[med-svn] [r-cran-pscbs] branch master updated (e6aa158 -> 6020efa)
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 change to branch master
in repository r-cran-pscbs.
from e6aa158 FIx test dependencies
new 9fd2d72 New upstream version 0.62.0
new ac861f1 Merge tag 'upstream/0.62.0'
new 20381b6 New upstream version
new 78b6d07 Convert to dh-r
new c77a7dd cme fix dpkg-control
new 1ab0444 Canonical homepage for CRAN
new 7934c13 update d/copyright
new 5401993 d/watch: version=4
new 6020efa Upload to unstable
The 9 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 +++
debian/changelog | 12 +
debian/control | 17 +-
debian/copyright | 15 +-
debian/rules | 4 +-
debian/watch | 6 +-
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 +
109 files changed, 2324 insertions(+), 1510 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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