[med-svn] [r-bioc-limma] branch master updated (c30f250 -> dfe5b16)
Andreas Tille
tille at debian.org
Thu Oct 16 13:05:03 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository r-bioc-limma.
from c30f250 Updated copyright information
new ae68131 Imported Upstream version 3.22.0+dfsg
new 579a4f2 Merge tag 'upstream/3.22.0+dfsg'
new 9de02f0 New upstream version
new b54e628 Skip test needing GO.db since we will not finish packaging this for Jessie right in time
new 9ea4d6f Suggests r-bioc-go.db since this is used in test suite but not yet packaged
new d3f0f1e Make sure we enforce C locale in test
new f759eb7 Skip test needing GO.db which is not yet packaged
new dfe5b16 debian/patches/do_not_attempt_GO.db_test.patch is considered as binary file ...
The 8 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 | 8 +-
NAMESPACE | 10 +
R/arrayWeights.R | 384 ++++++++++++++-----------
R/barcodeplot.R | 382 +++++++++++++++++++-----
R/diffSplice.R | 121 +++++---
R/geneset-roast.R | 12 +-
R/geneset-romer.R | 8 +-
R/goana.R | 236 +++++++++++++++
R/lmfit.R | 3 +-
R/plot.R | 82 +++---
R/plotExons.R | 100 +++++++
R/plotWithHighlights.R | 91 ++++++
R/plotdensities.R | 28 +-
R/plots-ma.R | 243 +++++-----------
R/read-ilmn.R | 20 +-
R/read-maimages.R | 46 +--
R/voom.R | 2 +-
R/vooma.R | 77 +++--
debian/changelog | 8 +
debian/control | 5 +-
debian/patches/do_not_attempt_GO.db_test.patch | Bin 0 -> 4642 bytes
debian/patches/series | 1 +
debian/source/include-binaries | 1 +
debian/tests/run-unit-test | 4 +-
inst/NEWS.Rd | 109 +++++++
inst/doc/changelog.txt | 125 +++++++-
inst/doc/intro.pdf | Bin 46191 -> 46191 bytes
inst/doc/usersguide.pdf | Bin 1017047 -> 0 bytes
man/10GeneSetTests.Rd | 4 +-
man/EList.Rd | 32 ++-
man/TestResults.Rd | 2 +-
man/alias2Symbol.Rd | 3 +
man/anova-method.Rd | 4 +-
man/arrayWeights.Rd | 8 +-
man/asdataframe.Rd | 2 +-
man/backgroundcorrect.Rd | 3 +-
man/barcodeplot.Rd | 87 ++++--
man/camera.Rd | 8 +-
man/diffSplice.Rd | 24 +-
man/genas.Rd | 4 +-
man/geneSetTest.Rd | 6 +-
man/gls.series.Rd | 4 +-
man/goana.MArrayLM.Rd | 89 ++++++
man/goana.Rd | 77 +++++
man/heatdiagram.Rd | 6 +-
man/ids2indices.Rd | 46 +++
man/imageplot.Rd | 4 +-
man/imageplot3by2.Rd | 4 +-
man/kooperberg.Rd | 2 +-
man/lmFit.Rd | 6 +-
man/loessfit.Rd | 2 +-
man/ma3x3.Rd | 9 +-
man/mdplot.Rd | 15 +-
man/mrlm.Rd | 4 +-
man/nec.Rd | 10 +-
man/normalizeCyclicLoess.Rd | 2 +-
man/normalizeMedianAbsValues.Rd | 2 +-
man/normalizeRobustSpline.Rd | 3 +-
man/normalizeVSN.Rd | 4 +-
man/normalizeWithinArrays.Rd | 2 +-
man/normalizebetweenarrays.Rd | 7 +-
man/normalizeprintorder.Rd | 2 +-
man/normalizequantiles.Rd | 5 +-
man/plot.Rd | 87 +++---
man/plotDensities.Rd | 20 +-
man/plotExons.Rd | 48 ++++
man/plotFB.Rd | 6 +-
man/plotRLDF.Rd | 4 +-
man/plotSA.Rd | 4 +-
man/plotSplice.Rd | 14 +-
man/plotlines.Rd | 4 +-
man/plotma.Rd | 106 ++++---
man/plotma3by2.Rd | 10 +-
man/plotprinttiploess.Rd | 4 +-
man/qqt.Rd | 3 +-
man/qualwt.Rd | 2 +-
man/read.columns.Rd | 6 +-
man/read.idat.Rd | 3 +-
man/read.ilmn.Rd | 2 +-
man/read.ilmn.targets.Rd | 5 +-
man/read.maimages.Rd | 2 +-
man/readGPRHeader.Rd | 7 +-
man/readSpotTypes.Rd | 2 +-
man/readTargets.Rd | 4 +-
man/readgal.Rd | 8 +-
man/removeBatchEffect.Rd | 4 +-
man/roast.Rd | 8 +-
man/romer.Rd | 7 +-
man/selectmodel.Rd | 4 +-
man/strsplit2.Rd | 2 +-
man/summary.Rd | 4 +-
man/symbols2indices.Rd | 28 --
man/topGO.Rd | 38 +++
man/topRomer.Rd | 4 +-
man/topSplice.Rd | 20 +-
man/tricubeMovingAverage.Rd | 12 +-
man/volcanoplot.Rd | 4 +-
man/voom.Rd | 6 +-
man/voomWithQualityWeights.Rd | 73 +++++
man/vooma.Rd | 8 +-
man/weightedLowess.Rd | 2 +-
man/writefit.Rd | 2 +-
man/zscore.Rd | 4 +-
tests/limma-Tests.R | 5 +
tests/limma-Tests.Rout.save | 163 ++++++-----
105 files changed, 2371 insertions(+), 976 deletions(-)
create mode 100644 R/goana.R
create mode 100644 R/plotExons.R
create mode 100644 R/plotWithHighlights.R
create mode 100644 debian/patches/do_not_attempt_GO.db_test.patch
create mode 100644 debian/source/include-binaries
delete mode 100644 inst/doc/usersguide.pdf
create mode 100644 man/goana.MArrayLM.Rd
create mode 100644 man/goana.Rd
create mode 100644 man/ids2indices.Rd
create mode 100644 man/plotExons.Rd
delete mode 100644 man/symbols2indices.Rd
create mode 100644 man/topGO.Rd
create mode 100644 man/voomWithQualityWeights.Rd
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