[med-svn] [r-bioc-edger] branch upstream updated (2285a83 -> 358f03f)

[Andreas Tille]

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

      from  2285a83   Imported Upstream version 3.6.2+dfsg
       new  358f03f   Imported Upstream version 3.6.7+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                          |    16 +-
 NAMESPACE                            |    16 +-
 R/DGEList.R                          |    15 +-
 R/aveLogCPM.R                        |     4 +-
 R/edgeRUsersGuide.R                  |     2 +-
 R/maximizeQuadratic.R                |     4 +-
 R/residDF.R                          |    39 +-
 R/subsetting.R                       |     3 +-
 build/vignette.rds                   |   Bin 228 -> 229 bytes
 data/NC1.txt                         | 17704 -------------------------
 data/NC2.txt                         | 16271 -----------------------
 data/Tu102.txt                       | 22714 ---------------------------------
 data/Tu98.txt                        | 18795 ---------------------------
 data/datalist                        |     4 -
 inst/NEWS.Rd                         |     8 +
 inst/doc/edgeR.pdf                   |   Bin 48051 -> 48051 bytes
 man/DGEExact-class.Rd                |    10 +-
 man/DGEGLM-class.Rd                  |    37 +-
 man/DGELRT-class.Rd                  |    24 +-
 man/DGEList-class.Rd                 |    28 +-
 man/DGEList.Rd                       |     5 +-
 man/Tu102.Rd                         |    22 -
 man/WLEB.Rd                          |     3 +-
 man/aveLogCPM.Rd                     |    11 +-
 man/dispBinTrend.Rd                  |     5 +-
 man/dispCoxReidInterpolateTagwise.Rd |     6 +-
 man/edgeRUsersGuide.Rd               |     2 +-
 man/estimateDisp.Rd                  |    16 +-
 man/estimateGLMCommonDisp.Rd         |     7 +-
 man/estimateGLMRobustDisp.Rd         |     5 +-
 man/estimateGLMTagwiseDisp.Rd        |     7 +-
 man/estimateGLMTrendedDisp.Rd        |     3 +-
 man/gof.Rd                           |     3 +-
 man/meanvar.Rd                       |    22 +-
 man/normalizeChIPtoInput.Rd          |     6 +-
 man/plotExonUsage.Rd                 |     3 +-
 man/plotMDS.DGEList.Rd               |     6 +-
 man/plotSmear.Rd                     |     3 +-
 man/spliceVariants.Rd                |     3 +-
 src/R_cr_adjust.cpp                  |     2 +-
 src/adj_coxreid.cpp                  |    17 +-
 tests/edgeR-Tests.Rout.save          |   183 +-
 42 files changed, 309 insertions(+), 75725 deletions(-)
 delete mode 100755 data/NC1.txt
 delete mode 100755 data/NC2.txt
 delete mode 100755 data/Tu102.txt
 delete mode 100755 data/Tu98.txt
 delete mode 100644 data/datalist
 delete mode 100644 man/Tu102.Rd

-- 
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