[med-svn] [r-bioc-edger] branch master updated (62f6a93 -> 4bb740d)
Andreas Tille
tille at debian.org
Fri Sep 8 20:33:32 UTC 2017
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 62f6a93 Adapt patch to new version
new 0d54e2c New upstream version 3.14.0+dfsg
new e9d58fa Stick to old version since new upstream versions need non-free locfit
new 0755691 Explain upgrade issue in README.Debian
new 4bb740d Standards-Version: 4.1.0 (no changes needed)
The 4 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
debian/README.Debian | 5 +
debian/changelog | 7 +-
debian/control | 2 +-
debian/patches/do_not_attempt_locfit_test.patch | 38 +-
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 +++++++++++------------
90 files changed, 1531 insertions(+), 3239 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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