[med-svn] [r-bioc-limma] branch master updated (2aa5678 -> 7a8ffe6)

[Charles Plessy]

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

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

      from  2aa5678   New upstream release; no new copyright nor license notice.
       new  5c7fc4d   Imported Upstream version 3.18.0~dfsg
       new  e77d8aa   Merge tag 'upstream/3.18.0_dfsg'
       new  7a8ffe6   New upstream release; no new copyright nor license notice.

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                 |   12 +--
 NAMESPACE                   |    4 +
 R/alias2Symbol.R            |    6 +-
 R/beadCountWeights.R        |   99 +++++++++++++++++
 R/contrastAsCoef.R          |   26 +++++
 R/genas.R                   |  228 +++++++++++++++++++++------------------
 R/geneset-roast.R           |   27 ++---
 R/lmfit.R                   |   98 ++++++++++++-----
 R/loessFit.R                |   50 ++++-----
 R/norm.R                    |    4 +-
 R/plots-ma.R                |  251 ++++++++++++++++++++++++++-----------------
 R/predFCm.R                 |    2 +-
 R/read-ilmn.R               |   36 +++++--
 R/subsetting.R              |    3 +-
 R/toptable.R                |  184 +++++++++++++++++++++----------
 R/treat.R                   |   63 ++++++++---
 build/vignette.rds          |  Bin 0 -> 219 bytes
 debian/changelog            |    4 +-
 debian/copyright            |    2 +-
 inst/doc/changelog.txt      |  180 +++++++++++++++++++++++++++----
 inst/doc/limma.R            |    2 -
 inst/doc/limma.pdf          |  Bin 45597 -> 45597 bytes
 man/01Introduction.Rd       |    3 +-
 man/06linearmodels.Rd       |    3 +-
 man/asmalist.Rd             |    7 ++
 man/beadCountWeights.Rd     |   61 +++++++++++
 man/contrastAsCoef.Rd       |   48 +++++++++
 man/contrasts.fit.Rd        |    2 +-
 man/ebayes.Rd               |   15 ++-
 man/fitfdist.Rd             |    4 +-
 man/genas.Rd                |   88 ++++++++++-----
 man/getEAWP.Rd              |    8 +-
 man/lmFit.Rd                |    3 +
 man/loessfit.Rd             |   86 +++++++++------
 man/plotma.Rd               |    9 +-
 man/predFCm.Rd              |    1 +
 man/propTrueNull.Rd         |    1 +
 man/removeBatchEffect.Rd    |    4 +-
 man/roast.Rd                |    1 +
 man/squeezeVar.Rd           |   23 +++-
 man/targetsA2C.Rd           |    2 +-
 man/toptable.Rd             |   15 ++-
 src/normexp.c               |    4 +-
 tests/limma-Tests.R         |   13 ++-
 tests/limma-Tests.Rout.save |  229 +++++++++++++++++++++++----------------
 45 files changed, 1350 insertions(+), 561 deletions(-)
 create mode 100644 R/beadCountWeights.R
 create mode 100644 R/contrastAsCoef.R
 create mode 100644 build/vignette.rds
 delete mode 100644 inst/doc/limma.R
 create mode 100644 man/beadCountWeights.Rd
 create mode 100644 man/contrastAsCoef.Rd

-- 
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.git