[med-svn] [r-bioc-gviz] 01/05: New upstream version 1.22.0

[Andreas Tille]

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in repository r-bioc-gviz.

commit 76748b876575ec6516a763c34f396dbd5283b750
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 9 11:04:42 2017 +0100

    New upstream version 1.22.0
---
 DESCRIPTION        |   4 ++--
 R/Gviz-methods.R   |   4 ++--
 Rplots.pdf         | Bin 3611 -> 3611 bytes
 build/vignette.rds | Bin 224 -> 225 bytes
 inst/doc/Gviz.Rnw  |   1 +
 inst/doc/Gviz.pdf  | Bin 1498771 -> 1550601 bytes
 vignettes/Gviz.Rnw |   1 +
 7 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9fa85de..248a0b4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: Gviz
-Version: 1.20.0
+Version: 1.22.0
 Title: Plotting data and annotation information along genomic
         coordinates
 Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09 at imperial.ac.uk>, Lance Parsons <lparsons at princeton.edu>, Shraddha Pai <shraddha.pai at utoronto.ca>
@@ -20,4 +20,4 @@ Collate: Gviz.R AllGenerics.R AllClasses.R Gviz-methods.R
 License: Artistic-2.0
 LazyLoad: yes
 NeedsCompilation: no
-Packaged: 2017-04-24 23:15:45 UTC; biocbuild
+Packaged: 2017-10-30 23:27:01 UTC; biocbuild
diff --git a/R/Gviz-methods.R b/R/Gviz-methods.R
index 116833d..2702f2d 100644
--- a/R/Gviz-methods.R
+++ b/R/Gviz-methods.R
@@ -4245,9 +4245,9 @@ setMethod(".buildRange", signature("TxDb"),
                   ## restore the old values after we are done
                   oldAct <- seqlevels(range)
                   oldRange <- range
-                  on.exit({restoreSeqlevels(oldRange); seqlevels(oldRange, force=TRUE) <- oldAct})
+                  on.exit({restoreSeqlevels(oldRange); seqlevels(oldRange, pruning.mode="coarse") <- oldAct})
                   restoreSeqlevels(range)
-                  seqlevels(range, force=TRUE) <- chromosome
+                  seqlevels(range, pruning.mode="coarse") <- chromosome
                   sl <- seqlengths(range)
                   if(is.null(tstart))
                       tstart <- rep(1, length(chromosome))
diff --git a/Rplots.pdf b/Rplots.pdf
index d2d4018..fd1fdae 100644
Binary files a/Rplots.pdf and b/Rplots.pdf differ
diff --git a/build/vignette.rds b/build/vignette.rds
index 11d785e..a3fc0e1 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/Gviz.Rnw b/inst/doc/Gviz.Rnw
index 5e68eec..938a621 100644
--- a/inst/doc/Gviz.Rnw
+++ b/inst/doc/Gviz.Rnw
@@ -29,6 +29,7 @@ BiocStyle::latex()
 \newcommand{\mgg}[0]{\Rpackage{Gviz} }
 \newcommand{\Reference}[1]{{\texttt{#1}}}
 \newcommand{\link}[1]{{#1}}
+\soulregister{\link}{1}% necessary for compatibility with LaTeX soul package used by BiocStyle for inline code highlighting
 \newcommand{\RR}[0]{{\texttt{R}}}
 
 \title{The Gviz User Guide}
diff --git a/inst/doc/Gviz.pdf b/inst/doc/Gviz.pdf
index a0fab7d..7aaefaf 100644
Binary files a/inst/doc/Gviz.pdf and b/inst/doc/Gviz.pdf differ
diff --git a/vignettes/Gviz.Rnw b/vignettes/Gviz.Rnw
index 5e68eec..938a621 100644
--- a/vignettes/Gviz.Rnw
+++ b/vignettes/Gviz.Rnw
@@ -29,6 +29,7 @@ BiocStyle::latex()
 \newcommand{\mgg}[0]{\Rpackage{Gviz} }
 \newcommand{\Reference}[1]{{\texttt{#1}}}
 \newcommand{\link}[1]{{#1}}
+\soulregister{\link}{1}% necessary for compatibility with LaTeX soul package used by BiocStyle for inline code highlighting
 \newcommand{\RR}[0]{{\texttt{R}}}
 
 \title{The Gviz User Guide}

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