[med-svn] [r-bioc-edger] branch master updated (dcbad9f -> c928b88)

[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-edger.

      from  dcbad9f   Add todo item
       new  2ff3cea   Adapt test style to other tests of R packages
       new  9804fdf   Versioned (Build-)Depends r-bioc-limma
       new  867e835   Remove wrong output from test
       new  63f604a   Update documentation for testing
       new  19d9e56   Patch is considered as binary
       new  c885038   Fix unit test
       new  279b010   Document difference in unit test
       new  358f03f   Imported Upstream version 3.6.7+dfsg
       new  2cee69b   Merge tag 'upstream/3.6.7+dfsg'
       new  d088dd0   New upstream version
       new  1c9228e   d/rules: Remove now redundant explicite xz compression
       new  c928b88   Ignore the change in the saved file for test comparison since its not critical for the test and creates unneeded maintenance burden

The 12 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 -
 debian/README.test                   |    16 +-
 debian/changelog                     |    13 +-
 debian/control                       |     7 +-
 debian/docs                          |     1 +
 debian/rules                         |     2 -
 debian/source/include-binaries       |     1 +
 debian/tests/control                 |     5 +-
 debian/tests/run-unit-test           |    23 +
 debian/tests/upstream                |    18 -
 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 +-
 51 files changed, 362 insertions(+), 75758 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
 create mode 100644 debian/source/include-binaries
 create mode 100644 debian/tests/run-unit-test
 delete mode 100755 debian/tests/upstream
 delete mode 100644 man/Tu102.Rd

-- 
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