[med-svn] [r-bioc-iranges] 01/04: New upstream version 2.10.5
Andreas Tille
tille at debian.org
Mon Oct 9 12:42:53 UTC 2017
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tille pushed a commit to branch master
in repository r-bioc-iranges.
commit bf67f3dfefb24d0dedc0a654a4b2466819a75295
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 9 14:40:08 2017 +0200
New upstream version 2.10.5
---
DESCRIPTION | 4 ++--
R/AtomicList-utils.R | 2 +-
R/Ranges-comparison.R | 3 ++-
R/Vector-class-leftovers.R | 1 +
R/nearest-methods.R | 5 +++--
build/vignette.rds | Bin 224 -> 225 bytes
inst/doc/IRangesOverview.pdf | Bin 230632 -> 230670 bytes
inst/unitTests/test_nearest-methods.R | 20 +++++++++++++-------
man/Ranges-comparison.Rd | 2 +-
9 files changed, 23 insertions(+), 14 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 455d787..3d12fb4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -8,7 +8,7 @@ Description: Provides efficient low-level and highly reusable S4
list-like classes for storing, transforming and aggregating
large grouped data, i.e., collections of atomic vectors and
DataFrames.
-Version: 2.10.2
+Version: 2.10.5
Encoding: UTF-8
Author: H. Pagès, P. Aboyoun and M. Lawrence
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
@@ -38,4 +38,4 @@ Collate: Vector-class-leftovers.R List-class-leftovers.R
nearest-methods.R cbind-Rle-methods.R tile-methods.R
bind-arrays.R zzz.R
NeedsCompilation: yes
-Packaged: 2017-05-24 22:14:44 UTC; biocbuild
+Packaged: 2017-10-07 22:27:32 UTC; biocbuild
diff --git a/R/AtomicList-utils.R b/R/AtomicList-utils.R
index 6956d16..84589d8 100644
--- a/R/AtomicList-utils.R
+++ b/R/AtomicList-utils.R
@@ -820,7 +820,7 @@ setMethod("rank", "CompressedAtomicList",
setMethod("order", "CompressedAtomicList",
function (..., na.last = TRUE, decreasing = FALSE,
- method = c("shell", "radix"))
+ method = c("auto", "shell", "radix"))
{
args <- list(...)
if (length(args) != 1L)
diff --git a/R/Ranges-comparison.R b/R/Ranges-comparison.R
index dd0dcdf..0478806 100644
--- a/R/Ranges-comparison.R
+++ b/R/Ranges-comparison.R
@@ -78,7 +78,8 @@ setMethod("selfmatch", "Ranges",
### 'na.last' is pointless (Ranges objects don't contain NAs) so is ignored.
### 'method' is also ignored at the moment.
setMethod("order", "Ranges",
- function(..., na.last=TRUE, decreasing=FALSE, method=c("shell", "radix"))
+ function(..., na.last=TRUE, decreasing=FALSE,
+ method=c("auto", "shell", "radix"))
{
if (!isTRUEorFALSE(decreasing))
stop("'decreasing' must be TRUE or FALSE")
diff --git a/R/Vector-class-leftovers.R b/R/Vector-class-leftovers.R
index 2f47d25..c447200 100644
--- a/R/Vector-class-leftovers.R
+++ b/R/Vector-class-leftovers.R
@@ -83,6 +83,7 @@ setMethod("subset", "Vector",
setGeneric("mstack", function(..., .index.var = "name")
standardGeneric("mstack"), signature = "...")
+BiocGenerics:::apply_hotfix73465(getGeneric("mstack"))
setMethod("mstack", "Vector", function(..., .index.var = "name") {
if (!isSingleString(.index.var))
diff --git a/R/nearest-methods.R b/R/nearest-methods.R
index e5951e2..22446d4 100644
--- a/R/nearest-methods.R
+++ b/R/nearest-methods.R
@@ -94,10 +94,11 @@ setMethod("nearest", c("Ranges", "RangesORmissing"),
{
select <- match.arg(select)
if (!missing(subject)) {
- ol <- findOverlaps(x, subject, select = select)
+ ol <- findOverlaps(x, subject, minoverlap = 0L, select = select)
} else {
subject <- x
- ol <- findOverlaps(x, select = select, drop.self = TRUE)
+ ol <- findOverlaps(x, minoverlap = 0L, select = select,
+ drop.self = TRUE)
}
if (select == "all") {
olv <- selectHits(ol, select="first")
diff --git a/build/vignette.rds b/build/vignette.rds
index eb6a78b..32eb36d 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/IRangesOverview.pdf b/inst/doc/IRangesOverview.pdf
index b3e9999..3183370 100644
Binary files a/inst/doc/IRangesOverview.pdf and b/inst/doc/IRangesOverview.pdf differ
diff --git a/inst/unitTests/test_nearest-methods.R b/inst/unitTests/test_nearest-methods.R
index d5dc22d..4574d46 100644
--- a/inst/unitTests/test_nearest-methods.R
+++ b/inst/unitTests/test_nearest-methods.R
@@ -120,22 +120,28 @@ test_Ranges_distance <- function()
test_Ranges_distanceToNearest <- function()
{
target <- Hits(sort.by.query=TRUE)
- current <- quiet(distanceToNearest(IRanges(), IRanges()))
+ current <- distanceToNearest(IRanges(), IRanges())
checkIdentical(queryHits(current), queryHits(target))
checkIdentical(subjectHits(current), subjectHits(target))
checkIdentical(queryLength(current), queryLength(target))
- query <- IRanges(5, 10)
+ x <- IRanges(5, 10)
subject <- IRanges(c(1, 1, 1), c(4, 5, 6))
- current <- quiet(distanceToNearest(query, subject, select="all"))
- checkIdentical(subjectHits(current), c(2L, 3L))
+ current <- distanceToNearest(x, subject, select="all")
+ checkIdentical(subjectHits(current), 1:3)
- current <- quiet(distanceToNearest(query, rev(subject), select="all"))
- checkIdentical(subjectHits(current), c(1L, 2L))
+ current <- distanceToNearest(x, rev(subject), select="all")
+ checkIdentical(subjectHits(current), 1:3)
- current <- distanceToNearest(query, IRanges())
+ current <- distanceToNearest(x, IRanges())
checkIdentical(length(current), 0L)
checkIdentical(queryLength(current), 1L)
checkIdentical(subjectLength(current), 0L)
+
+ x <- IRanges(c(2, 4, 12, 15), c(2, 3, 13, 14))
+ subject <- IRanges(1, 10)
+ current <- distanceToNearest(x, subject)
+ checkIdentical(queryHits(current), 1:4)
+ checkIdentical(mcols(current)$distance, c(0L, 0L, 1L, 4L))
}
diff --git a/man/Ranges-comparison.Rd b/man/Ranges-comparison.Rd
index a1ce60c..078ba1d 100644
--- a/man/Ranges-comparison.Rd
+++ b/man/Ranges-comparison.Rd
@@ -30,7 +30,7 @@
## order()
## -------
-\S4method{order}{Ranges}(..., na.last=TRUE, decreasing=FALSE, method=c("shell", "radix"))
+\S4method{order}{Ranges}(..., na.last=TRUE, decreasing=FALSE, method=c("auto", "shell", "radix"))
## Generalized parallel comparison of 2 Ranges objects
## ---------------------------------------------------
--
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