SVN: Bioconductor (release)

Revision 76863 by t.yin

t.yin — Fri, 24 May 2013 03:52:10 GMT

version bump

(Fri, 24 May 2013 03:52:10 GMT)

Modified

/branches/RELEASE_2_12/madman/Rpacks/biovizBase/DESCRIPTION

Revision 76862 by t.yin

t.yin — Fri, 24 May 2013 03:51:39 GMT

fix bugs in rect to circle transformation

(Fri, 24 May 2013 03:51:39 GMT)

Modified

/branches/RELEASE_2_12/madman/Rpacks/biovizBase/R/transform.R

Revision 76844 by k.uziela

k.uziela — Thu, 23 May 2013 21:54:52 GMT

Added an option to return ExpressionSet object

(Thu, 23 May 2013 21:54:52 GMT)

Modified	/branches/RELEASE_2_12/madman/Rpacks/prebs/DESCRIPTION
Modified	/branches/RELEASE_2_12/madman/Rpacks/prebs/vignettes/prebs.Rnw
Modified	/branches/RELEASE_2_12/madman/Rpacks/prebs/R/PREBS.R
Modified	/branches/RELEASE_2_12/madman/Rpacks/prebs/man/calc_prebs.Rd

Revision 76824 by h.bengtsson

h.bengtsson — Thu, 23 May 2013 01:19:32 GMT

DOCUMENTATION: Dropped an extra 'both' in the help page of normalizeAffine().

(Thu, 23 May 2013 01:19:32 GMT)

Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/normalizeAffine.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/R/normalizeAffine.matrix.R

Revision 76807 by p.mcmurdie

p.mcmurdie — Wed, 22 May 2013 18:40:18 GMT

phyloseq 1.4.4 - Fix issue with URL in description file.

(Wed, 22 May 2013 18:40:18 GMT)

Modified

/branches/RELEASE_2_12/madman/Rpacks/phyloseq/DESCRIPTION

Revision 76786 by p.mcmurdie

p.mcmurdie — Tue, 21 May 2013 22:27:02 GMT

phyloseq 1.4.3 - Speed improvement for import_biom

(Tue, 21 May 2013 22:27:02 GMT)

Modified	/branches/RELEASE_2_12/madman/Rpacks/phyloseq/R/IO-methods.R
Modified	/branches/RELEASE_2_12/madman/Rpacks/phyloseq/inst/NEWS
Modified	/branches/RELEASE_2_12/madman/Rpacks/phyloseq/DESCRIPTION

Revision 76776 by a.honkela

a.honkela — Tue, 21 May 2013 12:11:04 GMT

tigre 1.14.1: bug fixes for non-cascade model

(Tue, 21 May 2013 12:11:04 GMT)

Modified	/branches/RELEASE_2_12/madman/Rpacks/tigre/DESCRIPTION
Modified	/branches/RELEASE_2_12/madman/Rpacks/tigre/R/GPrank.R
Modified	/branches/RELEASE_2_12/madman/Rpacks/tigre/R/gpsimLinearFunctions.R
Modified	/branches/RELEASE_2_12/madman/Rpacks/tigre/R/GPPlot.R
Modified	/branches/RELEASE_2_12/madman/Rpacks/tigre/inst/NEWS

Revision 76774 by s.aibar

s.aibar — Tue, 21 May 2013 10:30:13 GMT

Deleted manual from inst/docs

(Tue, 21 May 2013 10:30:13 GMT)

Deleted

/branches/RELEASE_2_12/madman/Rpacks/geNetClassifier/inst/doc/geNetClassifier-manual.pdf

Revision 76773 by s.aibar

s.aibar — Tue, 21 May 2013 10:19:60 GMT

Bugfix: PlotExpression profiles sample order

(Tue, 21 May 2013 10:19:60 GMT)

Modified	/branches/RELEASE_2_12/madman/Rpacks/geNetClassifier/DESCRIPTION
Modified	/branches/RELEASE_2_12/madman/Rpacks/geNetClassifier/R/function.main.R
Modified	/branches/RELEASE_2_12/madman/Rpacks/geNetClassifier/NEWS

Revision 76769 by h.bengtsson

h.bengtsson — Tue, 21 May 2013 02:08:24 GMT

Version: 1.32.1 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.

(Tue, 21 May 2013 02:08:24 GMT)

Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfSetDimension.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfMergeAlleles.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCelUnits.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfOrderBy.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfOrderColumnsBy.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/compareCdfs.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfAddBaseMmCounts.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCdfNbrOfCellsPerUnitGroup.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCcg.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCdfGroupNames.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/updateCelUnits.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/writeCdfUnits.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfAddPlasqTypes.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfGetGroups.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/findCdf.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCdfDataFrame.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/copyCel.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/9._Advanced_-_Cell-index_maps_for_reading_and_writing.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/1._Dictionary.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/DESCRIPTION
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/applyCdfGroupFields.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/updateCel.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfMergeToQuartets.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/inst/NEWS
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfMergeStrands.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCdfUnits.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/writeCdfQcUnits.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/writeCdfHeader.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCdfIsPm.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfGetFields.Rd
Added	/branches/RELEASE_2_12/madman/Rpacks/affxparser/.Rbuildignore
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCdfUnitsWriteMap.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCelRectangle.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/createCel.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/2._Cell_coordinates_and_cell_indices.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/arrangeCelFilesByChipType.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfAddProbeOffsets.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCdfCellIndices.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/writeCelHeader.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCdf.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/convertCdf.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/compareCels.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfGtypeCelToPQ.Rd
Added	/branches/RELEASE_2_12/madman/Rpacks/affxparser/Makefile
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/isCelFile.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/readCcgHeader.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/applyCdfGroups.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/findFiles.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/parseDatHeaderString.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/convertCel.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/invertMap.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/affxparser/man/cdfHeaderToCelHeader.Rd

Revision 76767 by h.bengtsson

h.bengtsson — Tue, 21 May 2013 01:07:47 GMT

Version: 1.30.2 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.

(Tue, 21 May 2013 01:07:47 GMT)

Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/fitNaiveGenotypes.numeric.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/DESCRIPTION
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/plotXYCurve.numeric.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/iwpca.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/plotMvsAPairs.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/plotXYCurve.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/plotMvsA.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/fitIWPCA.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/calibrateMultiscan.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/inst/NEWS
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/fitXYCurve.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/normalizeCurveFit.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/normalizeAffine.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/normalizeQuantileRank.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/robustSmoothSpline.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/plotMvsMPairs.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/likelihood.smooth.spline.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/normalizeFragmentLength.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/plotDensity.list.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/wpca.matrix.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/callNaiveGenotypes.numeric.Rd
Modified	/branches/RELEASE_2_12/madman/Rpacks/aroma.light/man/normalizeTumorBoost.numeric.Rd