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commit 1820e1a33393b13e0a36afb9c23645372c48ffac Author: Andreas Tille <[email protected]> Date: Wed Apr 27 20:59:10 2016 +0200 Imported Upstream version 0.16.1 --- DESCRIPTION | 12 ++++++------ R/is.unsorted.R | 14 +++++++++++++- man/BiocGenerics-package.Rd | 3 +++ man/is.unsorted.Rd | 10 ++++++++-- 4 files changed, 30 insertions(+), 9 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8168ee6..b32c706 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: BiocGenerics Title: S4 generic functions for Bioconductor Description: S4 generic functions needed by many Bioconductor packages. -Version: 0.16.0 +Version: 0.16.1 Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <[email protected]> biocViews: Infrastructure @@ -14,13 +14,13 @@ License: Artistic-2.0 Collate: S3-classes-as-S4-classes.R normarg-utils.R replaceSlots.R append.R as.data.frame.R as.list.R as.vector.R cbind.R do.call.R duplicated.R eval.R Extremes.R funprog.R get.R grep.R - IQR.R is.unsorted.R lapply.R lengths.R mad.R mapply.R match.R - nrow.R order.R paste.R rank.R rep.R row_colnames.R sets.R - sort.R start.R subset.R table.R tapply.R unique.R unlist.R - unsplit.R relist.R boxplot.R image.R density.R residuals.R + is.unsorted.R lapply.R lengths.R mapply.R match.R nrow.R + order.R paste.R rank.R rep.R row_colnames.R sets.R sort.R + start.R subset.R table.R tapply.R unique.R unlist.R unsplit.R + relist.R boxplot.R image.R density.R IQR.R mad.R residuals.R weights.R xtabs.R clusterApply.R annotation.R combine.R dbconn.R dge.R fileName.R normalize.R organism_species.R plotMA.R plotPCA.R score.R strand.R updateObject.R testPackage.R test_BiocGenerics_package.R zzz.R NeedsCompilation: no -Packaged: 2015-10-14 02:13:19 UTC; biocbuild +Packaged: 2015-11-06 03:02:04 UTC; biocbuild diff --git a/R/is.unsorted.R b/R/is.unsorted.R index 9f9abe9..0c60cbe 100644 --- a/R/is.unsorted.R +++ b/R/is.unsorted.R @@ -2,4 +2,16 @@ ### The is.unsorted() generic ### ------------------------------------------------------------------------- -setGeneric("is.unsorted", signature = "x") +### base::is.unsorted() doesn't have the ellipsis. We add it to the generic +### function defined below so methods can support additional arguments (e.g. +### the 'ignore.strand' argument for the method for GenomicRanges objects). + +.is.unsorted.useAsDefault <- function(x, na.rm=FALSE, strictly=FALSE, ...) + base::is.unsorted(x, na.rm, strictly, ...) + +setGeneric("is.unsorted", signature="x", + function(x, na.rm=FALSE, strictly=FALSE, ...) + standardGeneric("is.unsorted"), + useAsDefault=.is.unsorted.useAsDefault +) + diff --git a/man/BiocGenerics-package.Rd b/man/BiocGenerics-package.Rd index b0e6d7a..4e28266 100644 --- a/man/BiocGenerics-package.Rd +++ b/man/BiocGenerics-package.Rd @@ -53,6 +53,9 @@ \item \code{BiocGenerics::\link[BiocGenerics]{get}}, \code{BiocGenerics::\link[BiocGenerics]{mget}} + \item \code{BiocGenerics::\link[BiocGenerics]{grep}}, + \code{BiocGenerics::\link[BiocGenerics]{grepl}} + \item \code{BiocGenerics::\link[BiocGenerics]{is.unsorted}} \item \code{BiocGenerics::\link[BiocGenerics]{lapply}}, diff --git a/man/is.unsorted.Rd b/man/is.unsorted.Rd index 332a86d..b9b4dc4 100644 --- a/man/is.unsorted.Rd +++ b/man/is.unsorted.Rd @@ -12,11 +12,11 @@ See \code{?base::\link[base]{is.unsorted}} for the default method (defined in the \pkg{base} package). Bioconductor packages can define specific methods for objects - not supported by the default method. + (typically vector-like) not supported by the default method. } \usage{ -is.unsorted(x, na.rm=FALSE, strictly=FALSE) +is.unsorted(x, na.rm=FALSE, strictly=FALSE, ...) } \arguments{ @@ -27,6 +27,12 @@ is.unsorted(x, na.rm=FALSE, strictly=FALSE) See \code{?base::\link[base]{is.unsorted}} for a description of these arguments. } + \item{...}{ + Additional arguments, for use in specific methods. + + Note that \code{base::\link[base]{is.unsorted}} (the default method) only + takes the \code{x}, \code{na.rm}, and \code{strictly} arguments. + } } \value{ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-biocgenerics.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
