[med-svn] [r-bioc-biocgenerics] branch upstream updated (52b69ed -> 1de16c4)

[Andreas Tille]

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

      from  52b69ed   Imported Upstream version 0.12.0
       new  1de16c4   Imported Upstream version 0.14.0

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                     |  27 +++++-----
 NAMESPACE                       |  26 ++++++++--
 R/S3-classes-as-S4-classes.R    |   2 +
 R/{image.R => fileName.R}       |   6 +--
 R/normarg-utils.R               |  10 ++++
 R/organism_species.R            |  16 ++++++
 R/plotPCA.R                     |   3 ++
 R/score.R                       |  10 ++++
 R/show-utils.R                  |  81 ++++++++++++++++++++++--------
 R/testPackage.R                 |  14 +++---
 R/{update.R => update-utils.R}  |   8 ++-
 inst/CITATION                   |  14 ++++++
 man/BiocGenerics-package.Rd     |  13 +++++
 man/S3-classes-as-S4-classes.Rd |   5 +-
 man/fileName.Rd                 |  51 +++++++++++++++++++
 man/organism_species.Rd         | 108 ++++++++++++++++++++++++++++++++++++++++
 man/{plotMA.Rd => plotPCA.Rd}   |  25 +++++-----
 man/rank.Rd                     |   4 +-
 man/score.Rd                    |  63 +++++++++++++++++++++++
 man/strand.Rd                   |   6 +++
 20 files changed, 426 insertions(+), 66 deletions(-)
 copy R/{image.R => fileName.R} (61%)
 create mode 100644 R/organism_species.R
 create mode 100644 R/plotPCA.R
 create mode 100644 R/score.R
 rename R/{update.R => update-utils.R} (86%)
 create mode 100644 inst/CITATION
 create mode 100644 man/fileName.Rd
 create mode 100644 man/organism_species.Rd
 copy man/{plotMA.Rd => plotPCA.Rd} (53%)
 create mode 100644 man/score.Rd

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