[med-svn] [r-bioc-limma] branch master updated (8425d59 -> 7118c17)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

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

      from  8425d59   Move debian/upstream to debian/upstream/metadata
       new  a2a7358   Use generic way to remove files from upstream tarball
       new  fc78793   Imported Upstream version 3.20.7+dfsg
       new  aefefa5   Merge tag 'upstream/3.20.7+dfsg'
       new  7118c17   Luckily new upstream version does nt depend from r-cran-locfit any more ...

The 4 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                  |  25 ++--
 NAMESPACE                    |  12 +-
 R/barcodeplot.R              | 183 ++++++++++++++++++------
 R/beadCountWeights.R         |  28 ++--
 R/diffSplice.R               | 210 ++++++++++++++++++++++++++++
 R/dups.R                     |   7 +-
 R/fitFDistRobustly.R         |  13 +-
 R/geneset-camera.R           |  53 ++++---
 R/geneset-roast.R            | 325 +++++++++++++++++++++++--------------------
 R/geneset-romer.R            |  24 ++--
 R/lmfit.R                    |   6 +-
 R/loessFit.R                 | 106 ++++++++++----
 R/plot.R                     |  70 ++++++++++
 R/plotMDS.R                  |  53 ++++---
 R/plots-ma.R                 |  28 +++-
 R/read-ilmn.R                |  10 +-
 R/read.idat.R                |  41 ++++++
 R/removeBatchEffect.R        |  16 +--
 R/subsetting.R               |   6 +-
 R/toptable.R                 |  31 +++--
 R/treat.R                    |  16 ++-
 R/tricubeMovingAverage.R     |  18 +++
 R/utility.R                  |   6 +-
 R/weightedLowess.R           |  49 +++++++
 R/zscore.R                   |  25 +++-
 build/vignette.rds           | Bin 229 -> 230 bytes
 debian/README.source         |   3 -
 debian/changelog             |   6 +-
 debian/control               |   3 +-
 debian/gbp.conf              |   6 -
 debian/rules                 |   3 +
 debian/watch                 |   2 +-
 inst/NEWS.Rd                 | 117 ++++++++++++++++
 inst/doc/changelog.txt       | 251 ++++++++++++++++++++++++++++++---
 inst/doc/intro.pdf           | Bin 46191 -> 46191 bytes
 man/01Introduction.Rd        |  30 +++-
 man/02classes.Rd             |   2 +-
 man/03reading.Rd             |   4 +-
 man/04Background.Rd          |   2 +-
 man/05Normalization.Rd       |   2 +-
 man/06linearmodels.Rd        |   2 +-
 man/07SingleChannel.Rd       |   2 +-
 man/08Tests.Rd               |   2 +-
 man/09Diagnostics.Rd         |   4 +-
 man/10GeneSetTests.Rd        |  36 +++++
 man/10Other.Rd               |  10 --
 man/11RNAseq.Rd              |  31 +++++
 man/EList.Rd                 |  25 ++--
 man/PrintLayout.Rd           |   9 +-
 man/alias2Symbol.Rd          |   7 +-
 man/arrayWeights.Rd          |  11 +-
 man/arrayWeightsQuick.Rd     |   6 +-
 man/asMatrixWeights.Rd       |   1 -
 man/avearrays.Rd             |   3 +-
 man/barcodeplot.Rd           |  17 ++-
 man/beadCountWeights.Rd      |   8 +-
 man/blockDiag.Rd             |  12 +-
 man/camera.Rd                |  22 +--
 man/changelog.Rd             |   4 +
 man/classifytests.Rd         |   2 +
 man/controlStatus.Rd         |  12 +-
 man/diffSplice.Rd            |  41 ++++++
 man/ebayes.Rd                |   6 +-
 man/genas.Rd                 |   2 +-
 man/geneSetTest.Rd           |   7 +-
 man/heatdiagram.Rd           |   8 +-
 man/imageplot3by2.Rd         |   3 +-
 man/kooperberg.Rd            |   6 +-
 man/lmFit.Rd                 |  14 +-
 man/loessfit.Rd              |  37 +++--
 man/nec.Rd                   |  10 +-
 man/normalizeWithinArrays.Rd |   4 +-
 man/normalizeprintorder.Rd   |   9 +-
 man/{plotma.Rd => plot.Rd}   |  55 +++++---
 man/plotMDS.Rd               |  17 ++-
 man/plotSA.Rd                |   3 +-
 man/plotSplice.Rd            |  29 ++++
 man/plotma.Rd                |  13 +-
 man/plotma3by2.Rd            |   5 +-
 man/poolvar.Rd               |   6 -
 man/printtipWeights.Rd       |  34 +++--
 man/qqt.Rd                   |   6 +-
 man/read.columns.Rd          |   4 +-
 man/read.idat.Rd             |  70 ++++++++++
 man/read.ilmn.Rd             |  27 ++--
 man/read.ilmn.targets.Rd     |   2 +-
 man/read.maimages.Rd         |   5 +-
 man/readGPRHeader.Rd         |  12 +-
 man/removeBatchEffect.Rd     |  19 ++-
 man/roast.Rd                 |  24 ++--
 man/romer.Rd                 |   8 +-
 man/symbols2indices.Rd       |   2 +
 man/targetsA2C.Rd            |   5 +-
 man/topRomer.Rd              |   7 +-
 man/topSplice.Rd             |  34 +++++
 man/toptable.Rd              |  13 +-
 man/tricubeMovingAverage.Rd  |  36 +++++
 man/volcanoplot.Rd           |   4 +-
 man/voom.Rd                  |   7 +-
 man/vooma.Rd                 |   3 +-
 man/weightedLowess.Rd        |  72 ++++++++++
 man/writefit.Rd              |   3 +-
 man/zscore.Rd                |  40 ++++--
 src/weighted_lowess.c        | 271 ++++++++++++++++++++++++++++++++++++
 tests/limma-Tests.R          |  17 ++-
 tests/limma-Tests.Rout.save  | 139 ++++++++++--------
 106 files changed, 2441 insertions(+), 716 deletions(-)
 create mode 100644 R/diffSplice.R
 create mode 100644 R/plot.R
 create mode 100644 R/read.idat.R
 create mode 100644 R/tricubeMovingAverage.R
 create mode 100644 R/weightedLowess.R
 delete mode 100644 debian/README.source
 create mode 100644 man/10GeneSetTests.Rd
 delete mode 100644 man/10Other.Rd
 create mode 100644 man/11RNAseq.Rd
 create mode 100644 man/diffSplice.Rd
 copy man/{plotma.Rd => plot.Rd} (60%)
 mode change 100755 => 100644
 create mode 100644 man/plotSplice.Rd
 create mode 100644 man/read.idat.Rd
 create mode 100644 man/topSplice.Rd
 create mode 100644 man/tricubeMovingAverage.Rd
 create mode 100644 man/weightedLowess.Rd
 create mode 100644 src/weighted_lowess.c

-- 
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