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Revision: 76821
Author: sdurinck
Date: Wed, 22 May 2013 23:26:29 GMT
Paths:
Modified  /trunk/madman/Rpacks/biomaRt/DESCRIPTION
Modified  /trunk/madman/Rpacks/biomaRt/R/biomaRt.R
Using native BioMart header info to name column names of getBM result
Revision: 76816
Author: m.mccall
Date: Wed, 22 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/ternarynet/DESCRIPTION
Modified  /trunk/madman/Rpacks/ternarynet/src/tnetfuncs.cc
fixed minor bug in tnetfuncs.cc
Revision: 76813
Author: l.zhu
Date: Wed, 22 May 2013 20:49:30 GMT
Paths:
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/R/makeVennDiagram.R
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/R/findOverlappingPeaks.R
fixed makeVennDiagram nooverlap problem on May 22 2013
Revision: 76812
Author: v.obenchain
Date: Wed, 22 May 2013 19:43:08 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/man/summarizeOverlaps.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/R/summarizeOverlaps.R
Modify 'colData' slot of SummarizedExperiment output from summarizeOverlaps().
This now holds the class type and length of 'reads'.
Revision: 76811
Author: k.horan
Date: Wed, 22 May 2013 19:25:30 GMT
Paths:
Modified  /trunk/madman/Rpacks/eiR/src/f2c/Makefile
Modified  /trunk/madman/Rpacks/eiR/src/f2c/main.c
Modified  /trunk/madman/Rpacks/eiR/src/Makevars.win
hopefully a fix for building on windows
Revision: 76810
Author: k.horan
Date: Wed, 22 May 2013 19:25:23 GMT
Paths:
Modified  /trunk/madman/Rpacks/eiR/DESCRIPTION
new version for similarity update
Revision: 76809
Author: k.horan
Date: Wed, 22 May 2013 19:25:15 GMT
Paths:
Modified  /trunk/madman/Rpacks/eiR/man/eiCluster.Rd
Modified  /trunk/madman/Rpacks/eiR/inst/unitTests/test_main.R
Modified  /trunk/madman/Rpacks/eiR/man/eiQuery.Rd
Modified  /trunk/madman/Rpacks/eiR/R/core.R
finished adding option to return similarity results
Revision: 76808
Author: p.mcmurdie
Date: Wed, 22 May 2013 18:44:47 GMT
Paths:
Modified  /trunk/madman/Rpacks/phyloseq/inst/NEWS
Modified  /trunk/madman/Rpacks/phyloseq/R/transform_filter-methods.R
Modified  /trunk/madman/Rpacks/phyloseq/DESCRIPTION
Added  /trunk/madman/Rpacks/phyloseq/inst/tests/test-rarefy.R
Modified  /trunk/madman/Rpacks/phyloseq/man/rarefy_even_depth.Rd
phyloseq 1.5.17 - rarefy_even_depth(), and minor improvements
Revision: 76806
Author: l.chavez
Date: Wed, 22 May 2013 17:50:46 GMT
Paths:
Modified  /trunk/madman/Rpacks/MEDIPS/R/MEDIPS.meth.R
Modified  /trunk/madman/Rpacks/MEDIPS/DESCRIPTION
Modified  /trunk/madman/Rpacks/MEDIPS/inst/doc/MEDIPS.Rnw
Manual update: ratio direction
Revision: 76805
Author: v.obenchain
Date: Wed, 22 May 2013 17:43:47 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/R/methods-BamFile.R
Modified  /trunk/madman/Rpacks/Rsamtools/man/BamFile-class.Rd
Add output of countBam() to 'colData' slot of SummarizedExperiment created by
summarizeOverlaps() with BamFile or BamFileList.
Revision: 76804
Author: p.shannon
Date: Wed, 22 May 2013 16:49:18 GMT
Paths:
Modified  /trunk/madman/Rpacks/RCytoscape/DESCRIPTION
fixed setNodeShapeDirect man page
Revision: 76803
Author: p.shannon
Date: Wed, 22 May 2013 16:47:33 GMT
Paths:
Modified  /trunk/madman/Rpacks/RCytoscape/man/setNodeShapeDirect.Rd
added getNodeShapes to example
Revision: 76802
Author: stvjc
Date: Wed, 22 May 2013 16:45:44 GMT
Paths:
Modified  /trunk/madman/Rpacks/GGtools/R/fdr.all.cis.R
Modified  /trunk/madman/Rpacks/GGtools/DESCRIPTION
All.cis needs to match seqlevels of output ranges to names of smlSet smList
Revision: 76801
Author: p.shannon
Date: Wed, 22 May 2013 16:38:57 GMT
Paths:
Modified  /trunk/madman/Rpacks/RCytoscape/man/setNodeShapeDirect.Rd
fixed see also type
Revision: 76800
Author: v.haberle
Date: Wed, 22 May 2013 16:30:15 GMT
Paths:
Added  /trunk/madman/Rpacks/CAGEr/NEWS
Added NEWS file
Revision: 76799
Author: v.haberle
Date: Wed, 22 May 2013 16:26:22 GMT
Paths:
Modified  /trunk/madman/Rpacks/CAGEr/R/ImportMethods.R
Modified  /trunk/madman/Rpacks/CAGEr/DESCRIPTION
Modified  /trunk/madman/Rpacks/CAGEr/man/getCTSS.Rd
Fixed column classes in CTSS data.frame when reading the data from bam files
Revision: 76797
Author: t.yates
Date: Wed, 22 May 2013 14:54:24 GMT
Paths:
Modified  /trunk/madman/Rpacks/annmap/DESCRIPTION
Modified  /trunk/madman/Rpacks/annmap/inst/cookbook/cookbook.Rnw
Updated cookbook to include cds example. v1.3.2
Revision: 76796
Author: t.yates
Date: Wed, 22 May 2013 14:54:12 GMT
Paths:
Modified  /trunk/madman/Rpacks/annmap/R/coords.R
Modified  /trunk/madman/Rpacks/annmap/man/annmap.coords.Rd
Allow transcriptCoordsToGenome to take CDS region into account
Revision: 76795
Author: whuber
Date: Wed, 22 May 2013 12:16:25 GMT
Paths:
Modified  /trunk/madman/Rpacks/cellHTS2/R/readPlateList.R
Modified  /trunk/madman/Rpacks/cellHTS2/R/methods-cellHTS.R
Modified  /trunk/madman/Rpacks/cellHTS2/DESCRIPTION
Fixed a typo and some minor reformatting of comments.
Revision: 76794
Author: m.mccall
Date: Wed, 22 May 2013 04:19:23 GMT
Paths:
Modified  /trunk/madman/Rpacks/ternarynet/R/attractorSummary.R
Modified  /trunk/madman/Rpacks/ternarynet/R/plotFit.R
Modified  /trunk/madman/Rpacks/ternarynet/DESCRIPTION
Modified  /trunk/madman/Rpacks/ternarynet/man/tnetpost.Rd
Modified  /trunk/madman/Rpacks/ternarynet/R/tnetpost.R
altered default values in tnetpost
Revision: 76792
Author: y.liao
Date: Tue, 21 May 2013 23:24:44 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
Trimming spaces before gene_id
Revision: 76790
Author: r.tautenhahn
Date: Tue, 21 May 2013 23:16:16 GMT
Paths:
Modified  /trunk/madman/Rpacks/xcms/inst/NEWS
fixed bug in patternVsRowScore (group.nearest) that was introduced by the
modifications in rev 65169 and caused features to be aligned that were far outside the given m/z and retention time windows.
Revision: 76789
Author: r.tautenhahn
Date: Tue, 21 May 2013 23:12:18 GMT
Paths:
Modified  /trunk/madman/Rpacks/xcms/DESCRIPTION
fixed bug in patternVsRowScore (group.nearest) that was introduced by the
modifications in rev 65169 and caused features to be aligned that were far outside the given m/z and retention time windows.
Revision: 76788
Author: r.tautenhahn
Date: Tue, 21 May 2013 23:10:35 GMT
Paths:
Modified  /trunk/madman/Rpacks/xcms/R/xcmsSet.R
fixed bug in patternVsRowScore (group.nearest) that was introduced by the
modifications in rev 65169 and caused features to be aligned that were far outside the given m/z and retention time windows.
Revision: 76787
Author: v.obenchain
Date: Tue, 21 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/src/vcffile.c
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/readVcf-methods.Rd
readVcf() now creates rownames with format CHROM:POS_REF/ALT for variants with ID=".".
Revision: 76785
Author: t.yin
Date: Tue, 21 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/man/tracks.Rd
Modified  /trunk/madman/Rpacks/ggbio/R/tracks.R
add cbind/rbind for tracks object and change top margin to 1
Revision: 76784
Author: t.yin
Date: Tue, 21 May 2013 19:48:04 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/man/tracks.Rd
Modified  /trunk/madman/Rpacks/ggbio/R/tracks.R
Modified  /trunk/madman/Rpacks/ggbio/NAMESPACE
Modified  /trunk/madman/Rpacks/ggbio/R/Plot-class.R
Add combination methods for tracks and add get_gtable function to get gtable from tracks object.
Revision: 76780
Author: v.haberle
Date: Tue, 21 May 2013 15:59:29 GMT
Paths:
Modified  /trunk/madman/Rpacks/CAGEr/DESCRIPTION
Modified  /trunk/madman/Rpacks/CAGEr/R/AllClasses.R
Modified  /trunk/madman/Rpacks/CAGEr/inst/doc/CAGEr.Rnw
Allowed use of custom built genomes by excluding the check of presence of genome name in the available.genomes list
Revision: 76779
Author: n.servant
Date: Tue, 21 May 2013 15:20:15 GMT
Paths:
Modified  /trunk/madman/Rpacks/HiTC/R/import.R
Modified  /trunk/madman/Rpacks/HiTC/NEWS
Modified  /trunk/madman/Rpacks/HiTC/man/importC.Rd
Modified  /trunk/madman/Rpacks/HiTC/R/HTCexp-class.R
Modified  /trunk/madman/Rpacks/HiTC/man/mapC.Rd
Modified  /trunk/madman/Rpacks/HiTC/R/mapC.R
Modified  /trunk/madman/Rpacks/HiTC/DESCRIPTION
small bugs fixed
Revision: 76778
Author: khansen
Date: Tue, 21 May 2013 14:59:45 GMT
Paths:
Modified  /trunk/madman/Rpacks/minfi/man/mapToGenome-methods.Rd
Modified  /trunk/madman/Rpacks/minfi/NAMESPACE
Added  /trunk/madman/Rpacks/minfi/man/RatioSet-class.Rd
Modified  /trunk/madman/Rpacks/minfi/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/minfi/R/rset.R
Added  /trunk/madman/Rpacks/minfi/man/ratioConvert-methods.Rd
Modified  /trunk/madman/Rpacks/minfi/R/generics.R
Modified  /trunk/madman/Rpacks/minfi/R/gmset.R
Modified  /trunk/madman/Rpacks/minfi/man/MethylSet-class.Rd
Modified  /trunk/madman/Rpacks/minfi/man/GenomicMethylSet-class.Rd
Modified  /trunk/madman/Rpacks/minfi/DESCRIPTION
Modified  /trunk/madman/Rpacks/minfi/R/grset.R
Modified  /trunk/madman/Rpacks/minfi/R/mset.R
added RatioSet class and ratioConvert() method
Revision: 76777
Author: a.honkela
Date: Tue, 21 May 2013 12:13:19 GMT
Paths:
Modified  /trunk/madman/Rpacks/tigre/DESCRIPTION
Modified  /trunk/madman/Rpacks/tigre/R/GPrank.R
Modified  /trunk/madman/Rpacks/tigre/R/gpsimLinearFunctions.R
Modified  /trunk/madman/Rpacks/tigre/R/GPPlot.R
Modified  /trunk/madman/Rpacks/tigre/inst/NEWS
tigre 1.15.1: bug fixes to non-cascade model (identical to tigre 1.14.1)
Revision: 76775
Author: r.stojnic
Date: Tue, 21 May 2013 10:58:04 GMT
Paths:
Modified  /trunk/madman/Rpacks/PWMEnrich/R/MotifEnrichmentResults-methods.R
Fixed a typo
Revision: 76772
Author: radivot
Date: Tue, 21 May 2013 09:50:44 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/simulate.r
Added  /trunk/madman/Rpacks/SBMLR/inst/models/sbmlrDemo.R
Modified  /trunk/madman/Rpacks/SBMLR/inst/models/sod.xml
Modified  /trunk/madman/Rpacks/SBMLR/inst/models/sod.R
Modified  /trunk/madman/Rpacks/SBMLR/inst/models/sodNatural.R
fixed sod example. Source of integration instability was my clipping of negative concentrations to zero. So I fixed simulate to no longer do this.
Revision: 76771
Author: t.yin
Date: Tue, 21 May 2013 05:47:50 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/tracks.R
Modified  /trunk/madman/Rpacks/ggbio/R/Grob-class.R
Modified  /trunk/madman/Rpacks/ggbio/R/Tracked-class.R
Modified  /trunk/madman/Rpacks/ggbio/R/Plot-class.R
fix tracks bugs for labeling and remove Grob class subclass, this may be confusing
Revision: 76770
Author: t.yin
Date: Tue, 21 May 2013 03:56:42 GMT
Paths:
Modified  /trunk/madman/Rpacks/biovizBase/R/addStepping-method.R
Modified  /trunk/madman/Rpacks/biovizBase/man/addStepping-method.Rd
add fix arguments
Revision: 76768
Author: h.bengtsson
Date: Tue, 21 May 2013 02:08:09 GMT
Paths:
Modified  /trunk/madman/Rpacks/affxparser/man/convertCdf.Rd
Modified  /trunk/madman/Rpacks/affxparser/man/readCdfDataFrame.Rd
Modified  /trunk/madman/Rpacks/affxparser/Makefile
Modified  /trunk/madman/Rpacks/affxparser/man/readCcgHeader.Rd
Modified  /trunk/madman/Rpacks/affxparser/man/readCelUnits.Rd
Modified  /trunk/madman/Rpacks/affxparser/DESCRIPTION
Modified  /trunk/madman/Rpacks/affxparser/man/convertCel.Rd
Modified  /trunk/madman/Rpacks/affxparser/man/updateCel.Rd
Modified  /trunk/madman/Rpacks/affxparser/man/arrangeCelFilesByChipType.Rd
Modified  /trunk/madman/Rpacks/affxparser/man/readCdfCellIndices.Rd
Modified  /trunk/madman/Rpacks/affxparser/inst/NEWS
Modified  /trunk/madman/Rpacks/affxparser/man/readCdfUnits.Rd
Version: 1.33.1 [2013-05-20]
o Same updates as in release v1.32.1.

Version: 1.32.1 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
Revision: 76766
Author: h.bengtsson
Date: Tue, 21 May 2013 01:05:52 GMT
Paths:
Modified  /trunk/madman/Rpacks/aroma.light/man/callNaiveGenotypes.numeric.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/wpca.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeTumorBoost.numeric.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/fitNaiveGenotypes.numeric.Rd
Modified  /trunk/madman/Rpacks/aroma.light/DESCRIPTION
Modified  /trunk/madman/Rpacks/aroma.light/man/plotXYCurve.numeric.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/iwpca.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotMvsAPairs.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotXYCurve.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotMvsA.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/fitIWPCA.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/calibrateMultiscan.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/inst/NEWS
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeCurveFit.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/fitXYCurve.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeAffine.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeQuantileRank.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotMvsMPairs.matrix.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/robustSmoothSpline.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/likelihood.smooth.spline.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/normalizeFragmentLength.Rd
Modified  /trunk/madman/Rpacks/aroma.light/man/plotDensity.list.Rd
Version: 1.31.2 [2013-05-20]
o Same updates as in v1.30.2.

Version: 1.30.2 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
Revision: 76765
Author: y.liao
Date: Mon, 20 May 2013 23:48:58 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor improvement of featureCounts
Revision: 76764
Author: t.yin
Date: Mon, 20 May 2013 18:51:14 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/man/tracks.Rd
Modified  /trunk/madman/Rpacks/ggbio/R/ideogram.R
Modified  /trunk/madman/Rpacks/ggbio/R/tracks.R
Modified  /trunk/madman/Rpacks/ggbio/R/GGbio-class.R
Modified  /trunk/madman/Rpacks/ggbio/NAMESPACE
Modified  /trunk/madman/Rpacks/ggbio/R/Tracked-class.R
Modified  /trunk/madman/Rpacks/ggbio/R/Plot-class.R
fix major broken issues of tracks function, need to support old accessor API too I guess though
Revision: 76761
Author: j.hon
Date: Mon, 20 May 2013 17:59:40 GMT
Paths:
Modified  /trunk/madman/Rpacks/triplex/man/triplex.3D.Rd
Modified  /trunk/madman/Rpacks/triplex/NAMESPACE
Modified  /trunk/madman/Rpacks/triplex/R/triplex.3D.R
Modified  /trunk/madman/Rpacks/triplex/DESCRIPTION
rgl moved from Depends into Suggests
Revision: 76760
Author: radivot
Date: Mon, 20 May 2013 17:48:31 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/inst/models/sod.R
Added  /trunk/madman/Rpacks/SBMLR/inst/models/sodNatural.R
added sodNatural.R, but I can't seem to make it work
Revision: 76759
Author: j.muller
Date: Mon, 20 May 2013 17:36:52 GMT
Paths:
Modified  /trunk/madman/Rpacks/TransView/NEWS
Modified  /trunk/madman/Rpacks/TransView/man/meltPeak.Rd
Modified  /trunk/madman/Rpacks/TransView/DESCRIPTION
Modified  /trunk/madman/Rpacks/TransView/R/TransView_tools.R
Modified  /trunk/madman/Rpacks/TransView/man/TransView-package.Rd
CHANGES IN VERSION 1.5.3
------------------------

NEW FEATURES

    o meltPeak can return loess smoothed scores.
Revision: 76758
Author: l.chavez
Date: Mon, 20 May 2013 17:20:23 GMT
Paths:
Modified  /trunk/madman/Rpacks/MEDIPS/DESCRIPTION
Modified  /trunk/madman/Rpacks/MEDIPS/inst/doc/MEDIPS.Rnw
Manual distance=1 update
Revision: 76757
Author: p.haverty
Date: Mon, 20 May 2013 17:13:02 GMT
Paths:
Modified  /trunk/madman/Rpacks/genoset/man/segs2RleDataFrame.Rd
Modified  /trunk/madman/Rpacks/genoset/NAMESPACE
Modified  /trunk/madman/Rpacks/genoset/man/segs2RangedData.Rd
Modified  /trunk/madman/Rpacks/genoset/R/segments.R
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Fixed roxygen2 segments family see also
Revision: 76756
Author: p.haverty
Date: Mon, 20 May 2013 17:10:14 GMT
Paths:
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Now importing width from GenomicRanges
Revision: 76755
Author: p.haverty
Date: Mon, 20 May 2013 16:34:38 GMT
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
IRanges now both Depends and Imports
Revision: 76754
Author: t.yates
Date: Mon, 20 May 2013 15:57:12 GMT
Paths:
Modified  /trunk/madman/Rpacks/annmap/DESCRIPTION
Modified  /trunk/madman/Rpacks/annmap/inst/unitTests/runit.coords.R
Modified  /trunk/madman/Rpacks/annmap/R/coords.R
Modified  /trunk/madman/Rpacks/annmap/inst/NEWS.Rd
Fix for transcriptCoordsToGenome

* ANNMAP112:
  Up to v1.3.1
  Added NEWS of fix
  Fix for ANNMAP-112 use as.integer rather than as.numeric
  Unit test for ANNMAP-112 bug with transcript/protein CoordsToGenome
Revision: 76753
Author: y.liao
Date: Mon, 20 May 2013 15:55:12 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor improvement of featureCounts
Revision: 76751
Author: radivot
Date: Mon, 20 May 2013 12:01:57 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/man/simulate.Rd
Added  /trunk/madman/Rpacks/SBMLR/inst/models/curtoNatural.R
Added  /trunk/madman/Rpacks/SBMLR/inst/models/sod.xml
Added  /trunk/madman/Rpacks/SBMLR/inst/models/sod.R
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/summary.SBML.r
Modified  /trunk/madman/Rpacks/SBMLR/NEWS
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBML.r
added SOD model and curtoNatural.R to models. Removed need for reversible flag in SBMLR model files.
Revision: 76750
Author: j.hon
Date: Mon, 20 May 2013 09:52:05 GMT
Paths:
Modified  /trunk/madman/Rpacks/triplex/DESCRIPTION
Stric rgl dependency
Revision: 76748
Author: y.liao
Date: Mon, 20 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/sambam-file.h
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
Modified  /trunk/madman/Rpacks/Rsubread/src/sambam-file.c
removed wrong message from featureCounts
Revision: 76747
Author: g.yu
Date: Mon, 20 May 2013 05:33:44 GMT
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/NEWS
Modified  /trunk/madman/Rpacks/clusterProfiler/R/utilities.R
Modified  /trunk/madman/Rpacks/clusterProfiler/R/enrichKEGG.R
enrichGO and enrichKEGG support rat organism <2013-05-20, Mon>
Revision: 76746
Author: p.murrell
Date: Mon, 20 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/hyperdraw/inst/doc/hyperdraw.Rnw
Modified  /trunk/madman/Rpacks/hyperdraw/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/hyperdraw/R/draw.R
add "start" option for "arrowLoc"
Revision: 76745
Author: p.murrell
Date: Mon, 20 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/hyperdraw/R/hypergraph.R
Modified  /trunk/madman/Rpacks/hyperdraw/inst/doc/hyperdraw.Rnw
Modified  /trunk/madman/Rpacks/hyperdraw/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/hyperdraw/R/draw.R
add "both" option for "arrowLoc";  bug fix for conversion from Hypregraph to graphBPH
Revision: 76744
Author: y.liao
Date: Sun, 19 May 2013 23:30:44 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
removed wrong message from featureCounts
Revision: 76743
Author: t.yin
Date: Sun, 19 May 2013 22:51:54 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/man/tracks.Rd
Modified  /trunk/madman/Rpacks/ggbio/DESCRIPTION
update manual of tracks
Revision: 76742
Author: t.yin
Date: Sun, 19 May 2013 22:51:33 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/tests/runTests.R
Added  /trunk/madman/Rpacks/ggbio/tests
add test folder and file
Revision: 76741
Author: t.yin
Date: Sun, 19 May 2013 22:50:35 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/inst/tests/test_grob.R
update test
Revision: 76740
Author: t.yin
Date: Sun, 19 May 2013 22:50:20 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/NAMESPACE
update NAMESPACE
Revision: 76739
Author: t.yin
Date: Sun, 19 May 2013 22:36:24 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/tracks.R
Modified  /trunk/madman/Rpacks/ggbio/R/GGbio-class.R
Modified  /trunk/madman/Rpacks/ggbio/R/utils.R
tweak and move around functions
Revision: 76738
Author: t.yin
Date: Sun, 19 May 2013 22:34:38 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/ggplot-method.R
remove ggplot,Any
Revision: 76737
Author: t.yin
Date: Sun, 19 May 2013 22:34:14 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/AllClasses.R
add numericORNULL
Revision: 76736
Author: t.yin
Date: Sun, 19 May 2013 22:32:02 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/plotRangesLinkedToData.R
fix a typo
Revision: 76735
Author: t.yin
Date: Sun, 19 May 2013 22:31:40 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/man/Plot-class.Rd
Added  /trunk/madman/Rpacks/ggbio/R/Plot-class.R
add Plot Class
Revision: 76734
Author: t.yin
Date: Sun, 19 May 2013 22:31:18 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/man/Grob-class.Rd
Added  /trunk/madman/Rpacks/ggbio/R/Grob-class.R
add Grob class
Revision: 76733
Author: t.yin
Date: Sun, 19 May 2013 21:28:40 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/inst/tests/test_grob.R
Added  /trunk/madman/Rpacks/ggbio/inst/tests
add test directory
Revision: 76732
Author: t.yin
Date: Sun, 19 May 2013 21:24:56 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/R/Cache-class.R
Added  /trunk/madman/Rpacks/ggbio/man/Cache-class.Rd
add Cache class
Revision: 76731
Author: t.yin
Date: Sun, 19 May 2013 21:24:28 GMT
Paths:
Added  /trunk/madman/Rpacks/ggbio/man/Tracked-class.Rd
Added  /trunk/madman/Rpacks/ggbio/R/Tracked-class.R
add Tracked class
Revision: 76730
Author: mtmorgan
Date: Sun, 19 May 2013 12:13:41 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/R/SnapshotFunction-helpers.R
Modified  /trunk/madman/Rpacks/ShortRead/R/Snapshot.R
Modified  /trunk/madman/Rpacks/ShortRead/R/spViewPerFeature.R
Modified  /trunk/madman/Rpacks/ShortRead/man/Snapshot-class.Rd
quieten warnings from Snapshot

- use seqlevels<-
- avoid setting scales in update() -- bug in lattice??
Revision: 76728
Author: mtmorgan
Date: Sun, 19 May 2013 04:01:52 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/NEWS
DESCRIPTION and NEWS update
Revision: 76727
Author: mtmorgan
Date: Sun, 19 May 2013 02:36:24 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_trimEnds.R
Added  /trunk/madman/Rpacks/ShortRead/R/trimEnds.R
Modified  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_trimTails.R
Modified  /trunk/madman/Rpacks/ShortRead/man/trimTails.Rd
trim*,character-methods using filterFastq
Revision: 76726
Author: mtmorgan
Date: Sun, 19 May 2013 02:35:41 GMT
Paths:
Added  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_filterFastq.R
Added  /trunk/madman/Rpacks/ShortRead/man/filterFastq.Rd
Added  /trunk/madman/Rpacks/ShortRead/R/filterFastq.R
filterFastq methods
Revision: 76725
Author: mtmorgan
Date: Sat, 18 May 2013 19:19:18 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_writeFastq_test.R
Modified  /trunk/madman/Rpacks/ShortRead/R/methods-ShortReadQ.R
write 0-length fastq files
Revision: 76724
Author: mtmorgan
Date: Sat, 18 May 2013 19:16:25 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/R/methods-QualityScore.R
Modified  /trunk/madman/Rpacks/ShortRead/man/QualityScore-class.Rd
Modified  /trunk/madman/Rpacks/ShortRead/NAMESPACE
encoding,QualityScore-methods
Revision: 76723
Author: mtmorgan
Date: Sat, 18 May 2013 19:06:16 GMT
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/R/XStringQuality-class.R
Modified  /trunk/madman/Rpacks/Biostrings/NAMESPACE
Modified  /trunk/madman/Rpacks/Biostrings/DESCRIPTION
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringQuality-class.Rd
alphabet and encoding methods for XStringQuality
Revision: 76722
Author: hpages
Date: Sat, 18 May 2013 04:56:45 GMT
Paths:
Modified  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/SplicingGraphs.Rnw
small tweaks to vignette
Revision: 76721
Author: radivot
Date: Sat, 18 May 2013 03:09:57 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/simulate.r
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/summary.SBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBML.r
got it to pass check with VV additions

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