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Revision: 108208
Author: x.zheng
Date: 2015-09-05T00:07:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqVarTools/R/setVariantID.R
Modified  /trunk/madman/Rpacks/SeqVarTools/inst/unitTests/test_alternateAlleleDetection.R
Modified  /trunk/madman/Rpacks/SeqVarTools/inst/unitTests/test_duplicateDiscordance.R
call seqClose instead of closefn.gds
Revision: 108207
Author: m.conomos
Date: 2015-09-04T23:23:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/GENESIS/DESCRIPTION
Modified  /trunk/madman/Rpacks/GENESIS/NAMESPACE
Added  /trunk/madman/Rpacks/GENESIS/R/getBlocks.R
Added  /trunk/madman/Rpacks/GENESIS/R/getScanIndex.R
Added  /trunk/madman/Rpacks/GENESIS/R/getSnpIndex.R
Modified  /trunk/madman/Rpacks/GENESIS/R/pcair.R
Modified  /trunk/madman/Rpacks/GENESIS/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/GENESIS/man/pcair.Rd
Changed some default values.  Added helper functions to get SNP and scan index and blocks.
Revision: 108205
Author: v.obenchain
Date: 2015-09-04T21:20:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/R/bpvec-methods.R
Modified  /trunk/madman/Rpacks/BiocParallel/inst/unitTests/test_bpvec.R
fix bug in bpvec() related to splitting X
Revision: 108204
Author: w.luo
Date: 2015-09-04T21:14:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/pathview/DESCRIPTION
Modified  /trunk/madman/Rpacks/pathview/NAMESPACE
new version 1.9.1
Revision: 108202
Author: d.tenenbaum
Date: 2015-09-04T20:58:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/R/repository.R
make sure PackageStatus field ends up in VIEWS file
bump version
Revision: 108201
Author: x.zheng
Date: 2015-09-04T20:36:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqArray/NAMESPACE
Modified  /trunk/madman/Rpacks/SeqArray/R/Conversion.R
Modified  /trunk/madman/Rpacks/SeqArray/R/Utilities.R
Modified  /trunk/madman/Rpacks/SeqArray/README.md
Modified  /trunk/madman/Rpacks/SeqArray/man/seqParallelSetup.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 63be5607163bf7a335dba1893782745a84cd621c

    export `.Last.lib()`

Revision: 108200
Author: v.obenchain
Date: 2015-09-04T20:26:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/vignettes/GenomicFiles.Rnw
use library instead of loadNamespace for worker function
Revision: 108199
Author: hpages
Date: 2015-09-04T20:14:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/coordinate-mapping-methods.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/unitTests/test_coordinate-mapping-methods.R
a couple of leftovers from the ellipisis cleanup
Revision: 108198
Author: hpages
Date: 2015-09-04T19:44:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGFF.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
makeTxDbFromGFF() now loads only the columns and tags it needs from the GFF
file.
Revision: 108197
Author: hpages
Date: 2015-09-04T19:37:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/coordinate-mapping-methods.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/man/coordinate-mapping-methods.Rd
Fix codoc mismatch for pmapFromTranscripts,Ranges,GRangesList method.
Remove uneeded ellipisis from the argument list of various coordinate mapping
methods.
Revision: 108196
Author: x.zhenyu
Date: 2015-09-04T19:02:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/tilingArray/DESCRIPTION
Updated the outdated email address
Revision: 108195
Author: d.tenenbaum
Date: 2015-09-04T18:52:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/webAccessFunctions.R
fix suggested by Martin for issue related to ftp URLs that was
breaking build in windows
Revision: 108194
Author: hpages
Date: 2015-09-04T18:49:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
... and reset 'z' to 0
Revision: 108192
Author: d.tenenbaum
Date: 2015-09-04T18:19:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
bump version, make 'y' odd for devel
Revision: 108191
Author: m.lawrence
Date: 2015-09-04T18:13:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/unitTests/test_coordinate-mapping-methods.R
fix unit tests for changes to recycling contract in pmap* functions
Revision: 108190
Author: hpages
Date: 2015-09-04T17:49:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
bump version
Revision: 108189
Author: hpages
Date: 2015-09-04T17:48:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
update Title
Revision: 108185
Author: d.tenenbaum
Date: 2015-09-04T17:24:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
bump version
Revision: 108184
Author: p.stempor
Date: 2015-09-04T17:21:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/.gitignore
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/global.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/server.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui.R
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/bootstrap.min.js
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/fav.ico
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/help.html
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_01.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_01.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_02.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_03.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_04.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_05.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_06.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_07.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_08.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_09.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_10.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_11.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_12.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/03_01.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/03_01b.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/03_02.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/03_03.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/03_04.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/05_01.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/05_02.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/05_03.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/05_04.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/06/06_01.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/06/06_02.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/06/06_03.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/06/06_04.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_01.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_02.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_03.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_04.png
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_05.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_05_06.png
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/07_06.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_01.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_02.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_03.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_04.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/08_05.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/09_01.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/09_02.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/09_03.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/09_04.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/10_00.png
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/10_01.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/11_01.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/fav.ico
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/ico.png
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Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/img/icos.png
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/index_files
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/bootstrap.min.css
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/fonts
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/fonts/Ubuntu.ttf
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Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts
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Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/index_files/jquery-1.11.0
Added  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/index_files/jquery-1.11.0/jquery.min.js
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/jquery-ui.min.js
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Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/prettify.min.js
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Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/LICENSE
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/README.md
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Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/simplex.min.css
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/slate.min.css
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/spacelab.min.css
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/spruce.min.css
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/superhero.min.css
Deleted  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/help/themes/united.min.css
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/main.js
Merge branch 'master' into devel

* master:
  bump to new devel version
  help update
  Installing/removing genomes bring immediate effect in GUI
  Improved help pages

From: przemol <pstempor@gmail.com>
Revision: 108172
Author: r.stojnic
Date: 2015-09-04T15:34:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/PWMEnrich/R/pwm.R
Remove defunct function
Revision: 108170
Author: b.mifsud
Date: 2015-09-04T15:17:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOTHiC/R/GOTHiC.R
fixed cisBinNumber calculation
Revision: 108169
Author: r.stojnic
Date: 2015-09-04T15:16:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/PWMEnrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/PWMEnrich/R/pwm.R
Modified  /trunk/madman/Rpacks/PWMEnrich/inst/NEWS
Modified  /trunk/madman/Rpacks/PWMEnrich/vignettes/PWMEnrich.Rnw
Add P-value calculation for human sequences
Revision: 108168
Author: t.girke
Date: 2015-09-04T14:37:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/systemPipeR/README
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 429ae61cc1245523f566cf6d287a0f100a2c55c4

    vignette updates

Revision: 108167
Author: t.girke
Date: 2015-09-04T14:37:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeChIPseq.Rnw
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeRIBOseq.Rnw
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeRIBOseq.pdf
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeRNAseq.Rnw
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeRNAseq.pdf
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeVARseq.Rnw
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 82aeba97d513f655b32bcac13a540c2cb7197b32

    some edits

Revision: 108166
Author: m.hummel
Date: 2015-09-04T14:29:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/TEQC/NEWS
updated NEWS file
Revision: 108165
Author: a.oles
Date: 2015-09-04T14:28:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
Modified  /trunk/madman/Rpacks/EBImage/NAMESPACE
Modified  /trunk/madman/Rpacks/EBImage/R/Image.R
Modified  /trunk/madman/Rpacks/EBImage/R/computeFeatures.R
Modified  /trunk/madman/Rpacks/EBImage/R/drawCircle.R
Modified  /trunk/madman/Rpacks/EBImage/R/floodFill.R
Modified  /trunk/madman/Rpacks/EBImage/man/combine.Rd
Modified  /trunk/madman/Rpacks/EBImage/man/computeFeatures.Rd
Modified  /trunk/madman/Rpacks/EBImage/src/EBImage.c
Modified  /trunk/madman/Rpacks/EBImage/src/floodFill.cpp
Modified  /trunk/madman/Rpacks/EBImage/src/objects.c
Modified  /trunk/madman/Rpacks/EBImage/src/tools.c
Modified  /trunk/madman/Rpacks/EBImage/tests/test.R
Modified  /trunk/madman/Rpacks/EBImage/tests/test.Rout.save
version 4.11.14
  - fix to 'stackObjects' when no objects are present
  - preserve storage.mode in 'fillHull'
  - add methods allowing to combine an image list containing NULL elements
  - faster argument validation in 'floodFill'
  - refactored code of 'drawCircle' and fixed xy offset issue
  - increase test coverage of 'computeFeatures'
Revision: 108164
Author: m.hummel
Date: 2015-09-04T14:22:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/TEQC/DESCRIPTION
Modified  /trunk/madman/Rpacks/TEQC/NEWS
Modified  /trunk/madman/Rpacks/TEQC/R/TEQCreport.R
Modified  /trunk/madman/Rpacks/TEQC/R/chrom.barplot.R
Modified  /trunk/madman/Rpacks/TEQC/man/chrom.barplot.Rd
new parameter to chrom.barplot; bug fix regarding Offset in TEQCreport
Revision: 108162
Author: a.colaprico
Date: 2015-09-04T13:50:09+00:00
Paths:
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/CITATION
Added  /trunk/madman/Rpacks/TCGAbiolinks/man/.Rapp.history
Added  /trunk/madman/Rpacks/TCGAbiolinks/man/TCGAVisualize_volcano.Rd
Added  /trunk/madman/Rpacks/TCGAbiolinks/man/TCGAanalyze_Clustering.Rd
Added  /trunk/madman/Rpacks/TCGAbiolinks/man/TCGAanalyze_DEA_Affy.Rd
Added  /trunk/madman/Rpacks/TCGAbiolinks/man/TCGAprepare_Affy.Rd
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Added  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/elmer2.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/elmer3.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/elmer4.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/figure4cluster.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/figure4surv.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/figure5exp.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/figure5met.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/figure5star.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/tcgaBiolinks.pdf
updates in vignette
Revision: 108161
Author: j.gehring
Date: 2015-09-04T12:29:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/SomaticSignatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/SomaticSignatures/NAMESPACE
Modified  /trunk/madman/Rpacks/SomaticSignatures/R/motif-matrix.R
Modified  /trunk/madman/Rpacks/SomaticSignatures/R/mutation-context.R
Modified  /trunk/madman/Rpacks/SomaticSignatures/R/signature-plots.R
Modified  /trunk/madman/Rpacks/SomaticSignatures/man/mutation-context.Rd
Modified  /trunk/madman/Rpacks/SomaticSignatures/man/number-signatures.Rd
Modified  /trunk/madman/Rpacks/SomaticSignatures/vignettes/SomaticSignatures-vignette.Rhtml
Modified  /trunk/madman/Rpacks/SomaticSignatures/vignettes/SomaticSignatures-vignette.org
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a4b99d5bf2bed790725eca3bac6e8570048c3473

    2.4.8: Bugfixes

    - Full motif matrix even if certain motifs are not represented in the data (patch from Bernd Fischer). Drop import of reshape2::acast with this.
    - Specifiy Lab colorspace for ggplot2 gradients explicitly due to deprecation
    - Stricter check in 'motifMatrix': Only allow DNA bases and SNV substitutions
    - Correct typos in personalized genomes section in vignette
    - Reformatting of vignette due to new orgmode version

Revision: 108158
Author: hpages
Date: 2015-09-04T08:08:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/seqlevels-wrappers.R
fix misuse of dropSeqlevels()
Revision: 108157
Author: ddiez
Date: 2015-09-04T08:01:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/codelink/DESCRIPTION
Version bumped.
Revision: 108156
Author: ddiez
Date: 2015-09-04T07:59:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/codelink/R/CodelinkSet-methods.R
Modified  /trunk/madman/Rpacks/codelink/R/CodelinkSet-tools.R
Modified  /trunk/madman/Rpacks/codelink/R/plot.R
Fixes to MA plot when dealing with data processed with Codelink suite.
Revision: 108154
Author: hpages
Date: 2015-09-04T07:24:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
makeTxDbFromGRanges() and makeTxDbFromGFF() now also import features of type
pseudogenic_transcript and pseudogenic_exon.
Revision: 108153
Author: hpages
Date: 2015-09-04T07:01:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/src/readGFF.c
readGFFPragmas() now removes the trailing LF or CRLF from the pragma lines
Revision: 108152
Author: hpages
Date: 2015-09-04T06:06:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/TxDb-class.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/man/TxDb-class.Rd
make the seqlevels(x) <- seqlevels0(x) idiom work on TxDb objects
Revision: 108149
Author: x.zheng
Date: 2015-09-04T02:05:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqArray/DESCRIPTION
Modified  /trunk/madman/Rpacks/SeqArray/NAMESPACE
Modified  /trunk/madman/Rpacks/SeqArray/NEWS
Modified  /trunk/madman/Rpacks/SeqArray/R/Conversion.R
Modified  /trunk/madman/Rpacks/SeqArray/R/Internal.R
Added  /trunk/madman/Rpacks/SeqArray/man/seqBED2GDS.Rd
Added  /trunk/madman/Rpacks/SeqArray/src/ConvToGDS.cpp
Modified  /trunk/madman/Rpacks/SeqArray/src/SeqArray.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: d98d475ccf800fe825b3b5748f4bf2e7ee78a4eb

    new function seqBED2GDS(): PLINK BED => GDS, close #8

Revision: 108148
Author: ying.hu
Date: 2015-09-04T01:23:35+00:00
Paths:
 /trunk/madman/Rpacks/OmicCircos/vignettes/OmicCircos_vignette.Rnw
updated OmicCircos 1.5.1
Revision: 108147
Author: ying.hu
Date: 2015-09-04T01:22:35+00:00
Paths:
Added  /trunk/madman/Rpacks/OmicCircos/data/TCGA.BC_Her2_cnv_exp.RData
Added TCGA.BC_Her2_cnv_exp.RData
Revision: 108146
Author: ying.hu
Date: 2015-09-04T01:21:48+00:00
Paths:
Deleted  /trunk/madman/Rpacks/OmicCircos/data/TCGA.BC_Her2_cnv_exp.RData
Deleted TCGA.BC_Her2_cnv_exp.RData
Revision: 108145
Author: ying.hu
Date: 2015-09-04T01:19:56+00:00
Paths:
Added  /trunk/madman/Rpacks/OmicCircos/data/TCGA.BC.gene.exp.2k.60.RData
Added TCGA.BC.gene.exp.2k.60.RData
Revision: 108144
Author: ying.hu
Date: 2015-09-04T01:18:57+00:00
Paths:
Deleted  /trunk/madman/Rpacks/OmicCircos/data/TCGA.BC.gene.exp.2k.60.RData
Delete TCGA.BC.gene.exp.2k.60.RData
Revision: 108143
Author: ying.hu
Date: 2015-09-04T01:17:53+00:00
Paths:
Added  /trunk/madman/Rpacks/OmicCircos/data/TCGA.BC.cnv.2k.60.RData
Added TCGA.BC.cnv.2k.60.RData
Revision: 108142
Author: ying.hu
Date: 2015-09-04T01:16:31+00:00
Paths:
Deleted  /trunk/madman/Rpacks/OmicCircos/data/TCGA.BC.cnv.2k.60.RData
Delete TCGA.BC.cnv.2k.60.RData
Revision: 108141
Author: hpages
Date: 2015-09-04T00:32:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/DESCRIPTION
bump version
Revision: 108140
Author: hpages
Date: 2015-09-04T00:29:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/NAMESPACE
Modified  /trunk/madman/Rpacks/rtracklayer/R/gff.R
Modified  /trunk/madman/Rpacks/rtracklayer/R/ranges.R
Modified  /trunk/madman/Rpacks/rtracklayer/R/readGFF.R
Modified  /trunk/madman/Rpacks/rtracklayer/inst/unitTests/test_gff.R
Modified  /trunk/madman/Rpacks/rtracklayer/src/readGFF.c
"import" method for GFFFile objects now uses readGFF()
Revision: 108136
Author: v.obenchain
Date: 2015-09-03T21:30:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_AnnotationHubConstructor.R
Deleted  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_EnsemblImportPreparer-classes.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_ImportPreparer-class.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_recipe.R
unit tests

- remove redundant test_EnsemblImportPreparer-classes.R
- identify tests that take too long; fup w/ Sonali
- NCBIImportPreparer test is broken; working on a solution

Revision: 108135
Author: d.tenenbaum
Date: 2015-09-03T20:59:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/seq2pathway/DESCRIPTION
add
PackageStatus: Deprecated
and bump version
Revision: 108134
Author: z.gu
Date: 2015-09-03T20:42:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/rGREAT/DESCRIPTION
non-sense commit
Revision: 108133
Author: z.gu
Date: 2015-09-03T20:42:17+00:00
Paths:
Deleted  /trunk/madman/Rpacks/rGREAT/.DS_Store
Modified  /trunk/madman/Rpacks/rGREAT/.gitignore
remove DS_Store
Revision: 108131
Author: z.gu
Date: 2015-09-03T20:32:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/ComplexHeatmap/.DS_Store
Added  /trunk/madman/Rpacks/ComplexHeatmap/.gitignore
Modified  /trunk/madman/Rpacks/ComplexHeatmap/DESCRIPTION
Modified  /trunk/madman/Rpacks/ComplexHeatmap/NAMESPACE
Modified  /trunk/madman/Rpacks/ComplexHeatmap/NEWS
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/00_S4_generic_methods.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/AdditiveUnit-class.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/Heatmap-class.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/HeatmapAnnotation-class.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/HeatmapList-class.R
Added  /trunk/madman/Rpacks/ComplexHeatmap/R/HeatmapList-get_order.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/SingleAnnotation-class.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/annotation_fun.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/decorate.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/densityHeatmap.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/global.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/is_abs_unit.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/oncoPrint.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/plotDataFrame.R
Added  /trunk/madman/Rpacks/ComplexHeatmap/R/select.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/utils.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/AdditiveUnit.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/ComplexHeatmap-package.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/Heatmap-class.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/Heatmap.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/HeatmapAnnotation.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/HeatmapList-class.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/SingleAnnotation.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/add.AdditiveUnit.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/columnAnnotation.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/column_anno_barplot.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/column_anno_boxplot.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/column_anno_density.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/column_anno_histogram.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/column_anno_points.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/column_anno_text.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/column_dend-Heatmap-method.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/column_dend-HeatmapList-method.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/column_dend-dispatch.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/column_order-Heatmap-method.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/column_order-HeatmapList-method.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/column_order-dispatch.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_annotation.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_column_dend.rd
Deleted  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_column_hclust.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_column_names.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_column_title.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_dend.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_dimnames.rd
Deleted  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_hclust.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_heatmap_body.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_row_dend.rd
Deleted  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_row_hclust.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_row_names.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_row_title.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/decorate_title.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/densityHeatmap.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/draw-HeatmapList-method.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_dend-Heatmap-method.rd
Deleted  /trunk/madman/Rpacks/ComplexHeatmap/man/draw_hclust-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/get_color_mapping_param_list-HeatmapAnnotation-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/grid.dendrogram.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/ht_global_opt.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/is_abs_unit.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/make_column_cluster-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/make_layout-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/make_row_cluster-Heatmap-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/max_text_height.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/max_text_width.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/oncoPrint.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/plotDataFrame.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/rowAnnotation.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/row_anno_barplot.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/row_anno_boxplot.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/row_anno_density.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/row_anno_histogram.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/row_anno_points.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/row_anno_text.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/row_dend-Heatmap-method.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/row_dend-HeatmapList-method.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/row_dend-dispatch.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/row_order-Heatmap-method.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/row_order-HeatmapList-method.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/row_order-dispatch.rd
Added  /trunk/madman/Rpacks/ComplexHeatmap/man/select.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/show-ColorMapping-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/show-HeatmapAnnotation-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/show-HeatmapList-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/show-SingleAnnotation-method.rd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s1.introduction.Rmd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s2.single_heatmap.Rmd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s3.a_list_of_heatmaps.Rmd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s4.heatmap_annotation.Rmd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s5.legend.Rmd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s6.heatmap_decoration.Rmd
Deleted  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s7.examples.Rmd
Added  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s7.interactive.Rmd
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s8.oncoprint.Rmd
Added  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/s9.examples.Rmd
Added  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/select_region.gif
resolve conflict from master branch
Revision: 108130
Author: v.obenchain
Date: 2015-09-03T20:20:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/vignettes/GenomicFiles.Rnw
tidy vignette examples
Revision: 108129
Author: v.obenchain
Date: 2015-09-03T19:48:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/inst/unitTests/test_BamViews.R
close connections in scanBam,BamViews and countBam,BamViews unit tests
Revision: 108127
Author: t.creasy
Date: 2015-09-03T19:33:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/DESCRIPTION
updated author list
Revision: 108126
Author: v.obenchain
Date: 2015-09-03T19:27:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/src/BamIterator.h
Modified  /trunk/madman/Rpacks/Rsamtools/src/BamRangeIterator.h
clean up old FIXMEs
Revision: 108125
Author: t.creasy
Date: 2015-09-03T19:27:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/DESCRIPTION
updated author list and formatting
Revision: 108124
Author: t.creasy
Date: 2015-09-03T19:23:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/DESCRIPTION
updated bibtex author list
Revision: 108121
Author: j.hester
Date: 2015-09-03T19:08:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/DESCRIPTION
Bump version

From: Jim Hester <james.f.hester@gmail.com>
Revision: 108120
Author: j.hester
Date: 2015-09-03T19:06:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/DESCRIPTION
Modified  /trunk/madman/Rpacks/SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R
Modified  /trunk/madman/Rpacks/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd
Add ellipsis to makeSummarizedExperimentFromExpressionSet
Revision: 108119
Author: t.creasy
Date: 2015-09-03T19:05:54+00:00
Paths:
Deleted  /trunk/madman/Rpacks/BubbleTree/inst/doc/BubbleTree-vignette.html
removed file
Revision: 108118
Author: t.creasy
Date: 2015-09-03T19:04:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/vignettes/BubbleTree-vignette.Rmd
updated vignette
Revision: 108117
Author: t.creasy
Date: 2015-09-03T18:55:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/vignettes/BubbleTree-vignette.Rmd
updated vignette
Revision: 108116
Author: t.creasy
Date: 2015-09-03T18:29:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/vignettes/BubbleTree-vignette.Rmd
updated vignette
Revision: 108115
Author: t.creasy
Date: 2015-09-03T18:21:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/R/BTreePlotter.R
Modified  /trunk/madman/Rpacks/BubbleTree/vignettes/BubbleTree-vignette.Rmd
removed warnings from geom_point
Revision: 108114
Author: t.creasy
Date: 2015-09-03T18:14:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/vignettes/BubbleTree-vignette.Rmd
updated vignette
Revision: 108113
Author: t.creasy
Date: 2015-09-03T18:11:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/R/BTreePlotter.R
Modified  /trunk/madman/Rpacks/BubbleTree/vignettes/BubbleTree-vignette.Rmd
removed warnings from geom_segment; updated vignette
Revision: 108112
Author: t.creasy
Date: 2015-09-03T17:50:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree
not sure why it's making me commit this
Revision: 108111
Author: t.creasy
Date: 2015-09-03T17:45:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/man/drawFeatures.Rd
updated documentation
Revision: 108110
Author: t.creasy
Date: 2015-09-03T17:40:13+00:00
Paths:
Added  /trunk/madman/Rpacks/BubbleTree/inst/doc/BubbleTree-vignette.html
updated html vignette

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