[med-svn] [r-bioc-genomicranges] 01/03: Imported Upstream version 1.28.6

[Graham Inggs]

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ginggs pushed a commit to branch master
in repository r-bioc-genomicranges.

commit c1b9488569eaa4255ec05816fab5822e40cec6ab
Author: Graham Inggs <ginggs at debian.org>
Date:   Fri Oct 13 17:46:15 2017 +0200

    Imported Upstream version 1.28.6
---
 DESCRIPTION                                 |   4 ++--
 R/GenomicRanges-comparison.R                |   3 ++-
 inst/doc/ExtendingGenomicRanges.pdf         | Bin 103241 -> 103036 bytes
 inst/doc/GRanges_and_GRangesList_slides.pdf | Bin 250940 -> 250940 bytes
 inst/doc/GenomicRangesHOWTOs.pdf            | Bin 195193 -> 195126 bytes
 inst/doc/GenomicRangesIntroduction.pdf      | Bin 159460 -> 159556 bytes
 inst/doc/Ten_things_slides.pdf              | Bin 138327 -> 138327 bytes
 man/GenomicRanges-comparison.Rd             |   2 +-
 man/makeGRangesFromDataFrame.Rd             |   8 +++++---
 9 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4b2db37..7a8e09c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -11,7 +11,7 @@ Description: The ability to efficiently represent and manipulate genomic
 	summarization of an experiment, are defined in the GenomicAlignments
 	and SummarizedExperiment packages respectively. Both packages build
 	on top of the GenomicRanges infrastructure.
-Version: 1.28.5
+Version: 1.28.6
 Encoding: UTF-8
 Author: P. Aboyoun, H. Pagès, and M. Lawrence
 Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
@@ -49,4 +49,4 @@ Collate: utils.R phicoef.R transcript-utils.R constraint.R
         tileGenome.R tile-methods.R genomicvars.R zzz.R
 RoxygenNote: 5.0.1.9000
 NeedsCompilation: yes
-Packaged: 2017-09-06 22:51:36 UTC; biocbuild
+Packaged: 2017-10-03 22:49:24 UTC; biocbuild
diff --git a/R/GenomicRanges-comparison.R b/R/GenomicRanges-comparison.R
index 95ad0f1..a039f13 100644
--- a/R/GenomicRanges-comparison.R
+++ b/R/GenomicRanges-comparison.R
@@ -250,7 +250,8 @@ order_GenomicRanges <- function(x, decreasing=FALSE, ignore.strand=FALSE)
 ### ignored.
 ### 'method' is also ignored at the moment.
 setMethod("order", "GenomicRanges",
-    function(..., na.last=TRUE, decreasing=FALSE, method=c("shell", "radix"))
+    function(..., na.last=TRUE, decreasing=FALSE,
+                  method=c("auto", "shell", "radix"))
     {
         ## Turn off this warning for now since it triggers spurious warnings
         ## when calling sort() on a GRangesList object. The root of the
diff --git a/inst/doc/ExtendingGenomicRanges.pdf b/inst/doc/ExtendingGenomicRanges.pdf
index 209de0a..a128de4 100644
Binary files a/inst/doc/ExtendingGenomicRanges.pdf and b/inst/doc/ExtendingGenomicRanges.pdf differ
diff --git a/inst/doc/GRanges_and_GRangesList_slides.pdf b/inst/doc/GRanges_and_GRangesList_slides.pdf
index 2cb8e5d..59dab1f 100644
Binary files a/inst/doc/GRanges_and_GRangesList_slides.pdf and b/inst/doc/GRanges_and_GRangesList_slides.pdf differ
diff --git a/inst/doc/GenomicRangesHOWTOs.pdf b/inst/doc/GenomicRangesHOWTOs.pdf
index 7fb18db..baf21be 100644
Binary files a/inst/doc/GenomicRangesHOWTOs.pdf and b/inst/doc/GenomicRangesHOWTOs.pdf differ
diff --git a/inst/doc/GenomicRangesIntroduction.pdf b/inst/doc/GenomicRangesIntroduction.pdf
index 7d1266b..4577996 100644
Binary files a/inst/doc/GenomicRangesIntroduction.pdf and b/inst/doc/GenomicRangesIntroduction.pdf differ
diff --git a/inst/doc/Ten_things_slides.pdf b/inst/doc/Ten_things_slides.pdf
index 3b478a9..42b99cc 100644
Binary files a/inst/doc/Ten_things_slides.pdf and b/inst/doc/Ten_things_slides.pdf differ
diff --git a/man/GenomicRanges-comparison.Rd b/man/GenomicRanges-comparison.Rd
index 34752f5..616dda6 100644
--- a/man/GenomicRanges-comparison.Rd
+++ b/man/GenomicRanges-comparison.Rd
@@ -44,7 +44,7 @@
 
 \S4method{is.unsorted}{GenomicRanges}(x, na.rm=FALSE, strictly=FALSE, ignore.strand=FALSE)
 
-\S4method{order}{GenomicRanges}(..., na.last=TRUE, decreasing=FALSE, method=c("shell", "radix"))
+\S4method{order}{GenomicRanges}(..., na.last=TRUE, decreasing=FALSE, method=c("auto", "shell", "radix"))
 
 \S4method{sort}{GenomicRanges}(x, decreasing=FALSE, ignore.strand=FALSE, by)
 
diff --git a/man/makeGRangesFromDataFrame.Rd b/man/makeGRangesFromDataFrame.Rd
index 899144e..bf392c8 100644
--- a/man/makeGRangesFromDataFrame.Rd
+++ b/man/makeGRangesFromDataFrame.Rd
@@ -203,19 +203,21 @@ makeGRangesFromDataFrame(df)
 if (require(rtracklayer)) {
   session <- browserSession()
   genome(session) <- "sacCer2"
-  query <- ucscTableQuery(session, "Most Conserved")
+  query <- ucscTableQuery(session, "Assembly")
   df <- getTable(query)
 
   ## A common pitfall is to forget that the UCSC Table Browser uses the
   ## "0-based start" convention:
-  gr0 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)
+  gr0 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
+                                  start.field="chromStart", end.field="chromEnd")
   head(gr0)
   min(start(gr0))
 
   ## The start positions need to be converted into 1-based positions,
   ## to adhere to the convention used in Bioconductor:
   gr1 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
-                                  starts.in.df.are.0based=TRUE)
+                                  starts.in.df.are.0based=TRUE,
+                                  start.field="chromStart", end.field="chromEnd")
   head(gr1)
 }
 }

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