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Revision: 100014
Author: g.yu
Date: 2015-03-01T06:18:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/DESCRIPTION
Modified  /trunk/madman/Rpacks/ggtree/NEWS
Modified  /trunk/madman/Rpacks/ggtree/R/phylopic.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2484901a46377834f43aafe3e79326741b42deae

    change .png to .PNG to satisfy WINDOWS

Revision: 100013
Author: g.yu
Date: 2015-03-01T05:45:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/ReactomePA/DESCRIPTION
Modified  /trunk/madman/Rpacks/ReactomePA/NEWS
Modified  /trunk/madman/Rpacks/ReactomePA/R/gseAnalyzer.R
Modified  /trunk/madman/Rpacks/ReactomePA/man/getGeneSet.Reactome.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6c98e2262d8ef472dbefdbac2457e4d23f355408

    rm tmp file


Commit id: 73c89b6535cac3273e2f35563e6ef2ac37c55cb9

    add use_internal_data parameter according to DOSE

Revision: 100012
Author: g.yu
Date: 2015-03-01T05:33:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/DESCRIPTION
Modified  /trunk/madman/Rpacks/clusterProfiler/R/compareCluster.R
Modified  /trunk/madman/Rpacks/clusterProfiler/man/plot-methods.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4438c02e942b423d8bdea58cb0177f247b74b8a2

    update man to fix warning

Revision: 100011
Author: smyth
Date: 2015-03-01T04:54:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/R/plotdensities.R
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
1 March 2015: limma 3.23.10

- fix bug in the MAList method for plotDensities introduced with
  the use of NextMethod() in version 3.21.16.
Revision: 100010
Author: hpages
Date: 2015-03-01T04:48:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/DESCRIPTION
Version bump only to trigger propagation and re-installation on the user side.
This is to avoid the "multiple methods tables found for ‘score’ and ‘score<-’"
warnings the user gets when loading rtracklayer after updating to the latest
BiocGenerics and IRanges.
Revision: 100008
Author: stvjc
Date: 2015-02-28T21:19:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/edxBioc/vignettes/vjcbioc.Rmd
added info on probe packages
Revision: 100007
Author: hpages
Date: 2015-02-28T20:42:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/VanillaICE/man/IO.Rd
remove R CMD check WARNING caused by recent fileName() changes
Revision: 100006
Author: hpages
Date: 2015-02-28T20:35:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Version bump only to trigger propagation and re-installation on the user side.
This is to avoid the "multiple methods tables found for ‘score’ and ‘score<-’"
warnings the user gets when loading GenomicRanges after updating to the latest
BiocGenerics and IRanges.
Revision: 100005
Author: v.obenchain
Date: 2015-02-28T18:06:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/man/mapCoords-methods.Rd
remove deprecated mapCoords() examples
Revision: 100004
Author: stvjc
Date: 2015-02-28T17:49:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/edxBioc/vignettes/vjcbioc.Rmd
some minor additions to vignette
Revision: 100003
Author: s.neumann
Date: 2015-02-28T14:26:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzR/DESCRIPTION
Modified  /trunk/madman/Rpacks/mzR/NAMESPACE
Modified  /trunk/madman/Rpacks/mzR/NEWS
Modified  /trunk/madman/Rpacks/mzR/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/mzR/R/methods-mzRident.R
Modified  /trunk/madman/Rpacks/mzR/R/methods-mzRnetCDF.R
Modified  /trunk/madman/Rpacks/mzR/R/methods-mzRpwiz.R
Modified  /trunk/madman/Rpacks/mzR/R/methods-mzRramp.R
Modified  /trunk/madman/Rpacks/mzR/man/metadata.Rd
Modified  /trunk/madman/Rpacks/mzR/man/mzR-class.Rd
Modified  /trunk/madman/Rpacks/mzR/man/openMSfile.Rd
Modified  /trunk/madman/Rpacks/mzR/man/peaks.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6599b4e00f742fc668f41353450efbaf98f0bbf1

    using the generic functions from ProtGenerics and BiocGenerics

Revision: 99999
Author: stvjc
Date: 2015-02-28T13:18:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/edxBioc/DESCRIPTION
wrong host, added some suggests, depends
Revision: 99998
Author: stvjc
Date: 2015-02-28T13:17:32+00:00
Paths:
Added  /trunk/madman/Rpacks/edxBioc/R/methods.R
methods code also added
Revision: 99997
Author: stvjc
Date: 2015-02-28T13:01:45+00:00
Paths:
Added  /trunk/madman/Rpacks/edxBioc/vignettes/pngs/databaseTypes.png
need databaseTypes png file
Revision: 99996
Author: stvjc
Date: 2015-02-28T13:00:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/edxBioc/DESCRIPTION
Modified  /trunk/madman/Rpacks/edxBioc/NAMESPACE
Added  /trunk/madman/Rpacks/edxBioc/R/seqc-eSet.R
Modified  /trunk/madman/Rpacks/edxBioc/vignettes/vjcbioc.Rmd
adding seqc infrastructure that is not being distributed
Revision: 99995
Author: stvjc
Date: 2015-02-28T12:09:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/edxBioc/vignettes/vjcbioc.Rmd
basic new material questions
Revision: 99994
Author: stvjc
Date: 2015-02-28T11:52:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/edxBioc/DESCRIPTION
Added  /trunk/madman/Rpacks/edxBioc/vignettes/pngs/GDSbrow.png
Added  /trunk/madman/Rpacks/edxBioc/vignettes/pngs/asthGEO.png
Modified  /trunk/madman/Rpacks/edxBioc/vignettes/vjcbioc.Rmd
more questions and materials
Revision: 99992
Author: l.gatto
Date: 2015-02-28T11:52:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/Pbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/Pbase/NEWS
revert bump in remotes branch
Revision: 99991
Author: l.gatto
Date: 2015-02-28T11:52:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/Pbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/Pbase/NEWS
new devel version
Revision: 99990
Author: hpages
Date: 2015-02-28T10:48:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/VanillaICE/DESCRIPTION
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-ArrayViews.R
Modified  /trunk/madman/Rpacks/VanillaICE/man/IO.Rd
the 1st arg of the fileName() generic is 'object' again
Revision: 99989
Author: hpages
Date: 2015-02-28T10:44:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-accessors.R
Sync "fileName" method definition with renaming of 1st arg ('x' -> 'object')
in the definition of the fileName() generic in BiocGenerics.
Revision: 99988
Author: hpages
Date: 2015-02-28T10:40:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/annotate/DESCRIPTION
Modified  /trunk/madman/Rpacks/annotate/R/html.R
Modified  /trunk/madman/Rpacks/annotate/man/HTMLPage-class.Rd
Sync "fileName" method definition with renaming of 1st arg ('x' -> 'object')
in the definition of the fileName() generic in BiocGenerics.
Revision: 99987
Author: hpages
Date: 2015-02-28T10:31:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocGenerics/R/fileName.R
Modified  /trunk/madman/Rpacks/BiocGenerics/man/fileName.Rd
rename fileName() 1st arg 'x' -> 'object'
Revision: 99986
Author: hpages
Date: 2015-02-28T10:28:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/topGO/DESCRIPTION
Modified  /trunk/madman/Rpacks/topGO/NAMESPACE
Modified  /trunk/madman/Rpacks/topGO/R/topGOmethods.R
Remove score() and `score<-`() local generics and use new generics from
BiocGenerics instead.
Revision: 99985
Author: hpages
Date: 2015-02-28T10:26:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/graph/DESCRIPTION
Modified  /trunk/madman/Rpacks/graph/NAMESPACE
Modified  /trunk/madman/Rpacks/graph/man/fromGXL-methods.Rd
remove unneeded imports
Revision: 99984
Author: hpages
Date: 2015-02-28T10:00:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/RangedData-class.R
Deleted  /trunk/madman/Rpacks/IRanges/man/score.Rd
Remove score() and `score<-`() local generics and use new generics from
BiocGenerics instead.
Revision: 99983
Author: hpages
Date: 2015-02-28T09:49:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocGenerics/R/testPackage.R
get rid of R CMD check "no visible global function definition" NOTE
Revision: 99980
Author: l.gatto
Date: 2015-02-28T04:26:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/Pbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/Pbase/NAMESPACE
Modified  /trunk/madman/Rpacks/Pbase/NEWS
Modified  /trunk/madman/Rpacks/Pbase/R/coordinate-mapping-methods.R
Added  /trunk/madman/Rpacks/Pbase/R/plotting.R
Merge branch 'master' into remotes/hedgehog
Revision: 99979
Author: stvjc
Date: 2015-02-28T03:39:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/edxBioc/vignettes/vjcbioc.Rmd
various emendations to vig
Revision: 99978
Author: x.zheng
Date: 2015-02-28T03:00:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/src/gdsfmt.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6646acd4a99f763eca705999a98e5d2afa328ff9

    Oops, the bug in 'objdesp.gdsn' still exists, fixed!

Revision: 99977
Author: n.hayden
Date: 2015-02-28T01:48:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/BitSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/BitSeq/configure.ac
revert to AC_SUBST on OPENMP_CXXFLAGS
Revision: 99975
Author: hpages
Date: 2015-02-28T01:20:59+00:00
Paths:
Deleted  /trunk/madman/Rpacks/Rsamtools/pileup_notes.txt
don't need this anymore
Revision: 99974
Author: n.hayden
Date: 2015-02-28T01:18:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/BitSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/BitSeq/configure
Modified  /trunk/madman/Rpacks/BitSeq/configure.ac
Deleted  /trunk/madman/Rpacks/BitSeq/m4
Modified  /trunk/madman/Rpacks/BitSeq/src/Makevars.in
Modified  /trunk/madman/Rpacks/BitSeq/src/Makevars.win
Modified  /trunk/madman/Rpacks/BitSeq/src/Makevars.win.in
Adhere to new Rsamtools recommendations, rely on autoconf AC_OPENMP
Revision: 99973
Author: s.arora
Date: 2015-02-28T01:09:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEpigenomeRoadmap.R
code update

- correct recipe for Epigenome Roadmap files
Revision: 99972
Author: s.arora
Date: 2015-02-28T00:43:37+00:00
Paths:
Added  /trunk/madman/Rpacks/SELEX
Added  /trunk/madman/Rpacks/SELEX/DESCRIPTION
Added  /trunk/madman/Rpacks/SELEX/NAMESPACE
Added  /trunk/madman/Rpacks/SELEX/R
Added  /trunk/madman/Rpacks/SELEX/R/SELEX.R
Added  /trunk/madman/Rpacks/SELEX/R/onLoad.R
Added  /trunk/madman/Rpacks/SELEX/inst
Added  /trunk/madman/Rpacks/SELEX/inst/extdata
Added  /trunk/madman/Rpacks/SELEX/inst/extdata/R0.fastq.gz
Added  /trunk/madman/Rpacks/SELEX/inst/extdata/R2.fastq.gz
Added  /trunk/madman/Rpacks/SELEX/inst/extdata/config.xml
Added  /trunk/madman/Rpacks/SELEX/inst/java
Added  /trunk/madman/Rpacks/SELEX/inst/java/selex.jar
Added  /trunk/madman/Rpacks/SELEX/java
Added  /trunk/madman/Rpacks/SELEX/java/src
Added  /trunk/madman/Rpacks/SELEX/java/src/Makefile
Added  /trunk/madman/Rpacks/SELEX/java/src/base
Added  /trunk/madman/Rpacks/SELEX/java/src/base/ArraysMerger.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/ArraysMergerHeap.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/CountObject.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/CountObjectIterator.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/DebugLog.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/FatalException.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/MarkovModelInfo.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/MarkovModelOption.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/QuickSort.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/RegexOption.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/SELEXConfigReader.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/Sequence.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/SequenceComparator.java
Added  /trunk/madman/Rpacks/SELEX/java/src/base/Util.java
Added  /trunk/madman/Rpacks/SELEX/java/src/data
Added  /trunk/madman/Rpacks/SELEX/java/src/data/selex
Added  /trunk/madman/Rpacks/SELEX/java/src/data/selex/filelist
Added  /trunk/madman/Rpacks/SELEX/java/src/main
Added  /trunk/madman/Rpacks/SELEX/java/src/main/CountFileReader.java
Added  /trunk/madman/Rpacks/SELEX/java/src/main/FastQFileScanner.java
Added  /trunk/madman/Rpacks/SELEX/java/src/main/SELEX.java
Added  /trunk/madman/Rpacks/SELEX/java/src/main/SELEXConfigGUI.java
Added  /trunk/madman/Rpacks/SELEX/java/src/main/SampleDataFileExtractor.java
Added  /trunk/madman/Rpacks/SELEX/java/src/main/SimpleKmerCount.java
Added  /trunk/madman/Rpacks/SELEX/java/src/selex.jar
Added  /trunk/madman/Rpacks/SELEX/java/src/selex.xsd
Added  /trunk/madman/Rpacks/SELEX/java/src/test
Added  /trunk/madman/Rpacks/SELEX/java/src/test/CountFileReaderTest.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/ExecutorTest.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/IntegerHolder.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/Kmer.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/MappedMemTest.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/MinHeap.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/MinHeapTest.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/RadixSortTest.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/RegTest.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/SELEXTest1.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/SELEXTest2.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/SequenceTest.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/Sorting.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/SortingTest.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/UtilTest.java
Added  /trunk/madman/Rpacks/SELEX/java/src/test/ZipfileTest.java
Added  /trunk/madman/Rpacks/SELEX/man
Added  /trunk/madman/Rpacks/SELEX/man/SELEX.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.affinities.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.config.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.countSummary.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.counts.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.defineSample.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.exampledata.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.fastqPSFM.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.getAttributes.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.getRound0.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.getSeqfilter.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.infogain.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.infogainSummary.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.jvmStatus.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.kmax.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.kmerPSFM.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.loadAnnotation.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.mm.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.mmProb.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.mmSummary.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.revcomp.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.run.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.sample.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.samplePSFM.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.sampleSummary.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.saveAnnotation.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.seqfilter.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.setwd.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.split.Rd
Added  /trunk/madman/Rpacks/SELEX/man/selex.summary.Rd
Added  /trunk/madman/Rpacks/SELEX/vignettes
Added  /trunk/madman/Rpacks/SELEX/vignettes/SELEX.Rnw
Modified  /trunk/madman/Rpacks/bioc_3.1.manifest
Added  /trunk/madman/Rpacks/sigsquared
Added  /trunk/madman/Rpacks/sigsquared/DESCRIPTION
Added  /trunk/madman/Rpacks/sigsquared/NAMESPACE
Added  /trunk/madman/Rpacks/sigsquared/R
Added  /trunk/madman/Rpacks/sigsquared/R/GeneSignature.R
Added  /trunk/madman/Rpacks/sigsquared/R/SolnSpace.R
Added  /trunk/madman/Rpacks/sigsquared/data
Added  /trunk/madman/Rpacks/sigsquared/data/BrCa443.RData
Added  /trunk/madman/Rpacks/sigsquared/inst
Added  /trunk/madman/Rpacks/sigsquared/inst/unitTests
Added  /trunk/madman/Rpacks/sigsquared/inst/unitTests/test_ensembleAdjustable.R
Added  /trunk/madman/Rpacks/sigsquared/inst/unitTests/test_geneSignaturehelpers.R
Added  /trunk/madman/Rpacks/sigsquared/man
Added  /trunk/madman/Rpacks/sigsquared/man/BrCa443.Rd
Added  /trunk/madman/Rpacks/sigsquared/man/analysisPipeline.Rd
Added  /trunk/madman/Rpacks/sigsquared/man/ensembleAdjustable.Rd
Added  /trunk/madman/Rpacks/sigsquared/man/geneSignature-class.Rd
Added  /trunk/madman/Rpacks/sigsquared/man/setGeneSignature.Rd
Added  /trunk/madman/Rpacks/sigsquared/man/sigsquared.Rd
Added  /trunk/madman/Rpacks/sigsquared/tests
Added  /trunk/madman/Rpacks/sigsquared/tests/runTests.R
Added  /trunk/madman/Rpacks/sigsquared/vignettes
Added  /trunk/madman/Rpacks/sigsquared/vignettes/bpmsnetwork.png
Added  /trunk/madman/Rpacks/sigsquared/vignettes/sigsquared.Rnw
Added  /trunk/madman/Rpacks/skewr
Added  /trunk/madman/Rpacks/skewr/DESCRIPTION
Added  /trunk/madman/Rpacks/skewr/NAMESPACE
Added  /trunk/madman/Rpacks/skewr/R
Added  /trunk/madman/Rpacks/skewr/R/snFuncs.R
Added  /trunk/madman/Rpacks/skewr/R/snMixFuncs.R
Added  /trunk/madman/Rpacks/skewr/R/snPlots.R
Added  /trunk/madman/Rpacks/skewr/R/snUtils.R
Added  /trunk/madman/Rpacks/skewr/Thumbs.db
Added  /trunk/madman/Rpacks/skewr/inst
Added  /trunk/madman/Rpacks/skewr/man
Added  /trunk/madman/Rpacks/skewr/man/getBarcodes.Rd
Added  /trunk/madman/Rpacks/skewr/man/getMethyLumiSet.Rd
Added  /trunk/madman/Rpacks/skewr/man/getSNparams.Rd
Added  /trunk/madman/Rpacks/skewr/man/panelPlots.Rd
Added  /trunk/madman/Rpacks/skewr/man/preprocess.Rd
Added  /trunk/madman/Rpacks/skewr/man/subsetProbes.Rd
Added  /trunk/madman/Rpacks/skewr/vignettes
Added  /trunk/madman/Rpacks/skewr/vignettes/skewr.Rnw
Added  /trunk/madman/Rpacks/skewr/vignettes/skewr.bib
Added  /trunk/madman/Rpacks/skewr/vignettes/unsrturl.bst
adding packages: sigaquared , SELEX, skewr

Revision: 99970
Author: m.carlson
Date: 2015-02-28T00:27:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/man/AnnotationHubMetadata-class.Rd
Changes the check code so that the constructor can police the new sourcetype values correctly
Revision: 99969
Author: hpages
Date: 2015-02-28T00:25:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/annotate/R/html.R
oops, need to rename arg all the way...
Revision: 99968
Author: hpages
Date: 2015-02-28T00:24:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/VanillaICE/DESCRIPTION
Modified  /trunk/madman/Rpacks/VanillaICE/NAMESPACE
Modified  /trunk/madman/Rpacks/VanillaICE/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/VanillaICE/R/methods-ArrayViews.R
Modified  /trunk/madman/Rpacks/VanillaICE/man/IO.Rd
remove local fileName() generic and use new generic from BiocGenerics instead
Revision: 99967
Author: hpages
Date: 2015-02-28T00:13:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/NAMESPACE
forgot to import fileName
Revision: 99966
Author: hpages
Date: 2015-02-28T00:06:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/DESCRIPTION
depends on latest version of BiocGenerics
Revision: 99965
Author: hpages
Date: 2015-02-28T00:06:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/annotate/DESCRIPTION
depends on latest version of BiocGenerics
Revision: 99964
Author: hpages
Date: 2015-02-28T00:04:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocGenerics/DESCRIPTION
Oops, bump version in the wrond direction. Corrected now.
Revision: 99963
Author: hpages
Date: 2015-02-28T00:01:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/easyRNASeq/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-accessors.R
remove local fileName() generic and use new generic from BiocGenerics instead
Revision: 99961
Author: hpages
Date: 2015-02-27T23:56:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/annotate/DESCRIPTION
Modified  /trunk/madman/Rpacks/annotate/R/html.R
Modified  /trunk/madman/Rpacks/annotate/man/HTMLPage-class.Rd
remove local fileName() generic and use new generic from BiocGenerics instead
Revision: 99960
Author: x.zheng
Date: 2015-02-27T23:49:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/HIBAG/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 348641a70f9e92bf4ae256c387cd7ccb9713777a

    Recover .travis.yml since multiple R versions are tested

Revision: 99958
Author: m.carlson
Date: 2015-02-27T23:43:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/UniProt.ws/DESCRIPTION
Modified  /trunk/madman/Rpacks/UniProt.ws/inst/extdata/keytypes.txt
Bug fix to prevent issues with a name clash in keytypes.
Revision: 99957
Author: s.arora
Date: 2015-02-27T23:40:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/KEGGgraph/DESCRIPTION
Modified  /trunk/madman/Rpacks/KEGGprofile/DESCRIPTION
Modified  /trunk/madman/Rpacks/PathNet/DESCRIPTION
Modified  /trunk/madman/Rpacks/attract/DESCRIPTION
Modified  /trunk/madman/Rpacks/clipper/DESCRIPTION
Modified  /trunk/madman/Rpacks/keggorthology/DESCRIPTION
Modified  /trunk/madman/Rpacks/neaGUI/DESCRIPTION
Modified  /trunk/madman/Rpacks/pcot2/DESCRIPTION
biocView update

- add KEGG and other suitable biocViews using recommendBiocViews() output

Revision: 99956
Author: x.zheng
Date: 2015-02-27T23:34:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/HIBAG/.travis.yml
Modified  /trunk/madman/Rpacks/HIBAG/appveyor.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 814ea8c6916d6a1ee2cc91c372abd13c8ecf3c7e

    simply AppVeyor and Travis rules to save checking time

    BioC is being at r99955 in svn, who will be the lucky person making the
    100,000th commit?

Revision: 99955
Author: m.jiang
Date: 2015-02-27T23:15:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/INSTALL
Modified  /trunk/madman/Rpacks/flowWorkspace/configure
Modified  /trunk/madman/Rpacks/flowWorkspace/configure.ac
Modified  /trunk/madman/Rpacks/flowWorkspace/src/GatingHierarchy.cpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/Makevars.in
Deleted  /trunk/madman/Rpacks/flowWorkspace/src/README
Modified  /trunk/madman/Rpacks/flowWorkspace/src/boost_serialization/README
Added  /trunk/madman/Rpacks/flowWorkspace/src/protobuf-2.6.0.tgz
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 473bd8c2756271fab715e2a092e3d51994b33509

    Merge branch 'trunk'


Commit id: 9c197c1435c12043e88fe20eb08a97737824e32b

    bundle protobuf-2.6.0 into package

    fix ambiguous 'abs' call on mac.

    protobuffix automake issue on mac


Commit id: 0de75d1b016f1f3a97055cc664d1bbe0168e1b0e

    bundle protobuf-2.6.0 into package

Revision: 99954
Author: d.tenenbaum
Date: 2015-02-27T22:20:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b268398d86abf7c7a8559ef1241116cdee6d45b1

    ...and make sure unit tests still pass

Revision: 99953
Author: d.tenenbaum
Date: 2015-02-27T22:08:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/R/checks.R
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: dae7e9bb5d9c18a355e706aa4017305cb4362c00

    Infrastructure packages are not required to have vignettes. Closes #32.

Revision: 99952
Author: x.zheng
Date: 2015-02-27T21:48:36+00:00
Paths:
Added  /trunk/madman/Rpacks/HIBAG/.Rbuildignore
Added  /trunk/madman/Rpacks/HIBAG/.gitattributes
Modified  /trunk/madman/Rpacks/HIBAG/.travis.yml
Modified  /trunk/madman/Rpacks/HIBAG/DESCRIPTION
Modified  /trunk/madman/Rpacks/HIBAG/NAMESPACE
Modified  /trunk/madman/Rpacks/HIBAG/NEWS
Modified  /trunk/madman/Rpacks/HIBAG/R/DataUtilities.R
Modified  /trunk/madman/Rpacks/HIBAG/R/HIBAG.R
Modified  /trunk/madman/Rpacks/HIBAG/README.md
Added  /trunk/madman/Rpacks/HIBAG/appveyor.yml
Modified  /trunk/madman/Rpacks/HIBAG/inst/CITATION
Modified  /trunk/madman/Rpacks/HIBAG/inst/doc/GeneInfo_hg18.txt
Modified  /trunk/madman/Rpacks/HIBAG/inst/doc/GeneInfo_hg19.txt
Modified  /trunk/madman/Rpacks/HIBAG/inst/doc/GeneInfo_hg20.txt
Added  /trunk/madman/Rpacks/HIBAG/inst/extdata/ModelList.RData
Deleted  /trunk/madman/Rpacks/HIBAG/inst/extdata/ModelListTest.RData
Added  /trunk/madman/Rpacks/HIBAG/inst/extdata/OutOfBag.RData
Deleted  /trunk/madman/Rpacks/HIBAG/inst/unitTests/test_model.R
Modified  /trunk/madman/Rpacks/HIBAG/man/HIBAG-package.Rd
Modified  /trunk/madman/Rpacks/HIBAG/man/hlaAttrBagging.Rd
Modified  /trunk/madman/Rpacks/HIBAG/man/hlaGenoSwitchStrand.Rd
Modified  /trunk/madman/Rpacks/HIBAG/man/hlaLociInfo.Rd
Modified  /trunk/madman/Rpacks/HIBAG/man/hlaModelFromObj.Rd
Modified  /trunk/madman/Rpacks/HIBAG/man/hlaParallelAttrBagging.Rd
Modified  /trunk/madman/Rpacks/HIBAG/man/hlaReport.Rd
Modified  /trunk/madman/Rpacks/HIBAG/src/HIBAG.cpp
Modified  /trunk/madman/Rpacks/HIBAG/src/LibHLA.cpp
Modified  /trunk/madman/Rpacks/HIBAG/src/LibHLA.h
Deleted  /trunk/madman/Rpacks/HIBAG/src/Makevars
Modified  /trunk/madman/Rpacks/HIBAG/tests/runTests.R
Modified  /trunk/madman/Rpacks/HIBAG/vignettes/HIBAG_Ref.bib
Modified  /trunk/madman/Rpacks/HIBAG/vignettes/HIBAG_Tutorial.Rnw
Added  /trunk/madman/Rpacks/HIBAG/vignettes/HIBAG_Tutorial_html.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f5f3df94771e943f98b623b89ac4aa261d9b730f

    Merge pull request #1 from zhengxwen/dev

    Commit to BioC: v1.3.1

Commit id: 0b15add64ade43f39466d177f657f7d99260c0d0

    hlaGDS2Geno: uses "warning" instead of "stop"

    when “gdsfmt” and “SNPRelate” are not available.


Commit id: 196c3914f2e15a7eb3917c1b2b92eec5c6384bbc

    R+AppVeyor

    the integration for R projects on Windows, using AppVeyor -- a CI
    testing service similar to Travis-CI


Commit id: 3d28da538b8d5e1a6066058b50dd7db27eee393c

    add ".Rbuildignore"


Commit id: 829fe738161d891f1c670842fca1aa03760938b4

    Update README.md


Commit id: cd512134b7c470f2b9756be0443eb38b10049639

    modify the unit tests to be compatible with multiple platforms


Commit id: 116d7008d23437341259a0271f6a0d0c5529632a

    a new html vignette

    * add a new html vignette (Rmd file)
    * hlaReport() outputs text with markdown format


Commit id: 918efc8848e4f7fe222296ae4dccbacdb651af47

    R/C++ interface: .C ==> .Call

    R-exts: .Call interface is much to be preferred


Commit id: 03c4abe90647ada6ef11759a2c1a65881af1caee

    remove non-standard char in “GeneInfo_hg18.txt”

    chr6 ==> 6, in “inst/doc/GeneInfo_hg18.txt”,
    “inst/doc/GeneInfo_hg19.txt” and “inst/doc/GeneInfo_hg20.txt”.


Commit id: 8f46ec6b4a7cae1855f2aa10d84ddd8c0dd7ef75

    .C ==> .Call and remove unused functions


Commit id: 941e56fea7b01328ac5b8d87271e52fa9e460976

    update .travis.yml


Commit id: 5f153cb03af764585d3f26500f01f876d99dffe9

    Reduce time of vignettes (R CMD check)


Commit id: 38664d012701cf7f7ff334dcba90afce3b746115

    Reduce the running time of "R CMD check"


Commit id: e4e5b5f99eceb097143b97ed389cc5c8ff208d94

    fix R-devel (R-3.2) checking NOTE

    Found the following apparent S3 methods exported but not registered


Commit id: 4cae330fb1094ff8efa9d28927794d4ddf84018c

    simplify 'hlaLociInfo'

    compatible with old R version (<3.1)

Revision: 99951
Author: d.tenenbaum
Date: 2015-02-27T21:45:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocCheck/R/BiocCheck.R
Modified  /trunk/madman/Rpacks/BiocCheck/R/checks.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: bffad9f37c4d9502da4ffb13e4ca19e771609dd1

    Check if package already exists in CRAN

    If (--new-packages is specified, check in Bioconductor as well).
    Closes #35

Revision: 99949
Author: l.gatto
Date: 2015-02-27T20:38:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/ProtGenerics/DESCRIPTION
Added  /trunk/madman/Rpacks/ProtGenerics/NEWS
added news file
Revision: 99948
Author: l.gatto
Date: 2015-02-27T20:38:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/ProtGenerics/DESCRIPTION
remove extra blank lines
Revision: 99947
Author: stvjc
Date: 2015-02-27T20:37:30+00:00
Paths:
Added  /trunk/madman/Rpacks/edxBioc/vignettes/pngs/asthFull.png
Added  /trunk/madman/Rpacks/edxBioc/vignettes/pngs/reactomeBrow.png
new pics for pathways
Revision: 99946
Author: s.arora
Date: 2015-02-27T20:24:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHubResource-class.R
code update

- add client code to handle zip file and return a
pointer to the unzipped file
Revision: 99945
Author: s.arora
Date: 2015-02-27T20:22:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeChEA.R
code update

- get chea file from website
- the file is too big to read into memory with R
- just unzip it and return a file pointer to user. 
Revision: 99944
Author: m.carlson
Date: 2015-02-27T20:07:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/vignettes/AnnotationHubRecipes.Rmd
updates the vignette that tells people how to write their own recipes.
Revision: 99943
Author: n.hayden
Date: 2015-02-27T20:06:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/TransView/DESCRIPTION
update to require proper version of Rsamtools
Revision: 99942
Author: n.hayden
Date: 2015-02-27T20:02:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqbias/DESCRIPTION
update to require proper Rsamtools version
Revision: 99941
Author: n.hayden
Date: 2015-02-27T19:32:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/qrqc/DESCRIPTION
update to depend on proper version of Rsamtools
Revision: 99940
Author: n.hayden
Date: 2015-02-27T19:27:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/h5vc/DESCRIPTION
Modified  /trunk/madman/Rpacks/h5vc/src/Makevars
Modified  /trunk/madman/Rpacks/h5vc/src/Makevars.common
Modified  /trunk/madman/Rpacks/h5vc/src/Makevars.win
fix getting Rsamtools lib dependencies
Revision: 99939
Author: m.carlson
Date: 2015-02-27T19:17:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
Helpful comment about how to document new preparerClasses
Revision: 99938
Author: n.hayden
Date: 2015-02-27T19:16:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/DiffBind/DESCRIPTION
update to require proper version of Rsamtools
Revision: 99935
Author: n.hayden
Date: 2015-02-27T18:56:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/deepSNV/DESCRIPTION
Modified  /trunk/madman/Rpacks/deepSNV/src/Makevars.common
Modified  /trunk/madman/Rpacks/deepSNV/src/Makevars.in
Modified  /trunk/madman/Rpacks/deepSNV/src/Makevars.win
fix getting Rsamtools libs dependencies
Revision: 99934
Author: s.gibb
Date: 2015-02-27T18:49:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/cleaver/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: cf992c20136ab16d84bda62c4c7ee590b48d1b24

    add bioc-required:true

Committed by: Sebastian Gibb
Author Name: Sebastian Gibb
Commit date: 2015-02-27 19:50:02 +0100
Author date: 2015-02-27 19:50:02 +0100
Revision: 99933
Author: s.gibb
Date: 2015-02-27T18:48:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/cleaver/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 95ee81078dde54d4402f57fd325accdba6f88a59

    update .travis.yml for native R support

Committed by: Sebastian Gibb
Author Name: Sebastian Gibb
Commit date: 2015-02-27 19:48:27 +0100
Author date: 2015-02-27 19:48:27 +0100
Revision: 99932
Author: n.hayden
Date: 2015-02-27T18:43:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
increase min Rsamtools version
Revision: 99929
Author: n.hayden
Date: 2015-02-27T18:33:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/Rsamtools.mk.win
include ZLIB_CFLAGS in SAMTOOLS_CPPFLAGS
Revision: 99928
Author: s.arora
Date: 2015-02-27T18:29:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/data/biocViewsVocab.rda
Modified  /trunk/madman/Rpacks/biocViews/inst/dot/biocViewsVocab.dot
Modified  /trunk/madman/Rpacks/biocViews/inst/extdata/biocViewsVocab.sqlite
biocView update

- add KEGG, Reactome, BioCarta, NCINatureCurated to biocViews

Revision: 99925
Author: n.hayden
Date: 2015-02-27T15:33:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/QuasR/DESCRIPTION
Modified  /trunk/madman/Rpacks/QuasR/src/Makevars
Modified  /trunk/madman/Rpacks/QuasR/src/Makevars.win
revert last commit
Revision: 99924
Author: m.love
Date: 2015-02-27T15:00:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rnw
add to vignette
Revision: 99922
Author: stvjc
Date: 2015-02-27T11:00:31+00:00
Paths:
Added  /trunk/madman/Rpacks/edxBioc/vignettes/pngs/asthDetail.png
new asthma detail pathway
Revision: 99921
Author: stvjc
Date: 2015-02-27T10:57:38+00:00
Paths:
Added  /trunk/madman/Rpacks/edxBioc/vignettes/pngs/KEGGORTHpic.png
new pic for KEGGORTH
Revision: 99919
Author: k.uziela
Date: 2015-02-27T09:52:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/prebs/DESCRIPTION
Modified  /trunk/madman/Rpacks/prebs/NAMESPACE
Modified  /trunk/madman/Rpacks/prebs/R/PREBS.R
Corrected NAMESPACE class constructor imports
Revision: 99918
Author: x.zheng
Date: 2015-02-27T07:55:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/DESCRIPTION
Modified  /trunk/madman/Rpacks/gdsfmt/NEWS
Modified  /trunk/madman/Rpacks/gdsfmt/R/gdsfmt-main.r
Modified  /trunk/madman/Rpacks/gdsfmt/README.md
Modified  /trunk/madman/Rpacks/gdsfmt/appveyor.yml
Modified  /trunk/madman/Rpacks/gdsfmt/inst/include/R_GDS.h
Modified  /trunk/madman/Rpacks/gdsfmt/man/objdesp.gdsn.Rd
Modified  /trunk/madman/Rpacks/gdsfmt/src/gdsfmt.cpp
Modified  /trunk/madman/Rpacks/gdsfmt/vignettes/gdsfmt_vignette.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 0bf3211dbc8738a86b0411cd51ff7dbc24eedbc4

    new examples in vignette / improve 'objdesp.gdsn'

Committed by: Xiuwen Zheng
Author Name: Xiuwen Zheng
Commit date: 2015-02-26 23:56:04 -0800
Author date: 2015-02-26 23:56:04 -0800
Revision: 99917
Author: g.yu
Date: 2015-02-27T06:31:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/R/plotAnno.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 296e117a5fa0ae4f6f102c8cb81d73710128334b

    bug fixed in anno stats

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-02-27 14:31:18 +0800
Author date: 2015-02-27 14:31:18 +0800
Revision: 99916
Author: l.collado-torres
Date: 2015-02-27T04:32:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/regionReport/R/derfinderReport.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: abb55552f5f2f43f5247146274ef1fd899b97eaa

    Fixed default option for 'clean'

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2015-02-26 23:31:41 -0500
Author date: 2015-02-26 23:31:41 -0500
Revision: 99914
Author: l.collado-torres
Date: 2015-02-27T04:15:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/regionReport/DESCRIPTION
Modified  /trunk/madman/Rpacks/regionReport/NEWS
Modified  /trunk/madman/Rpacks/regionReport/R/derfinderReport.R
Modified  /trunk/madman/Rpacks/regionReport/README.md
Modified  /trunk/madman/Rpacks/regionReport/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c5187f119addb8be2fd763f3a3a219cbdeced820

    v1.1.7 -- Allow more control on render options in derfinderReport()

    Allow the user to supply 'clean' and 'output_format' options when running
    derfinderReport()

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2015-02-26 23:12:20 -0500
Author date: 2015-02-26 23:12:20 -0500

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