[med-svn] [r-cran-pscbs] branch upstream updated (1b810ae -> 9fd2d72)
Andreas Tille
tille at debian.org
Tue Nov 15 20:29:04 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository r-cran-pscbs.
from 1b810ae Imported Upstream version 0.61.0
new 9fd2d72 New upstream version 0.62.0
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:
.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 +
.../segmentByCBS,knownSegments.Rex | 59 +--
incl/segmentByCBS,plot.Rex | 6 +
incl/segmentByCBS,pruneBySdUndo.Rex | 33 ++
incl/segmentByCBS,tests.Rex | 84 ++++
.../segmentByCBS.Rex | 16 +-
.../segmentByNonPairedPSCBS.Rex | 32 +-
incl/segmentByPairedPSCBS,HetsAndHoms.Rex | 62 +++
incl/segmentByPairedPSCBS,allLOH.Rex | 43 ++
.../segmentByPairedPSCBS.Rex | 44 +-
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, 2295 insertions(+), 1485 deletions(-)
create mode 100644 .Rbuildignore
create mode 100644 .Rinstignore
create mode 100644 .gitignore
create mode 100644 .make/Makefile
create mode 100644 .travis.yml
create mode 100644 CONDUCT.md
create mode 100644 INSTALL.md
delete mode 100644 MD5
create mode 100644 Makefile
create mode 100644 README.md
create mode 100644 appveyor.yml
delete mode 100644 build/vignette.rds
create mode 100644 cran-comments.md
create mode 100644 incl/999.missingdocs.txt
create mode 100644 incl/BengtssonH_etal_2010.Rd
create mode 100644 incl/OlshenA_etal_2011.Rd
create mode 100644 incl/OlshenVenkatraman_2004.Rd
create mode 100644 incl/VenkatramanOlshen_2007.Rd
create mode 100644 incl/as.DNAcopy.Rex
create mode 100644 incl/segmentByCBS,calls.Rex
copy tests/segmentByCBS.R => incl/segmentByCBS,knownSegments.Rex (63%)
create mode 100644 incl/segmentByCBS,plot.Rex
create mode 100644 incl/segmentByCBS,pruneBySdUndo.Rex
create mode 100644 incl/segmentByCBS,tests.Rex
rename tests/segmentByCBS,flavors.R.HIDE => incl/segmentByCBS.Rex (56%)
copy tests/segmentByNonPairedPSCBS,medianDH.R => incl/segmentByNonPairedPSCBS.Rex (75%)
create mode 100644 incl/segmentByPairedPSCBS,HetsAndHoms.Rex
create mode 100644 incl/segmentByPairedPSCBS,allLOH.Rex
copy tests/segmentByNonPairedPSCBS,medianDH.R => incl/segmentByPairedPSCBS.Rex (68%)
delete mode 100644 inst/doc/CBS.R
delete mode 100644 inst/doc/CBS.pdf
delete mode 100644 inst/doc/CBS.tex.rsp
delete mode 100644 inst/doc/PairedPSCBS.R
delete mode 100644 inst/doc/PairedPSCBS.pdf
delete mode 100644 inst/doc/PairedPSCBS.tex.rsp
create mode 100644 man/estimateDeltaCN.PairedPSCBS.Rd
create mode 100644 man/normalizeTotalCNs.AbstractCBS.Rd
create mode 100644 revdep/README.md
create mode 100644 revdep/check.R
create mode 100644 revdep/problems.md
create mode 100644 revdep/timing.md
delete mode 100644 tests/PairedPSCBS,plot.R.HIDE
create mode 100644 vignettes/.install_extras
create mode 100644 vignettes/Makefile
create mode 100644 vignettes/dummy.Rnw
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