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Revision: 126937
Author: e.henrich
Date: 2017-02-24T00:28:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION_BACKUP_1615
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION_BASE_1615
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION_LOCAL_1615
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION_REMOTE_1615
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.gitignore
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn/entries
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Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn/pristine/db/dbfb87b9bac19d82f234f8528462d5be748f19c3.svn-base
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Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn/wc.db
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn/wc.db-journal
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/DESCRIPTION
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/NAMESPACE
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/CreateConnection.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/ImmuneSpace.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/ImmuneSpaceR.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/getDataset.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/getGEMatrix.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/quick_plot.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/utils.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/zzz.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/README.md
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/inst/NEWS
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/inst/extdata/saved_con.rds
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/inst/img/qpHai.png
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/inst/ssl_certs/README.txt
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/inst/ssl_certs/ca-bundle.crt
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/inst/testthat/global_variable.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/inst/testthat/test-framework.R
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man/CreateConnection.Rd
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man/ISpalette.Rd
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Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/Using_RImmuneSpace.Rmd
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/arrays.Rmd
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/getDataset.Rmd
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/img/getDataset-views.png
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/report_SDY144.Rmd
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/report_SDY180.Rmd
Deleted  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/report_SDY269.Rmd
bump edited

From: ehfhcrc <ehenrich@fredhutch.org>
Revision: 126936
Author: e.henrich
Date: 2017-02-24T00:28:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION
Merge branch 'dev' into devel

* dev:
  bump to 1.3.2

From: ehfhcrc <ehenrich@fredhutch.org>
Revision: 126935
Author: e.henrich
Date: 2017-02-23T23:24:59+00:00
Paths:
Added  /trunk/madman/Rpacks/ImmuneSpaceR/.travis.yml
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION
Added  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION_BACKUP_1615
Added  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION_BASE_1615
Added  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION_LOCAL_1615
Added  /trunk/madman/Rpacks/ImmuneSpaceR/DESCRIPTION_REMOTE_1615
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.gitignore
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn/entries
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn/format
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn/pristine
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn/pristine/0b
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/.svn/pristine/0b/0bd1d03a912abb40570412a1ae7bb8963b14cacb.svn-base
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Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/ImmuneSpace.R
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Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/R/getGEMatrix.R
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Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/README.md
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/inst
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Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/inst/testthat/test-framework.R
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man/CreateConnection.Rd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man/ISpalette.Rd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man/ImmuneSpaceConnection-class.Rd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man/ImmuneSpaceR-package.Rd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man/loadConnection.Rd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man/theme_IS.Rd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/man/write_netrc.Rd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/Using_RImmuneSpace.Rmd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/arrays.Rmd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/getDataset.Rmd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/img
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/img/getDataset-views.png
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/report_SDY144.Rmd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/report_SDY180.Rmd
Added  /trunk/madman/Rpacks/ImmuneSpaceR/ImmuneSpaceR/vignettes/report_SDY269.Rmd
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/R/CreateConnection.R
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/R/utils.R
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/README.md
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/man/CreateConnection.Rd
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/man/ISpalette.Rd
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/man/ImmuneSpaceConnection-class.Rd
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/man/ImmuneSpaceR-package.Rd
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/man/loadConnection.Rd
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/man/theme_IS.Rd
Modified  /trunk/madman/Rpacks/ImmuneSpaceR/man/write_netrc.Rd
resolved merge conflicts

From: ehfhcrc <ehenrich@fredhutch.org>
Revision: 126934
Author: m.jiang
Date: 2017-02-23T22:08:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/CytoML/DESCRIPTION
bump
Revision: 126932
Author: t.silva
Date: 2017-02-23T20:04:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/vignettes/index.Rmd
update
Revision: 126931
Author: t.silva
Date: 2017-02-23T19:53:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/vignettes/index.Rmd
update
Revision: 126930
Author: t.creasy
Date: 2017-02-23T19:34:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/DESCRIPTION
Modified  /trunk/madman/Rpacks/BubbleTree/NAMESPACE
Modified  /trunk/madman/Rpacks/BubbleTree/R/BTreePlotter.R
Modified  /trunk/madman/Rpacks/BubbleTree/Rprofile
Removed "rainbow" function as it relies on the rgl packages that causes a warning on headless hosts
Revision: 126928
Author: m.love
Date: 2017-02-23T18:44:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/NEWS
Modified  /trunk/madman/Rpacks/DESeq2/R/RcppExports.R
Modified  /trunk/madman/Rpacks/DESeq2/R/core.R
Added  /trunk/madman/Rpacks/DESeq2/R/fitNbinomGLMs.R
Added  /trunk/madman/Rpacks/DESeq2/R/wrappers.R
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeq.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeq2-package.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqDataSet.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqResults.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqTransform.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/coef.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/collapseReplicates.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/counts.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/design.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/dispersionFunction.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/dispersions.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateBetaPriorVar.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateDispersions.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateDispersionsGeneEst.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateSizeFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateSizeFactorsForMatrix.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/fpkm.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/fpm.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/lfcShrink.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/makeExampleDESeqDataSet.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/nbinomLRT.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/nbinomWaldTest.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/normTransform.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/normalizationFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/normalizeGeneLength.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotCounts.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotDispEsts.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotMA.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotPCA.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotSparsity.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/replaceOutliers.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/results.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/rlog.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/show.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/sizeFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/summary.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/varianceStabilizingTransformation.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/vst.Rd
Modified  /trunk/madman/Rpacks/DESeq2/src/DESeq2.cpp
Modified  /trunk/madman/Rpacks/DESeq2/src/RcppExports.cpp
Modified  /trunk/madman/Rpacks/DESeq2/tests/testthat/test_disp_fit.R
Modified  /trunk/madman/Rpacks/DESeq2/tests/testthat/test_weights.R
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rmd
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2_pdf.Rmd
finishing off weights implementation
Revision: 126927
Author: hpages
Date: 2017-02-23T18:17:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/man/SNPlocs-class.Rd
escape % in %within% in examples
Revision: 126926
Author: l.gatto
Date: 2017-02-23T17:26:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/MSnbase/NAMESPACE
Modified  /trunk/madman/Rpacks/MSnbase/NEWS.md
Modified  /trunk/madman/Rpacks/MSnbase/R/combineFeatures.R
Modified  /trunk/madman/Rpacks/MSnbase/R/functions-MSnSet.R
Modified  /trunk/madman/Rpacks/MSnbase/R/functions-Spectrum.R
Modified  /trunk/madman/Rpacks/MSnbase/R/methods-filters.R
Added  /trunk/madman/Rpacks/MSnbase/man/aggvar.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/combineFeatures.Rd
Added  /trunk/madman/Rpacks/MSnbase/man/nFeatures.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/navMS.Rd
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_MSnSet.R
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_Spectrum.R
Merge branch 'master' into devel

* master:
  don't call nFeatures in combineFeatures
  document nFeatures when combining
  new nFeatures function - close issue 192
  document aggvar in news
  add aggvar man
  add hint about changing breaks on the RHS because of #190
  addapt unit test for bin_Spectrum (see #191)
  remove useless :::
  add NEWS entry for fixed binning
  fix breaks calculation for binning single (closes #191) and multiple (closes #190) spectra
  add aggvar test
  aggvar, ragnars' offspring function will rip your guts and serve them to the gods
  add agg function - currently unexported
  coding style
  new github devel version

From: Laurent <lg390@cam.ac.uk>
Revision: 126925
Author: l.shepherd
Date: 2017-02-23T15:53:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/TODO.md
Update TODO
Revision: 126924
Author: t.silva
Date: 2017-02-23T15:25:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/app/server/elmer.R
 updating vignettes
Revision: 126923
Author: t.silva
Date: 2017-02-23T15:25:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/vignettes/analysis.Rmd
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/vignettes/data.Rmd
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/vignettes/integrative.Rmd
 updating vignettes
Revision: 126922
Author: t.creasy
Date: 2017-02-23T15:08:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/DESCRIPTION
updated maintainers
Revision: 126921
Author: i.nassiri
Date: 2017-02-23T14:32:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/SRGnet/DESCRIPTION
Version revised.
Revision: 126920
Author: i.nassiri
Date: 2017-02-23T14:30:47+00:00
Paths:
Added  /trunk/madman/Rpacks/SRGnet/R/SRGnet.R
Deleted  /trunk/madman/Rpacks/SRGnet/R/SRGnet_function.R
Deleted  /trunk/madman/Rpacks/SRGnet/inst/doc/vignette.Rmd
Deleted  /trunk/madman/Rpacks/SRGnet/inst/doc/vignette.html
Deleted  /trunk/madman/Rpacks/SRGnet/man/SRG.Rd
Extra files were removed.
Revision: 126919
Author: l.shepherd
Date: 2017-02-23T14:10:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocFileCache/vignettes/BiocFileCache.Rmd
Don't run use case
Revision: 126918
Author: l.shepherd
Date: 2017-02-23T14:00:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/TODO.md
Modified  /trunk/madman/Rpacks/BiocFileCache/vignettes/BiocFileCache.Rmd
Add use section in vignette
Revision: 126917
Author: t.silva
Date: 2017-02-23T13:56:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/app/server/elmer.R
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/app/ui/elmer_analysis.R
update
Revision: 126915
Author: t.silva
Date: 2017-02-23T13:00:02+00:00
Paths:
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/include
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/include/after_body.html
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/include/before_body.html
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/include/header.html
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/include/logo.png
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/include/site.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/include/symbol.png
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/flatly.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/Lato.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/LatoBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/LatoItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/NewsCycle.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/NewsCycleBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/OpenSans.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/OpenSansBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/OpenSansBoldItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/OpenSansItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/OpenSansLight.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/OpenSansLightItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/Raleway.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/RalewayBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/Roboto.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/RobotoBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/RobotoLight.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/RobotoMedium.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/SourceSansPro.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/SourceSansProBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/SourceSansProItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/SourceSansProLight.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/css/fonts/Ubuntu.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/fonts
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Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/fonts/glyphicons-halflings-regular.svg
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/fonts/glyphicons-halflings-regular.ttf
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Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/js/bootstrap.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/shim
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/shim/html5shiv.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap/shim/respond.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/bootstrap-theme.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/bootstrap-theme.css.map
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/bootstrap-theme.min.css
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Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/flatly.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts
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Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/LatoItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/NewsCycle.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/NewsCycleBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/OpenSans.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/OpenSansBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/OpenSansBoldItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/OpenSansItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/OpenSansLight.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/OpenSansLightItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/fonts/Raleway.ttf
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Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/readable.min.css
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Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/united.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/css/yeti.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/fonts
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.eot
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.svg
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff2
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/js/bootstrap.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/js/bootstrap.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/js/npm.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/shim
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/shim/html5shiv.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/bootstrap-3.3.5/shim/respond.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/datatables-binding
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/datatables-binding/datatables.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core/css/jquery.dataTables.extra.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core/css/jquery.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core/js/jquery.dataTables.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core-bootstrap
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core-bootstrap/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core-bootstrap/css/dataTables.bootstrap.extra.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core-bootstrap/css/dataTables.bootstrap.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core-bootstrap/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core-bootstrap/js/dataTables.bootstrap.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-core-bootstrap/js/jquery.dataTables.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-autofill
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-autofill/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-autofill/css/autoFill.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-autofill/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-autofill/js/dataTables.autoFill.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-buttons
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-buttons/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-buttons/css/buttons.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-buttons/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-buttons/js/buttons.colVis.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-buttons/js/buttons.flash.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-buttons/js/buttons.html5.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-buttons/js/buttons.print.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-buttons/js/dataTables.buttons.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-colreorder
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-colreorder/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-colreorder/css/colReorder.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-colreorder/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-colreorder/js/dataTables.colReorder.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedcolumns
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedcolumns/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedcolumns/css/fixedColumns.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedcolumns/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedcolumns/js/dataTables.fixedColumns.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedheader
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedheader/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedheader/css/fixedHeader.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedheader/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-fixedheader/js/dataTables.fixedHeader.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-keytable
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-keytable/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-keytable/css/keyTable.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-keytable/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-keytable/js/dataTables.keyTable.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-responsive
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-responsive/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-responsive/css/responsive.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-responsive/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-responsive/js/dataTables.responsive.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-rowreorder
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-rowreorder/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-rowreorder/css/rowReorder.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-rowreorder/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-rowreorder/js/dataTables.rowReorder.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-scroller
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-scroller/css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-scroller/css/scroller.dataTables.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-scroller/js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-ext-scroller/js/dataTables.scroller.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-plugin-natural
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-plugin-natural/natural.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-plugin-searchhighlight
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-plugin-searchhighlight/dataTables.searchHighlight.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-plugin-searchhighlight/dataTables.searchHighlight.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/dt-plugin-searchhighlight/jquery.highlight.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/htmlwidgets
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/htmlwidgets/htmlwidgets.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jquery
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jquery/jquery.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jquery-1.11.3
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jquery-1.11.3/jquery.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/README
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/images
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/images/ui-icons_444444_256x240.png
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/images/ui-icons_555555_256x240.png
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/images/ui-icons_777620_256x240.png
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/images/ui-icons_777777_256x240.png
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/images/ui-icons_cc0000_256x240.png
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/images/ui-icons_ffffff_256x240.png
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/index.html
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/jquery-ui.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/jquery-ui.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/jquery-ui.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/jquery-ui.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/jquery-ui.structure.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/jquery-ui.structure.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/jquery-ui.theme.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jqueryui-1.11.4/jquery-ui.theme.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jszip
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/jszip/jszip.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/navigation-1.1
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/navigation-1.1/FileSaver.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/navigation-1.1/codefolding.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/navigation-1.1/sourceembed.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/navigation-1.1/tabsets.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/nouislider
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/nouislider/jquery.nouislider.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/nouislider/jquery.nouislider.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/pdfmake
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/pdfmake/pdfmake.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/pdfmake/vfs_fonts.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/selectize
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/selectize/selectize.bootstrap3.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/selectize/selectize.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/tocify-1.9.1
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/tocify-1.9.1/jquery.tocify.css
Added  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/doc/libs/tocify-1.9.1/jquery.tocify.js
adding missing lib
Revision: 126914
Author: l.shepherd
Date: 2017-02-23T12:57:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocFileCache/R/BiocFileCache-class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/TODO.md
Change how web resources are downloaded

  - save to temporary file in cache first
  - if successful move to official location in cache
Revision: 126913
Author: t.silva
Date: 2017-02-23T12:43:53+00:00
Paths:
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/include
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/include/after_body.html
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/include/before_body.html
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/include/header.html
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/include/logo.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/include/site.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/include/symbol.png
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/flatly.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/Lato.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/LatoBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/LatoItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/NewsCycle.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/NewsCycleBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/OpenSans.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/OpenSansBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/OpenSansBoldItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/OpenSansItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/OpenSansLight.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/OpenSansLightItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/Raleway.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/RalewayBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/Roboto.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/RobotoBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/RobotoLight.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/RobotoMedium.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/SourceSansPro.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/SourceSansProBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/SourceSansProItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/SourceSansProLight.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/css/fonts/Ubuntu.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/fonts
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/fonts/glyphicons-halflings-regular.eot
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/fonts/glyphicons-halflings-regular.svg
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/fonts/glyphicons-halflings-regular.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/fonts/glyphicons-halflings-regular.woff
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/fonts/glyphicons-halflings-regular.woff2
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/js
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/js/bootstrap.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/shim
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/shim/html5shiv.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap/shim/respond.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/bootstrap-theme.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/bootstrap-theme.css.map
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/bootstrap-theme.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/bootstrap.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/bootstrap.css.map
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/bootstrap.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/cerulean.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/cosmo.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/flatly.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/fonts
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/fonts/Lato.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/fonts/LatoBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/fonts/LatoItalic.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/fonts/NewsCycle.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/fonts/NewsCycleBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/fonts/OpenSans.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/fonts/OpenSansBold.ttf
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/bootstrap-3.3.5/css/fonts/OpenSansBoldItalic.ttf
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Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/nouislider/jquery.nouislider.min.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/nouislider/jquery.nouislider.min.js
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Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/pdfmake/pdfmake.min.js
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Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/selectize/selectize.min.js
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/tocify-1.9.1
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/tocify-1.9.1/jquery.tocify.css
Added  /trunk/madman/Rpacks/TCGAbiolinks/inst/doc/libs/tocify-1.9.1/jquery.tocify.js
fixing?
Revision: 126912
Author: g.tan
Date: 2017-02-23T12:09:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/CNEr/DESCRIPTION
Modified  /trunk/madman/Rpacks/CNEr/NAMESPACE
Modified  /trunk/madman/Rpacks/CNEr/NEWS
Modified  /trunk/madman/Rpacks/CNEr/R/Axt-methods.R
Modified  /trunk/madman/Rpacks/CNEr/R/WholeGenomeAlignment.R
Modified  /trunk/madman/Rpacks/CNEr/R/ceScan.R
Modified  /trunk/madman/Rpacks/CNEr/man/Axt-class.Rd
Added  /trunk/madman/Rpacks/CNEr/man/makeAxtTracks.Rd
Modified  /trunk/madman/Rpacks/CNEr/tests/testthat/test_Axt.R
version 1.11.7


Update from Bioconductor and remove `fill` in `geom_text`
Revision: 126911
Author: m.love
Date: 2017-02-23T03:18:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/R/core.R
Modified  /trunk/madman/Rpacks/DESeq2/src/DESeq2.cpp
Modified  /trunk/madman/Rpacks/DESeq2/tests/testthat/test_weights.R
tweaks to weights implementation
Revision: 126910
Author: d.low
Date: 2017-02-23T03:09:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/CONFESS/DESCRIPTION
Modified  /trunk/madman/Rpacks/CONFESS/R/internal_fluo_est.R
fixed stat_contour error caused by ggplot

From: Diana Low <lowdiana@gmail.com>
Revision: 126909
Author: l.collado-torres
Date: 2017-02-22T22:06:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/recount/DESCRIPTION
Modified  /trunk/madman/Rpacks/recount/NEWS
Modified  /trunk/madman/Rpacks/recount/R/coverage_matrix.R
Modified  /trunk/madman/Rpacks/recount/tests/testthat/test-data.R
v1.1.18 -- fix a bug in the helper function .read_pheno() which affects coverage_matrix()
Revision: 126907
Author: j.hon
Date: 2017-02-22T22:03:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/DESCRIPTION
Version bump.
Revision: 126906
Author: j.hon
Date: 2017-02-22T22:02:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/vignettes/pqsfinder.Rmd
Histogram plot in ggplot2.
Revision: 126905
Author: j.hon
Date: 2017-02-22T21:56:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/DESCRIPTION
Replace biomaRt by ggplot2 in Suggests.
Revision: 126904
Author: j.hon
Date: 2017-02-22T21:47:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/vignettes/pqsfinder.Rmd
Fixed mistake in the scoring option table.
Revision: 126903
Author: j.hon
Date: 2017-02-22T21:45:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/vignettes/pqsfinder.Rmd
Removed comments prepended to each line of GFF and FASTA file contents.
Revision: 126902
Author: hpages
Date: 2017-02-22T21:36:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/phyloseq/DESCRIPTION
Bump version in order to trigger rebuild of binary package by build system. The
recent renaming of union class vectorORfactor -> vector_OR_factor in S4Vectors
seems to break the phyloseq Windows and Mac binaries that are currently
available in the public repos.
Revision: 126899
Author: l.myint
Date: 2017-02-22T21:16:33+00:00
Paths:
Added  /trunk/madman/Rpacks/yamss/inst/CITATION
Modified  /trunk/madman/Rpacks/yamss/inst/NEWS.Rd
Add paper citation and update news

From: Leslie Myint <leslie.myint@gmail.com>
Revision: 126898
Author: l.myint
Date: 2017-02-22T21:16:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/yamss/DESCRIPTION
Bump version

From: Leslie Myint <leslie.myint@gmail.com>
Revision: 126897
Author: t.creasy
Date: 2017-02-22T21:09:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/BubbleTree/DESCRIPTION
Modified  /trunk/madman/Rpacks/BubbleTree/R/BTreePredictor.R
Updated to new version after bug fix in BTreePredictor
Revision: 126896
Author: s.white
Date: 2017-02-22T20:49:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/KEGGlincs/NAMESPACE
Modified  /trunk/madman/Rpacks/KEGGlincs/R/get_dd_tables.R
modify drug table output

From: vandersm <vandersm@mail.uc.edu>
Revision: 126895
Author: m.love
Date: 2017-02-22T19:39:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/R/core.R
Modified  /trunk/madman/Rpacks/DESeq2/src/DESeq2.cpp
Modified  /trunk/madman/Rpacks/DESeq2/tests/testthat/test_weights.R
more work on weights
Revision: 126894
Author: l.shepherd
Date: 2017-02-22T18:43:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocFileCache/R/BiocFileCache-class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/man/BiocFileCache-class.Rd
Minor documentation fixes
Revision: 126893
Author: l.shepherd
Date: 2017-02-22T18:35:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocFileCache/R/BiocFileCache-class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/TODO.md
Modified  /trunk/madman/Rpacks/BiocFileCache/man/BiocFileCache-class.Rd
Modified  /trunk/madman/Rpacks/BiocFileCache/tests/testthat/test_BiocFileCache_class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/vignettes/BiocFileCache.Rmd
bfcupdate now takes multiple rids

  - does not error when file not found b/c of multi rids
  - arguments given must match length of rids
  - assumes arguments in given order of rids
Revision: 126890
Author: l.shepherd
Date: 2017-02-22T17:21:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocFileCache/R/BiocFileCache-class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/R/sql.R
Modified  /trunk/madman/Rpacks/BiocFileCache/TODO.md
Modified  /trunk/madman/Rpacks/BiocFileCache/man/BiocFileCache-class.Rd
Modified  /trunk/madman/Rpacks/BiocFileCache/tests/testthat/test_BiocFileCache_class.R
bfcneedsupdate now takes multiple rids

  - also defaults to checking entire object
  - filters out non web resources, but gives message
  - ignores invalid rids
  - if not valid web resources returns NULL

Revision: 126880
Author: l.shepherd
Date: 2017-02-22T16:13:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocFileCache/R/BiocFileCache-class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/TODO.md
Modified  /trunk/madman/Rpacks/BiocFileCache/man/BiocFileCache-class.Rd
Modified  /trunk/madman/Rpacks/BiocFileCache/tests/testthat/test_BiocFileCache_class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/vignettes/BiocFileCache.Rmd
Multiple ids as bfcrpath argument

  - named character vector changed to rid instead of "localFile"
Revision: 126879
Author: l.shepherd
Date: 2017-02-22T15:37:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocFileCache/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocFileCache/R/BiocFileCache-class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/R/sql.R
Modified  /trunk/madman/Rpacks/BiocFileCache/TODO.md
Fix dimension displayed
Revision: 126877
Author: l.shepherd
Date: 2017-02-22T14:40:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocFileCache/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocFileCache/R/BiocFileCache-class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/TODO.md
Modified  /trunk/madman/Rpacks/BiocFileCache/man/BiocFileCache-class.Rd
Modified  /trunk/madman/Rpacks/BiocFileCache/tests/testthat/test_BiocFileCache_class.R
Modified  /trunk/madman/Rpacks/BiocFileCache/vignettes/BiocFileCache.Rmd
Updates based on Val suggestion

  - rename bfclist to bfcinfo
  - remove output of bfcinfo from show method
  - add message to show method for further investigation
  - add method specific value sections
  - include invisible return values for update functions
  - add function bfcrpath to just output rpath
  - update documentation, vignette, and tests to match

Revision: 126876
Author: c.page
Date: 2017-02-22T13:59:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/DMRScan/DESCRIPTION
Modified  /trunk/madman/Rpacks/DMRScan/vignettes/DMRScan.Rmd
update
Revision: 126874
Author: a.mayakonda
Date: 2017-02-22T11:37:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/maftools/DESCRIPTION
Modified  /trunk/madman/Rpacks/maftools/NAMESPACE
Modified  /trunk/madman/Rpacks/maftools/R/TrinucleotideMatrix.R
Modified  /trunk/madman/Rpacks/maftools/R/annovarToMaf.R
Modified  /trunk/madman/Rpacks/maftools/R/coOncoplot.R
Modified  /trunk/madman/Rpacks/maftools/R/extractSignatures.R
Modified  /trunk/madman/Rpacks/maftools/R/icgc_to_maf.R
Modified  /trunk/madman/Rpacks/maftools/R/lollipopPlot.R
Modified  /trunk/madman/Rpacks/maftools/R/mathScore.R
Modified  /trunk/madman/Rpacks/maftools/R/oncoplot.R
Modified  /trunk/madman/Rpacks/maftools/R/oncostrip.R
Added  /trunk/madman/Rpacks/maftools/R/pancanAnalysis.R
Modified  /trunk/madman/Rpacks/maftools/R/plotSignatures.R
Modified  /trunk/madman/Rpacks/maftools/R/plotTiTv.R
Added  /trunk/madman/Rpacks/maftools/R/prepareMutSig.R
Modified  /trunk/madman/Rpacks/maftools/R/rainfallPlot.R
Modified  /trunk/madman/Rpacks/maftools/R/read_maf_dt.R
Modified  /trunk/madman/Rpacks/maftools/R/summarizeMaf.R
Modified  /trunk/madman/Rpacks/maftools/R/titv.R
Modified  /trunk/madman/Rpacks/maftools/R/validateMaf.R
Modified  /trunk/madman/Rpacks/maftools/README.md
Modified  /trunk/madman/Rpacks/maftools/inst/NEWS
Added  /trunk/madman/Rpacks/maftools/inst/extdata/LAML_sig_genes.txt.gz
Added  /trunk/madman/Rpacks/maftools/inst/extdata/hugo_to_mutSigSymbol.txt.gz
Added  /trunk/madman/Rpacks/maftools/inst/extdata/pancan.txt.gz
Modified  /trunk/madman/Rpacks/maftools/inst/extdata/prot_len.txt.gz
Modified  /trunk/madman/Rpacks/maftools/inst/extdata/protein_domains.txt.gz
Modified  /trunk/madman/Rpacks/maftools/inst/extdata/signatures.txt
Modified  /trunk/madman/Rpacks/maftools/inst/extdata/tcga_laml.maf.gz
Modified  /trunk/madman/Rpacks/maftools/man/coOncoplot.Rd
Modified  /trunk/madman/Rpacks/maftools/man/extractSignatures.Rd
Modified  /trunk/madman/Rpacks/maftools/man/lollipopPlot.Rd
Modified  /trunk/madman/Rpacks/maftools/man/oncoplot.Rd
Modified  /trunk/madman/Rpacks/maftools/man/oncostrip.Rd
Added  /trunk/madman/Rpacks/maftools/man/pancanComparision.Rd
Modified  /trunk/madman/Rpacks/maftools/man/plotSignatures.Rd
Modified  /trunk/madman/Rpacks/maftools/man/plotTiTv.Rd
Added  /trunk/madman/Rpacks/maftools/man/prepareMutSig.Rd
Modified  /trunk/madman/Rpacks/maftools/vignettes/maftools.Rmd
version bump
Revision: 126873
Author: hpages
Date: 2017-02-22T11:32:34+00:00
Paths:
Deleted  /trunk/madman/Rpacks/HDF5Array/src
delete src/ folder
Revision: 126869
Author: t.silva
Date: 2017-02-22T03:34:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/mutation.Rmd
Modified  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/tcgaBiolinks.Rmd
adding maf hg19
Revision: 126868
Author: t.silva
Date: 2017-02-22T02:41:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/DESCRIPTION
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/vignettes/vignette.Rmd
bugfix
Revision: 126867
Author: m.love
Date: 2017-02-22T02:17:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/R/core.R
Modified  /trunk/madman/Rpacks/DESeq2/tests/testthat/test_weights.R
more weights implementation
Revision: 126864
Author: t.silva
Date: 2017-02-21T20:24:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/DESCRIPTION
Modified  /trunk/madman/Rpacks/TCGAbiolinks/NAMESPACE
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAInternal.R
bug fix
Revision: 126863
Author: t.silva
Date: 2017-02-21T20:06:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/DESCRIPTION
version bump
Revision: 126862
Author: t.silva
Date: 2017-02-21T20:05:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/DESCRIPTION
version bump
Revision: 126860
Author: t.silva
Date: 2017-02-21T20:00:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/app/server/getmolecular.R
Modified  /trunk/madman/Rpacks/TCGAbiolinksGUI/inst/app/ui/getmolecular.R
adding table
Revision: 126859
Author: t.silva
Date: 2017-02-21T19:59:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAInternal.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAQuery.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAvisualize.R
bugfix
Revision: 126854
Author: hpages
Date: 2017-02-21T19:26:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biobase/DESCRIPTION
Bump version in order to trigger rebuild of binary package by build system. The
recent renaming of union class vectorORfactor -> vector_OR_factor in S4Vectors
seems to break the Biobase binary that is currently available in the public
repos.
Revision: 126853
Author: s.white
Date: 2017-02-21T18:16:40+00:00
Paths:
Added  /trunk/madman/Rpacks/KEGGlincs/R/get_dd_tables.R
Added  /trunk/madman/Rpacks/KEGGlincs/man/get_drug_table.Rd
add DD table functions

From: vandersm <vandersm@mail.uc.edu>
Revision: 126851
Author: n.xiao
Date: 2017-02-21T17:20:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/sevenbridges/DESCRIPTION
Modified  /trunk/madman/Rpacks/sevenbridges/NEWS
Modified  /trunk/madman/Rpacks/sevenbridges/NEWS.md
GitHub release v1.5.8
Revision: 126849
Author: n.xiao
Date: 2017-02-21T17:02:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/sevenbridges/DESCRIPTION
Modified  /trunk/madman/Rpacks/sevenbridges/NAMESPACE
Modified  /trunk/madman/Rpacks/sevenbridges/NEWS
Modified  /trunk/madman/Rpacks/sevenbridges/NEWS.md
Modified  /trunk/madman/Rpacks/sevenbridges/R/api-http.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/api-utils.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-all.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-app.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-auth-utils.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-auth.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-billing.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-cwl.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-files.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-filesystem.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-flow.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-folders.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-item.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-meta.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-project.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-task.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-tool.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-upload.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/class-volume.R
Modified  /trunk/madman/Rpacks/sevenbridges/R/sevenbridges-package.R
Modified  /trunk/madman/Rpacks/sevenbridges/README.md
Modified  /trunk/madman/Rpacks/sevenbridges/appveyor.yml
Modified  /trunk/madman/Rpacks/sevenbridges/logo.png
Modified  /trunk/madman/Rpacks/sevenbridges/man/Auth-class.Rd
Modified  /trunk/madman/Rpacks/sevenbridges/vignettes/api.Rmd
Modified  /trunk/madman/Rpacks/sevenbridges/vignettes/cgc-sparql.Rmd
Modified  /trunk/madman/Rpacks/sevenbridges/vignettes/rstudio.Rmd
GitHub release v1.5.7
Revision: 126848
Author: k.dey
Date: 2017-02-21T16:50:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/Logolas/DESCRIPTION
Modified  /trunk/madman/Rpacks/Logolas/README.md
updated README
Revision: 126847
Author: k.dey
Date: 2017-02-21T16:47:46+00:00
Paths:
Added  /trunk/madman/Rpacks/Logolas/.DS_Store
Modified  /trunk/madman/Rpacks/Logolas/DESCRIPTION
Modified  /trunk/madman/Rpacks/Logolas/R/ic_computer.R
Added  /trunk/madman/Rpacks/Logolas/update_remotes.sh
Added  /trunk/madman/Rpacks/Logolas/vignettes/.DS_Store
Added  /trunk/madman/Rpacks/Logolas/vignettes/figure/demofig0.png
Added  /trunk/madman/Rpacks/Logolas/vignettes/figure/demofig1.png
Added  /trunk/madman/Rpacks/Logolas/vignettes/figure/demofig2.png
Added  /trunk/madman/Rpacks/Logolas/vignettes/figure/demofig3.png
Added  /trunk/madman/Rpacks/Logolas/vignettes/figure/demofig4.png
Modified  /trunk/madman/Rpacks/Logolas/vignettes/figure/logolas_use-1.png
Modified  /trunk/madman/Rpacks/Logolas/vignettes/figure/logolas_use_0-1.png
Modified  /trunk/madman/Rpacks/Logolas/vignettes/figure/logolas_use_10-1.png
Modified  /trunk/madman/Rpacks/Logolas/vignettes/figure/logolas_use_12-1.png
Modified  /trunk/madman/Rpacks/Logolas/vignettes/figure/logolas_use_17-1.png
Modified  /trunk/madman/Rpacks/Logolas/vignettes/figure/logolas_use_2-1.png
Modified  /trunk/madman/Rpacks/Logolas/vignettes/figure/logolas_use_7-1.png
Modified  /trunk/madman/Rpacks/Logolas/vignettes/figure/logolas_use_7_0-1.png
Added  /trunk/madman/Rpacks/Logolas/vignettes/figure/test.R
Modified  /trunk/madman/Rpacks/Logolas/vignettes/logolas.Rnw
Modified  /trunk/madman/Rpacks/Logolas/vignettes/logolas.pdf
Added  /trunk/madman/Rpacks/Logolas/vignettes/logolas.synctex.gz
Modified  /trunk/madman/Rpacks/Logolas/vignettes/logolas.tex
Modified  /trunk/madman/Rpacks/Logolas/vignettes/logolas.toc
updated the ic computer function and modified the vignette
Revision: 126846
Author: jmacdon
Date: 2017-02-21T16:42:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/utils.R
Updated genome2org to include several new organisms at UCSC. Also modified dbEasyPrepareQuery to use dbGetQuery rather than dbGetPreparedQuery, which is deprecated.
Revision: 126845
Author: b.mifsud
Date: 2017-02-21T16:15:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOTHiC/DESCRIPTION
Modified  /trunk/madman/Rpacks/GOTHiC/R/GOTHiC.R
fixed fragment mapping in GOTHiChicup function
Revision: 126842
Author: m.smith
Date: 2017-02-21T15:21:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/R/markdownToLatex.R
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/inst/rmarkdown/templates/f1000_article/skeleton/skeleton.Rmd
Minor updates to skeleton.Rmd and changing deprecated pandoc wrapping parameter
Revision: 126838
Author: p.angerer
Date: 2017-02-21T12:23:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/NAMESPACE
Modified  /trunk/madman/Rpacks/destiny/R/diffusionmap.r
Fixed n_samples

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