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Revision: 89140
Author: l.gatto
Date: 2014-04-17T19:19:37+00:00
Paths:
Added  /trunk/madman/Rpacks/MSnbase/man/compare_Spectra.Rd
Added  /trunk/madman/Rpacks/MSnbase/man/bin-methods.Rd
Modified  /trunk/madman/Rpacks/MSnbase/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/MSnbase/R/functions-Spectrum2.R
Added  /trunk/madman/Rpacks/MSnbase/R/matching.R
Modified  /trunk/madman/Rpacks/MSnbase/man/MSnSet-class.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/MSnExp-class.Rd
Modified  /trunk/madman/Rpacks/MSnbase/NAMESPACE
Added  /trunk/madman/Rpacks/MSnbase/R/functions-fragments.R
Modified  /trunk/madman/Rpacks/MSnbase/man/pSet-class.Rd
Added  /trunk/madman/Rpacks/MSnbase/R/plotting-Spectrum.R
Modified  /trunk/madman/Rpacks/MSnbase/man/makePEP.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/writeMzTabData.Rd
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_utils.R
Modified  /trunk/madman/Rpacks/MSnbase/man/grepEcols.Rd
Added  /trunk/madman/Rpacks/MSnbase/man/plotSpectrumSpectrum-methods.Rd
Modified  /trunk/madman/Rpacks/MSnbase/R/methods-Spectrum.R
Modified  /trunk/madman/Rpacks/MSnbase/man/Spectrum2-class.Rd
Added  /trunk/madman/Rpacks/MSnbase/man/dotproduct.Rd
Modified  /trunk/madman/Rpacks/MSnbase/inst/scripts/make_msx.R
Modified  /trunk/madman/Rpacks/MSnbase/R/functions-Spectrum.R
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_MSnExp.R
Modified  /trunk/madman/Rpacks/MSnbase/R/methods-MSnSet.R
Modified  /trunk/madman/Rpacks/MSnbase/man/makePRT.Rd
Modified  /trunk/madman/Rpacks/MSnbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/MSnbase/man/Spectrum-class.Rd
Added  /trunk/madman/Rpacks/MSnbase/man/calculateFragments-methods.Rd
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/MSnbase-demo.Rnw
Added  /trunk/madman/Rpacks/MSnbase/man/calculateFragments_Spectrum2.Rd
Added  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_fragments.R
Added  /trunk/madman/Rpacks/MSnbase/man/compareSpectra-methods.Rd
Added  /trunk/madman/Rpacks/MSnbase/R/methods-fragments.R
Added  /trunk/madman/Rpacks/MSnbase/man/numberOfCommonPeaks.Rd
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_quant.R
Added  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_matching.R
Added  /trunk/madman/Rpacks/MSnbase/man/commonPeaks.Rd
Added  /trunk/madman/Rpacks/MSnbase/man/matchPeaks.Rd
Modified  /trunk/madman/Rpacks/MSnbase/R/utils.R
Modified  /trunk/madman/Rpacks/MSnbase/man/makeMTD.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/featureCV.Rd
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_Spectrum.R
Modified  /trunk/madman/Rpacks/MSnbase/man/getVariableName.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/nQuants.Rd
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat/test_MSnSet.R
Modified  /trunk/madman/Rpacks/MSnbase/R/methods-MSnExp.R
Modified  /trunk/madman/Rpacks/MSnbase/NEWS
Added  /trunk/madman/Rpacks/MSnbase/man/plotSpectrumVsSpectrum.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/addIdentificationData-methods.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/ReporterIons-class.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/formatRt.Rd
Added  /trunk/madman/Rpacks/MSnbase/man/relaxedMatch.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/quantify-methods.Rd
Modified  /trunk/madman/Rpacks/MSnbase/R/functions-MSnExp.R
Modified  /trunk/madman/Rpacks/MSnbase/man/readMzTabData.Rd
Modified  /trunk/madman/Rpacks/MSnbase/inst/extdata/msx.rda
Merge branch 'master' into local-hedgehog
Revision: 89137
Author: hpages
Date: 2014-04-17T18:32:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioc_3.0.manifest
add S4Vectors to the builds
Revision: 89136
Author: s.gogarten
Date: 2014-04-17T18:11:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/GWASTools/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/GWASTools/man/qqPlot.Rd
Modified  /trunk/madman/Rpacks/GWASTools/R/qqPlot.R
Modified  /trunk/madman/Rpacks/GWASTools/DESCRIPTION
added ylim argument to qqPlot
Revision: 89135
Author: m.lawrence
Date: 2014-04-17T17:40:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
export new as.list.Vector S3 method
Revision: 89129
Author: m.love
Date: 2014-04-17T15:43:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/exomeCopy/R/helper_functions.R
Modified  /trunk/madman/Rpacks/exomeCopy/DESCRIPTION
fixing bug in generateBackground
Revision: 89127
Author: q.declerck
Date: 2014-04-17T15:08:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/inSilicoDb/R/basic.R
Modified  /trunk/madman/Rpacks/inSilicoDb/DESCRIPTION
remove testing url
Revision: 89125
Author: stvjc
Date: 2014-04-17T12:32:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GGtools/R/basicappraise.R
various steps to achieve functionality of appraise
Revision: 89123
Author: hpages
Date: 2014-04-17T06:21:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantTools/man/pileupVariants.Rd
Modified  /trunk/madman/Rpacks/VariantTools/R/pileupVariants.R
Use ApplyPileupsParam() instead of PileupParam().
Revision: 89122
Author: hpages
Date: 2014-04-17T06:17:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/SigFuge/vignettes/SigFuge.Rnw
Modified  /trunk/madman/Rpacks/SigFuge/DESCRIPTION
Use ApplyPileupsParam() instead of PileupParam().
Revision: 89121
Author: hpages
Date: 2014-04-17T06:13:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/genpb/DESCRIPTION
Modified  /trunk/madman/Rpacks/genpb/R/getPupc.R
Use ApplyPileupsParam() instead of PileupParam().
Revision: 89120
Author: hpages
Date: 2014-04-17T06:11:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/biovizBase/DESCRIPTION
Modified  /trunk/madman/Rpacks/biovizBase/man/pileupAsGRanges.Rd
Modified  /trunk/madman/Rpacks/biovizBase/vignettes/intro.Rnw
Modified  /trunk/madman/Rpacks/biovizBase/NAMESPACE
Modified  /trunk/madman/Rpacks/biovizBase/R/pileup.R
Use ApplyPileupsParam() instead of PileupParam().
Revision: 89119
Author: hpages
Date: 2014-04-17T06:01:11+00:00
Paths:
Added  /trunk/madman/Rpacks/S4Vectors/tests
Added  /trunk/madman/Rpacks/S4Vectors/src
Added  /trunk/madman/Rpacks/S4Vectors/vignettes
Added  /trunk/madman/Rpacks/S4Vectors/inst
Added  /trunk/madman/Rpacks/S4Vectors/inst/unitTests
Added  /trunk/madman/Rpacks/S4Vectors/inst/include
add standard folders (empty for now)
Revision: 89118
Author: hpages
Date: 2014-04-17T05:56:00+00:00
Paths:
Added  /trunk/madman/Rpacks/S4Vectors/R
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Added  /trunk/madman/Rpacks/S4Vectors/TODO
Added  /trunk/madman/Rpacks/S4Vectors/man
Added  /trunk/madman/Rpacks/S4Vectors/NAMESPACE
add TODO file
Revision: 89115
Author: hpages
Date: 2014-04-17T05:49:29+00:00
Paths:
Added  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
add DESCRIPTION file
Revision: 89114
Author: hpages
Date: 2014-04-17T05:28:18+00:00
Paths:
Added  /trunk/madman/Rpacks/S4Vectors
Add empty folder for upcoming S4Vectors package.
Revision: 89113
Author: hpages
Date: 2014-04-17T05:22:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/classNameForDisplay-methods.R
Modified  /trunk/madman/Rpacks/IRanges/man/classNameForDisplay-methods.Rd
remove unneeded "classNameForDisplay" methods
Revision: 89112
Author: stvjc
Date: 2014-04-17T05:05:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/DESCRIPTION
Added  /trunk/madman/Rpacks/GGtools/man/EqAppr-class.Rd
add EqAppr class doc, prepare to expose
Revision: 89111
Author: stvjc
Date: 2014-04-17T05:04:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/NAMESPACE
drop bindgwava
Revision: 89110
Author: stvjc
Date: 2014-04-17T03:39:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GGtools/R/basicappraise.R
Added  /trunk/madman/Rpacks/GGtools/R/Eqappr.R
add object system for model appraisal, and drop interim serializations in appraisal function, keep it functional
Revision: 89109
Author: stvjc
Date: 2014-04-17T03:38:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/R/basicappraise.R
 some interim changes to allow conditional serialization of interim results
Revision: 89108
Author: m.lawrence
Date: 2014-04-17T02:19:15+00:00
Paths:
Added  /trunk/madman/Rpacks/LazyList/R/Array-class.R
rebirth of Array-class.R
Revision: 89103
Author: m.castro
Date: 2014-04-16T23:56:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/RTN/DESCRIPTION
updated version
Revision: 89101
Author: m.castro
Date: 2014-04-16T23:50:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/RedeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/RedeR/inst/java/reder.jar
update version
Revision: 89098
Author: v.obenchain
Date: 2014-04-16T21:27:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/Grouping-class.R
minor edit to validity method for PartitioningMap
Revision: 89097
Author: hpages
Date: 2014-04-16T21:22:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/XVector/DESCRIPTION
Modified  /trunk/madman/Rpacks/XVector/R/XVectorList-class.R
Stuff that was Deprecated is now Defunct.
Revision: 89096
Author: g.zararsiz
Date: 2014-04-16T21:18:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLSeq/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: 8d0f8492a2044e05300f4c81644db304b1aa2c0c
    Commit message:
    Update DESCRIPTION

    Third version bump after creating 2.14 release
    Committed by gokmenzararsiz 
    Commit date: 2014-04-17T00:18:37+03:00

From: Bioconductor Git-SVN Bridge 
Revision: 89094
Author: g.zararsiz
Date: 2014-04-16T21:14:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLSeq/README
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: 8e05fd5b5f694afb82ff41bb32b2296df18500f3
    Commit message:
    Update README
    Committed by gokmenzararsiz 
    Commit date: 2014-04-17T00:14:40+03:00

From: Bioconductor Git-SVN Bridge 
Revision: 89093
Author: hpages
Date: 2014-04-16T21:12:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/seqinfo.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GRangesList-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/makeSeqnameIds.R
stuff that was Deprecated is now Defunct.
Revision: 89089
Author: m.carlson
Date: 2014-04-16T20:54:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubServer/metadata_schema.txt
Modified  /trunk/madman/Rpacks/AnnotationHubServer/inst/scripts/populateMySQLDB.R
updates script and schema to autoincrement the primary key.
Revision: 89088
Author: hpages
Date: 2014-04-16T20:54:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/HitsList-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/extractList.R
Modified  /trunk/madman/Rpacks/IRanges/man/inter-range-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/R/inter-range-methods.R
Modified  /trunk/madman/Rpacks/IRanges/R/DataFrame-utils.R
Deprecated stuff is now defunct.
Revision: 89083
Author: m.carlson
Date: 2014-04-16T19:50:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubServer/inst/scripts/populateMySQLDB.R
So this is a good stopping point (since everything just loaded)
Revision: 89082
Author: m.carlson
Date: 2014-04-16T19:12:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubServer/metadata_schema.txt
Modified  /trunk/madman/Rpacks/AnnotationHubServer/inst/scripts/populateMySQLDB.R
Changes the schema and the script that populates the data tables
Revision: 89081
Author: v.obenchain
Date: 2014-04-16T18:31:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/IRanges/man/Grouping-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/R/Grouping-class.R
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
remove 'mapEnd' slot in PartitioningMap class

Decided to keep PartitioningMap after all. The class contains
PartitioningByEnd and one additional slot, 'mapOrder', used
to track the order of unpack()ed ranges (see pack() and
unpack() in GenomicFiles).
Revision: 89077
Author: m.jiang
Date: 2014-04-16T17:52:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCore/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowCore/R/in-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: 608c28b4023ad55976d187331a2b05f6b5aba4b5
    Commit message:
    1.remove dependeancy on feature package 2.fix ellipse gating error

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flowCore@89012 bc3139a8-67e5-0310-9ffc-ced21a209358
    Committed by m.jiang 
    Commit date: 2014-04-15T18:28:36Z

From: Bioconductor Git-SVN Bridge 
Revision: 89075
Author: k.horan
Date: 2014-04-16T17:17:59+00:00
Paths:
Added  /trunk/madman/Rpacks/ChemmineR/profiling/test_fpSim.R
Added  /trunk/madman/Rpacks/ChemmineR/profiling
Modified  /trunk/madman/Rpacks/ChemmineR/R/sim.R
Modified  /trunk/madman/Rpacks/ChemmineR/inst/unitTests/test_general.R
Modified  /trunk/madman/Rpacks/ChemmineR/NAMESPACE
Modified  /trunk/madman/Rpacks/ChemmineR/DESCRIPTION
Added  /trunk/madman/Rpacks/ChemmineR/src/fingerprints.cc
Commit made by the Bioconductor Git-SVN bridge.
Consists of 4 commit(s).

Commit information:

    Commit id: 47d37821ae48f3291576f43c26daf977fd03aacd
    Commit message:
    c-version working now. seems to have a 2x speedup
    Committed by khoran 
    Commit date: 2014-04-15T17:49:24-07:00

    Commit id: b6fd7b5eebd2532ac70d70f7dd3abdb52ceea18c
    Commit message:
    change fpSim to the c-version and renamed original to fpSimOrig
    Committed by khoran 
    Commit date: 2014-04-16T10:12:55-07:00

    Commit id: a959eebdc8fe0e304924560a93a845b32e227ea5
    Commit message:
    Merge branch 'fpsim_speedup'
    Committed by khoran 
    Commit date: 2014-04-16T10:16:36-07:00

    Commit id: 1277c52c1f88ad08e4862b82240d218dfa6419f9
    Commit message:
    bump version
    Committed by khoran 
    Commit date: 2014-04-16T10:17:25-07:00

From: Bioconductor Git-SVN Bridge 
Revision: 89073
Author: d.tenenbaum
Date: 2014-04-16T17:03:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubServer/inst/scripts/getNewResources.R
Add 3.0 to versions in script that generates new resources.
Revision: 89068
Author: n.wang
Date: 2014-04-16T13:51:02+00:00
Paths:
Added  /trunk/madman/Rpacks/UNDO/man/dimension_reduction.Rd
Added  /trunk/madman/Rpacks/UNDO/R/dimension_reduction.R
The new function is missed in the last commit.
Revision: 89063
Author: a.oles
Date: 2014-04-16T09:04:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/vignettes/LatexStyle.Rnw
version 1.3.1
- removed 'helvet' from the list of latex packages in the vignette
Revision: 89062
Author: j.bogojeska
Date: 2014-04-16T07:10:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rtreemix/src/Makevars.win
Updated flag -Wno-unused to -Wno-unused-value
Revision: 89061
Author: j.bogojeska
Date: 2014-04-16T07:10:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rtreemix/src/Makevars
Updated flag -Wno-unused to -Wno-unused-value
Revision: 89060
Author: j.bogojeska
Date: 2014-04-16T06:55:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rtreemix/DESCRIPTION
Removed packages from Depends and left them only in Imports
Revision: 89057
Author: m.lawrence
Date: 2014-04-16T04:30:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/rsbml/inst/sbml/GlycolysisLayout.xml
update GlycolysisLayout.xml to L2V2 so that the layout extension works
Revision: 89055
Author: mtmorgan
Date: 2014-04-16T00:50:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/R/XStringQuality-class.R
Modified  /trunk/madman/Rpacks/Biostrings/DESCRIPTION
PhredQuality maximum quality is 126 - 33
Revision: 89047
Author: m.lawrence
Date: 2014-04-15T22:56:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantTools/NAMESPACE
Modified  /trunk/madman/Rpacks/VariantTools/R/tallyVariants.R
Modified  /trunk/madman/Rpacks/VariantTools/DESCRIPTION
cleanup tiling in tallyVariants
Revision: 89046
Author: m.lawrence
Date: 2014-04-15T22:10:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/rsbml/inst/sbml/GlycolysisLayout.xml
fixes to GlycolysisLayout.xml to pass the L3V1 libsbml checks (not
clear why this was needed, since we declare L2)
Revision: 89045
Author: m.carlson
Date: 2014-04-15T22:01:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubServer/inst/scripts/populateMySQLDB.R
fixes a bug in the script that produces the mySQL db from AHMs
Revision: 89044
Author: m.carlson
Date: 2014-04-15T21:24:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubServer/inst/scripts/populateMySQLDB.R
bug fix for AddOneRecord()
Revision: 89043
Author: m.carlson
Date: 2014-04-15T21:10:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubServer/inst/scripts/populateMySQLDB.R
tiny bug fix for function that removes a record
Revision: 89042
Author: m.carlson
Date: 2014-04-15T21:05:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubServer/inst/scripts/populateMySQLDB.R
Working script for the first couple of AHMs (at least)

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