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Revision: 92713
Author: g.imholte
Date: 2014-07-22T19:20:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/iBMQ/DESCRIPTION
bump minor version
Revision: 92712
Author: g.imholte
Date: 2014-07-22T19:15:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/iBMQ/src/main_parallel_sparse_constC.c
fix omp.h inclusion and parallelism
Revision: 92708
Author: hpages
Date: 2014-07-22T18:01:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
minor code simplification
Revision: 92707
Author: j.gadin
Date: 2014-07-22T17:04:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/initialize-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/ASEset-accessors.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/locationplot-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 4 commits.

Commit information:

Commit id: 495c548f1ca4a4e164741d5634b0f4687191d520
Commit message: added new method glocationplot, it works but may be in need of some checks
Committed by: Jesper Gådin
Author Name: Jesper Gådin
Commit date: 2014-07-22 19:02:26 +0200
Author date: 2014-07-22 19:02:26 +0200

Commit id: 7cab8ab9214c717a31dcf7c7266bf143edc72f36
Commit message: removed del column from countLists
Committed by: Jesper Gådin
Author Name: Jesper Gådin
Commit date: 2014-07-21 13:45:44 +0200
Author date: 2014-07-21 13:45:44 +0200

Commit id: c60929b76cff1924c7dca6891e951f86b776c76f
Commit message: new function arank that returns the order of total counts among all samples for each allele
Committed by: Jesper Gådin
Author Name: Jesper Gådin
Commit date: 2014-07-21 10:41:35 +0200
Author date: 2014-07-21 10:41:35 +0200

Commit id: 5837b28cd1b6d0389392f6aa46449a13d419de7f
Commit message: NaN as default when counts are missing in fraction function
Committed by: Jesper Gådin
Author Name: Jesper Gådin
Commit date: 2014-07-21 10:15:17 +0200
Author date: 2014-07-21 10:15:17 +0200

Revision: 92706
Author: d.gatti
Date: 2014-07-22T17:02:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/man/assoc.plot.Rd
Modified  /trunk/madman/Rpacks/DOQTL/R/assoc.map.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 392154a959f3b0172581a16440fbee147383815b
Commit message: Fixed highlight in assoc.plot().
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-07-22 13:01:56 -0400
Author date: 2014-07-22 13:01:56 -0400

Revision: 92704
Author: l.gatto
Date: 2014-07-22T13:47:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/Pbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/Pbase/vignettes/mapping.Rmd
Modified  /trunk/madman/Rpacks/Pbase/vignettes/mapping.html
Modified  /trunk/madman/Rpacks/Pbase/vignettes/Pbase-data.Rmd
Modified  /trunk/madman/Rpacks/Pbase/NEWS
Modified  /trunk/madman/Rpacks/Pbase/vignettes/mapping.md
Merge branch 'master' into remotes/hedgehog
Revision: 92703
Author: g.tan
Date: 2014-07-22T11:03:13+00:00
Paths:
Added  /trunk/madman/Rpacks/CNEr/R/DB.R
Modified  /trunk/madman/Rpacks/CNEr/NAMESPACE
Modified  /trunk/madman/Rpacks/CNEr/DESCRIPTION
Added  /trunk/madman/Rpacks/CNEr/man/queryCNEData.Rd
add queryCNEData
Revision: 92702
Author: l.gatto
Date: 2014-07-22T10:27:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRoloc/R/plotting.R
Modified  /trunk/madman/Rpacks/pRoloc/man/highlightOnPlot.Rd
Modified  /trunk/madman/Rpacks/pRoloc/DESCRIPTION
Modified  /trunk/madman/Rpacks/pRoloc/NEWS
Merge branch 'master' into remotes/hedgehog
Revision: 92701
Author: hpages
Date: 2014-07-22T04:45:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
a couple of minor cosmetic changes
Revision: 92700
Author: hpages
Date: 2014-07-22T04:29:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Represent NCList object as an ordinary integer vector. This makes it even more
compact in memory and serializable.
Revision: 92699
Author: k.hebestreit
Date: 2014-07-22T03:35:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiSeq/R/summarizeRegions.R
emoved a warning caused by not using the full name of a data.frame columns in summerizeRegions().

Revision: 92698
Author: likun.wang
Date: 2014-07-22T03:22:17+00:00
Paths:
Deleted  /trunk/madman/Rpacks/cisPath/R/addProteinNames.R
function improvement
Revision: 92697
Author: likun.wang
Date: 2014-07-22T03:19:25+00:00
Paths:
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/cisPath.js
Modified  /trunk/madman/Rpacks/cisPath/R/networkView.R
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/images/ui-bg_glass_75_dadada_1x400.png
Modified  /trunk/madman/Rpacks/cisPath/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/cisPath/NAMESPACE
Deleted  /trunk/madman/Rpacks/cisPath/inst/extdata/name2prot.txt
Deleted  /trunk/madman/Rpacks/cisPath/man/addProteinNames.rd
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/jquery-ui.css
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/cisPath.css
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/images/cisPath.png
Modified  /trunk/madman/Rpacks/cisPath/R/getResults.R
Modified  /trunk/madman/Rpacks/cisPath/src/cisPath.cpp
Deleted  /trunk/madman/Rpacks/cisPath/inst/extdata/network.html
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/wait1.gif
Modified  /trunk/madman/Rpacks/cisPath/vignettes/cisPath.Rnw
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/images/ui-bg_flat_75_ffffff_40x100.png
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/images/close.png
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/images/ui-bg_glass_65_ffffff_1x400.png
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/d3.min.js
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/jquery-ui.js
Modified  /trunk/madman/Rpacks/cisPath/inst/extdata/easyEditor.html
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/images
Modified  /trunk/madman/Rpacks/cisPath/DESCRIPTION
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/jquery-1.11.0.js
Modified  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/app.css
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/images/ui-bg_glass_75_e6e6e6_1x400.png
Modified  /trunk/madman/Rpacks/cisPath/inst/NEWS
Modified  /trunk/madman/Rpacks/cisPath/R/cisPath.R
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/cisPathWeb.html
Modified  /trunk/madman/Rpacks/cisPath/man/networkView.rd
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/cisPath.html
Modified  /trunk/madman/Rpacks/cisPath/inst/extdata/graphView.html
Modified  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/app.js
Modified  /trunk/madman/Rpacks/cisPath/R/easyEditor.R
Modified  /trunk/madman/Rpacks/cisPath/man/cisPath.rd
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/images/wait1.gif
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/cisPathWorker.js
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/images/ui-bg_flat_0_aaaaaa_40x100.png
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/jquery.jsonp-2.4.0.min.js
Added  /trunk/madman/Rpacks/cisPath/inst/extdata/D3/cisPathWeb.js
function improvement
Revision: 92689
Author: v.obenchain
Date: 2014-07-21T22:56:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/vignettes/Overview.Rnw
finish vignette AMI section
Revision: 92688
Author: hpages
Date: 2014-07-21T22:38:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
gracefully handle malloc()/realloc() failures
Revision: 92687
Author: l.zhu
Date: 2014-07-21T21:15:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/R/compare2Sequences.R
fixed bugs in compare2Sequences
Revision: 92686
Author: hpages
Date: 2014-07-21T20:53:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
tweak internal C structs to make NCList objects more compact in memory
Revision: 92684
Author: hpages
Date: 2014-07-21T20:23:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
5% speedup to IRanges:::findOverlaps_NCList()
Revision: 92682
Author: j.paulson
Date: 2014-07-21T19:06:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagenomeSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/fitZig.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/fitZig.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/correlationTest.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/correlationTest.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 231a97dea2c05662ce29a094906d6c7e7025aa49
Commit message: Tweaking man pages
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-21 15:06:31 -0400
Author date: 2014-07-21 15:06:31 -0400

Revision: 92680
Author: v.obenchain
Date: 2014-07-21T18:33:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
remove duplicate rows from .spliceSites()
Revision: 92679
Author: v.obenchain
Date: 2014-07-21T18:33:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-locateVariants.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
remove duplicate output rows from .spliceSites()
Revision: 92678
Author: m.jiang
Date: 2014-07-21T18:22:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingSet-Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 123d75cade23dc4a3576c87d6e11e654f1273a4c
Commit message: Merge branch 'trunk'
Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-07-21 11:21:29 -0700
Author date: 2014-07-21 11:21:29 -0700

Commit id: 6e1fb1e00fd59cfa93ae65aba66abb6150ad2a9c
Commit message: make the error message of load_gs more meaningful
Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-07-21 11:21:20 -0700
Author date: 2014-07-21 11:21:20 -0700

Revision: 92677
Author: c.soneson
Date: 2014-07-21T18:13:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/compcodeR/man/voom.limma.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/NOISeq.prenorm.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/DESeq.GLM.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/DESeq.nbinom.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/voom.ttest.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/compData.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/baySeq.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/NBPSeq.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/DSS.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/SAMseq.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/checkDataObject.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/runComparisonGUI.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/compcodeR-package.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/EBSeq.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/check_compData_results.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/checkTableConsistency.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/ttest.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/summarizeSyntheticDataSet.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/vst.limma.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/generateSyntheticData.Rd
Modified  /trunk/madman/Rpacks/compcodeR/R/generateRmdCodeDiffExp.R
Modified  /trunk/madman/Rpacks/compcodeR/man/vst.ttest.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/show-compData-method.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/logcpm.limma.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/check_compData.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/convertListTocompData.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/convertcompDataToList.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/DESeq2.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/compData-class.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/HTSDiff.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/sqrtcpm.limma.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/NEWS
Modified  /trunk/madman/Rpacks/compcodeR/man/generateCodeHTMLs.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/edgeR.exact.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/runComparison.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/listcreateRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/compcodeR/man/edgeR.GLM.createRmd.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/runDiffExp.Rd
Modified  /trunk/madman/Rpacks/compcodeR/man/TCC.createRmd.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e992ceb1a8b0a3b6449d72fc251ed2774d7bd777
Commit message: Added full reference information to the TCC package. Version 1.1.2.
Committed by: Charlotte Soneson
Author Name: Charlotte Soneson
Commit date: 2014-07-21 20:13:05 +0200
Author date: 2014-07-21 20:13:05 +0200

Revision: 92676
Author: m.jiang
Date: 2014-07-21T17:55:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/COMPASS/man/COMPASS-package.Rd
Modified  /trunk/madman/Rpacks/COMPASS/scratch/digamma_compare.cpp
Modified  /trunk/madman/Rpacks/COMPASS/DESCRIPTION
Modified  /trunk/madman/Rpacks/COMPASS/man/summary.COMPASSContainer.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/merge.COMPASSContainer.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/COMPASSContainer.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/subset.COMPASSContainer.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/UniqueCombinations.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/COMPASSContainer-data.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/SimpleCOMPASS.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/metadata.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/shinyCOMPASS.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/plot.COMPASSResult.Rd
Modified  /trunk/madman/Rpacks/COMPASS/src/RcppExports.cpp
Modified  /trunk/madman/Rpacks/COMPASS/man/GetThresholdedIntensities.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/Combinations.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/categories.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/shinyCOMPASSDeps.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/print.COMPASSResult.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/pheatmap.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/summary.COMPASSResult.Rd
Modified  /trunk/madman/Rpacks/COMPASS/R/GatingSetToCOMPASS.R
Modified  /trunk/madman/Rpacks/COMPASS/man/melt_.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/plot2.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/COMPASSContainerFromGatingSet.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/print.COMPASSContainer.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/markers.Rd
Modified  /trunk/madman/Rpacks/COMPASS/R/plotMeanGamma.R
Modified  /trunk/madman/Rpacks/COMPASS/man/COMPASS.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/COMPASSDescription.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/transpose_list.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/CellCounts.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/COMPASSResult-data.Rd
Modified  /trunk/madman/Rpacks/COMPASS/NAMESPACE
Modified  /trunk/madman/Rpacks/COMPASS/man/TotalCellCounts.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/FunctionalityScore.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/Posterior.Rd
Modified  /trunk/madman/Rpacks/COMPASS/man/COMPASSResult-accessors.Rd
Modified  /trunk/madman/Rpacks/COMPASS/R/COMPASS.R
Modified  /trunk/madman/Rpacks/COMPASS/man/PolyfunctionalityScore.Rd
setting up git-svn bridge
Revision: 92675
Author: r.castelo
Date: 2014-07-21T17:48:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/NAMESPACE
Modified  /trunk/madman/Rpacks/qpgraph/R/AllClass.R
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
Modified  /trunk/madman/Rpacks/qpgraph/R/qpgraph.R
Added  /trunk/madman/Rpacks/qpgraph/R/qpGraph-methods.R
Modified  /trunk/madman/Rpacks/qpgraph/R/AllGeneric.R
Created the class qpGraph and replaced old qpGraph() function by a constructor. Addded deprecation message when old function is used.
Revision: 92674
Author: m.love
Date: 2014-07-21T16:04:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/inst/script/testsuite.Rmd
Modified  /trunk/madman/Rpacks/DESeq2/R/results.R
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
fix replace outlier + addMLE bug
Revision: 92673
Author: g.yu
Date: 2014-07-21T15:50:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE/DESCRIPTION
Modified  /trunk/madman/Rpacks/DOSE/R/gseAnalyzer.R
Modified  /trunk/madman/Rpacks/DOSE/NEWS
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e4289365bcc38a7898c025c9a3d61e8372a0b493
Commit message: return ggplot2 objects in gseaplot <2014-07-21, Mon>
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-07-21 23:50:27 +0800
Author date: 2014-07-21 23:50:27 +0800

Revision: 92672
Author: l.gatto
Date: 2014-07-21T15:09:42+00:00
Paths:
Deleted  /trunk/madman/Rpacks/pRolocGUI/vignettes/pRolocVis.Rmd
rm old vig
Revision: 92670
Author: g.yu
Date: 2014-07-21T11:36:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/NEWS
Modified  /trunk/madman/Rpacks/ChIPseeker/R/tagMatrix.R
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPseeker/R/plotChrCov.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 22de2cc00eca49cced65f2d46db75555fb260c33
Commit message: bug fixed in plotChrCov
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-07-21 19:36:36 +0800
Author date: 2014-07-21 19:36:36 +0800

Revision: 92667
Author: raffaele.calogero
Date: 2014-07-21T04:51:37+00:00
Paths:
Added  /trunk/madman/Rpacks/chimera/man/newfSet.Rd
Fixing some bugs in various help man
Revision: 92666
Author: raffaele.calogero
Date: 2014-07-21T04:51:10+00:00
Paths:
Deleted  /trunk/madman/Rpacks/chimera/inst/etc
Fixing some bugs in various help man
Revision: 92664
Author: hpages
Date: 2014-07-21T03:36:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
tweak memory management strategy
Revision: 92661
Author: g.imholte
Date: 2014-07-21T03:23:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/iBMQ/src/main_parallel_sparse.c
remove extra omp.h include
Revision: 92657
Author: g.imholte
Date: 2014-07-21T02:28:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/iBMQ
update configure file
Revision: 92656
Author: g.imholte
Date: 2014-07-21T02:03:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/iBMQ/configure
replace old configure file
Revision: 92655
Author: g.imholte
Date: 2014-07-21T01:46:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/iBMQ/DESCRIPTION
Change package maintainer to greg imholte
Revision: 92654
Author: hpages
Date: 2014-07-21T01:24:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Optimize NCList code (no more huge slow down on NCList objects with a lot of
nesting).
Revision: 92652
Author: hpages
Date: 2014-07-20T21:50:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
More testing of the new NCList code. Current code is not performing very well
on NCList objects with a lot of nesting (note that duplicate ranges add nesting
levels). Could be a problem with current implementation but could also be an
intrinsic property of the NCList representation.
Revision: 92651
Author: r.romoli
Date: 2014-07-20T20:41:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/flagme/DESCRIPTION
addXCMSPeaks.R and addXCMSPeaks.Rd
Revision: 92650
Author: hpages
Date: 2014-07-20T08:54:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
add "length", "start", "end", "width", and "names" methods for NCList objects
Revision: 92648
Author: d.henderson
Date: 2014-07-20T07:41:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/src/inbreed.cc
Let's see if this works.
Revision: 92643
Author: stvjc
Date: 2014-07-19T12:18:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGBase/vignettes/ggbase.Rnw
Modified  /trunk/madman/Rpacks/GGBase/DESCRIPTION
fix up the vignette and suggest GGtools
Revision: 92642
Author: hpages
Date: 2014-07-19T10:27:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/NCL.c
More playing with Nested Containment List. Initial testing shows it's 3x-6x
faster than IntervalTree and uses about twice less memory (this was with a
subject containing 55 millions simulated short reads covering Human chr1
uniformly).
Revision: 92641
Author: hpages
Date: 2014-07-19T09:14:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/NCL.c
more playing with Nested Containment List
Revision: 92640
Author: smyth
Date: 2014-07-19T09:02:56+00:00
Paths:
Added  /trunk/madman/Rpacks/edgeR/src/init.cpp
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
svn adding init.cpp
Revision: 92639
Author: p.pyl
Date: 2014-07-19T08:51:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/h5vc/R/plotting.R
Modified  /trunk/madman/Rpacks/h5vc/DESCRIPTION
Modified  /trunk/madman/Rpacks/h5vc/man/mismatchPlot.Rd
Modified  /trunk/madman/Rpacks/h5vc/vignettes/h5vc.tour.Rmd
Overhauled mismatchPlot function
Revision: 92638
Author: m.lawrence
Date: 2014-07-19T04:27:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/inst/unitTests/test_VRanges-class.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VRanges-class.R
attempt to fix broken tests
Revision: 92637
Author: hpages
Date: 2014-07-19T01:40:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Added  /trunk/madman/Rpacks/IRanges/src/NCL.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
start playing with Nested Containment List
Revision: 92634
Author: p.shannon
Date: 2014-07-18T22:36:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
row selection now happens, row repainted as light red, not way yet to read off pmid,A,B
Revision: 92633
Author: p.shannon
Date: 2014-07-18T22:02:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
before switching over to the rowSelect DataTable
Revision: 92632
Author: m.love
Date: 2014-07-18T20:59:34+00:00
Paths:
Added  /trunk/madman/Rpacks/DESeq2/inst/script/testsuite.Rmd
Added  /trunk/madman/Rpacks/DESeq2/inst/script
Modified  /trunk/madman/Rpacks/DESeq2/R/results.R
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
minor fix MLE colnames
Revision: 92630
Author: hpages
Date: 2014-07-18T17:29:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-class.R
Make new "granges" method for GenomicRanges objects behave like discussed on the
mailing list, that is:
  - 'use.mcols' arg is supported,
  - metadata columns are not propagated by default,
  - metadata slot never propagates.
Revision: 92629
Author: p.shannon
Date: 2014-07-18T17:29:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
created (emulating interactiveDisplay/R/dataframe.R) a
scriptsAndStyles function, which injects html header (mostly css)
into the document.

i added the nowrap-within-cells css to this, see that it works, thereby establishing that
the other table-row-selection css seems to work
Revision: 92627
Author: p.shannon
Date: 2014-07-18T16:59:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
4 tabs now, with spiked-in pmid, geneIDs for A and B, in addition to main results tab
Revision: 92626
Author: hpages
Date: 2014-07-18T16:56:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/SplicingGraphs/R/utils.R
Modified  /trunk/madman/Rpacks/SplicingGraphs/DESCRIPTION
Modified  /trunk/madman/Rpacks/SplicingGraphs/inst/scripts/TSPC-utils.R
fix bug in internal utility commonStrand.RleList()
Revision: 92625
Author: m.lawrence
Date: 2014-07-18T16:18:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/IRanges/R/List-class.R
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
add pc() function for parallel c() of list-like objects; like
GenomicAlignments:::.pcombine but seems a bit faster for our use cases
Revision: 92624
Author: p.shannon
Date: 2014-07-18T15:39:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
very simple use of two tabs
Revision: 92623
Author: p.shannon
Date: 2014-07-18T15:28:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
added css to uiWidgets to prevent wrapping of lines in the DataTable
Revision: 92622
Author: d.gatti
Date: 2014-07-18T15:14:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/R/assoc.map.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 6855a1989c272b4bd5bf9092b2e28bda41bf8969
Commit message: Fixed assoc.plot() bug in which xlim was not handled correctly
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-07-18 11:14:23 -0400
Author date: 2014-07-18 11:14:23 -0400

Revision: 92621
Author: t.morris
Date: 2014-07-18T14:00:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.lasso.R
Modified  /trunk/madman/Rpacks/ChAMP/man/ChAMP-package.Rd
Added  /trunk/madman/Rpacks/ChAMP/inst/doc/ChAMP.pdf
Modified  /trunk/madman/Rpacks/ChAMP/DESCRIPTION
Fixed bug in champ.lasso.
Revision: 92620
Author: t.morris
Date: 2014-07-18T12:34:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChAMP/vignettes/ChAMP.Rnw
Modified  /trunk/madman/Rpacks/ChAMP/vignettes/450k.bib
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.load.R
Modified  /trunk/madman/Rpacks/ChAMP/man/ChAMP-package.Rd
Modified  /trunk/madman/Rpacks/ChAMP/DESCRIPTION
Fixed bug in champ.load and made some updates to vignette.
Revision: 92619
Author: c.isella
Date: 2014-07-18T11:21:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/Mulcom/src/mulLibs.cc
Modified  /trunk/madman/Rpacks/Mulcom/DESCRIPTION
Update to 3.0
Revision: 92617
Author: yang.cao
Date: 2014-07-18T05:48:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/mmnet/vignettes/mmnet.Rnw
add code of installing release version
Revision: 92616
Author: yang.cao
Date: 2014-07-18T05:34:08+00:00
Paths:
Deleted  /trunk/madman/Rpacks/mmnet/R/.Rhistory
Modified  /trunk/madman/Rpacks/mmnet/DESCRIPTION
samll change of vignette

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