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Revision: 97028
Author: m.jiang
Date: 2014-11-22T00:39:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 0 commit.

Commit information:


Revision: 97027
Author: m.carlson
Date: 2014-11-22T00:36:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/vignettes/AnnotationDbi.Rnw
Modified  /trunk/madman/Rpacks/AnnotationDbi/vignettes/IntroToAnnotationPackages.Rnw
Updates vignette to no longer use SweaveOpts
Revision: 97024
Author: s.arora
Date: 2014-11-21T23:02:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/R/recommendBiocViews.R
code update

- expt data packages do not have man pages or vignettes
- so modify code to recommend biocViews for packages
which do not have man pages or vignettes
Revision: 97022
Author: sdurinck
Date: 2014-11-21T21:59:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/biomaRt/DESCRIPTION
Modified  /trunk/madman/Rpacks/biomaRt/R/biomaRt.R
update of listEnsembl and useEnsembl functions. changed funcgen to regulation
Revision: 97021
Author: v.obenchain
Date: 2014-11-21T21:10:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpiterate.Rd
edit bpiterate() example re: number of available cores
Revision: 97019
Author: hpages
Date: 2014-11-21T20:05:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/findOverlaps-methods.R
Optimize strategy for preprocessing input of "findOverlaps" method for
GenomicRanges objects when 'algorithm' is "nclist".
Revision: 97018
Author: hpages
Date: 2014-11-21T19:56:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/findOverlaps-methods.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
improve NCLists_find_overlaps_and_combine()
Revision: 97016
Author: stvjc
Date: 2014-11-21T19:12:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLbase/R/storeFuncs.R
Modified  /trunk/madman/Rpacks/gQTLbase/R/storeS4.R
Modified  /trunk/madman/Rpacks/gQTLbase/vignettes/gqtlBase.Rmd
fixes to vignette
Revision: 97014
Author: f.marini
Date: 2014-11-21T18:42:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowcatchR/R/auxiliary.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c6e03c3528992c3112193c270db1c5d709ee8a75

    fixed behaviour in select.Frames when selecting a single frame

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 19:35:28 +0100
Author date: 2014-11-21 19:35:28 +0100
Revision: 97012
Author: f.marini
Date: 2014-11-21T17:10:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowcatchR/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowcatchR/NEWS
Modified  /trunk/madman/Rpacks/flowcatchR/R/preprocessing.R
Modified  /trunk/madman/Rpacks/flowcatchR/README.md
Modified  /trunk/madman/Rpacks/flowcatchR/vignettes/flowcatchR-vignette.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 5 commits.

Commit information:

Commit id: cd7d031049a9413c13bfada96de491d97f31cd78

    added couple of info in readme.md for suggesting developments

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 18:09:52 +0100
Author date: 2014-11-21 18:09:52 +0100

Commit id: 34c43f9ce319000886768d1c2eb221aadfab44ff

    release version 1.0.1

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 18:02:42 +0100
Author date: 2014-11-21 18:02:42 +0100

Commit id: f8ab7fe7f437d7787a722dcb88b2d7b0fe6bee46

    reset version in DESCRIPTION before creating the git svn bridge for bioconductor

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 17:29:13 +0100
Author date: 2014-11-21 17:29:13 +0100

Commit id: 6d0482037cf0056d8428facd89796afe6c12a3b4

    fixed parameters name in the vignettes

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-21 16:13:26 +0100
Author date: 2014-11-21 16:13:26 +0100

Commit id: 328eb3a051a80e205fb8833b027d6bc2c48e3c0a

    placeholder for a todo set in the preprocessing

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-11-18 17:56:50 +0100
Author date: 2014-11-18 17:56:50 +0100
Revision: 97009
Author: l.gatto
Date: 2014-11-21T16:40:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/synapter/DESCRIPTION
Modified  /trunk/madman/Rpacks/synapter/NAMESPACE
Modified  /trunk/madman/Rpacks/synapter/NEWS
Modified  /trunk/madman/Rpacks/synapter/R/gui.R
Modified  /trunk/madman/Rpacks/synapter/README.md
Merge branch 'master' into local-hedgehog
Revision: 97008
Author: f.comoglio
Date: 2014-11-21T16:33:49+00:00
Paths:
Added  /trunk/madman/Rpacks/wavClusteR/DESCRIPTION
Added  /trunk/madman/Rpacks/wavClusteR/NAMESPACE
Added  /trunk/madman/Rpacks/wavClusteR/R/FDRbyRSF.R
Added  /trunk/madman/Rpacks/wavClusteR/R/annotateClusters.R
Added  /trunk/madman/Rpacks/wavClusteR/R/export.R
Added  /trunk/madman/Rpacks/wavClusteR/R/filterClusters.R
Added  /trunk/madman/Rpacks/wavClusteR/R/fitMixtureModel.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getAllSub.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getClusters.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getExpInterval.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getHighConfSub.R
Added  /trunk/madman/Rpacks/wavClusteR/R/getMeta.R
Added  /trunk/madman/Rpacks/wavClusteR/R/plotSizeDistribution.R
Added  /trunk/madman/Rpacks/wavClusteR/R/plotStatistics.R
Added  /trunk/madman/Rpacks/wavClusteR/R/plotSubstitutions.R
Added  /trunk/madman/Rpacks/wavClusteR/R/processMD.R
Added  /trunk/madman/Rpacks/wavClusteR/R/readSortedBam.R
Added  /trunk/madman/Rpacks/wavClusteR/R/wavCWTPeaksCF.R
Added  /trunk/madman/Rpacks/wavClusteR/README.md
Added  /trunk/madman/Rpacks/wavClusteR/inst/CITATION
Added  /trunk/madman/Rpacks/wavClusteR/inst/extdata/example.bam
Added  /trunk/madman/Rpacks/wavClusteR/inst/extdata/example.bam.bai
Added  /trunk/madman/Rpacks/wavClusteR/man/FitMixtureModel.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/annotateClusters.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/estimateFDR.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/exportClusters.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/exportCoverage.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/exportHighConfSub.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/exportSequences.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/filterClusters.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getAllSub.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getClusters.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getExpInterval.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getHighConfSub.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getMetaCoverage.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getMetaGene.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/getMetaTSS.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/model.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/plotSizeDistribution.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/plotStatistics.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/plotSubstitutions.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/readSortedBam.Rd
Added  /trunk/madman/Rpacks/wavClusteR/man/wavClusteR-package.Rd
Added  /trunk/madman/Rpacks/wavClusteR/vignettes/AGO2annotation.pdf
Added  /trunk/madman/Rpacks/wavClusteR/vignettes/AGO2metagene.pdf
Added  /trunk/madman/Rpacks/wavClusteR/vignettes/wavCluster_vignette.Rnw
Added  /trunk/madman/Rpacks/wavClusteR/vignettes/wavCluster_vignette.pdf
Added  /trunk/madman/Rpacks/wavClusteR/wavClusteR_1.99.0.tar.gz
Added  /trunk/madman/Rpacks/wavClusteR/wavClusteR_1.99.1.tar.gz
Added  /trunk/madman/Rpacks/wavClusteR/wavClusteR_1.99.2.tar.gz
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 52ac07b205705bbf15b83c59774e0df0784c95ee

    pushing changed to GitHub, to become effective via GH-SVN bridge.

Committed by: FC
Author Name: FC
Commit date: 2014-11-21 17:33:18 +0100
Author date: 2014-11-21 17:33:18 +0100
Revision: 97006
Author: l.collado-torres
Date: 2014-11-21T16:10:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderPlot/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c370d50a56f886be22e6befbc03f0c318c79277f

    Run build and check separately

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-21 11:10:06 -0500
Author date: 2014-11-21 11:10:06 -0500
Revision: 97005
Author: l.collado-torres
Date: 2014-11-21T16:09:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/.travis.yml
Modified  /trunk/madman/Rpacks/derfinder/R/findRegions.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 16acd6866ded1115c35a611cbd4ac93e48c6cd91

    Run build and check separately

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-21 11:09:11 -0500
Author date: 2014-11-21 11:09:11 -0500
Revision: 97004
Author: l.collado-torres
Date: 2014-11-21T16:08:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/regionReport/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: cdcb65041b66ca6915e6b0018329804637f535db

    Run build and check separately

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-21 11:08:55 -0500
Author date: 2014-11-21 11:08:55 -0500
Revision: 97003
Author: l.collado-torres
Date: 2014-11-21T16:08:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderHelper/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 9f21311b355ed3576956bba8a3b8164dff76e674

    Run build and check separately

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-21 11:08:36 -0500
Author date: 2014-11-21 11:08:36 -0500
Revision: 97002
Author: z.ji
Date: 2014-11-21T13:57:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSCA/inst/shiny/ui.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 13c0367b2254180e046d0c5e5d39dfc97de242a6

    Merge branch 'master' of https://github.com/zji90/GSCA

    Conflicts:
        inst/shiny/ui.R

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-21 08:57:13 -0500
Author date: 2014-11-21 08:57:13 -0500

Commit id: 867060d17e58c4d185763f6a784aa33206119c80

    Changed UI appearances

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-12 14:21:53 -0500
Author date: 2014-11-12 14:21:53 -0500
Revision: 97001
Author: z.ji
Date: 2014-11-21T13:56:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/TSCAN/R/TSCANorder.R
Modified  /trunk/madman/Rpacks/TSCAN/R/exprmclust.R
Modified  /trunk/madman/Rpacks/TSCAN/R/plotmclust.R
Modified  /trunk/madman/Rpacks/TSCAN/inst/shiny/server.R
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/shinyapps
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/shinyapps/zhiji
Added  /trunk/madman/Rpacks/TSCAN/inst/shiny/shinyapps/zhiji/TSCAN.dcf
Modified  /trunk/madman/Rpacks/TSCAN/inst/shiny/ui.R
Modified  /trunk/madman/Rpacks/TSCAN/man/TSCANorder.Rd
Modified  /trunk/madman/Rpacks/TSCAN/man/exprmclust.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 1b2d331b30c6dd414b348496bd7d826a50c600b7

    updating UI

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-21 08:56:49 -0500
Author date: 2014-11-21 08:56:49 -0500

Commit id: 3c5f9502984e7c3b2da5b8e8f3b3d90f2b9900ca

    Revised TSCANorder func to report multiple branches

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-12 14:21:41 -0500
Author date: 2014-11-12 14:21:41 -0500
Revision: 96997
Author: b.knapp
Date: 2014-11-21T07:50:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/NAMESPACE
update pacakge for the use with time series
Revision: 96996
Author: b.knapp
Date: 2014-11-21T07:48:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/NAMESPACE
update pacakge for the use with time series
Revision: 96995
Author: b.knapp
Date: 2014-11-21T07:42:31+00:00
Paths:
Added  /trunk/madman/Rpacks/lpNet/man/generateTimeSeriesNetStates.Rd
Added  /trunk/madman/Rpacks/lpNet/man/getBaseline.Rd
add manuals
Revision: 96993
Author: b.knapp
Date: 2014-11-21T07:39:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/DESCRIPTION
update of lpNet for the use with time series data
Revision: 96992
Author: hpages
Date: 2014-11-21T07:38:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Speed up findOverlaps_GNCList() by taking advantage of latest
IRanges:::NCLists_find_overlaps_and_combine() improvements.
Revision: 96991
Author: hpages
Date: 2014-11-21T07:35:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Add 'select' arg to NCLists_find_overlaps_and_combine(). Hit selection is
entirely done in C.
Revision: 96990
Author: b.knapp
Date: 2014-11-21T07:26:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpNet/DESCRIPTION
update of lpNet for the use with time series data
Revision: 96989
Author: hpages
Date: 2014-11-21T07:14:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
NCLists_find_overlaps_and_combine() now handles the space of the ranges at the
C level. This will be used by GenomicRanges:::findOverlaps_GNCList() to handle
the ignore.strand=FALSE case more efficiently.
Revision: 96988
Author: d.strbenac
Date: 2014-11-21T07:00:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/rankPlot.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/selectionPlot.R
Modified  /trunk/madman/Rpacks/ClassifyR/man/selectionPlot.Rd
Preserve order of levels appearing in results list for rankPlot and selectionPlot.
Revision: 96986
Author: s.xu
Date: 2014-11-21T04:21:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/sapFinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/sapFinder/inst/NEWS
Modified  /trunk/madman/Rpacks/sapFinder/inst/parser4sapFinder.jar
To modify FDR method
Revision: 96985
Author: hpages
Date: 2014-11-21T03:38:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Add more tests for when the input of NCList() and findOverlaps_NCList() is on a
circular space.
Revision: 96984
Author: j.maksimovic
Date: 2014-11-21T02:58:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/missMethyl/DESCRIPTION
Modified  /trunk/madman/Rpacks/missMethyl/vignettes/missMethyl.Rnw
Made change in vignette to deal with minfi bug fix in read.450k.exp. Path should now be correctly constructed when a targets file is included.
Revision: 96983
Author: hpages
Date: 2014-11-21T01:53:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Add tests for when the input of NCList() and findOverlaps_NCList() are ranges
on a circular space.
Revision: 96982
Author: m.carlson
Date: 2014-11-21T00:57:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/vignettes/IntroToAnnotationPackages.Rnw
Mentions mapIds in the vignette
Revision: 96981
Author: m.carlson
Date: 2014-11-21T00:53:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/safe/DESCRIPTION
Modified  /trunk/madman/Rpacks/safe/R/safe.toptable.R
Bug fix to safe.toptable function.

Replaces a call to mget with a call to mapIds
Revision: 96980
Author: m.carlson
Date: 2014-11-20T23:59:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/man/AnnotationDb-class.Rd
Better description of many to one relationships in the manual page.
Revision: 96979
Author: m.carlson
Date: 2014-11-20T23:40:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/inst/unitTests/test_mapIds.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/man/AnnotationDb-class.Rd
Modified  /trunk/madman/Rpacks/AnnotationDbi/man/Bimap-envirAPI.Rd
Documents mapIds function and removes warnings about 1:many mappings
Revision: 96978
Author: r.castelo
Date: 2014-11-20T23:09:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/R/commonFunctions.R
Fixed .cDNAloc()
Revision: 96976
Author: d.strbenac
Date: 2014-11-20T23:00:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/rankPlot.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/selectionPlot.R
Commonality plots now work for a comparison factor with three or more levels.
Revision: 96975
Author: m.carlson
Date: 2014-11-20T22:13:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R
Added  /trunk/madman/Rpacks/AnnotationDbi/inst/unitTests/test_mapIds.R
Adds unit tests and makes behavior for mapIds more consistent.
Revision: 96974
Author: a.lun
Date: 2014-11-20T22:04:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Added Aaron to maintainer list.
Revision: 96973
Author: stvjc
Date: 2014-11-20T21:30:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/parody/DESCRIPTION
testing from rex2
Revision: 96972
Author: stvjc
Date: 2014-11-20T21:10:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/parody/DESCRIPTION
testing svn write priv
Revision: 96971
Author: hpages
Date: 2014-11-20T21:06:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
fix bug in C code behind findOverlaps_NCList(), findOverlaps_NCLists(), and
NCLists_find_overlaps_and_combine()
Revision: 96970
Author: hpages
Date: 2014-11-20T20:44:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
GNCList() and findOverlaps_GNCList() now support circular underlying sequences
Revision: 96969
Author: hpages
Date: 2014-11-20T20:41:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
NCList now support ranges on circular spaces
Revision: 96968
Author: d.tenenbaum
Date: 2014-11-20T20:04:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/PICS/DESCRIPTION
Modified  /trunk/madman/Rpacks/PICS/NAMESPACE
Modified  /trunk/madman/Rpacks/PING/DESCRIPTION
Modified  /trunk/madman/Rpacks/PING/NAMESPACE
NAMESPACE tweaks
Revision: 96967
Author: m.carlson
Date: 2014-11-20T19:15:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
More tidying for code that gets a new DB

Also makes sure that the new DB is valid
Revision: 96965
Author: v.obenchain
Date: 2014-11-20T18:59:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/vignettes/IntroductionToBiocParallel.Rnw
add note to vignette re: module load in template file
Revision: 96964
Author: d.tenenbaum
Date: 2014-11-20T18:55:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
safer transfer of highest id
Revision: 96963
Author: stvjc
Date: 2014-11-20T18:17:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/parody/DESCRIPTION
testing from rex
Revision: 96962
Author: hpages
Date: 2014-11-20T17:28:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
minor simplification
Revision: 96959
Author: hpages
Date: 2014-11-20T11:52:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Another findOverlaps_GNCList() speedup by using new
IRanges:::NCLists_find_overlaps_and_combine() instead of
IRanges:::findOverlaps_NCLists().
Revision: 96958
Author: hpages
Date: 2014-11-20T11:47:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Add NCLists_find_overlaps_and_combine() (non-exported) as the new workhorse
behind GenomicRanges:::findOverlaps_GNCList().
Revision: 96957
Author: hpages
Date: 2014-11-20T09:31:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
tidy up code
Revision: 96955
Author: d.strbenac
Date: 2014-11-20T06:00:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Added  /trunk/madman/Rpacks/ClassifyR/R/rankPlot.R
Deleted  /trunk/madman/Rpacks/ClassifyR/R/rankStabilityPlot.R
Added  /trunk/madman/Rpacks/ClassifyR/R/selectionPlot.R
Added  /trunk/madman/Rpacks/ClassifyR/man/rankPlot.Rd
Deleted  /trunk/madman/Rpacks/ClassifyR/man/rankStabilityPlot.Rd
Added  /trunk/madman/Rpacks/ClassifyR/man/selectionPlot.Rd
rankStabilityPlot changed to rankPlot. Now does both stability and commonality between analyses. More options for plot margins and labels.
Revision: 96954
Author: hpages
Date: 2014-11-20T05:33:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
more work on internal helper NCLists_find_overlaps()
Revision: 96952
Author: l.collado-torres
Date: 2014-11-20T05:10:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/README.md
Modified  /trunk/madman/Rpacks/derfinder/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 6160296c8d23459d5a623bae8a7baa9f60f83a4b

    Update version in citation

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-20 00:10:48 -0500
Author date: 2014-11-20 00:10:48 -0500
Revision: 96951
Author: l.collado-torres
Date: 2014-11-20T05:08:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/R/coverageToExon.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e13416de9257101d21fbc31a1e02023870950b15

    Don't need library() and ::: for coverageToExon() as revealed by R CMD check with and without them

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-20 00:08:38 -0500
Author date: 2014-11-20 00:08:38 -0500
Revision: 96950
Author: l.collado-torres
Date: 2014-11-20T04:50:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/derfinder/R/coverageToExon.R
Modified  /trunk/madman/Rpacks/derfinder/R/fullCoverage.R
Modified  /trunk/madman/Rpacks/derfinder/tests/testthat/test_data.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ca2e02cac0d004e31a0b5e2801f71311d4f0a37f

    v1.1.13 -- fixed coverageToExon() use with multiple cores. Testing if ::: is needed

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-11-19 23:49:52 -0500
Author date: 2014-11-19 23:49:52 -0500
Revision: 96948
Author: v.obenchain
Date: 2014-11-20T02:43:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/R/MulticoreParam-class.R
Modified  /trunk/madman/Rpacks/BiocParallel/inst/unitTests/test_bpiterate.R
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpiterate.Rd
modify bpiterate() man pages example for windows
Revision: 96947
Author: hpages
Date: 2014-11-20T02:41:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicAlignments/R/GAlignmentPairs-class.R
Modified  /trunk/madman/Rpacks/GenomicAlignments/R/GAlignments-class.R
internal utility makeClassinfoRowForCompactPrinting() is now in S4Vectors
Revision: 96946
Author: hpages
Date: 2014-11-20T02:38:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/R/BSgenomeViews-class.R
internal utility makeClassinfoRowForCompactPrinting() is now in S4Vectors
Revision: 96945
Author: hpages
Date: 2014-11-20T02:36:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/utils.R
internal utility makeClassinfoRowForCompactPrinting() is now in S4Vectors
Revision: 96944
Author: n.malani
Date: 2014-11-20T02:36:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/hiAnnotator/DESCRIPTION
Modified  /trunk/madman/Rpacks/hiAnnotator/NEWS
Modified  /trunk/madman/Rpacks/hiAnnotator/R/hiAnnotator.R
added allSubjectCols & overlapType params to getSitesInFeature
Revision: 96943
Author: smyth
Date: 2014-11-20T02:34:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/edgeR/R/plotMDS.DGEList.R
Modified  /trunk/madman/Rpacks/edgeR/man/glmfit.Rd
Modified  /trunk/madman/Rpacks/edgeR/man/plotMDS.DGEList.Rd
plotMDS.DGEList now has argument pch and col argument is removed.
Revision: 96942
Author: v.obenchain
Date: 2014-11-20T02:31:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/mapCoords-methods.R
add .listCumsumShifted() helper back
Revision: 96941
Author: hpages
Date: 2014-11-20T02:29:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/Hits-class-leftovers.R
Remove old and sluggish "show" method for Hits object (there is now a fast
method in S4Vectors that produces output with a more ``modern'' look).
Revision: 96940
Author: hpages
Date: 2014-11-20T02:17:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/R/Hits-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/R/utils.R
Modified  /trunk/madman/Rpacks/S4Vectors/man/Hits-class.Rd
Add ``modern'' "show" method for Hits objects (will become effective when old
and sluggish method defined in IRanges is removed).
Revision: 96939
Author: m.carlson
Date: 2014-11-20T01:21:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
Fixes bug that was remaining disconnected to older DB.
Revision: 96938
Author: m.carlson
Date: 2014-11-20T00:59:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
fixes tricky bug that sometimes looked at wrong online resource for the 'highest id'
Revision: 96937
Author: mtmorgan
Date: 2014-11-20T00:52:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeUCSCChain.R
minor makeUCSC* cleanup
Revision: 96935
Author: j.zhu
Date: 2014-11-20T00:30:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/SRAdb/DESCRIPTION
Bump the version to 1.21.4
Revision: 96933
Author: hpages
Date: 2014-11-19T23:41:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Significant findOverlaps_GNCList() speedup by taking advantage of fast
IRanges:::findOverlaps_NCLists().
Revision: 96932
Author: m.carlson
Date: 2014-11-19T23:35:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R
changes arguement names and names of values.
Revision: 96931
Author: h.corradabravo
Date: 2014-11-19T23:17:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizData-class.R
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizWigData-class.R
Modified  /trunk/madman/Rpacks/epivizr/R/register-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b6032e36dc4b2175061e3713232c4e5e5e294313

    fix 'useOffset' error

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-11-19 18:17:09 -0500
Author date: 2014-11-19 18:17:09 -0500
Revision: 96930
Author: m.carlson
Date: 2014-11-19T23:13:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R
bug fix for new function mapIds
Revision: 96929
Author: hpages
Date: 2014-11-19T23:12:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
address a couple of small mistakes in findOverlaps_NCLists()
Revision: 96928
Author: h.redestig
Date: 2014-11-19T23:10:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/pcaMethods/.gitignore
Modified  /trunk/madman/Rpacks/pcaMethods/DESCRIPTION
Deleted  /trunk/madman/Rpacks/pcaMethods/LICENSE
Modified  /trunk/madman/Rpacks/pcaMethods/NAMESPACE
Modified  /trunk/madman/Rpacks/pcaMethods/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/pcaMethods/R/methods-pcaRes.R
Modified  /trunk/madman/Rpacks/pcaMethods/R/nipalsPca.R
Modified  /trunk/madman/Rpacks/pcaMethods/R/pcaMethods-package.R
Modified  /trunk/madman/Rpacks/pcaMethods/R/robustPca.R
Modified  /trunk/madman/Rpacks/pcaMethods/R/vector2matrices.R
Modified  /trunk/madman/Rpacks/pcaMethods/man/BPCA_dostep.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/BPCA_initmodel.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/DModX-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/DModX.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/Q2.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/R2VX-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/R2VX.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/R2cum-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/R2cum.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/RnipalsPca.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/asExprSet.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/biplot-methods.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/biplot.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/biplot.pcaRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/bpca.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/center-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/center.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/centered-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/centered.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/checkData.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/completeObs-nniRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/completeObs.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/cvseg.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/cvstat-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/cvstat.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/deletediagonals.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/derrorHierarchic.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/dim.pcaRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/errorHierarchic.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/fitted-methods.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/fitted.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/fitted.pcaRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/forkNlpcaNet.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/getHierarchicIdx.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/helix.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/kEstimate.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/kEstimateFast.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/leverage-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/leverage.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/lineSearch.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/linr.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/listPcaMethods.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/llsImpute.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/loadings-ANY-method.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/loadings-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/loadings.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/loadings.pcaRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/metaboliteData.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/metaboliteDataComplete.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/method-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/method.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/nObs-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/nObs.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/nP-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/nP.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/nPcs-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/nPcs.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/nVar-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/nVar.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/nipalsPca.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/nlpca.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/nmissing-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/nmissing.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/nni.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/nniRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/optiAlgCgd.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/orth.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/pca.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/pcaMethods-deprecated.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/pcaMethods.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/pcaNet.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/pcaRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/plot.pcaRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/plotPcs.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/ppca.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/predict-methods.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/predict.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/predict.pcaRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/prep.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/print.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/rediduals-methods.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/repmat.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/resid.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/residuals.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/residuals.pcaRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/robustPca.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/robustSvd.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/sDev-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/sDev.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/scaled-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/scaled.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/scl-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/scl.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/scores-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/scores.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/scores.pcaRes.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/show-methods.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/show.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/showNniRes.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/showPcaRes.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/simpleEllipse.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/slplot-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/slplot.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/sortFeatures.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/summary.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/svdImpute.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/svdPca.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/tempFixNas.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/vector2matrices-matrix-method.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/vector2matrices-nlpcaNet-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/vector2matrices.Rd
Added  /trunk/madman/Rpacks/pcaMethods/man/wasna-pcaRes-method.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/man/wasna.Rd
Modified  /trunk/madman/Rpacks/pcaMethods/man/weightsAccount.Rd
Deleted  /trunk/madman/Rpacks/pcaMethods/src/Makevars
Deleted  /trunk/madman/Rpacks/pcaMethods/src/Makevars.win
Added  /trunk/madman/Rpacks/pcaMethods/src/RcppExports.cpp
Modified  /trunk/madman/Rpacks/pcaMethods/src/nipals.cpp
Commit made by the Bioconductor Git-SVN bridge.
Consists of 4 commits.

Commit information:

Commit id: 08b7fc9456072ec456fa2dd1c02cc52443d4423c

    continued cleanup

Committed by: Henning Redestig
Author Name: Henning Redestig
Commit date: 2014-11-20 00:06:27 +0100
Author date: 2014-11-20 00:06:27 +0100

Commit id: b59e61f4c08517259050bfb6c55125d3940bdbc4

    Merge branch 'master' of https://github.com/hredestig/pcaMethods

    Conflicts:
        DESCRIPTION

Committed by: Henning Redestig
Author Name: Henning Redestig
Commit date: 2014-11-17 22:11:59 +0100
Author date: 2014-11-17 22:11:59 +0100

Commit id: fdd14fbf6f8047ebc2dc295bb2614e56a8569d91

    squash! cleanup action

Committed by: Henning Redestig
Author Name: Henning Redestig
Commit date: 2014-11-17 22:09:25 +0100
Author date: 2014-11-17 22:09:25 +0100

Commit id: d29a57cde2c8d1bf6efcd1c5404033f0c597a155

    cleanup action

    - stop using Makevars scripts as new Rcpp does not need them
    - get rid of R cmd check warnings

Committed by: Henning Redestig
Author Name: Henning Redestig
Commit date: 2014-11-17 21:47:24 +0100
Author date: 2014-11-17 21:46:13 +0100

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