[med-svn] [r-bioc-limma] branch master updated (00175e1 -> 7679d3f)

[Gordon Ball]

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

      from  00175e1   Tests depend on r-cran-mass
       new  decb5cf   Imported Upstream version 3.28.10+dfsg
       new  1cd4735   Merge tag 'upstream/3.28.10+dfsg'
       new  7679d3f   New upstream: 3.28.10

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                                    |  17 +-
 NAMESPACE                                      |   4 +-
 R/alias2Symbol.R                               | 100 ++--
 R/detectionPValues.R                           |  41 ++
 R/diffSplice.R                                 |  15 +-
 R/dups.R                                       |   2 +-
 R/ebayes.R                                     |  48 +-
 R/{squeezeVar.R => fitFDist.R}                 |  59 +--
 R/fitFDistRobustly.R                           |  66 ++-
 R/fitmixture.R                                 |  48 ++
 R/geneset-camera.R                             |  11 +-
 R/geneset-fry.R                                | 232 +++++----
 R/geneset-roast.R                              | 633 +++++++++++--------------
 R/geneset-romer.R                              |  15 +-
 R/goana.R                                      |  50 +-
 R/kegga.R                                      | 211 ++++++---
 R/lmEffects.R                                  | 139 ++++++
 R/lmfit.R                                      |  39 +-
 R/loessFit.R                                   |   2 +-
 R/neqc.R                                       |   4 +-
 R/norm.R                                       |   7 +-
 R/plotrldf.R                                   | 133 ++++--
 R/propTrueNull.R                               |   6 +-
 R/read-maimages.R                              |   1 +
 R/read.R                                       |  14 +-
 R/read.idat.R                                  | 127 +++--
 R/sepchannel.R                                 |   2 +-
 R/squeezeVar.R                                 | 203 ++------
 R/tricubeMovingAverage.R                       |  15 +-
 R/voom.R                                       |  15 +-
 build/vignette.rds                             | Bin 230 -> 229 bytes
 debian/changelog                               |   8 +
 debian/patches/do_not_attempt_GO.db_test.patch |  66 +--
 inst/NEWS.Rd                                   | 225 +++++++++
 inst/doc/changelog.txt                         | 234 ++++++++-
 inst/doc/intro.pdf                             | Bin 46191 -> 46191 bytes
 man/03reading.Rd                               |   1 +
 man/10GeneSetTests.Rd                          |   2 +-
 man/alias2Symbol.Rd                            |  14 +-
 man/camera.Rd                                  |  40 +-
 man/detectionPValue.Rd                         |  58 +++
 man/dupcor.Rd                                  |  40 +-
 man/ebayes.Rd                                  |  14 +-
 man/fitfdist.Rd                                |  28 +-
 man/fitmixture.Rd                              |  66 +++
 man/fitted.MArrayLM.Rd                         |   5 +-
 man/getEAWP.Rd                                 |  25 +-
 man/gls.series.Rd                              |   4 +-
 man/goana.Rd                                   |  53 ++-
 man/ids2indices.Rd                             |   6 +-
 man/lmFit.Rd                                   |   2 +-
 man/logcosh.Rd                                 |  26 +
 man/marraylm.Rd                                |   1 +
 man/nec.Rd                                     |   1 +
 man/plotRLDF.Rd                                |  70 ++-
 man/propexpr.Rd                                |  44 +-
 man/read.idat.Rd                               |  77 ++-
 man/read.maimages.Rd                           |   3 +-
 man/removeext.Rd                               |  13 +-
 man/roast.Rd                                   |  63 +--
 man/romer.Rd                                   |   5 +-
 man/squeezeVar.Rd                              |  10 +-
 man/targetsA2C.Rd                              |   6 +
 man/venn.Rd                                    |  22 +-
 man/voom.Rd                                    |  12 +-
 tests/limma-Tests.R                            |   4 +
 tests/limma-Tests.Rout.save                    |  81 ++--
 67 files changed, 2372 insertions(+), 1216 deletions(-)
 create mode 100644 R/detectionPValues.R
 copy R/{squeezeVar.R => fitFDist.R} (66%)
 create mode 100644 R/fitmixture.R
 create mode 100644 R/lmEffects.R
 create mode 100644 man/detectionPValue.Rd
 create mode 100644 man/fitmixture.Rd
 create mode 100644 man/logcosh.Rd

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