[med-svn] [r-bioc-biocgenerics] branch upstream updated (d2469c7 -> cbaf052)

[Charles Plessy]

This is an automated email from the git hooks/post-receive script.

plessy pushed a change to branch upstream
in repository r-bioc-biocgenerics.

      from  d2469c7   Imported Upstream version 0.6.0
       new  cbaf052   Imported Upstream version 0.8.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 DESCRIPTION                 |   22 ++++++------
 NAMESPACE                   |   27 +++++++++++++--
 R/annotation.R              |    7 ++--
 R/{unique.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/{image.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, 1148 insertions(+), 430 deletions(-)
 copy R/{unique.R => append.R} (52%)
 copy R/{tapply.R => as.vector.R} (57%)
 create mode 100644 R/dge.R
 create mode 100644 R/is.unsorted.R
 copy R/{image.R => normalize.R} (58%)
 create mode 100644 R/normarg-utils.R
 create mode 100644 R/plotMA.R
 create mode 100644 R/show-utils.R
 create mode 100644 R/update.R
 create mode 100644 man/append.Rd
 create mode 100644 man/as.vector.Rd
 create mode 100644 man/dge.Rd
 create mode 100644 man/evalq.Rd
 create mode 100644 man/is.unsorted.Rd
 create mode 100644 man/normalize.Rd
 create mode 100644 man/plotMA.Rd

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