[med-svn] [r-bioc-limma] branch master updated (9ec05b1 -> 8ae68ad)

[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-limma.

      from  9ec05b1   Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/r-bioc-limma
       new  3913647   Imported Upstream version 3.18.4+dfsg
       new  b8d0515   Merge tag 'upstream/3.18.4+dfsg'
       new  f9c130a   New upstream version has working testsuite
       new  2c4f3d8   Re-add README.test
       new  d40eea4   Slight updates of d/control + d/copyright
       new  826518d   XS-Testsuite: autopkgtest
       new  8ae68ad   Needs r-cran-locfit (svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-locfit/trunk/)

The 7 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                                 |   8 ++
 R/dups.R                                  |  36 +++--
 R/genas.R                                 |  91 ++++++-------
 R/{plotFG.R => plotFB.R}                  |  24 +++-
 R/plotdensities.R                         | 211 +++++++++++++-----------------
 R/plots-ma.R                              |  10 +-
 R/read-ilmn.R                             |   3 +-
 R/squeezeVar.R                            |  23 +++-
 R/toptable.R                              |   6 +-
 build/vignette.rds                        | Bin 219 -> 229 bytes
 debian/README.test                        |   6 +
 debian/changelog                          |  19 ++-
 debian/control                            |   8 +-
 debian/copyright                          |   2 +-
 debian/tests/control                      |   4 +-
 inst/doc/changelog.txt                    |  46 +++++++
 inst/doc/index.html                       |   3 +-
 inst/doc/{limma.Rnw => intro.Rnw}         |   6 +-
 inst/doc/{limma.pdf => intro.pdf}         | Bin 45597 -> 46191 bytes
 man/09Diagnostics.Rd                      |   2 +-
 man/EList.Rd                              |   6 +-
 man/auROC.Rd                              |  12 +-
 man/avereps.Rd                            |  16 ++-
 man/backgroundcorrect.Rd                  |   6 +-
 man/beadCountWeights.Rd                   |  35 ++++-
 man/nec.Rd                                |   9 +-
 man/normalizebetweenarrays.Rd             |   2 +-
 man/plotDensities.Rd                      | 102 +++++----------
 man/plotFB.Rd                             |  14 +-
 man/read.ilmn.Rd                          |  30 +++--
 man/voom.Rd                               |   1 +
 man/vooma.Rd                              |   1 +
 inst/doc/limma.Rnw => vignettes/intro.Rnw |   6 +-
 34 files changed, 424 insertions(+), 330 deletions(-)
 rename R/{plotFG.R => plotFB.R} (51%)
 create mode 100644 debian/README.test
 copy inst/doc/{limma.Rnw => intro.Rnw} (89%)
 mode change 100755 => 100644
 rename inst/doc/{limma.pdf => intro.pdf} (73%)
 rename inst/doc/limma.Rnw => vignettes/intro.Rnw (89%)
 mode change 100755 => 100644

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