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Revision: 89438
Author: i.scheinin
Date: 2014-04-24T09:53:49+00:00
Paths:
Deleted  /trunk/madman/Rpacks/QDNAseq/.tm_properties
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: d3587b0a27ab4182576a6532655c47f310256b25
    Commit message:
    Remove .tm_properties file from repository.
    Committed by Ilari Scheinin 
    Commit date: 2014-04-24T11:53:43+02:00

From: Bioconductor Git-SVN Bridge 
Revision: 89437
Author: i.scheinin
Date: 2014-04-24T09:48:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/QDNAseq/R/binReadCounts.R
Modified  /trunk/madman/Rpacks/QDNAseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/QDNAseq/R/estimateCorrection.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/smoothOutlierBins.R
Modified  /trunk/madman/Rpacks/QDNAseq/NEWS
Modified  /trunk/madman/Rpacks/QDNAseq/R/normalizeBins.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/plot-methods.R
conflicts resolved while setting up Git-SVN bridge

From: Bioconductor Git-SVN Bridge 
Revision: 89436
Author: t.peters
Date: 2014-04-24T06:23:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/DMRcate/DESCRIPTION
Modified  /trunk/madman/Rpacks/DMRcate/R/functions.R
Modified  /trunk/madman/Rpacks/DMRcate/vignettes/DMRcate.Rnw
conflicts resolved while setting up Git-SVN bridge

From: Bioconductor Git-SVN Bridge 
Revision: 89433
Author: hpages
Date: 2014-04-24T00:52:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/subsetting-utils.R
more tweaks to normalizeSingleBracketSubscript() in preparation of the split
Revision: 89432
Author: hpages
Date: 2014-04-24T00:35:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/subsetting-utils.R
Prepare internal helper normalizeSingleBracketSubscript() for the
IRanges/S4Vectors split.
Revision: 89431
Author: mtmorgan
Date: 2014-04-23T23:55:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
mention FASTA in DESCRIPTION
Revision: 89430
Author: v.obenchain
Date: 2014-04-23T23:16:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/man/List-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/R/List-class.R
remove redundant check in as.data.frame,List method
Revision: 89429
Author: v.obenchain
Date: 2014-04-23T23:07:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_List-class.R
Modified  /trunk/madman/Rpacks/IRanges/man/List-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_DataFrameList.R
Modified  /trunk/madman/Rpacks/IRanges/R/List-class.R
Modified  /trunk/madman/Rpacks/IRanges/man/DataFrameList-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/R/DataFrameList-class.R
Add as.data.frame,List method, unit tests and documentation.
- remove as.data.frame,DataFrameList method
- modify test_SplitDataFrameList_as_data.frame() unit test
Revision: 89428
Author: mtmorgan
Date: 2014-04-23T22:45:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/NEWS
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/R/methods-BamSampler.R
scanBam,BamSampler-method does not mangle names, respects yieldSize
Revision: 89420
Author: mtmorgan
Date: 2014-04-23T22:15:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocInstaller/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocInstaller/R/updateBiocInstallerPackage.R
Modified  /trunk/madman/Rpacks/BiocInstaller/R/biocLite.R
Modified  /trunk/madman/Rpacks/BiocInstaller/R/useDevel.R
Modified  /trunk/madman/Rpacks/BiocInstaller/R/zzz.R
simplify flags and some logic

- set explicitly in zzz.R
- invoke .biocUpgrade() directly if BiocUpgrade in biocLite() arguments
Revision: 89417
Author: hpages
Date: 2014-04-23T21:43:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/man/Vector-class.Rd
add missing aliases for DataTableORNULL
Revision: 89411
Author: hpages
Date: 2014-04-23T21:35:41+00:00
Paths:
Added  /trunk/madman/Rpacks/S4Vectors/man/DataTable-class.Rd
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Added  /trunk/madman/Rpacks/S4Vectors/R/DataTable-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/TODO
Modified  /trunk/madman/Rpacks/S4Vectors/NAMESPACE
move DataTable class from IRanges
Revision: 89409
Author: hpages
Date: 2014-04-23T21:32:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocGenerics/man/row_colnames.Rd
document the 'value' argument
Revision: 89408
Author: hpages
Date: 2014-04-23T21:23:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocGenerics/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocGenerics/man/BiocGenerics-package.Rd
Modified  /trunk/madman/Rpacks/BiocGenerics/man/row_colnames.Rd
Modified  /trunk/madman/Rpacks/BiocGenerics/R/row_colnames.R
Modified  /trunk/madman/Rpacks/BiocGenerics/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocGenerics/man/xtabs.Rd
- Add rownames<- and colnames<- generics.
- Add S4Vectors to Suggests field.
Revision: 89406
Author: t.yin
Date: 2014-04-23T21:00:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/biovizBase/R/addStepping-method.R
Modified  /trunk/madman/Rpacks/biovizBase/DESCRIPTION
missing parathesis and bump version
Revision: 89405
Author: t.yin
Date: 2014-04-23T20:57:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/biovizBase/R/addStepping-method.R
Modified  /trunk/madman/Rpacks/biovizBase/DESCRIPTION
remove ignore.strand and bump version
Revision: 89395
Author: g.tan
Date: 2014-04-23T19:13:25+00:00
Paths:
Added  /trunk/madman/Rpacks/CNEr/src/alignment.c
Modified  /trunk/madman/Rpacks/CNEr/R/AllGenerics.R
Added  /trunk/madman/Rpacks/CNEr/R/Axt-methods.R
Modified  /trunk/madman/Rpacks/CNEr/DESCRIPTION
version 1.1.2. add some unfinished code
Revision: 89392
Author: g.yu
Date: 2014-04-23T18:18:02+00:00
Paths:
Added  /trunk/madman/Rpacks/ChIPseeker/man/plotPeakHeatmap.Rd
Added  /trunk/madman/Rpacks/ChIPseeker/R/tagMatrix.R
Added  /trunk/madman/Rpacks/ChIPseeker/man/plotPeakProf.Rd
Added  /trunk/madman/Rpacks/ChIPseeker/man/getPromoters.Rd
 add plotPeakProf and plotPeakHeatmap <2014-04-24, Thu>
Revision: 89391
Author: g.yu
Date: 2014-04-23T18:16:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/R/annotatePeak.R
Modified  /trunk/madman/Rpacks/ChIPseeker/NAMESPACE
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
 add plotPeakProf and plotPeakHeatmap <2014-04-24, Thu>
Revision: 89390
Author: a.stilp
Date: 2014-04-23T17:06:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GWASTools/R/manhattanPlot.R
Modified  /trunk/madman/Rpacks/GWASTools/man/qqPlot.Rd
Modified  /trunk/madman/Rpacks/GWASTools/R/qqPlot.R
Modified  /trunk/madman/Rpacks/GWASTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GWASTools/man/manhattanPlot.Rd
added thinThreshold argument to manhattanPlot and qqPlot functions to thin pvalues that are higher than a given threshold
Revision: 89388
Author: a.oles
Date: 2014-04-23T14:31:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/R/morphology.R
Fix to previous commit
Revision: 89386
Author: a.oles
Date: 2014-04-23T12:29:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/R/morphology.R
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
version 4.7.2
- fixed tolower conversion of 'shape' argument in 'makeBrush'
Revision: 89384
Author: s.balcome
Date: 2014-04-23T06:06:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/interactiveDisplay/NAMESPACE
Modified  /trunk/madman/Rpacks/interactiveDisplay/vignettes/interactiveDisplay.Rmd
Added  /trunk/madman/Rpacks/interactiveDisplay/man/gridtweak.Rd
Added  /trunk/madman/Rpacks/interactiveDisplay/R/gridtweak.R
Modified  /trunk/madman/Rpacks/interactiveDisplay/DESCRIPTION
Added a little function gridtweak().  It may be removed later, but I personally find it convenient.
Revision: 89383
Author: jq.sun
Date: 2014-04-23T02:10:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCC/man/TCC.Rd
Modified  /trunk/madman/Rpacks/TCC/NAMESPACE
delete legacy functions in TCC (warnings suppress).
Revision: 89382
Author: jq.sun
Date: 2014-04-23T00:42:05+00:00
Paths:
Deleted  /trunk/madman/Rpacks/TCC/man/do_TbT.Rd
Deleted  /trunk/madman/Rpacks/TCC/man/MAplot.Rd
Deleted  /trunk/madman/Rpacks/TCC/man/NB.Rd
Deleted  /trunk/madman/Rpacks/TCC/man/exactTestafterTbT.Rd
delete legacy functions in TCC (delete files).
Revision: 89381
Author: jq.sun
Date: 2014-04-23T00:41:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCC/R/TCC_0.4.R
Modified  /trunk/madman/Rpacks/TCC/NAMESPACE
Modified  /trunk/madman/Rpacks/TCC/NEWS
Modified  /trunk/madman/Rpacks/TCC/DESCRIPTION
delete legacy functions in TCC.
Revision: 89380
Author: d.tenenbaum
Date: 2014-04-23T00:39:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSCA/DESCRIPTION
bump version to 1.3.1 after it was down-bumped from 1.3.0 to 1.0.0.
Revision: 89374
Author: d.tenenbaum
Date: 2014-04-23T00:15:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rdisop/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rdisop/src/imslib/src/ims/utils/distribution.cpp
add an import so code will compile under clang++
Revision: 89373
Author: d.tenenbaum
Date: 2014-04-22T23:15:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/ExpressionView/DESCRIPTION
Modified  /trunk/madman/Rpacks/ExpressionView/src/orderclusters.cpp
include stdlib.h so clang++ can find rand().
Revision: 89372
Author: d.tenenbaum
Date: 2014-04-22T23:07:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/AffyTiling/DESCRIPTION
Modified  /trunk/madman/Rpacks/AffyTiling/src/AnnotateProbes.cpp
move extern "C" to fix clang++ compilation problem
Revision: 89371
Author: z.ji
Date: 2014-04-22T23:06:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSCA/DESCRIPTION
change” --username z.ji --password gJFShNa92f
svn commit -m change”
Revision: 89370
Author: d.tenenbaum
Date: 2014-04-22T23:01:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/GLAD/src/loopRemove.cpp
Modified  /trunk/madman/Rpacks/GLAD/DESCRIPTION
import stdlib.h to resolve clang++ compilation issue
Revision: 89369
Author: d.tenenbaum
Date: 2014-04-22T23:00:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/girafe/DESCRIPTION
Modified  /trunk/madman/Rpacks/girafe/src/coverage.cpp
move extern "C" to resolve clang++ compilation issue
Revision: 89358
Author: m.carlson
Date: 2014-04-22T21:03:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/data/biocViewsVocab.rda
Modified  /trunk/madman/Rpacks/biocViews/inst/extdata/biocViewsVocab.sqlite
Modified  /trunk/madman/Rpacks/biocViews/inst/dot/biocViewsVocab.dot
Adds new package type MeSHDb
Revision: 89357
Author: m.carlson
Date: 2014-04-22T20:29:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTranscriptDbFromGFF.R
Now when GTF files are processed into TxDbs with exon ranking being inferreed, if the exons are on separate chromosomes, we toss out that transcript (since we cannot possibly guess it correctly).
Revision: 89355
Author: m.castro
Date: 2014-04-22T20:25:51+00:00
Paths:
Added  /trunk/madman/Rpacks/RedeR/vignettes/fig7.pdf
Modified  /trunk/madman/Rpacks/RedeR/DESCRIPTION
Added  /trunk/madman/Rpacks/RedeR/vignettes/fig6.pdf
update version
Revision: 89353
Author: hpages
Date: 2014-04-22T19:58:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantTools/NAMESPACE
Modified  /trunk/madman/Rpacks/VariantTools/R/fisher_p.R
Modified  /trunk/madman/Rpacks/VariantTools/DESCRIPTION
need to import new S4Vectors package
Revision: 89352
Author: hpages
Date: 2014-04-22T19:49:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/TFBSTools/NAMESPACE
also need to import isConstant() from new S4Vectors package instead of IRanges
Revision: 89351
Author: hpages
Date: 2014-04-22T19:42:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/SomaticSignatures/NAMESPACE
Modified  /trunk/madman/Rpacks/SomaticSignatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/SomaticSignatures/man/granges-utils.Rd
Modified  /trunk/madman/Rpacks/SomaticSignatures/R/granges-utils.R
seqnameStyle() is defunct, using seqlevelsStyle() instead
Revision: 89350
Author: hpages
Date: 2014-04-22T19:38:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/oligoClasses/NAMESPACE
Modified  /trunk/madman/Rpacks/oligoClasses/DESCRIPTION
need to import new S4Vectors package
Revision: 89349
Author: hpages
Date: 2014-04-22T19:23:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/MinimumDistance/NAMESPACE
Modified  /trunk/madman/Rpacks/MinimumDistance/DESCRIPTION
Need to import new S4Vectors package.
Revision: 89348
Author: m.chen
Date: 2014-04-22T19:22:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/SomatiCA/DESCRIPTION
commit_change
Revision: 89347
Author: m.chen
Date: 2014-04-22T19:13:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/SomatiCA/R/refineSegment.R
commit_change
Revision: 89346
Author: hpages
Date: 2014-04-22T19:02:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/MeSHDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/MeSHDbi/NAMESPACE
Need to import the new S4Vectors package.
Revision: 89344
Author: hpages
Date: 2014-04-22T18:54:29+00:00
Paths:
Deleted  /trunk/madman/Rpacks/MeSHDbi/inst/doc/MeSHDbi.Rnw
Deleted  /trunk/madman/Rpacks/MeSHDbi/inst/doc/MeSHDbi.pdf
Deleted  /trunk/madman/Rpacks/MeSHDbi/vignettes/MeSHDbi.pdf
Removing files that don't belong to svn (they get generated by 'R CMD build').
Revision: 89343
Author: m.jiang
Date: 2014-04-22T17:31:16+00:00
Paths:
Added  /trunk/madman/Rpacks/openCyto/man/fcEllipsoidGate.Rd
Added  /trunk/madman/Rpacks/openCyto/man/fcEllipsoidGate-class.Rd
Modified  /trunk/madman/Rpacks/openCyto/R/gating-functions.R
Modified  /trunk/madman/Rpacks/openCyto/DESCRIPTION
Modified  /trunk/madman/Rpacks/openCyto/R/AllClasses.R
Modified  /trunk/madman/Rpacks/openCyto/R/functions.R
Modified  /trunk/madman/Rpacks/openCyto/NAMESPACE
conflicts resolved while setting up Git-SVN bridge

From: Bioconductor Git-SVN Bridge 
Revision: 89342
Author: m.jiang
Date: 2014-04-22T17:28:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
conflicts resolved while setting up Git-SVN bridge

From: Bioconductor Git-SVN Bridge 
Revision: 89340
Author: m.jiang
Date: 2014-04-22T17:22:52+00:00
Paths:
Deleted  /trunk/madman/Rpacks/flowCore/man/curv1Filter-class.Rd
Deleted  /trunk/madman/Rpacks/flowCore/man/curv2Filter-class.Rd
Deleted  /trunk/madman/Rpacks/flowCore/R/feature.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: bfc22e63999933f960dd8fe687460664a3d52911
    Commit message:
    resolve the svn and git conflicts by manuall remove 3 files
    Committed by mikejiang 
    Commit date: 2014-04-22T10:22:32-07:00

From: Bioconductor Git-SVN Bridge 
Revision: 89339
Author: m.jiang
Date: 2014-04-22T17:19:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCore/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: 4e2448b40f4f1790a3051641826295d0766314a5
    Commit message:
    bump version
    Committed by mikejiang 
    Commit date: 2014-04-22T10:19:28-07:00

From: Bioconductor Git-SVN Bridge 

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