[med-svn] [r-bioc-limma] branch upstream updated (d85c65f -> 75e8fab)

[Andreas Tille]

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

      from  d85c65f   Imported Upstream version 3.28.17+dfsg
       new  75e8fab   Imported Upstream version 3.30.0+dfsg

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                   |   6 +--
 R/cumOverlap.R                |  45 +++++++++++++++++
 R/dups.R                      |   9 ++--
 R/fitFDistRobustly.R          |  46 ++++++++---------
 R/geneset-fry.R               |   2 +-
 R/geneset-roast.R             |   2 +-
 R/norm.R                      |   6 +--
 R/plotMDS.R                   |  11 +++--
 R/plotrldf.R                  |  22 ++++++---
 R/voom.R                      |   5 +-
 inst/NEWS.Rd                  | 111 +++++++++++++++++++++++++++++++++++++++++-
 inst/doc/changelog.txt        |  77 ++++++++++++++++++++++-------
 inst/doc/intro.pdf            | Bin 46191 -> 43301 bytes
 man/01Introduction.Rd         |   5 ++
 man/cumOverlap.Rd             |  49 +++++++++++++++++++
 man/detectionPValue.Rd        |   2 +
 man/ebayes.Rd                 |   2 +-
 man/fitfdist.Rd               |   9 +---
 man/goana.Rd                  |  25 ++++++----
 man/ids2indices.Rd            |   6 +--
 man/plotMDS.Rd                |  10 ++--
 man/plotRLDF.Rd               |  19 +++++---
 man/squeezeVar.Rd             |   2 +-
 man/voom.Rd                   |  14 ++++--
 man/voomWithQualityWeights.Rd |  10 ++--
 tests/limma-Tests.Rout.save   |  56 ++++++++++-----------
 26 files changed, 418 insertions(+), 133 deletions(-)
 create mode 100644 R/cumOverlap.R
 create mode 100644 man/cumOverlap.Rd

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