[med-svn] [r-bioc-edger] branch upstream updated (104c7f6 -> 3caac50)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository r-bioc-edger.

      from  104c7f6   New upstream version 3.16.5+dfsg
       new  3caac50   New upstream version 3.18.1+dfsg

The 1 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                      |   9 ++----
 R/S3methods.R                  |   2 +-
 R/decidetestsDGE.R             |  57 +++++++++++++++++++++++++++++-----
 R/gini.R                       |  11 +++++--
 R/glmfit.R                     |   5 ++-
 R/normalizeChIPtoInput.R       |   6 ++--
 R/plotMD.R                     |  42 +++++++++++++++++++++----
 R/topTags.R                    |   2 +-
 build/vignette.rds             | Bin 228 -> 228 bytes
 inst/NEWS.Rd                   |  27 ++++++++++++++++
 inst/doc/edgeR.pdf             | Bin 45765 -> 45765 bytes
 man/addPriorCount.Rd           |   9 ++++++
 man/decidetestsDGE.Rd          |  68 ++++++++++++++++++++++++++++-------------
 man/dim.Rd                     |   7 -----
 man/estimateDisp.Rd            |   4 +--
 man/gini.Rd                    |   2 +-
 man/nbinomDeviance.Rd          |   6 ++--
 man/plotMD.Rd                  |  34 ++++++++++++---------
 man/topTags.Rd                 |   2 +-
 src/R_initialize_levenberg.cpp |  17 ++++++-----
 src/R_levenberg.cpp            |  26 +++++++++++-----
 src/adj_coxreid.cpp            |   1 +
 src/fmm_spline.c               |  17 ++++++-----
 src/glm_levenberg.cpp          |   7 +++--
 tests/edgeR-Tests.Rout.save    |  28 ++++++++---------
 26 files changed, 275 insertions(+), 120 deletions(-)

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