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Revision: 89278
Author: t.yin
Date: 2014-04-21T03:48:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/layout_linear-method.R
Modified  /trunk/madman/Rpacks/ggbio/R/autoplot-method.R
Modified  /trunk/madman/Rpacks/ggbio/R/ideogram.R
Modified  /trunk/madman/Rpacks/ggbio/man/plotSingleChrom.Rd
Modified  /trunk/madman/Rpacks/ggbio/man/ggplot-method.Rd
Modified  /trunk/madman/Rpacks/ggbio/R/Tracks-class.R
Modified  /trunk/madman/Rpacks/ggbio/R/GGbio-class.R
Modified  /trunk/madman/Rpacks/ggbio/man/layout_circle-method.Rd
Modified  /trunk/madman/Rpacks/ggbio/NAMESPACE
Modified  /trunk/madman/Rpacks/ggbio/R/utils.R
Modified  /trunk/madman/Rpacks/ggbio/inst/example/GGbio-class.R
Modified  /trunk/madman/Rpacks/ggbio/man/autoplot-method.Rd
Modified  /trunk/madman/Rpacks/ggbio/R/geom_alignment-method.R
Modified  /trunk/madman/Rpacks/ggbio/R/stat_coverage-method.R
Modified  /trunk/madman/Rpacks/ggbio/R/Cache-class.R
Modified  /trunk/madman/Rpacks/ggbio/R/hack.R
Modified  /trunk/madman/Rpacks/ggbio/R/layout_karyogram-method.R
Modified  /trunk/madman/Rpacks/ggbio/man/ggbio-class.Rd
Modified  /trunk/madman/Rpacks/ggbio/man/Grob-class.Rd
Modified  /trunk/madman/Rpacks/ggbio/R/layout_circle-method.R
Modified  /trunk/madman/Rpacks/ggbio/vignettes/realvignettes/ggbio.Rnw
Modified  /trunk/madman/Rpacks/ggbio/R/stat_reduce-method.R
Modified  /trunk/madman/Rpacks/ggbio/man/geom_alignment-method.Rd
Modified  /trunk/madman/Rpacks/ggbio/R/Plot-class.R
Modified  /trunk/madman/Rpacks/ggbio/DESCRIPTION
update part of the vignette and fix some bugs
Revision: 89277
Author: m.lawrence
Date: 2014-04-20T23:17:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/LazyList/R/Interaction-class.R
Modified  /trunk/madman/Rpacks/LazyList/R/Lapply-methods.R
preparing to embark on refactoring of Interaction and friends
Revision: 89276
Author: m.lawrence
Date: 2014-04-20T23:16:20+00:00
Paths:
Deleted  /trunk/madman/Rpacks/LazyList/R/Array-class.R
Modified  /trunk/madman/Rpacks/LazyList/R/tapply-methods.R
Modified  /trunk/madman/Rpacks/LazyList/R/DimensionDecorator-class.R
Modified  /trunk/madman/Rpacks/LazyList/R/LazyList-class.R
in a surprise move, get rid of the Array class and introduce DimensionDecorator
Revision: 89275
Author: m.lawrence
Date: 2014-04-20T23:15:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/LazyList/DESCRIPTION
Added  /trunk/madman/Rpacks/LazyList/R/extractList-methods.R
Deleted  /trunk/madman/Rpacks/LazyList/R/split-methods.R
move split methods to extractList-methods.R
Revision: 89273
Author: hpages
Date: 2014-04-20T20:09:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/vignettes/easyRNASeq.Rnw
need to library(IRanges) before calling RangedData() in the vignette
Revision: 89270
Author: h.corradabravo
Date: 2014-04-20T18:42:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: b2c9079e62fbf2c8343f961efb55aa0f808141a1
    Commit message:
    Update README.md
    Committed by hcorrada 
    Commit date: 2014-04-20T14:42:00-04:00

From: Bioconductor Git-SVN Bridge 
Revision: 89269
Author: h.corradabravo
Date: 2014-04-20T18:35:35+00:00
Paths:
Deleted  /trunk/madman/Rpacks/epivizr/TODO
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: e9053fa44a9ae9cce19bb96232b21675bf09411b
    Commit message:
    Delete TODO
    Committed by hcorrada 
    Commit date: 2014-04-20T14:35:29-04:00

From: Bioconductor Git-SVN Bridge 
Revision: 89265
Author: whuber
Date: 2014-04-20T18:04:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/man/localCurvature.Rd
Modified  /trunk/madman/Rpacks/EBImage/R/gblur.R
Modified  /trunk/madman/Rpacks/EBImage/man/morphology.Rd
Modified  /trunk/madman/Rpacks/EBImage/R/morphology.R
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
Fixed a typo.
Revision: 89262
Author: mtmorgan
Date: 2014-04-20T01:39:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocInstaller/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocInstaller/inst/scripts/biocLite.R
tools:::.Bioc_version_associated_with_R_version may be a function in R-devel
Revision: 89260
Author: g.zararsiz
Date: 2014-04-19T21:29:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLSeq/inst/doc/MLSeq.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: b8b7c6606ceafdf3d7a8691a17f5d8ae9802981d
    Commit message:
    Update MLSeq.Rnw
    Committed by Dinçer GÖKSÜLÜK 
    Commit date: 2014-04-20T00:29:00+03:00

From: Bioconductor Git-SVN Bridge 
Revision: 89257
Author: hpages
Date: 2014-04-19T20:29:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-package.R
Modified  /trunk/madman/Rpacks/easyRNASeq/NAMESPACE
resync with stuff moving from IRanges to S4Vectors
Revision: 89255
Author: hpages
Date: 2014-04-19T20:04:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/Gviz/DESCRIPTION
Modified  /trunk/madman/Rpacks/Gviz/NAMESPACE
need to have GenomicRanges in Depends
Revision: 89250
Author: mtmorgan
Date: 2014-04-19T18:27:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/NEWS
version and NEWS bump
Revision: 89249
Author: mtmorgan
Date: 2014-04-19T18:24:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/R/methods-QualityScore.R
Modified  /trunk/madman/Rpacks/ShortRead/man/QualityScore-class.Rd
Modified  /trunk/madman/Rpacks/ShortRead/man/alphabetScore.Rd
alphabetScore,Phred-quality method
Revision: 89248
Author: hpages
Date: 2014-04-19T18:13:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/DECIPHER/NAMESPACE
Modified  /trunk/madman/Rpacks/DECIPHER/DESCRIPTION
resync with stuff moving from IRanges to S4Vectors
Revision: 89247
Author: hpages
Date: 2014-04-19T17:58:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/CNEr/src/Makevars.common
Modified  /trunk/madman/Rpacks/CNEr/NAMESPACE
Modified  /trunk/madman/Rpacks/CNEr/DESCRIPTION
Modified  /trunk/madman/Rpacks/CNEr/src/CNEr.h
Added  /trunk/madman/Rpacks/CNEr/src/S4Vectors_stubs.c
resync with stuff moving from IRanges to S4Vectors
Revision: 89245
Author: hpages
Date: 2014-04-19T17:30:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
resync with stuff moving from IRanges to S4Vectors
Revision: 89244
Author: hpages
Date: 2014-04-19T17:19:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/R/SNPlocs-class.R
Modified  /trunk/madman/Rpacks/BSgenome/R/getSeq-methods.R
Modified  /trunk/madman/Rpacks/BSgenome/NAMESPACE
resync with stuff moving from IRanges to S4Vectors
Revision: 89243
Author: d.tenenbaum
Date: 2014-04-19T17:12:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
conflicts resolved while setting up Git-SVN bridge

From: Bioconductor Git-SVN Bridge 
Revision: 89242
Author: hpages
Date: 2014-04-19T17:02:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/biovizBase/R/addStepping-method.R
Modified  /trunk/madman/Rpacks/biovizBase/DESCRIPTION
fix misplaced parenthesis
Revision: 89241
Author: hpages
Date: 2014-04-19T16:58:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VRanges-class.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/NAMESPACE
resync with more stuff moving from IRanges to S4Vectors
Revision: 89240
Author: hpages
Date: 2014-04-19T16:57:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/R/methods-ScanBamParam.R
resync with more stuff moving from IRanges to S4Vectors
Revision: 89239
Author: hpages
Date: 2014-04-19T16:55:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/subsetting-utils.R
change spelling
Revision: 89238
Author: hpages
Date: 2014-04-19T16:39:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
cigarToWidth() is gone.
Revision: 89233
Author: hpages
Date: 2014-04-19T11:34:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/TODO
update TODO
Revision: 89232
Author: hpages
Date: 2014-04-19T10:48:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/NAMESPACE
now that GenomicAlignments::GappedReads() is exported, we can import it
Revision: 89231
Author: hpages
Date: 2014-04-19T10:44:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomicAlignments/man/GappedReads-class.Rd
export GappedReads() constructor
Revision: 89228
Author: hpages
Date: 2014-04-19T10:22:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/extractTranscriptSeqs.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/utils.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/transcriptsBy.R
resync with more stuff moving from IRanges to S4Vectors
Revision: 89223
Author: hpages
Date: 2014-04-19T09:03:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/nearest-methods.R
another internal renaming
Revision: 89222
Author: hpages
Date: 2014-04-19T08:58:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/IntervalTree-utils.R
Modified  /trunk/madman/Rpacks/IRanges/R/nearest-methods.R
internal renaming
Revision: 89221
Author: hpages
Date: 2014-04-19T08:30:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/XVector/DESCRIPTION
Modified  /trunk/madman/Rpacks/XVector/src/vector_copy.c
Modified  /trunk/madman/Rpacks/XVector/src/SharedVector_class.c
resync with more stuff moving from IRanges to S4Vectors
Revision: 89220
Author: hpages
Date: 2014-04-19T08:21:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/subsetting-utils.R
Modified  /trunk/madman/Rpacks/IRanges/R/Rle-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/inter_range_methods.c
Modified  /trunk/madman/Rpacks/IRanges/inst/include/_IRanges_stubs.c
Modified  /trunk/madman/Rpacks/IRanges/R/DataTable-API.R
Modified  /trunk/madman/Rpacks/IRanges/R/Grouping-class.R
Modified  /trunk/madman/Rpacks/IRanges/inst/include/IRanges_interface.h
Modified  /trunk/madman/Rpacks/IRanges/R/tile-methods.R
Modified  /trunk/madman/Rpacks/IRanges/R/CompressedList-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/read.Mask.R
Modified  /trunk/madman/Rpacks/IRanges/src/CompressedIRangesList_class.c
Deleted  /trunk/madman/Rpacks/IRanges/src/SEXP_utils.c
Modified  /trunk/madman/Rpacks/IRanges/R/Hits-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/setops-methods.R
Modified  /trunk/madman/Rpacks/IRanges/src/Ranges_comparison.c
Deleted  /trunk/madman/Rpacks/IRanges/src/int_utils.c
Modified  /trunk/madman/Rpacks/IRanges/R/List-comparison.R
Deleted  /trunk/madman/Rpacks/IRanges/man/str-utils.Rd
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges_class.c
Deleted  /trunk/madman/Rpacks/IRanges/R/eval-utils.R
Modified  /trunk/madman/Rpacks/IRanges/R/IRanges-utils.R
Modified  /trunk/madman/Rpacks/IRanges/R/Ranges-comparison.R
Deleted  /trunk/madman/Rpacks/IRanges/R/int-utils.R
Modified  /trunk/madman/Rpacks/IRanges/R/RangedData-utils.R
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/IRanges/R/RangedData-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/Vector_class.c
Deleted  /trunk/madman/Rpacks/IRanges/src/str_utils.c
Modified  /trunk/madman/Rpacks/IRanges/R/Views-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/nearest-methods.R
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/R/Vector-class.R
Deleted  /trunk/madman/Rpacks/IRanges/R/str-utils.R
Modified  /trunk/madman/Rpacks/IRanges/R/extractList.R
Deleted  /trunk/madman/Rpacks/IRanges/R/compact_bitvector.R
Modified  /trunk/madman/Rpacks/IRanges/R/intra-range-methods.R
Deleted  /trunk/madman/Rpacks/IRanges/src/compact_bitvector.c
Modified  /trunk/madman/Rpacks/IRanges/src/Rle_class.c
Modified  /trunk/madman/Rpacks/IRanges/R/List-class.R
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/Ranges-class.R
move more stuff to S4Vectors
Revision: 89218
Author: hpages
Date: 2014-04-19T03:06:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
minor edits
Revision: 89217
Author: hpages
Date: 2014-04-19T02:59:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
Add SequenceRole field to data frame returned by fetchExtendedChromInfoFromUCSC().
Revision: 89216
Author: hpages
Date: 2014-04-19T00:33:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
minor edit
Revision: 89213
Author: hpages
Date: 2014-04-19T00:21:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
minor edit
Revision: 89212
Author: hpages
Date: 2014-04-19T00:16:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports the sacCer2 genome.
Revision: 89211
Author: m.carlson
Date: 2014-04-19T00:16:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/saveFeatures.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/select-methods.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
defuncts some old deprecated packages.
Revision: 89210
Author: m.carlson
Date: 2014-04-19T00:15:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/OrganismDbi/R/methods-select.R
Modified  /trunk/madman/Rpacks/OrganismDbi/DESCRIPTION
defuncts some old deprecated packages.
Revision: 89209
Author: m.carlson
Date: 2014-04-19T00:15:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationDbi/NEWS
Modified  /trunk/madman/Rpacks/AnnotationDbi/inst/unitTests/test_select.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
defuncts some old deprecated packages.
Revision: 89207
Author: p.haverty
Date: 2014-04-18T23:53:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/inst/unitTests/test_DataFrame.R
Modified  /trunk/madman/Rpacks/genoset/R/DataFrame-methods.R
Version: 1.17.3. Added beginnings of RleDataFrame, including pseudocode for rowMeans.
Revision: 89206
Author: k.hebestreit
Date: 2014-04-18T23:30:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiSeq/man/clusterSites.Rd
Small bug in the manual.

Revision: 89202
Author: hpages
Date: 2014-04-18T23:02:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/Seqinfo-class.R
better eror message
Revision: 89200
Author: hpages
Date: 2014-04-18T22:27:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
Add "circular" field to data frame returned by fetchExtendedChromInfoFromUCSC().
Revision: 89194
Author: hpages
Date: 2014-04-18T21:26:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports the hg18 and mm9 genomes.
Revision: 89193
Author: h.zare
Date: 2014-04-18T20:31:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/Clomial/R/choose.best.R
Modified  /trunk/madman/Rpacks/Clomial/DESCRIPTION
more bug fixes for running in parallel
Revision: 89186
Author: hpages
Date: 2014-04-18T16:48:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggbio/NAMESPACE
Modified  /trunk/madman/Rpacks/ggbio/DESCRIPTION
resync with stuff moving from IRanges to S4Vectors
Revision: 89184
Author: hpages
Date: 2014-04-18T16:35:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_GRangesList-class.R
minor adjustment to unit tests
Revision: 89183
Author: hpages
Date: 2014-04-18T15:56:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GRangesList-class.R
"ranges" method for GRangesList objects should not propagate the inner
metadata columns by default.
Revision: 89181
Author: hpages
Date: 2014-04-18T15:07:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/zlibbioc/DESCRIPTION
version bump
Revision: 89180
Author: hpages
Date: 2014-04-18T15:07:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/zlibbioc/vignettes/UsingZlibbioc.Rnw
correct 'R CMD INSTALL' command on non-Windows platforms
Revision: 89179
Author: hpages
Date: 2014-04-18T15:04:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/gmapR/R/GmapBamReader-class.R
Modified  /trunk/madman/Rpacks/gmapR/NAMESPACE
Modified  /trunk/madman/Rpacks/gmapR/DESCRIPTION
resync with stuff moving from IRanges to S4Vectors
Revision: 89178
Author: m.lawrence
Date: 2014-04-18T12:52:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/LazyList/R/Array-class.R
Modified  /trunk/madman/Rpacks/LazyList/DESCRIPTION
Added  /trunk/madman/Rpacks/LazyList/R/Dimension-class.R
add Dimension; more thoughts on Array

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