[med-svn] [r-cran-pscbs] 02/09: Merge tag 'upstream/0.62.0'
Andreas Tille
tille at debian.org
Tue Nov 15 20:29:03 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-pscbs.
commit ac861f13b3657582a2a513a1973f525951d0c12f
Merge: e6aa158 9fd2d72
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 15 17:54:17 2016 +0100
Merge tag 'upstream/0.62.0'
Upstream version 0.62.0
.Rbuildignore | 58 +++
.Rinstignore | 7 +
.gitignore | 19 +
.make/Makefile | 475 +++++++++++++++++++++
.travis.yml | 48 +++
CONDUCT.md | 74 ++++
DESCRIPTION | 49 ++-
INSTALL.md | 39 ++
MD5 | 209 ---------
Makefile | 1 +
NAMESPACE | 5 +-
NEWS | 12 +-
R/AbstractCBS.HCLUST.R | 4 +-
R/AbstractCBS.PRUNE.R | 10 +-
R/AbstractCBS.R | 34 +-
R/AbstractCBS.RESTRUCT.R | 8 +-
R/CBS.CALL.R | 14 +-
R/CBS.EXTS.R | 8 +-
R/CBS.PLOT,many.R | 4 +-
R/CBS.PLOT.R | 12 +-
R/CBS.PRUNE.R | 4 +-
R/CBS.R | 20 +-
R/CBS.RESTRUCT.R | 4 +-
R/CBS.updateMeansTogether.R | 28 +-
R/DNAcopy.EXTS.R | 4 +-
R/NonPairedPSCBS.R | 8 +-
R/PSCBS.R | 37 +-
R/PSCBS.RESTRUCT.R | 2 +-
R/PairedPSCBS.BOOT.R | 10 +-
R/PairedPSCBS.BOOT.sets.R | 2 +-
R/PairedPSCBS.CALL.R | 4 +-
R/PairedPSCBS.EXTS.R | 50 ++-
R/PairedPSCBS.EXTS3.R | 34 +-
R/PairedPSCBS.PLOT,many.R | 12 +-
R/PairedPSCBS.PLOT.R | 22 +-
R/PairedPSCBS.PLOT2.R | 12 +-
R/PairedPSCBS.R | 48 ++-
R/PairedPSCBS.RESTRUCT.R | 4 +-
R/PairedPSCBS.applyByRegion.R | 2 +-
R/PairedPSCBS.callCopyNeutral.R | 40 ++
R/PairedPSCBS.callGNL.R | 2 +-
R/PairedPSCBS.callROH.R | 2 +-
R/PairedPSCBS.estimateKappa.R | 4 +-
R/PairedPSCBS.extractSegmentDataByLocus.R | 2 +-
R/PairedPSCBS.updateMeans.R | 2 +-
R/PairedPSCBS.updateMeansTogether.R | 2 +-
R/callSegmentationOutliers.R | 2 +-
R/findLargeGaps.R | 2 +-
R/segmentByCBS.R | 16 +-
R/segmentByPairedPSCBS.R | 24 +-
R/writeWIG.R | 2 +-
R/zzz.R | 2 +-
README.md | 40 ++
appveyor.yml | 78 ++++
build/vignette.rds | Bin 307 -> 0 bytes
cran-comments.md | 55 +++
incl/999.missingdocs.txt | 131 ++++++
incl/BengtssonH_etal_2010.Rd | 1 +
incl/OlshenA_etal_2011.Rd | 1 +
incl/OlshenVenkatraman_2004.Rd | 1 +
incl/VenkatramanOlshen_2007.Rd | 1 +
incl/as.DNAcopy.Rex | 13 +
incl/segmentByCBS,calls.Rex | 12 +
incl/segmentByCBS,knownSegments.Rex | 105 +++++
incl/segmentByCBS,plot.Rex | 6 +
incl/segmentByCBS,pruneBySdUndo.Rex | 33 ++
incl/segmentByCBS,tests.Rex | 84 ++++
.../segmentByCBS.Rex | 16 +-
incl/segmentByNonPairedPSCBS.Rex | 72 ++++
incl/segmentByPairedPSCBS,HetsAndHoms.Rex | 62 +++
incl/segmentByPairedPSCBS,allLOH.Rex | 43 ++
incl/segmentByPairedPSCBS.Rex | 78 ++++
inst/CITATION | 6 +-
inst/doc/CBS.R | 94 ----
inst/doc/CBS.pdf | Bin 250313 -> 0 bytes
inst/doc/CBS.tex.rsp | 305 -------------
inst/doc/PairedPSCBS.R | 92 ----
inst/doc/PairedPSCBS.pdf | Bin 283076 -> 0 bytes
inst/doc/PairedPSCBS.tex.rsp | 421 ------------------
inst/templates/rsp/CBS,report.tex.rsp | 4 +-
inst/templates/rsp/PairedPSCBS,report.tex.rsp | 15 +-
man/AbstractCBS.Rd | 1 +
man/CBS.Rd | 2 +-
man/Non-documented_objects.Rd | 3 -
man/NonPairedPSCBS.Rd | 4 +-
man/PSCBS.Rd | 3 +-
man/PairedPSCBS.Rd | 4 +-
man/estimateDeltaCN.PairedPSCBS.Rd | 52 +++
man/normalizeTotalCNs.AbstractCBS.Rd | 40 ++
man/segmentByCBS.Rd | 2 +-
revdep/README.md | 334 +++++++++++++++
revdep/check.R | 20 +
revdep/problems.md | 40 ++
revdep/timing.md | 17 +
tests/PairedPSCBS,plot.R.HIDE | 31 --
tests/segmentByCBS,futures.R | 7 +-
tests/segmentByCBS,shiftTCN.R | 4 +-
tests/segmentByPairedPSCBS,futures.R | 7 +-
vignettes/.install_extras | 8 +
vignettes/CBS.tex.rsp | 2 +-
vignettes/Makefile | 30 ++
vignettes/PSCBS.bib | 8 +-
vignettes/PairedPSCBS.tex.rsp | 2 +-
vignettes/dummy.Rnw | 11 +
104 files changed, 2512 insertions(+), 1388 deletions(-)
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