Subversion Logs

This is a list of recent commits to the development branch of the Bioconductor Subversion repository.

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Revision: 104146
Author: a.lun
Date: 2015-05-24T04:22:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/edgeR/R/processAmplicons.R
Modified  /trunk/madman/Rpacks/edgeR/src/R_process_hairpin_reads.c
Removed hard limits in R code, cleaned up temporary file removal and duplicate checking.
Revision: 104145
Author: j.lugo
Date: 2015-05-23T21:51:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/cnvGSA/R/cnvGSA.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9ece0ca6917a2df4d2f06befb326b814ffe0473b

    Fixed spacing

Revision: 104144
Author: y.assenov
Date: 2015-05-23T21:03:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/R/annotations.R
Bugfix in data.frame2GRanges
Revision: 104139
Author: mtmorgan
Date: 2015-05-23T17:11:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
Modified  /trunk/madman/Rpacks/AnnotationHub/inst/unitTests/test_AnnotationHub-class.R
(silently) coerce NA subscripts to FALSE
Revision: 104138
Author: a.akalin
Date: 2015-05-23T16:50:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/genomation/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9c264f415394c7735b922a02d23b8ec2064b45a7

    Update DESCRIPTION

Revision: 104137
Author: a.teschendorff
Date: 2015-05-23T15:15:28+00:00
Paths:
 /trunk/madman/Rpacks/DART/DESCRIPTION
 /trunk/madman/Rpacks/DART/NAMESPACE
 /trunk/madman/Rpacks/DART/R
Added  /trunk/madman/Rpacks/DART/R/BuildRN.R
Added  /trunk/madman/Rpacks/DART/R/DoDART.R
Added  /trunk/madman/Rpacks/DART/R/DoDARTCLQ.R
Added  /trunk/madman/Rpacks/DART/R/EvalConsNet.R
Added  /trunk/madman/Rpacks/DART/R/PredActScore.R
Added  /trunk/madman/Rpacks/DART/R/PruneNet.R
 /trunk/madman/Rpacks/DART/build
Added  /trunk/madman/Rpacks/DART/build/vignette.rds
 /trunk/madman/Rpacks/DART/data
Added  /trunk/madman/Rpacks/DART/data/dataDART.rda
Added  /trunk/madman/Rpacks/DART/data/datalist
 /trunk/madman/Rpacks/DART/inst
Added  /trunk/madman/Rpacks/DART/inst/CITATION
Added  /trunk/madman/Rpacks/DART/inst/NEWS
Added  /trunk/madman/Rpacks/DART/inst/doc
Added  /trunk/madman/Rpacks/DART/inst/doc/DART.R
Added  /trunk/madman/Rpacks/DART/inst/doc/DART.Rnw
Added  /trunk/madman/Rpacks/DART/inst/doc/DART.pdf
 /trunk/madman/Rpacks/DART/man
Added  /trunk/madman/Rpacks/DART/man/BuildRN.Rd
Added  /trunk/madman/Rpacks/DART/man/DART-package.Rd
Added  /trunk/madman/Rpacks/DART/man/DoDART.Rd
Added  /trunk/madman/Rpacks/DART/man/DoDARTCLQ.Rd
Added  /trunk/madman/Rpacks/DART/man/EvalConsNet.Rd
Added  /trunk/madman/Rpacks/DART/man/PredActScore.Rd
Added  /trunk/madman/Rpacks/DART/man/PruneNet.Rd
Added  /trunk/madman/Rpacks/DART/man/dataDART.Rd
 /trunk/madman/Rpacks/DART/vignettes
Added  /trunk/madman/Rpacks/DART/vignettes/DART.Rnw
value names changes
Revision: 104136
Author: mtmorgan
Date: 2015-05-23T02:17:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/vignettes/AnnotationHub-HOWTO.Rmd
minor tweaks to AnnotationHub-HOWTO vignette

- all sub-headings at same level
- liftOver is from hg19 --> hg38
- slightly more discriptive names for some important examples, e.g.,
  'peaks', 'variants'
- initial import in a hidden chunk, to avoid progress bar output if
  resource not in build-system cache
- mention help (e.g., ?readVcf) and other vignettes a little more
- additional minor tweaks
Revision: 104132
Author: m.carlson
Date: 2015-05-23T00:21:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEnsemblFasta.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/scripts/updateToLatestEnsembl.R
Some minor bug fixes for recipe in updateToLatestEnsembl.R
Revision: 104131
Author: s.arora
Date: 2015-05-23T00:10:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Added  /trunk/madman/Rpacks/AnnotationHubData/NEWS
Add a news file for AnnotationHubData
Revision: 104130
Author: s.arora
Date: 2015-05-22T23:35:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/inst/unitTests/test_AnnotationHub-class.R
unit Test update

the query test was testing if 11 records were returned( one for each ensembl
release) Since release 80 gtf files were added to the hub, this was breaking
 the unitTest as there are now 12 records!
So have updated the unitTest to not rely on the number of ensembl versions

Revision: 104129
Author: s.arora
Date: 2015-05-22T23:18:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/vignettes/AnnotationHub-HOWTO.Rmd
vignette update

- add third example for downloading vcf files from dbSNP
Revision: 104128
Author: s.arora
Date: 2015-05-22T22:45:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/vignettes/AnnotationHub-HOWTO.Rmd
vignette update

- remove progress bar from vignette for first time
users by using chunk option results='hide'
- use biocstyle for package name
- italicize objects
 
Revision: 104127
Author: hpages
Date: 2015-05-22T22:30:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/prepare_list_of_rda_files_to_update.R
more work on the "Find and update objects" procedure
Revision: 104121
Author: v.obenchain
Date: 2015-05-22T21:13:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/R/SnowParam-class.R
catch cluster options before dispatch to .SnowParam()
Revision: 104117
Author: hpages
Date: 2015-05-22T18:49:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/prepare_list_of_rda_files_to_update.R
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/scan_rda_files.R
more work on the "Find and update objects" procedure
Revision: 104116
Author: jmacdon
Date: 2015-05-22T18:39:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/affycoretools/R/plotma.R
Removed extra cruft from maplot().
Revision: 104114
Author: jmacdon
Date: 2015-05-22T18:37:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/affycoretools/DESCRIPTION
Modified  /trunk/madman/Rpacks/affycoretools/NAMESPACE
Modified  /trunk/madman/Rpacks/affycoretools/R/affycoretools.R
Modified  /trunk/madman/Rpacks/affycoretools/R/affystart.R
Modified  /trunk/madman/Rpacks/affycoretools/man/affycoretools.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/affystart.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/dataAndHeatmapPage.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/entrezLinks.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/fixHeaderAndGo.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/geneSetPage.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/getCols.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/getMainProbes.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/gsHeatmap.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/intNames.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/make.cl.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/makeGoGeneTable.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/makeGoTable.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/makeHmap.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/makeImages.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/makeIndices.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/makeVenn.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/maplot.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/mirna2mrna.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/outputRomer.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/pca.legend.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/plotDeg.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/plotPCA.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/runRomer.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/tableFilt.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/venn4Way.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/vennCounts2.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/vennPage.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/vennSelect2.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/writeFit.Rd
Fixes for changes made to maplot().
Revision: 104112
Author: p.bellot
Date: 2015-05-22T18:11:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/netbenchmark/R/experiments.bench.R
- Bug fix in experiments.bench dataset instead of datasource
Revision: 104109
Author: p.bellot
Date: 2015-05-22T17:36:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/netbenchmark/DESCRIPTION
Modified  /trunk/madman/Rpacks/netbenchmark/R/dataset.subsample.R
Modified  /trunk/madman/Rpacks/netbenchmark/R/evaluate.R
Modified  /trunk/madman/Rpacks/netbenchmark/R/experiments.bench.R
Modified  /trunk/madman/Rpacks/netbenchmark/R/netbenchmark.R
Modified  /trunk/madman/Rpacks/netbenchmark/R/noise.bench.R
Modified  /trunk/madman/Rpacks/netbenchmark/inst/NEWS
Modified  /trunk/madman/Rpacks/netbenchmark/inst/unitTests/test_evaluate.R
Modified  /trunk/madman/Rpacks/netbenchmark/man/experiments.bench.Rd
Modified  /trunk/madman/Rpacks/netbenchmark/man/netbenchmark.Rd
Modified  /trunk/madman/Rpacks/netbenchmark/man/netbenchmark.data.Rd
Modified  /trunk/madman/Rpacks/netbenchmark/man/noise.bench.Rd
Modified  /trunk/madman/Rpacks/netbenchmark/src/rate.cpp
- Better handling of ties between predictions in evaluation
- It is possible to specify the ranges of local.noise and global.noise
- Bug fix in experiments.bench.R, using the whole datasource
- Better summary table in netbenchmark.R
- Adding verbose obtion to all the benchmark
Revision: 104107
Author: u.bodenhofer
Date: 2015-05-22T15:34:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/podkat/DESCRIPTION
Modified  /trunk/madman/Rpacks/podkat/R/weights-methods.R
Modified  /trunk/madman/Rpacks/podkat/inst/NEWS
Fix of weights() method; version number bumped to 1.1.2
Revision: 104104
Author: khansen
Date: 2015-05-22T14:45:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/DESCRIPTION
Modified  /trunk/madman/Rpacks/minfi/R/compartments.R
Modified  /trunk/madman/Rpacks/minfi/man/preprocessFunnorm.Rd
Modified  /trunk/madman/Rpacks/minfi/man/preprocessNoob.Rd
Modified  /trunk/madman/Rpacks/minfi/man/preprocessQuantile.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 75bf0420afbecf45b36a44f241baa03afe3af79f

    bumped version; used dontrun{} in some examples which are also part of the testing suite

Revision: 104103
Author: m.lawrence
Date: 2015-05-22T14:42:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocGenerics/NAMESPACE
export grep and grepl generics
Revision: 104102
Author: b.fischer
Date: 2015-05-22T14:35:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/CHANGES
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
Modified  /trunk/madman/Rpacks/rhdf5/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/rhdf5/src/H5D.c
Memory allocation on heap instead of stack for reading large datasets (Thanks to a patch from Jimmy Jia)
Revision: 104101
Author: l.gatto
Date: 2015-05-22T13:57:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/DESCRIPTION
Modified  /trunk/madman/Rpacks/MSnbase/NEWS
Modified  /trunk/madman/Rpacks/MSnbase/R/utils.R
Added  /trunk/madman/Rpacks/MSnbase/inst/extdata/iTRAQ8plexPurityCorrections.csv
Modified  /trunk/madman/Rpacks/MSnbase/man/MSnSet-class.Rd
Modified  /trunk/madman/Rpacks/MSnbase/man/purityCorrect-methods.Rd
Modified  /trunk/madman/Rpacks/MSnbase/vignettes/MSnbase-demo.Rnw
Merge branch 'master' into local-hedgehog

iTRAQ 8-plex correction factors and impurity matrix
Revision: 104100
Author: g.yu
Date: 2015-05-22T09:09:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/NAMESPACE
Modified  /trunk/madman/Rpacks/ggtree/NEWS
Modified  /trunk/madman/Rpacks/ggtree/R/gplot.R
Added  /trunk/madman/Rpacks/ggtree/inst/examples/FluA_H3_AA.fas
Modified  /trunk/madman/Rpacks/ggtree/vignettes/ggtree.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b05c865913dd695504d01ae435cfc9d0eda40f0e

    update vignette

Revision: 104099
Author: g.yu
Date: 2015-05-22T08:47:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/DESCRIPTION
Modified  /trunk/madman/Rpacks/ggtree/NAMESPACE
Modified  /trunk/madman/Rpacks/ggtree/NEWS
Modified  /trunk/madman/Rpacks/ggtree/R/gplot.R
Modified  /trunk/madman/Rpacks/ggtree/TODO.md
Modified  /trunk/madman/Rpacks/ggtree/appveyor.yml
Added  /trunk/madman/Rpacks/ggtree/man/msaplot.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 48b838ee337e94cff1f69151d75091b17bd7257f

    msaplot


Commit id: 6083e201a71a1ff5ae2d11e635fb91e9e9c0b3fd

    update appveyor.yml

Revision: 104098
Author: hpages
Date: 2015-05-22T08:18:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/scan_rda_files.R
more work on the "Find and update objects" procedure
Revision: 104096
Author: z.gu
Date: 2015-05-22T07:05:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/ComplexHeatmap/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 746d856f48f8b99f98a81d56305995b3d9785474

    Update DESCRIPTION

Revision: 104095
Author: g.yu
Date: 2015-05-22T05:56:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/appveyor.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2211e2a3f29924eea047afcf278a8f9e3e769705

    appveyor

Revision: 104094
Author: g.yu
Date: 2015-05-22T05:50:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/appveyor.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 077875e2e0f582f4b3d0adc680ca34ad53820199

    appveyor

Revision: 104093
Author: g.yu
Date: 2015-05-22T05:48:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/README.md
Modified  /trunk/madman/Rpacks/ggtree/appveyor.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 68e1f93d5e04a52faa3e12fd9cd96dd4f6aaf575

    appveyor


Commit id: b71ca033ae39d57ef1342804552c86e0926ac078

    appveyor

Revision: 104091
Author: a.lun
Date: 2015-05-22T04:23:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/edgeR/R/processAmplicons.R
Modified  /trunk/madman/Rpacks/edgeR/man/processAmplicons.Rd
Modified  /trunk/madman/Rpacks/edgeR/src/R_process_hairpin_reads.c
Modified  /trunk/madman/Rpacks/edgeR/src/init.cpp
Modified  /trunk/madman/Rpacks/edgeR/src/utils.h
Change in processAmplicons interface, bug fixes.
Revision: 104090
Author: g.yu
Date: 2015-05-22T04:19:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/R/NJ.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: c2e913931369b253fe5536bb44aee4a0787b2a99

    remove non-ASCII character

Revision: 104088
Author: g.yu
Date: 2015-05-22T04:01:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/.Rbuildignore
Deleted  /trunk/madman/Rpacks/ggtree/TODO
Added  /trunk/madman/Rpacks/ggtree/TODO.md
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f3f2f4065c71fc16952e75fed6b0d658ce467e03

    TODO

Revision: 104087
Author: g.yu
Date: 2015-05-22T03:56:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/.travis.yml
Modified  /trunk/madman/Rpacks/ggtree/NEWS
Modified  /trunk/madman/Rpacks/ggtree/R/ggtree.R
Modified  /trunk/madman/Rpacks/ggtree/R/tree.R
Added  /trunk/madman/Rpacks/ggtree/TODO
Modified  /trunk/madman/Rpacks/ggtree/man/scaleClade.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 71e927079cd39a6640648cb63817e21f0b2a91cc

    add TODO


Commit id: c0e98b6afe6d0fd9b7bed0f92b5f909d1cb28f73

    vertical_only parameter in scaleClade


Commit id: d2029e826227000f0112629b025a91e14831a79e

    add apt_packages for compiling fftwtools pkg

Revision: 104086
Author: g.yu
Date: 2015-05-22T02:56:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/.travis.yml
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPseeker/NAMESPACE
Modified  /trunk/madman/Rpacks/ChIPseeker/NEWS
Modified  /trunk/madman/Rpacks/ChIPseeker/R/covplot.R
Modified  /trunk/madman/Rpacks/ChIPseeker/R/enrichOverlap.R
Modified  /trunk/madman/Rpacks/ChIPseeker/README.md
Modified  /trunk/madman/Rpacks/ChIPseeker/vignettes/ChIPseeker.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 7a1da11aec9b6b04d816601cb7b115c05b104369

    add travis

Revision: 104085
Author: g.yu
Date: 2015-05-22T02:55:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/README.md
Commit made by the Bioconductor Git-SVN bridge.

Commit id: ec4d8311fa3853de52b7831dfa7e457b6550cf21

    remove appveyor in readme

Revision: 104084
Author: g.yu
Date: 2015-05-22T02:49:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 354c38549313591b6a83b569f521d0801cdc1ee6

    .travis

Revision: 104083
Author: g.yu
Date: 2015-05-22T02:28:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 411ea08d5d93f2ba0a07fed5703bb7d4877fb7bc

    Update .travis.yml

    update .travis based on support of r language
Revision: 104081
Author: m.carlson
Date: 2015-05-22T01:01:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/OrganismDbi/DESCRIPTION
Modified  /trunk/madman/Rpacks/OrganismDbi/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/OrganismDbi/R/methods-select.R
Many thoughts on how to enhance selectByRanges.
Revision: 104080
Author: rscharpf
Date: 2015-05-22T00:33:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/VanillaICE/DESCRIPTION
Modified  /trunk/madman/Rpacks/VanillaICE/vignettes/crlmmDownstream.Rnw
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 81c55c9d8ad1ecdaa1e7c3be187ee541a85d22d4

    Remove unevaluated parallelization from crlmmDownstream vignette

Revision: 104078
Author: hpages
Date: 2015-05-22T00:12:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/prepare_list_of_rda_files_to_update.R
more tweaks to "Find and update objects" procedure
Revision: 104077
Author: m.lawrence
Date: 2015-05-21T23:14:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/gmapR/scripts/getGmapGstructSourceCode.R
gstruct should always use trunk
Revision: 104076
Author: m.lawrence
Date: 2015-05-21T23:14:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantTools/R/callGenotypes.R
use storage.mode instead of mode
Revision: 104075
Author: m.lawrence
Date: 2015-05-21T23:11:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/AllUtilities.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VRanges-class.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-genotypeToSnpMatrix.R
use storage.mode instead of mode; seems cleaner
Revision: 104074
Author: m.lawrence
Date: 2015-05-21T23:10:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-class.R
rename fixedColumnNames => parallelVectorNames
Revision: 104073
Author: m.lawrence
Date: 2015-05-21T23:08:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/R/Vector-comparison.R
fix typo in orderBy()
Revision: 104072
Author: m.lawrence
Date: 2015-05-21T23:07:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/NAMESPACE
Modified  /trunk/madman/Rpacks/S4Vectors/R/Rle-utils.R
add grep and grepl methods for Rle
Revision: 104071
Author: m.lawrence
Date: 2015-05-21T23:05:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/NAMESPACE
Modified  /trunk/madman/Rpacks/S4Vectors/R/Vector-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/man/Vector-class.Rd
fixedColumnNames() renamed to parallelVectorNames(); also, tweaks to rename()
Revision: 104070
Author: m.lawrence
Date: 2015-05-21T23:01:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/R/Rle-class.R
fixes to Rle sorting
Revision: 104069
Author: m.lawrence
Date: 2015-05-21T23:00:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/R/List-class.R
elementType,vector uses storage.mode() instead of mode()
Revision: 104068
Author: m.lawrence
Date: 2015-05-21T22:58:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocGenerics/R/show-utils.R
improvements to show utilities
Revision: 104067
Author: m.lawrence
Date: 2015-05-21T22:58:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocGenerics/DESCRIPTION
Added  /trunk/madman/Rpacks/BiocGenerics/R/grep.R
Added  /trunk/madman/Rpacks/BiocGenerics/man/grep.Rd
add grep, grepl generics
Revision: 104065
Author: hpages
Date: 2015-05-21T22:52:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/Find_and_update_objects.txt
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/prepare_list_of_rda_files_to_update.R
more tweaks to "Find and update objects" procedure
Revision: 104064
Author: s.arora
Date: 2015-05-21T22:48:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makedbSNPVCF.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/webAccessFunctions.R
recipe update - dbSNP

- Add vcf files from the following genome builds for humans
     "human_9606/VCF/clinical_vcf_set/",
     "human_9606_b141_GRCh37p13/VCF/",
     "human_9606_b142_GRCh37p13/VCF/",
     "human_9606_b142_GRCh37p13/VCF/clinical_vcf_set/"

- Make sure all VCF file formats are available for each build
  ("latest.vcf.gz" files were being excluded previously, they are
  now included)

- Add a news file to keep track of changes inside AHD.

- Bug fix -helper function .ftpFileInfo was not returning filename in fileurl

Revision: 104059
Author: p.haverty
Date: 2015-05-21T21:36:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/bigmemoryExtras/DESCRIPTION
Modified  /trunk/madman/Rpacks/bigmemoryExtras/R/BigMatrix.R
Version: 1.13.2. Always normalize path for backingpath
Revision: 104057
Author: c.meng
Date: 2015-05-21T20:34:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/omicade4/DESCRIPTION
Modified  /trunk/madman/Rpacks/omicade4/NAMESPACE
Modified  /trunk/madman/Rpacks/omicade4/inst/NEWS
add function topVar
Revision: 104056
Author: f.klein
Date: 2015-05-21T20:11:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/FourCSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/FourCSeq/R/reference_fragments.R
added fixed=subject to vmatchPattern querry to allow wild cards in the re enzyme patterns
Revision: 104055
Author: hpages
Date: 2015-05-21T19:57:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/Find_and_update_objects.txt
Modified  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/prepare_list_of_rda_files_to_update.R
some minor tweaks to "Find and update objects" procedure
Revision: 104053
Author: s.arora
Date: 2015-05-21T19:45:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEpigenomeRoadmap.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeHaemCode.R
bug fix

All bigwig file record's rdataclass was incorrectly specified as
"GRanges" - corrected it to have "BigWigFile" as the correct rdataclass
Revision: 104051
Author: hpages
Date: 2015-05-21T19:25:33+00:00
Paths:
Added  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts
Added  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/Find_and_update_objects.txt
Added  /trunk/madman/Rpacks/SummarizedExperiment/inst/scripts/prepare_list_of_rda_files_to_update.R
Start adding documentation and scripts for finding and updating serialized
objects located in a directory hierarchy.
Revision: 104050
Author: m.jiang
Date: 2015-05-21T19:16:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/.gitignore
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingSet-Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/inst/tests/InternalTestSuite.R
Modified  /trunk/madman/Rpacks/flowWorkspace/src/transformation.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3a723d7165f7250fd8eb071ad2c2fec3cd95c759

    add .fix_channel_slash routine to fix the slash issue of vX when transform range slot within transformRange. #90


Commit id: 826f4083a9ffbddd38bf8f5d8efc295c7e08210f

    tidy up transformRange


Commit id: 046316ffeb750ad5f8cc43dc263cc124063f644d

    downgrade transformation type to CALTBL explicitly in transformation::getInverseTransformation so that it is consistent with the object it returns

Revision: 104049
Author: s.arora
Date: 2015-05-21T19:05:19+00:00
Paths:
Added  /trunk/madman/Rpacks/ELMER
Added  /trunk/madman/Rpacks/ELMER/DESCRIPTION
Added  /trunk/madman/Rpacks/ELMER/NAMESPACE
Added  /trunk/madman/Rpacks/ELMER/R
Added  /trunk/madman/Rpacks/ELMER/R/Class.R
Added  /trunk/madman/Rpacks/ELMER/R/FetchTCGA.R
Added  /trunk/madman/Rpacks/ELMER/R/GetNearbyGenes.R
Added  /trunk/madman/Rpacks/ELMER/R/Main_function.R
Added  /trunk/madman/Rpacks/ELMER/R/Scatter.plot.R
Added  /trunk/madman/Rpacks/ELMER/R/Schematic.plot.R
Added  /trunk/madman/Rpacks/ELMER/R/Small.R
Added  /trunk/madman/Rpacks/ELMER/R/StatisticTest.R
Added  /trunk/madman/Rpacks/ELMER/R/TCGA_pipe.R
Added  /trunk/madman/Rpacks/ELMER/R/generic.R
Added  /trunk/madman/Rpacks/ELMER/R/methodAccess.R
Added  /trunk/madman/Rpacks/ELMER/R/motif.TF.Plots.R
Added  /trunk/madman/Rpacks/ELMER/inst
Added  /trunk/madman/Rpacks/ELMER/inst/extdata
Added  /trunk/madman/Rpacks/ELMER/inst/extdata/getTF.hypo.TFs.with.motif.pvalue.rda
Added  /trunk/madman/Rpacks/ELMER/inst/extdata/mee.example.rda
Added  /trunk/madman/Rpacks/ELMER/man
Added  /trunk/madman/Rpacks/ELMER/man/GetNearGenes.Rd
Added  /trunk/madman/Rpacks/ELMER/man/MEE.data-class.Rd
Added  /trunk/madman/Rpacks/ELMER/man/Pair-class.Rd
Added  /trunk/madman/Rpacks/ELMER/man/TCGA.pipe.Rd
Added  /trunk/madman/Rpacks/ELMER/man/TF.rank.plot.Rd
Added  /trunk/madman/Rpacks/ELMER/man/fetch.mee.Rd
Added  /trunk/madman/Rpacks/ELMER/man/fetch.pair.Rd
Added  /trunk/madman/Rpacks/ELMER/man/get.TFs.Rd
Added  /trunk/madman/Rpacks/ELMER/man/get.diff.meth.Rd
Added  /trunk/madman/Rpacks/ELMER/man/get.enriched.motif.Rd
Added  /trunk/madman/Rpacks/ELMER/man/get.feature.probe.Rd
Added  /trunk/madman/Rpacks/ELMER/man/get.pair.Rd
Added  /trunk/madman/Rpacks/ELMER/man/get.permu.Rd
Added  /trunk/madman/Rpacks/ELMER/man/get450K.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getClinic.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getExp.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getGeneID.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getGeneInfo.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getMeth.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getPair.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getProbeInfo.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getRNAseq.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getSample.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getSymbol.Rd
Added  /trunk/madman/Rpacks/ELMER/man/getTCGA.Rd
Added  /trunk/madman/Rpacks/ELMER/man/motif.enrichment.plot.Rd
Added  /trunk/madman/Rpacks/ELMER/man/promoterMeth.Rd
Added  /trunk/madman/Rpacks/ELMER/man/scatter.plot.Rd
Added  /trunk/madman/Rpacks/ELMER/man/schematic.plot.Rd
Added  /trunk/madman/Rpacks/ELMER/man/txs.Rd
Added  /trunk/madman/Rpacks/ELMER/vignettes
Added  /trunk/madman/Rpacks/ELMER/vignettes/vignettes.Rnw
Modified  /trunk/madman/Rpacks/bioc_3.2.manifest
add ELMER to the repository
Revision: 104048
Author: m.carlson
Date: 2015-05-21T18:23:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationForge/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationForge/R/NCBI_ftp.R
Modified  /trunk/madman/Rpacks/AnnotationForge/R/makeOrgPackageFromDataFrames.R
Changes the DB string in metadata from 'TAXID' to Taxonomy ID for consistency.

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