[med-svn] [r-bioc-edger] branch master updated (c6edb7c -> 62f6a93)

[Andreas Tille]

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

      from  c6edb7c   d/watch: version=4
       new  3caac50   New upstream version 3.18.1+dfsg
       new  94e059f   Updated version 3.18.1+dfsg from 'upstream/3.18.1+dfsg'
       new  62f6a93   Adapt patch to new version

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                                       |   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
 debian/changelog                                |   2 +-
 debian/patches/do_not_attempt_locfit_test.patch |   4 +-
 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 +++++-----
 28 files changed, 278 insertions(+), 123 deletions(-)

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