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Revision: 93504
Author: j.gadin
Date: 2014-08-21T08:55:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/ASEset-accessors.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: 4d21ae9acb67c56882ac488ae9f35cd4576fc680
Commit message: bump
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-21 10:54:47 +0200
Author date: 2014-08-21 10:54:47 +0200

Commit id: 060ba8de389cd58dbd1ff1a9f56a505dbb115756
Commit message: one sample in the correct way
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-21 10:49:47 +0200
Author date: 2014-08-21 10:49:47 +0200

Commit id: 848a6271a42c9b376c25ea606c93f058536a9cd1
Commit message: one sample works
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 20:27:14 +0200
Author date: 2014-08-20 20:27:14 +0200

Revision: 93503
Author: l.varemo
Date: 2014-08-21T07:02:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/piano/R/writeFilesForKiwi.R
Modified  /trunk/madman/Rpacks/piano/DESCRIPTION
Fixed bug in writeFilesForKiwi so that duplicate gene-names are now allowed to be used
Revision: 93500
Author: v.obenchain
Date: 2014-08-20T21:36:06+00:00
Paths:
Added  /trunk/madman/Rpacks/BiocParallel/vignettes/IntroductionToBiocParallel.Rnw
Deleted  /trunk/madman/Rpacks/BiocParallel/vignettes/Overview.Rnw
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
update vignette introduction and rename file
Revision: 93498
Author: b.fischer
Date: 2014-08-20T20:37:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/CHANGES
Added  /trunk/madman/Rpacks/rhdf5/src/H5P.h
Added  /trunk/madman/Rpacks/rhdf5/man/H5P.Rd
Modified  /trunk/madman/Rpacks/rhdf5/NAMESPACE
Added  /trunk/madman/Rpacks/rhdf5/R/H5P.R
Modified  /trunk/madman/Rpacks/rhdf5/R/h5checktype.R
Modified  /trunk/madman/Rpacks/rhdf5/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/rhdf5/src/H5constants.c
Modified  /trunk/madman/Rpacks/rhdf5/src/wrap.c
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
Added  /trunk/madman/Rpacks/rhdf5/src/H5P.c
Added support for the HDF5 property list H5P and added low level functions H5Pcreate, H5Pcopy, H5Pget_class, H5Pclose, H5Pclose_class
Revision: 93497
Author: mtmorgan
Date: 2014-08-20T19:29:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/SummarizedExperiment-class.R
missed arg on [rc]bind-method
Revision: 93496
Author: mtmorgan
Date: 2014-08-20T19:26:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/NEWS
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/SummarizedExperiment-class.R
[cr]bind,SummarizedExperiment-methods respect derived classes
Revision: 93495
Author: d.tenenbaum
Date: 2014-08-20T18:36:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/DESCRIPTION
Modified  /trunk/madman/Rpacks/GeneticsPed/NAMESPACE
move gdata to Imports: and import in NAMESPACE
Revision: 93494
Author: h.klein
Date: 2014-08-20T17:33:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/epigenomix/R/normalizeChIP.R
Modified normilzeChIP(x, method="scaleMedianRegion"), so that it works for large samples sizes

Revision: 93493
Author: j.gadin
Date: 2014-08-20T16:50:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Deleted  /trunk/madman/Rpacks/AllelicImbalance/tmp
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/AllGenerics.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 317bc409414ae63db658d4d1d14232ac82d95610
Commit message: a move from depends to imports
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 18:35:26 +0200
Author date: 2014-08-20 18:35:26 +0200

Revision: 93492
Author: k.horan
Date: 2014-08-20T16:11:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChemmineR/inst/CITATION
Modified  /trunk/madman/Rpacks/ChemmineR/R/sim.R
Modified  /trunk/madman/Rpacks/ChemmineR/R/compound_db.R
Modified  /trunk/madman/Rpacks/ChemmineR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 927f4f6a2d1d115a0b9d45cf74f01e1afff83a07
Commit message: fixed bug in selectInBatches, fixed CITATION file
Committed by: khoran
Author Name: khoran
Commit date: 2014-08-20 09:11:01 -0700
Author date: 2014-08-20 09:11:01 -0700

Revision: 93490
Author: m.schroeder
Date: 2014-08-20T13:19:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/survcomp/DESCRIPTION
Modified  /trunk/madman/Rpacks/survcomp/man/km.coxph.plot.Rd
Modified  /trunk/madman/Rpacks/survcomp/R/concordance.index.R
Modified  /trunk/madman/Rpacks/survcomp/R/km.coxph.plot.R
Modified  /trunk/madman/Rpacks/survcomp/man/survcomp-package.Rd
Modified  /trunk/madman/Rpacks/survcomp/vignettes/survcomp.Rnw
Minor bug fixes and new contact details. Version bump to 1.15.1.
Revision: 93489
Author: j.gadin
Date: 2014-08-20T12:47:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-glocationplot.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-lbarplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/initialize-ASEset.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/man/coverageMatrixListFromGAL.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Added  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-Gviz-tracks.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/man/barplot-lattice.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/GvizTrack-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-locationplot.Rd
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: 551c61847b53756e7291f69e6e35cb88498af669
Commit message: and the bump
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 14:47:00 +0200
Author date: 2014-08-20 14:47:00 +0200

Commit id: f6c5e00b7f0fea73fdf4d8da32b85b672f7eaff0
Commit message: R CMD check ok
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 14:45:00 +0200
Author date: 2014-08-20 14:45:00 +0200

Commit id: 7be7d3bea298d3d38274f6b47c4e7268db09fc0c
Commit message: updated docs
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 13:43:43 +0200
Author date: 2014-08-20 13:43:43 +0200

Commit id: c8cfe1005a5f1202d89184fc1562929fbf29c616
Commit message: fixed counts option bug for trellis plots
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-19 16:46:29 +0200
Author date: 2014-08-19 16:46:29 +0200

Revision: 93488
Author: m.schroeder
Date: 2014-08-20T11:42:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/genefu/DESCRIPTION
Updated R dependency >=2.10 for compressed data folder.
Revision: 93487
Author: m.schroeder
Date: 2014-08-20T11:32:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/genefu/R/gene70.R
Modified  /trunk/madman/Rpacks/genefu/vignettes/genefu.Rnw
Added  /trunk/madman/Rpacks/genefu/inst/extdata/filipits2011_sig_endopredict.csv
Modified  /trunk/madman/Rpacks/genefu/R/intrinsic.cluster.predict.R
Modified  /trunk/madman/Rpacks/genefu/man/genefu-package.Rd
Modified  /trunk/madman/Rpacks/genefu/DESCRIPTION
Updated contact details and version number. Fixed minor bugs.
Revision: 93486
Author: a.reyes
Date: 2014-08-20T09:16:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEXSeq/vignettes/DEXSeq.Rnw
Modified  /trunk/madman/Rpacks/DEXSeq/DESCRIPTION
added dispersion estimation changes from DESeq2
Revision: 93484
Author: h.corradabravo
Date: 2014-08-20T05:26:50+00:00
Paths:
Added  /trunk/madman/Rpacks/epivizr/vignettes/Makefile
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 032007b96f0436964bbc73171489cb43a3e1968f
Commit message: style the vignette
Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-08-20 01:16:16 -0400
Author date: 2014-08-20 01:16:16 -0400

Revision: 93482
Author: h.corradabravo
Date: 2014-08-20T03:24:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizDeviceMgr-class.R
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 21cae7eafb586ca090a9acb0b76f8b114f9ec724
Commit message: fix limit on slideshow; regenerate vignette
Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-08-19 23:23:42 -0400
Author date: 2014-08-19 23:23:42 -0400

Revision: 93480
Author: l.zhu
Date: 2014-08-19T22:20:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/tests/runTests.R
disable unit test
Revision: 93479
Author: l.zhu
Date: 2014-08-19T22:19:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/R/offTargetAnalysis.R
Modified  /trunk/madman/Rpacks/CRISPRseek/R/filterOffTarget.R
Modified  /trunk/madman/Rpacks/CRISPRseek/tests/runTests.R
Updated TranscriptDb to TxDb
Revision: 93478
Author: r.castelo
Date: 2014-08-19T22:10:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/NAMESPACE
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Added import method VariantAnnotation::samples() to NAMESPACE.
Revision: 93477
Author: q.sheng
Date: 2014-08-19T20:00:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/DupChecker/DESCRIPTION
Modified  /trunk/madman/Rpacks/DupChecker/vignettes/DupChecker.Rnw
Modified  /trunk/madman/Rpacks/DupChecker/NEWS
Modified  /trunk/madman/Rpacks/DupChecker/R/DupChecker.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: f036faccb2d3134a54ee92d07efe208adbe95ebf
Commit message:
Committed by: shengqh
Author Name: shengqh
Commit date: 2014-08-19 15:00:46 -0500
Author date: 2014-08-19 15:00:46 -0500

Revision: 93476
Author: v.obenchain
Date: 2014-08-19T20:00:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensemblVEP/README
Modified  /trunk/madman/Rpacks/ensemblVEP/DESCRIPTION
mention .profile in README
Revision: 93475
Author: d.tenenbaum
Date: 2014-08-19T18:47:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/DESCRIPTION
Added whitespace at start of biocViews continuation line
Revision: 93473
Author: d.gatti
Date: 2014-08-19T17:59:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/man/sdp.plot.Rd
Modified  /trunk/madman/Rpacks/DOQTL/man/assoc.plot.Rd
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Consists of 1 commit.

Commit information:

Commit id: e9a24b5ed7f4a6c13c17b497a15ba09998d4d3d6
Commit message: Fixed doc errors
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-08-19 13:59:30 -0400
Author date: 2014-08-19 13:59:30 -0400

Revision: 93470
Author: d.gatti
Date: 2014-08-19T17:42:06+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: 1931ae74204786bc6c9c1dbe7f4bec17648262f1
Commit message: Set sdp.plot x-axis to not plot when making an assoc.plot.
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-08-19 13:41:47 -0400
Author date: 2014-08-19 13:41:47 -0400

Revision: 93469
Author: v.obenchain
Date: 2014-08-19T17:03:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpiterate.Rd
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
clarify wording in bpiterate man page examples
Revision: 93468
Author: a.oles
Date: 2014-08-19T14:20:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/R/markdown.R
version 1.3.9
correct rendering of the Html style in R Studio when markdown v1 is used
Revision: 93466
Author: b.fischer
Date: 2014-08-19T09:19:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/man/h5write.Rd
Modified  /trunk/madman/Rpacks/rhdf5/CHANGES
Modified  /trunk/madman/Rpacks/rhdf5/NAMESPACE
Modified  /trunk/madman/Rpacks/rhdf5/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/rhdf5/R/h5readAttributes.R
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
New function h5readAttributes implemented that reads all HDF5 attributes of one object.
Revision: 93465
Author: g.klambauer
Date: 2014-08-19T08:48:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/cn.mops/R/normalizeChromosomes.R
Modified  /trunk/madman/Rpacks/cn.mops/DESCRIPTION
Modified  /trunk/madman/Rpacks/cn.mops/R/makeRobustCNVR.R
Modified  /trunk/madman/Rpacks/cn.mops/man/normalizeChromosomes.Rd
update in Rd files
Revision: 93464
Author: s.arora
Date: 2014-08-18T23:41:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
video update

- add video for GenomeInfoDb
Revision: 93463
Author: d.tenenbaum
Date: 2014-08-18T22:13:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/IPPD/DESCRIPTION
Modified  /trunk/madman/Rpacks/IPPD/R/internals.R
fix data set name
Revision: 93460
Author: b.afsari
Date: 2014-08-18T21:59:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSReg/R/internalFuncs.R
Updating internalFuncs.R. A minor bug was fixed.
Revision: 93459
Author: d.tenenbaum
Date: 2014-08-18T21:48:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/man/TDT.Rd
made geneFlowT example contingent on presence of gdata package.
if this example should always work, gdata should be moved to Depends/Imports.
Revision: 93457
Author: b.afsari
Date: 2014-08-18T20:33:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSReg/NAMESPACE
Modified  /trunk/madman/Rpacks/GSReg/DESCRIPTION
Modified  /trunk/madman/Rpacks/GSReg/vignettes/GSReg.Rnw
removing Sweave.sty
Revision: 93456
Author: b.afsari
Date: 2014-08-18T20:20:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSReg/man/GSReg_GeneSets_VReg..Rd
Replacing VReg by EVA.
Revision: 93455
Author: d.tenenbaum
Date: 2014-08-18T20:19:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/cn.mops/DESCRIPTION
Modified  /trunk/madman/Rpacks/cn.mops/NAMESPACE
Modified  /trunk/madman/Rpacks/cn.mops/R/getReadCountsFromBAM.R
fix imports (seqlengths and sortSeqlevels come from GenomeInfoDb)
Revision: 93454
Author: b.afsari
Date: 2014-08-18T20:11:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSReg/R/exportedFuncs.R
Replacing "VReg" by "EVA."
Revision: 93453
Author: b.afsari
Date: 2014-08-18T20:07:30+00:00
Paths:
Deleted  /trunk/madman/Rpacks/GSReg/vignettes/Sweave.sty
Removing Sweave.sty
Revision: 93452
Author: d.clayton
Date: 2014-08-18T19:51:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/snpStats/src/Makevars.win
Try again to replace indentation in Makevars.win
Revision: 93450
Author: d.tenenbaum
Date: 2014-08-18T19:05:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/DESCRIPTION
add gdata to Suggests since it is in VignetteDepends, bump version
Revision: 93448
Author: d.gatti
Date: 2014-08-18T18:12:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/R/scanone.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b55bddaa242999207b11b3f0b3a6447013a3fc7e
Commit message: Fixed bug in which the sex column was not being found correctly.
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-08-18 14:12:30 -0400
Author date: 2014-08-18 14:12:30 -0400

Revision: 93445
Author: d.gatti
Date: 2014-08-18T16:55:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/R/gene.plot.R
Modified  /trunk/madman/Rpacks/DOQTL/man/sdp.plot.Rd
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.
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Commit information:

Commit id: 503ccfe706c69514a2c4e87271a9b34205bbf58e
Commit message: Added SDP plot to assoc plot.
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-08-18 12:54:21 -0400
Author date: 2014-08-18 12:54:21 -0400

Revision: 93443
Author: a.frazee
Date: 2014-08-18T16:47:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/ballgown/NAMESPACE
Modified  /trunk/madman/Rpacks/ballgown/NEWS
Modified  /trunk/madman/Rpacks/ballgown/DESCRIPTION
Added  /trunk/madman/Rpacks/ballgown/man/exprfilter.Rd
Added  /trunk/madman/Rpacks/ballgown/R/exprfilter.R
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Commit information:

Commit id: 0a8e73bbde56499a583528a023ecc4e59b7265d3
Commit message: version bump + NEWS update
Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2014-08-18 12:47:25 -0400
Author date: 2014-08-18 12:47:25 -0400

Commit id: b6a1f431b080f3065836d9422276a0da7b1f1f76
Commit message: adds exprfilter function
Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2014-08-18 12:46:18 -0400
Author date: 2014-08-18 12:46:18 -0400

Revision: 93442
Author: g.feng
Date: 2014-08-18T16:46:42+00:00
Paths:
Deleted  /trunk/madman/Rpacks/GeneAnswers/R/getREACTOMEPATHTerms.R
remove one function
Revision: 93441
Author: k.horan
Date: 2014-08-18T16:34:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/eiR/DESCRIPTION
Modified  /trunk/madman/Rpacks/eiR/src/f2c.h
Modified  /trunk/madman/Rpacks/eiR/README
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Commit information:

Commit id: 02435debae0f8d833398c5fdd0c7a04810a49452
Commit message: revert -pedantic chagne and added a note about it in README. also fixed CITATIONS again
Committed by: khoran
Author Name: khoran
Commit date: 2014-08-18 09:34:39 -0700
Author date: 2014-08-18 09:34:39 -0700

Revision: 93440
Author: k.horan
Date: 2014-08-18T16:30:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/fmcsR/DESCRIPTION
Modified  /trunk/madman/Rpacks/fmcsR/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b987c5a4201ca72347d12a8c189fe8cce0754c7d
Commit message: added missing library call in CITATIONS file
Committed by: khoran
Author Name: khoran
Commit date: 2014-08-18 09:30:16 -0700
Author date: 2014-08-18 09:30:16 -0700

Revision: 93439
Author: g.feng
Date: 2014-08-18T14:59:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneAnswers/R/zzz.R
Modified  /branches/RELEASE_2_14/madman/Rpacks/GeneAnswers/DESCRIPTION
add new udpates
Revision: 93438
Author: j.ou
Date: 2014-08-18T14:32:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/trackViewer/DESCRIPTION
Modified  /trunk/madman/Rpacks/trackViewer/vignettes/trackViewer.Rnw
update vignettes
Revision: 93436
Author: r.romoli
Date: 2014-08-18T11:13:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/flagme/DESCRIPTION
Modified  /trunk/madman/Rpacks/flagme/R/addXCMSPeaks.R
debug addXCMSPeaks.R
Revision: 93435
Author: smyth
Date: 2014-08-18T09:40:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/man/topSplice.Rd
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
Modified  /trunk/madman/Rpacks/limma/man/diffSplice.Rd
Modified  /trunk/madman/Rpacks/limma/R/diffSplice.R
Modified  /trunk/madman/Rpacks/limma/inst/doc/usersguide.pdf
18 Aug 2014: limma 3.21.13

- Speed improvement for the calculation of Simes adjusted p-values by
  diffSplice().

- argument 'level' for diffSplice() renamed to 'test', with possible
  values "simes", "F" or "t".
Revision: 93434
Author: g.yu
Date: 2014-08-18T09:24:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/R/tagMatrix.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: f657f0afd503feec1af01d3b02a22a1af66f84f3
Commit message: update tagMatrix
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-08-18 17:24:35 +0800
Author date: 2014-08-18 17:24:35 +0800

Revision: 93433
Author: g.yu
Date: 2014-08-18T08:57:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/NAMESPACE
Modified  /trunk/madman/Rpacks/ChIPseeker/NEWS
Modified  /trunk/madman/Rpacks/ChIPseeker/vignettes/ChIPseeker.Rnw
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Deleted  /trunk/madman/Rpacks/ChIPseeker/R/plotChrCov.R
Added  /trunk/madman/Rpacks/ChIPseeker/man/covplot.Rd
Added  /trunk/madman/Rpacks/ChIPseeker/R/covplot.R
Modified  /trunk/madman/Rpacks/ChIPseeker/man/ChIPseeker-package.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 300728d971e2d087b2eb04e2a147a05ebf5bcb80
Commit message: deprecated plotChrCov to new function covplot
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-08-18 16:57:13 +0800
Author date: 2014-08-18 16:57:13 +0800

Revision: 93432
Author: m.iterson
Date: 2014-08-18T06:21:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/TurboNorm/NAMESPACE
Modified  /trunk/madman/Rpacks/TurboNorm/DESCRIPTION
fixed bug in NAMESPACE
Revision: 93430
Author: d.tenenbaum
Date: 2014-08-17T19:31:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/data/biocViewsVocab.rda
Modified  /trunk/madman/Rpacks/biocViews/inst/extdata/biocViewsVocab.sqlite
update rda and sqlite
Revision: 93429
Author: d.clayton
Date: 2014-08-17T15:33:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/snpStats/DESCRIPTION
Modified  /trunk/madman/Rpacks/snpStats/man/snpStats-package.Rd
Modified  /trunk/madman/Rpacks/snpStats/src/Makevars.win
Change blanks to tab in indented line in Makevars.win
Revision: 93427
Author: t.pedersen
Date: 2014-08-17T12:28:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzID/NEWS
Modified  /trunk/madman/Rpacks/mzID/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ddc3dfe80d404287581eeb1258af929a52a7f9f0
Commit message: Version bump
Committed by: Thomas Dybdal Pedersen
Author Name: Thomas Dybdal Pedersen
Commit date: 2014-08-17 14:28:23 +0200
Author date: 2014-08-17 14:28:23 +0200

Revision: 93425
Author: smyth
Date: 2014-08-17T03:50:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/man/estimateDisp.Rd
Modified  /trunk/madman/Rpacks/edgeR/src/init.cpp
Modified  /trunk/madman/Rpacks/edgeR/R/estimateDisp.R
Modified  /trunk/madman/Rpacks/edgeR/R/readDGE.R
Modified  /trunk/madman/Rpacks/edgeR/inst/doc/edgeRUsersGuide.pdf
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
edgeR 3.7.14.
- update to User's Guide section on pseudo-counts.
- estimateDisp has a new argument min.row.sum
Revision: 93424
Author: l.pantano
Date: 2014-08-16T13:24:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/DESCRIPTION
Added  /trunk/madman/Rpacks/DEGreport/data/geneInfo.rda
Modified  /trunk/madman/Rpacks/DEGreport/vignettes/DEGreport.Rnw
Deleted  /trunk/madman/Rpacks/DEGreport/vignettes/DEGreportHTML.Rmd
Modified  /trunk/madman/Rpacks/DEGreport/inst/NEWS
Added  /trunk/madman/Rpacks/DEGreport/man/geneInfo.Rd
Added  /trunk/madman/Rpacks/DEGreport/R/geneInfo.R
Modified  /trunk/madman/Rpacks/DEGreport/data/datalist
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c1d0ee8552bd40bb668e08ad81dbd7940ca7ced9
Commit message: remove biomart from vignettes due to unknown build issues in bioC checking.
Committed by: Lorena Pantano
Author Name: Lorena Pantano
Commit date: 2014-08-16 09:24:14 -0400
Author date: 2014-08-16 09:24:14 -0400

Revision: 93421
Author: r.flight
Date: 2014-08-16T02:58:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/categoryCompare/readme.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 624ae0dd2d6c93eaa40445e1c3e41a65092a7260
Commit message: added travis build to master readme
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-15 22:58:05 -0400
Author date: 2014-08-15 22:58:05 -0400

Revision: 93420
Author: r.flight
Date: 2014-08-16T02:56:17+00:00
Paths:
Added  /trunk/madman/Rpacks/categoryCompare/inst/doc/categoryCompare_vignette.R
Added  /trunk/madman/Rpacks/categoryCompare/inst/doc/categoryCompare_vignette.Rmd
Modified  /trunk/madman/Rpacks/categoryCompare/readme.md
Added  /trunk/madman/Rpacks/categoryCompare/inst/doc/categoryCompare_vignette.html
Added  /trunk/madman/Rpacks/categoryCompare/inst/doc
Modified  /trunk/madman/Rpacks/categoryCompare/vignettes/categoryCompare_vignette.Rmd
Added  /trunk/madman/Rpacks/categoryCompare/.Rbuildignore
Modified  /trunk/madman/Rpacks/categoryCompare/DESCRIPTION
Added  /trunk/madman/Rpacks/categoryCompare/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 22 commits.

Commit information:

Commit id: 3dcf470e3d20bfefe73cd72888fb1be40c707634
Commit message: merging in travis for build testing
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-15 22:54:33 -0400
Author date: 2014-08-15 22:54:33 -0400

Commit id: 8910dad0c7f889a737b7158b7160354ba785100f
Commit message: updating travis to not install Cytoscape
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-15 22:31:26 -0400
Author date: 2014-08-15 22:31:26 -0400

Commit id: 9671910d0f9d216e866b463390d2852fbd3c691f
Commit message: Merge branch 'travis' of https://github.com/rmflight/categoryCompare into travis
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-15 22:30:22 -0400
Author date: 2014-08-15 22:30:22 -0400

Commit id: 8fa53c1195c08fb8a467faf1af3247976827b6fe
Commit message: new vignettes with running code
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-15 22:29:38 -0400
Author date: 2014-08-15 22:29:38 -0400

Commit id: 3ca82e73ecf90502089ad5c8c986f130d176f419
Commit message: added runCy to all other sections
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-15 22:18:20 -0400
Author date: 2014-08-15 22:18:20 -0400

Commit id: d1cf1c6bd26cfa0b3c821af9a48f76b35f73371c
Commit message: setting up conditional cytoscape connection
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-15 22:16:39 -0400
Author date: 2014-08-15 22:16:39 -0400

Commit id: 351262b273354f98129671b02ae0d59575f7380e
Commit message: adding ipv4 stack to vmoptions for Cytoscape
Committed by: Robert M Flight
Author Name: Robert M Flight
Commit date: 2014-08-15 12:03:20 -0400
Author date: 2014-08-15 12:03:20 -0400

Commit id: f55615aa9615ca937b67e740e6798b1796851036
Commit message: trying with new version of cyrpc.conf
Committed by: Robert M Flight
Author Name: Robert M Flight
Commit date: 2014-08-15 11:28:01 -0400
Author date: 2014-08-15 11:28:01 -0400

Commit id: b4ebf36a99ce3992131110f69006700f82fe87b0
Commit message: adding webserver to the mix
Committed by: Robert M Flight
Author Name: Robert M Flight
Commit date: 2014-08-15 10:59:13 -0400
Author date: 2014-08-15 10:59:13 -0400

Commit id: 5d8a3181148c98acc4ae38ec37415c11f14c0a93
Commit message: adding sleep to allow Xvfb to startup
Committed by: Robert M Flight
Author Name: Robert M Flight
Commit date: 2014-08-15 10:47:41 -0400
Author date: 2014-08-15 10:47:41 -0400

Commit id: 3736a40b09d5b0bf4eca88dfffeb82b1e9d1b002
Commit message: trying running cytoscape as sudo
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-15 09:17:34 -0400
Author date: 2014-08-15 09:17:34 -0400

Commit id: f6c9036845940050994b2d23b4b4e630946e7552
Commit message: silly xvfb background
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 17:12:54 -0400
Author date: 2014-08-14 17:12:54 -0400

Commit id: 91590a60de1d373376d98e3b11da7f171e9448d8
Commit message: getting xvfb to work
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 17:04:05 -0400
Author date: 2014-08-14 17:04:05 -0400

Commit id: 798774bfb0167d7efc117a088faf1a08020b5b30
Commit message: trying rebuild the vignette
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 16:26:13 -0400
Author date: 2014-08-14 16:26:13 -0400

Commit id: d37b413282d311e29e3e3d81399a6c49fb0a6ad4
Commit message: correcting problem with xvfb
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 16:17:16 -0400
Author date: 2014-08-14 16:17:16 -0400

Commit id: e413bd313be3178dc00831cb7bec71574fedac7a
Commit message: added getting and starting cytoscape
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 16:09:50 -0400
Author date: 2014-08-14 16:09:50 -0400

Commit id: d1bb852134eebb7087febbd2e427b175b882b738
Commit message: added build status to readme
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 15:40:59 -0400
Author date: 2014-08-14 15:40:59 -0400

Commit id: 116adf47c736352cbab9d6e9895196d74412d6ec
Commit message: removing manual check
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 15:16:45 -0400
Author date: 2014-08-14 15:16:45 -0400

Commit id: ec6f8c99b72e83513112ee1bcae2e9ade79e56a4
Commit message: adding more args to R CMD Check
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 14:47:45 -0400
Author date: 2014-08-14 14:47:45 -0400

Commit id: 80b6d8cf88840551f80939b4ceaab6228a1fe957
Commit message: adding knitr to suggests field
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 14:21:18 -0400
Author date: 2014-08-14 14:21:18 -0400

Commit id: d794a28b0c755e9ec9d88c01f605a01de83754b4
Commit message: updating travis yml file
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 14:03:57 -0400
Author date: 2014-08-14 14:03:57 -0400

Commit id: 843da67b29417ad637392155b54388f61fad9659
Commit message: enable continuous integration via craigcitro/r-travis
Committed by: Robert Flight
Author Name: Robert Flight
Commit date: 2014-08-14 13:54:34 -0400
Author date: 2014-08-14 13:54:34 -0400

Revision: 93418
Author: m.carlson
Date: 2014-08-16T00:24:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/inst/dot/biocViewsVocab.dot
changes TxDb to TranscriptDb
Revision: 93416
Author: d.tenenbaum
Date: 2014-08-15T20:59:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/data/biocViewsVocab.rda
Modified  /trunk/madman/Rpacks/biocViews/inst/extdata/biocViewsVocab.sqlite
update rda and sqlite
Revision: 93415
Author: d.tenenbaum
Date: 2014-08-15T20:23:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/data/biocViewsVocab.rda
update rdata object
Revision: 93414
Author: s.arora
Date: 2014-08-15T20:13:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/inst/dot/biocViewsVocab.dot
biocViews update

- added 3 new biocViews - lipidomics, ImagingMassSpectrometry, StructuralEquationModels
Revision: 93412
Author: xi.wang
Date: 2014-08-15T20:06:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqGSEA/vignettes/SeqGSEA.Rnw
update citation
Revision: 93409
Author: t.hardcastle
Date: 2014-08-15T14:59:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/riboSeq/vignettes/riboSeq.Rnw
Modified  /trunk/madman/Rpacks/riboSeq/DESCRIPTION
0.99.13 minor adjustments to vignette.
Revision: 93408
Author: g.feng
Date: 2014-08-15T13:49:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneAnswers/R/getREACTOMEPATHTerms.R
fix reactome multimapping problem
Revision: 93407
Author: m.iterson
Date: 2014-08-15T13:32:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/TurboNorm/inst/CITATION
Modified  /trunk/madman/Rpacks/TurboNorm/R/panel.pspline.R
Modified  /trunk/madman/Rpacks/TurboNorm/R/turbotrend.R
Modified  /trunk/madman/Rpacks/TurboNorm/NAMESPACE
Added  /trunk/madman/Rpacks/TurboNorm/src/Rinit.c
Modified  /trunk/madman/Rpacks/TurboNorm/DESCRIPTION
added citation entry and registerd C-functions
Revision: 93406
Author: m.iterson
Date: 2014-08-15T13:08:59+00:00
Paths:
Added  /trunk/madman/Rpacks/SSPA/src/Rinit.c
add Rinit.c function
Revision: 93405
Author: m.iterson
Date: 2014-08-15T13:07:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/SSPA/inst/CITATION
Modified  /trunk/madman/Rpacks/SSPA/NAMESPACE
Modified  /trunk/madman/Rpacks/SSPA/DESCRIPTION
Added citation entry and registerd .C-functions
Revision: 93404
Author: l.gatto
Date: 2014-08-15T12:59:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/man/performance-analytics.Rd
Modified  /trunk/madman/Rpacks/MLInterfaces/R/performance-analytics.R
Merge branch 'master' into remotes/hedgehog

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