[med-svn] [r-bioc-edger] branch upstream updated (3caac50 -> 9f3654a)

[Andreas Tille]

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

      from  3caac50   New upstream version 3.18.1+dfsg
       new  9f3654a   New upstream version 3.14.0+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                    |   10 +-
 NAMESPACE                      |   12 +-
 R/DGEList.R                    |   15 +-
 R/S3methods.R                  |    2 +-
 R/addPriorCount.R              |   29 --
 R/adjustedProfileLik.R         |   68 ++-
 R/aveLogCPM.R                  |   60 ++-
 R/cpm.R                        |   25 +-
 R/decidetestsDGE.R             |   57 +--
 R/diffSpliceDGE.R              |    5 +-
 R/dispBinTrend.R               |    7 +-
 R/estimateDisp.R               |   82 +--
 R/estimateGLMCommonDisp.R      |    2 +-
 R/expandAsMatrix.R             |   18 +-
 R/geneset-DGEList.R            |   26 +-
 R/gini.R                       |   11 +-
 R/glmQLFTest.R                 |   61 ++-
 R/glmTreat.R                   |  132 ++---
 R/glmfit.R                     |   20 +-
 R/locfitByCol.R                |    5 +-
 R/makeCompressedMatrix.R       |  164 ------
 R/mglmLevenberg.R              |   60 ++-
 R/mglmOneGroup.R               |   36 +-
 R/mglmOneWay.R                 |   29 +-
 R/nbinomDeviance.R             |   50 +-
 R/normalizeChIPtoInput.R       |    6 +-
 R/plotMD.R                     |   45 +-
 R/plotMDS.DGEList.R            |   11 +-
 R/predFC.R                     |   34 +-
 R/readDGE.R                    |   18 +-
 R/scaleOffset.R                |   37 --
 R/spliceVariants.R             |   10 +-
 R/topTags.R                    |    2 +-
 build/vignette.rds             |  Bin 228 -> 228 bytes
 inst/CITATION                  |   37 +-
 inst/NEWS.Rd                   |   66 ---
 inst/doc/edgeR.pdf             |  Bin 45765 -> 48664 bytes
 man/addPriorCount.Rd           |   61 ---
 man/aveLogCPM.Rd               |    4 +-
 man/camera.DGEList.Rd          |   17 +-
 man/decidetestsDGE.Rd          |   68 +--
 man/dim.Rd                     |    7 +
 man/edgeR-package.Rd           |   25 +-
 man/estimateDisp.Rd            |    9 +-
 man/expandAsMatrix.Rd          |   21 +-
 man/gini.Rd                    |    2 +-
 man/glmQLFTest.Rd              |   21 +-
 man/glmTreat.Rd                |   20 +-
 man/goodTuring.Rd              |    6 +-
 man/makeCompressedMatrix.Rd    |  108 ----
 man/nbinomDeviance.Rd          |    6 +-
 man/plotMD.Rd                  |   31 +-
 man/plotMDS.DGEList.Rd         |    8 +-
 man/plotQLDisp.Rd              |   11 +-
 man/plotSmear.Rd               |   17 +-
 man/predFC.Rd                  |    7 +-
 man/processAmplicons.Rd        |   34 +-
 man/roast.DGEList.Rd           |   32 +-
 man/scaleOffset.Rd             |   35 --
 man/topTags.Rd                 |    2 +-
 src/R_add_prior_count.cpp      |   64 ---
 src/R_add_repeat_matrices.cpp  |   41 --
 src/R_ave_log_cpm.cpp          |   62 ---
 src/R_calculate_cpm.cpp        |   87 ----
 src/R_check_counts.cpp         |  137 -----
 src/R_check_poisson_bound.cpp  |   50 --
 src/R_compute_apl.cpp          |  111 -----
 src/R_compute_nbdev.cpp        |  113 ++---
 src/R_cr_adjust.cpp            |   43 ++
 src/R_get_one_way_fitted.cpp   |   60 ---
 src/R_initialize_levenberg.cpp |  209 --------
 src/R_levenberg.cpp            |  125 ++---
 src/R_one_group.cpp            |  136 ++---
 src/add_prior.cpp              |   54 --
 src/add_prior.h                |   25 -
 src/adj_coxreid.cpp            |   63 +--
 src/fmm_spline.c               |   17 +-
 src/glm.h                      |   17 +-
 src/glm_levenberg.cpp          |  123 +++--
 src/glm_one_group.cpp          |   20 +-
 src/init.cpp                   |   24 +-
 src/matvec_check.cpp           |  178 ++-----
 src/matvec_check.h             |   32 +-
 src/nbdev.cpp                  |    2 +-
 src/utils.h                    |   42 +-
 tests/edgeR-Tests.Rout.save    | 1079 ++++++++++++++++++++--------------------
 86 files changed, 1503 insertions(+), 3215 deletions(-)
 delete mode 100644 R/addPriorCount.R
 delete mode 100644 R/makeCompressedMatrix.R
 delete mode 100644 R/scaleOffset.R
 delete mode 100644 man/addPriorCount.Rd
 delete mode 100644 man/makeCompressedMatrix.Rd
 delete mode 100644 man/scaleOffset.Rd
 delete mode 100644 src/R_add_prior_count.cpp
 delete mode 100644 src/R_add_repeat_matrices.cpp
 delete mode 100644 src/R_ave_log_cpm.cpp
 delete mode 100644 src/R_calculate_cpm.cpp
 delete mode 100644 src/R_check_counts.cpp
 delete mode 100644 src/R_check_poisson_bound.cpp
 delete mode 100644 src/R_compute_apl.cpp
 create mode 100644 src/R_cr_adjust.cpp
 delete mode 100644 src/R_get_one_way_fitted.cpp
 delete mode 100644 src/R_initialize_levenberg.cpp
 delete mode 100644 src/add_prior.cpp
 delete mode 100644 src/add_prior.h

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