[med-svn] [r-bioc-rtracklayer] 02/05: New upstream version 1.36.6

[Andreas Tille]

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

commit a0babb9cd97ef245577a50a44366f2bd73cdaadf
Author: Andreas Tille <tille at debian.org>
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 at 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

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