[med-svn] [r-bioc-limma] branch master updated (b05eada -> 68f6f26)

[Steffen Möller]

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

      from  b05eada   New upstream version
       new  0ca9553   New upstream version 3.32.7+dfsg
       new  6d0b030   Updated version 3.32.7+dfsg from 'upstream/3.32.7+dfsg'
       new  68f6f26   New upstream version 3.32-7

The 3 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 +-
 NAMESPACE                                      |   8 +-
 R/alias2Symbol.R                               |  30 +++++
 R/barcodeplot.R                                |  22 ++--
 R/classes.R                                    |   8 +-
 R/diffSplice.R                                 |   8 +-
 R/fitFDist.R                                   |  42 +++---
 R/geneset-camera.R                             |   4 +-
 R/geneset-cameraPR.R                           |  89 +++++++++++++
 R/geneset-fry.R                                |   2 +-
 R/geneset-roast.R                              |   1 -
 R/kegga.R                                      | 171 +++++++++++++------------
 R/plotWithHighlights.R                         |   5 +-
 R/plots-fit.R                                  |  66 ++++++----
 R/read.idat.R                                  |  35 +++--
 R/toptable.R                                   |   4 +-
 R/wsva.R                                       |  42 ++++++
 build/vignette.rds                             | Bin 230 -> 231 bytes
 debian/changelog                               |   8 ++
 debian/control                                 |   2 +-
 debian/patches/do_not_attempt_GO.db_test.patch |  52 ++++----
 inst/NEWS.Rd                                   |  97 ++++++++++++++
 inst/doc/changelog.txt                         | 150 ++++++++++++++++++++--
 inst/doc/intro.pdf                             | Bin 43301 -> 43301 bytes
 man/08Tests.Rd                                 |   4 +-
 man/alias2Symbol.Rd                            |  18 ++-
 man/barcodeplot.Rd                             |  19 +--
 man/camera.Rd                                  |  17 ++-
 man/coolmap.Rd                                 |   6 +-
 man/detectionPValue.Rd                         |   4 +-
 man/dim.Rd                                     |   7 -
 man/ebayes.Rd                                  |   2 +-
 man/geneSetTest.Rd                             |  10 +-
 man/goana.Rd                                   |  28 +++-
 man/kooperberg.Rd                              |   4 +-
 man/plotSA.Rd                                  |  25 ++--
 man/plotWithHighlights.Rd                      |   2 +-
 man/propTrueNull.Rd                            |   3 +-
 man/propexpr.Rd                                |   4 +-
 man/volcanoplot.Rd                             |  20 +--
 man/wsva.Rd                                    |  40 ++++++
 src/init.c                                     |  32 +++++
 tests/limma-Tests.R                            |   4 +
 tests/limma-Tests.Rout.save                    | 131 +++++++++++--------
 44 files changed, 911 insertions(+), 321 deletions(-)
 create mode 100644 R/geneset-cameraPR.R
 create mode 100644 R/wsva.R
 create mode 100644 man/wsva.Rd
 create mode 100644 src/init.c

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