocbuild diff --git a/R/ucsc.R b/R/ucsc.R index 59f6c81..a039a30 100644 --- a/R/ucsc.R +++ b/R/ucsc.R @@ -442,7 +442,7 @@ setMethod("ucscSchemaDescription", "UCSCTableQuery", function(object) links <- new("UCSCLinks", genome = linkGenome, tableName = linkTable, fieldName = linkField, viaName = linkVia) } else links <- new("UCSCLinks") - sampNode <- getNodeSet(doc, "//div[@class = 'subheadingBar' and contains(text(), 'Sample')]/following::table[1]//table//table")[[1]] + sampNode <- getNodeSet(doc, "//div[contains(@class, 'subheadingBar') and contains(text(), 'Sample')]/following::table[1]//table//table")[[1]] sample <- getDataFrame(sampNode) schema <- new("UCSCSchema", schema, genome = genome, tableName = tableName, rowCount = rowCount, formatDescription = format) @@ -658,8 +658,9 @@ setMethod("browserView", "UCSCSession", view <- new("UCSCView", session = object) ## new hgsid for each browser launch doc <- ucscGet(object, "gateway") - node <- getNodeSet(doc, "//input[@name = 'hgsid']/@value")[[1]] - hgsid <- node ##xmlValue(node) + hgsid <- sub(".*=", "", + grep("hgsid=", getNodeSet(doc, "//a/@href"), + value=TRUE)[1L]) view@hgsid <- as.character(hgsid) ## figure out track modes origModes <- modes <- ucscTrackModes(view) diff --git a/build/vignette.rds b/build/vignette.rds index d410955..26cbafc 100644 Binary files a/build/vignette.rds and b/build/vignette.rds differ diff --git a/inst/doc/rtracklayer.pdf b/inst/doc/rtracklayer.pdf index f96e560..17aa4a3 100644 Binary files a/inst/doc/rtracklayer.pdf and b/inst/doc/rtracklayer.pdf differ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-rtracklayer.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
