[med-svn] [r-bioc-dnacopy] 01/05: Imported Upstream version 1.48.0

[Andreas Tille]

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

commit 439d719eb2bcb455b00bd20ac1d58f13d934d24f
Author: Andreas Tille <tille at debian.org>
Date:   Fri Oct 28 08:13:22 2016 +0200

    Imported Upstream version 1.48.0
---
 DESCRIPTION          |   4 ++--
 NAMESPACE            |   2 ++
 R/DNAcopyMethods.R   |   6 ++++++
 build/vignette.rds   | Bin 216 -> 218 bytes
 inst/CHANGES         |  13 +++++++++++++
 inst/doc/DNAcopy.pdf | Bin 234494 -> 218430 bytes
 6 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 329e992..34a7af5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: DNAcopy
 Title: DNA copy number data analysis
-Version: 1.46.0
+Version: 1.48.0
 Author: Venkatraman E. Seshan, Adam Olshen
 Description: Implements the circular binary segmentation (CBS) 
         algorithm to segment DNA copy number data and identify
@@ -10,4 +10,4 @@ LazyData: yes
 License: GPL (>= 2)
 biocViews: Microarray, CopyNumberVariation
 NeedsCompilation: yes
-Packaged: 2016-05-04 02:41:35 UTC; biocbuild
+Packaged: 2016-10-17 22:10:08 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index d281bcb..52091ca 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,7 @@
 useDynLib(DNAcopy)
 import(stats,graphics)
+importFrom("grDevices", "dev.cur", "dev.interactive", "dev.new")
+importFrom("utils", "data")
 export("CNA","exon.segment","getbdry","segment","segments.p","segments.summary","smooth.CNA","glFrequency","plotSample","zoomIntoRegion")
 S3method(print, CNA)
 S3method(plot, DNAcopy)
diff --git a/R/DNAcopyMethods.R b/R/DNAcopyMethods.R
index 0de13fa..8bad2ef 100644
--- a/R/DNAcopyMethods.R
+++ b/R/DNAcopyMethods.R
@@ -14,6 +14,12 @@ CNA <- function(genomdat, chrom, maploc, data.type=c("logratio","binary"),
       sortindex <- which(ina)
     }
     if (is.factor(chrom)) chrom <- as.character(chrom)
+    # added to allow arrays of single dimension - results from data.frame ops
+    if (is.array(genomdat)) {
+        if (length(dim(genomdat)) == 1) {
+            genomdat <- as.matrix(genomdat)
+        }
+    }
     if (is.vector(genomdat)) genomdat <- as.matrix(genomdat)
     if (!missing(sampleid)) {
       if (length(sampleid) != ncol(genomdat)) {
diff --git a/build/vignette.rds b/build/vignette.rds
index 5baebb0..539c469 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/CHANGES b/inst/CHANGES
index 72b02e4..48f341e 100644
--- a/inst/CHANGES
+++ b/inst/CHANGES
@@ -1,3 +1,16 @@
+Changes in Version 1.47.2
+
+   o Added a check to see if genomdat is a one-dimensional array 
+
+Changes in Version 1.47.1
+
+   o Added importFrom("grDevices", "dev.cur", "dev.interactive", "dev.new")
+     and importFrom("utils", "data") to NAMESPACE to resolve warnings
+
+
+1.41.3 became 1.42.0, 1.44.0 and 1.46.0 in Bioconductor 3.1, 3.2 & 3.3
+----------------------------------------------------------------------
+
 Changes in Version 1.41.3
 
    o Address the "malformed Description field" NOTE.
diff --git a/inst/doc/DNAcopy.pdf b/inst/doc/DNAcopy.pdf
index bf24aa5..972feee 100644
Binary files a/inst/doc/DNAcopy.pdf and b/inst/doc/DNAcopy.pdf differ

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