[med-svn] [r-bioc-limma] branch master updated (49a66bf -> 7b25c13)

[Andreas Tille]

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

      from  49a66bf   Merge remote-tracking branch 'origin/master'
      adds  58164b2   Team upload
       new  75e8fab   Imported Upstream version 3.30.0+dfsg
       new  0c109dc   Merge tag 'upstream/3.30.0+dfsg'
       new  420f511   New upstream version
       new  fb3a261   Generic BioConductor homepage, Switch to dh-r
       new  938714f   Adapt patch
       new  7b25c13   Upload to unstable

The 6 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 +-
 debian/changelog                               |   9 ++
 debian/control                                 |  11 ++-
 debian/copyright                               |   9 +-
 debian/patches/do_not_attempt_GO.db_test.patch |  58 ++++++-------
 debian/rules                                   |  24 ++++--
 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 ++++++-------
 31 files changed, 480 insertions(+), 182 deletions(-)
 create mode 100644 R/cumOverlap.R
 create mode 100644 man/cumOverlap.Rd

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