[med-svn] [r-bioc-biocgenerics] 03/05: Merge tag 'upstream/0.8.0'

[Charles Plessy]

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plessy pushed a commit to branch master
in repository r-bioc-biocgenerics.

commit 79bb382f1245d134b28883259943c69a45be56d4
Merge: bd18c77 cbaf052
Author: Charles Plessy <plessy at debian.org>
Date:   Thu Oct 17 15:03:33 2013 +0900

    Merge tag 'upstream/0.8.0'
    
    Upstream version 0.8.0
    
    # gpg: Signature made Thu 17 Oct 2013 15:03:29 JST using RSA key ID B3443334
    # gpg: Good signature from "Charles Plessy <plessy at riken.jp>"

 DESCRIPTION                 |   22 ++++++------
 NAMESPACE                   |   27 +++++++++++++--
 R/annotation.R              |    7 ++--
 R/{tapply.R => append.R}    |    8 ++---
 R/{tapply.R => as.vector.R} |    8 ++---
 R/combine.R                 |    2 +-
 R/dge.R                     |   18 ++++++++++
 R/eval.R                    |    4 +++
 R/is.unsorted.R             |    8 +++++
 R/normalize.R               |    8 +++++
 R/normarg-utils.R           |   31 +++++++++++++++++
 R/plotMA.R                  |   10 ++++++
 R/show-utils.R              |   60 ++++++++++++++++++++++++++++++++
 R/tapply.R                  |    4 +--
 R/update.R                  |   41 ++++++++++++++++++++++
 TODO                        |    4 ---
 man/BiocGenerics-package.Rd |   20 +++++++----
 man/Extremes.Rd             |   26 +++++++-------
 man/annotation.Rd           |   20 ++++++-----
 man/append.Rd               |   72 ++++++++++++++++++++++++++++++++++++++
 man/as.data.frame.Rd        |   32 +++++++++--------
 man/as.vector.Rd            |   73 +++++++++++++++++++++++++++++++++++++++
 man/boxplot.Rd              |   24 +++++++------
 man/cbind.Rd                |   32 +++++++++--------
 man/clusterApply.Rd         |   17 +++++----
 man/combine.Rd              |   28 ++++++++-------
 man/density.Rd              |   24 +++++++------
 man/dge.Rd                  |   51 +++++++++++++++++++++++++++
 man/duplicated.Rd           |   28 ++++++++-------
 man/eval.Rd                 |   25 ++++++++------
 man/evalq.Rd                |   51 +++++++++++++++++++++++++++
 man/funprog.Rd              |   34 +++++++++---------
 man/get.Rd                  |   26 +++++++-------
 man/image.Rd                |   24 +++++++------
 man/is.unsorted.Rd          |   80 +++++++++++++++++++++++++++++++++++++++++++
 man/lapply.Rd               |   28 ++++++++-------
 man/mapply.Rd               |   25 ++++++++------
 man/match.Rd                |   24 +++++++------
 man/normalize.Rd            |   61 +++++++++++++++++++++++++++++++++
 man/nrow.Rd                 |   28 ++++++++-------
 man/order.Rd                |   24 +++++++------
 man/paste.Rd                |   26 +++++++-------
 man/plotMA.Rd               |   55 +++++++++++++++++++++++++++++
 man/rank.Rd                 |   25 +++++++-------
 man/rep.Rd                  |   28 ++++++++-------
 man/residuals.Rd            |   24 +++++++------
 man/row_colnames.Rd         |   28 ++++++++-------
 man/sets.Rd                 |   28 ++++++++-------
 man/sort.Rd                 |   26 +++++++-------
 man/strand.Rd               |   20 ++++++-----
 man/table.Rd                |   24 +++++++------
 man/tapply.Rd               |   25 ++++++++------
 man/unique.Rd               |   31 +++++++++--------
 man/unlist.Rd               |   26 +++++++-------
 man/updateObject.Rd         |   24 +++++++------
 man/weights.Rd              |   24 +++++++------
 man/xtabs.Rd                |   25 ++++++++------
 57 files changed, 1152 insertions(+), 426 deletions(-)

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