[med-svn] [r-bioc-biovizbase] 01/04: New upstream version 1.26.0

[Andreas Tille]

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

commit 57de3f9552c3413e640130eb5738faf9f3c6c8fe
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 9 10:55:21 2017 +0100

    New upstream version 1.26.0
---
 DESCRIPTION        |   4 ++--
 R/crunch-method.R  |   4 ++--
 build/vignette.rds | Bin 234 -> 235 bytes
 inst/doc/intro.pdf | Bin 247927 -> 248141 bytes
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e5b75fa..f9e5a31 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: biovizBase
-Version: 1.24.0
+Version: 1.26.0
 Title: Basic graphic utilities for visualization of genomic data.
 Description: The biovizBase package is designed to provide a set of
         utilities, color schemes and conventions for genomic data. It
@@ -32,7 +32,7 @@ Collate: utils.R color.R AllGenerics.R crunch-method.R mold-method.R
         facets-method.R aes.R scale.R zzz.R biovizBase-package.R
 biocViews: Infrastructure, Visualization, Preprocessing
 NeedsCompilation: yes
-Packaged: 2017-04-24 23:08:22 UTC; biocbuild
+Packaged: 2017-10-30 23:18:48 UTC; biocbuild
 Author: Tengfei Yin [aut],
   Michael Lawrence [aut, ths, cre],
   Dianne Cook [aut, ths],
diff --git a/R/crunch-method.R b/R/crunch-method.R
index 3dadd76..3187d64 100644
--- a/R/crunch-method.R
+++ b/R/crunch-method.R
@@ -15,11 +15,11 @@ setMethod("crunch", "TxDb", function(obj, which,
 
     seqnms <- as.character(unique(seqnames(which)))
     if(seqnms %in% seqlevels(obj)){
-        seqlevels(obj, force = TRUE) <- seqnms
+        seqlevels(obj, pruning.mode="coarse") <- seqnms
     }else{
         stop(seqnms, " is not matched with seqlevels of your object, please rename your 'which' arguments ")
     }
-    ## seqlevels(obj, force = TRUE) <- seqnms
+    ## seqlevels(obj, pruning.mode="coarse") <- seqnms
     on.exit(restoreSeqlevels(obj))  # needed only because TxDb are reference
                                     # objects (unlike R objects in general that
                                     # have a copy-on-change semantics)
diff --git a/build/vignette.rds b/build/vignette.rds
index 35b8564..d3dadf1 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/intro.pdf b/inst/doc/intro.pdf
index d77fff5..e6673db 100644
Binary files a/inst/doc/intro.pdf and b/inst/doc/intro.pdf differ

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