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Revision: 95905
Author: mtmorgan
Date: 2014-10-22T23:43:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGFF.R
argh! further typo
Revision: 95904
Author: m.carlson
Date: 2014-10-22T23:15:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/scripts/updateToLatestEnsembl.R
updates notes for how to use s3 to fix broken files etc.
Revision: 95903
Author: v.obenchain
Date: 2014-10-22T23:00:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/R/GenomicFiles-class.R
modify show method for GenomicFiles class
Revision: 95902
Author: mtmorgan
Date: 2014-10-22T22:54:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGFF.R
further clarify(?) warning message

- makeTranscriptDbFromGFF is deprecated
- "inferring' spelled correctly
- sync initial part of message with (redundant!) message
- shorten by removing politeness, speculation in intention
Revision: 95901
Author: v.obenchain
Date: 2014-10-22T22:18:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/R/reduceByRange-methods.R
Modified  /trunk/madman/Rpacks/GenomicFiles/man/GenomicFiles-class.Rd
Modified  /trunk/madman/Rpacks/GenomicFiles/man/reduceByYield.Rd
fix bug in reduceByRange,GenomicFiles-method
Revision: 95900
Author: d.tenenbaum
Date: 2014-10-22T21:48:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/data/biocViewsVocab.rda
Modified  /trunk/madman/Rpacks/biocViews/inst/extdata/biocViewsVocab.sqlite
update rda and sqlite files
Revision: 95899
Author: p.stempor
Date: 2014-10-22T21:40:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Modified  /trunk/madman/Rpacks/seqplots/R/getPlotSetArray.R
Modified  /trunk/madman/Rpacks/seqplots/R/int_getSF.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: 403ee2a1fd3bfbabb074f404facaa44431d68366

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: przemol
Author Name: przemol
Commit date: 2014-10-22 22:39:37 +0100
Author date: 2014-10-22 22:39:37 +0100

Commit id: f6cef8fe6716d6bfb6863be2724826e82159d048

    version bump - 1.1.3

Committed by: przemol
Author Name: przemol
Commit date: 2014-10-22 22:39:22 +0100
Author date: 2014-10-22 22:39:22 +0100

Commit id: e431392419044d17bdfe77a62b4d00ac06aaf5e3

    fix bug causing dispersed anchored motif plot ends

Committed by: przemol
Author Name: przemol
Commit date: 2014-10-22 22:38:17 +0100
Author date: 2014-10-22 22:38:17 +0100
Revision: 95898
Author: s.arora
Date: 2014-10-22T21:20:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/inst/dot/biocViewsVocab.dot
spelling update

- update biocViews: Txdb to TxDb 
Revision: 95897
Author: s.arora
Date: 2014-10-22T21:17:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/seqlevelsStyle.R
Added  /trunk/madman/Rpacks/GenomeInfoDb/inst/extdata/dataFiles/Canis_familiaris.txt
Modified  /trunk/madman/Rpacks/GenomeInfoDb/inst/unitTests/test_seqlevels-wrappers.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/vignettes/Accept-organism-for-GenomeInfoDb.Rnw
code and file update

- add support for Canis familaris
- adjust failing unit test example
- add email address to vignette
- adjust 2 functions -seqlevelsInGroup() and
extractSeqlevelsByGroup() to account for changes in
.guessSpeciesStyle()
Revision: 95895
Author: s.aibar
Date: 2014-10-22T20:17:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/R/3_analyzeNetwork.R
Modified  /trunk/madman/Rpacks/FGNet/man/analyzeNetwork.Rd
Modified  /trunk/madman/Rpacks/FGNet/vignettes/FGNet.Rmd
typo: betweenness
Revision: 95893
Author: v.obenchain
Date: 2014-10-22T20:04:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/refLocsToLocalLocs-methods.Rd
clean up warnings in refLocsToLocalLocs() man page
Revision: 95890
Author: t.backman
Date: 2014-10-22T18:49:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioassayR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 0 commit.

Commit information:


Revision: 95889
Author: s.aibar
Date: 2014-10-22T18:06:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/DESCRIPTION
Modified  /trunk/madman/Rpacks/FGNet/NEWS
date update
Revision: 95887
Author: s.arora
Date: 2014-10-22T17:50:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/seqlevels-wrappers.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/seqlevelsStyle.R
code update

- .guessSpeciesStyle() should return all possible hits (instead of
first hit ) found.
- have adjusted seqlevelsStyle() and keepStandardChromosomes()
to accordingly handle multiple output from .guessSpeciesStyle()
Revision: 95885
Author: g.ha
Date: 2014-10-22T17:29:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/TitanCNA/TitanCNA_update_notes.txt
TitanCNA v1.5.2: improved speed of getPositionOverlap()
Revision: 95884
Author: g.ha
Date: 2014-10-22T17:28:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/TitanCNA/DESCRIPTION
TitanCNA v1.5.2: improved speed of getPositionOverlap()
Revision: 95883
Author: g.ha
Date: 2014-10-22T17:25:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/TitanCNA/R/utils.R
Modified  /trunk/madman/Rpacks/TitanCNA/TitanCNA_update_notes.txt
Modified  /trunk/madman/Rpacks/TitanCNA/man/TitanCNA-package.Rd
TitanCNA v1.5.2: improved speed of getPositionOverlap()
Revision: 95880
Author: p.stempor
Date: 2014-10-22T17:08:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: a9972354f723ed5f21fa83c1b8aafa2505c08c6b

    Update README.md

Committed by: Przemol
Author Name: Przemol
Commit date: 2014-10-22 18:07:58 +0100
Author date: 2014-10-22 18:07:58 +0100
Revision: 95879
Author: p.stempor
Date: 2014-10-22T17:07:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 60106c09fcc6f8115c239804615aad060a42dbbf

    Update README.md

Committed by: Przemol
Author Name: Przemol
Commit date: 2014-10-22 18:07:20 +0100
Author date: 2014-10-22 18:07:20 +0100
Revision: 95878
Author: h.corradabravo
Date: 2014-10-22T17:03:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
Modified  /trunk/madman/Rpacks/epivizr/NAMESPACE
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizBpData-class.R
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizData-class.R
Added  /trunk/madman/Rpacks/epivizr/R/EpivizDataCache-class.R
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizDeviceMgr-class.R
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizFeatureData-class.R
Added  /trunk/madman/Rpacks/epivizr/R/EpivizWigCache-class.R
Added  /trunk/madman/Rpacks/epivizr/R/EpivizWigData-class.R
Modified  /trunk/madman/Rpacks/epivizr/R/register-methods.R
Added  /trunk/madman/Rpacks/epivizr/inst/tests/test-coverage.r
Added  /trunk/madman/Rpacks/epivizr/inst/tests/test-wigcache.r
Commit made by the Bioconductor Git-SVN bridge.
Consists of 29 commits.

Commit information:

Commit id: 9b7d677e8e5f4733b5e82a1babaf69161542026e

    version bump

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-22 13:02:55 -0400
Author date: 2014-10-22 13:02:55 -0400

Commit id: 45090618000d532d4dc43481108d662414a1193d

    Merge branch 'coverage'

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-22 13:02:30 -0400
Author date: 2014-10-22 13:02:30 -0400

Commit id: cac5968cd9115bd3a5f4d5432883a5f4a9de8ccd

    Merge branch 'master' into coverage

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 13:48:40 -0400
Author date: 2014-10-06 13:48:40 -0400

Commit id: 7dd99e7f277d1b82a7f9b91d5a06e444cb79bcca

    testing with cache list

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 12:33:32 -0400
Author date: 2014-10-06 12:33:32 -0400

Commit id: 9925774257b2698508490401e8ea418f5ee7be3b

    add cahce list, works again with single cache

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 11:38:10 -0400
Author date: 2014-10-06 11:38:10 -0400

Commit id: bad3832807fc47b0f6082bd4acb2ec942bed965f

    testing on brain bigwig

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 09:57:24 -0400
Author date: 2014-10-06 09:57:24 -0400

Commit id: ff488b3c8ec6d1006256f9585fd4f69247622983

    index offseting tested on summary

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 06:18:36 -0400
Author date: 2014-10-06 06:18:36 -0400

Commit id: 040e269500f68c0524f1457968757765702bb2b2

    refactor wigcache test

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 06:09:05 -0400
Author date: 2014-10-06 06:09:05 -0400

Commit id: 14e9d5b69491635c716ba9ff8afc146eca2acb06

    refactor wigcache test

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 05:59:37 -0400
Author date: 2014-10-06 05:59:37 -0400

Commit id: 8381b72fa1d48038e664c808ed222bd2e8902313

    index offsetting tested on import.bw

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 05:49:17 -0400
Author date: 2014-10-06 05:49:17 -0400

Commit id: 887a33a197891aaa68d7a8fa1e94ee5a575edcaf

    stitching with summary

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 05:07:09 -0400
Author date: 2014-10-06 05:07:09 -0400

Commit id: 43280a84c15f2c7d6a02d1036a7540258f8a7a6e

    stitching on import.bw

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 04:14:32 -0400
Author date: 2014-10-06 04:14:32 -0400

Commit id: 804d97cf931567067925f9037fb3985e34cc7904

    using windowSize

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-10-06 03:09:33 -0400
Author date: 2014-10-06 03:09:33 -0400

Commit id: 74bb9024512aa99ab83ec9d4f767b43f1fb2d2d8

    fix verbosity issue

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-09-24 12:48:42 -0400
Author date: 2014-09-24 12:48:42 -0400

Commit id: 9201e1ecd5f354a95f8d49eed4717bdb1db6c0ae

    simplify coverage test

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-09-15 13:04:44 -0400
Author date: 2014-09-15 13:04:44 -0400

Commit id: 1aa4837cbcc405a566c2809a2daf4fba0f9e7333

    modify simple wig test

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-09-15 12:53:34 -0400
Author date: 2014-09-15 12:53:34 -0400

Commit id: 208f30bacad3e70ce71d2abb5a25ee3200f7321a

    testing wig cache works again

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-09-15 12:42:15 -0400
Author date: 2014-09-15 12:42:15 -0400

Commit id: b612d86a26ac7f78478b2b3586c65bc906599567

    Merge branch 'master' into coverage

Committed by: Hector Corrada Bravo
Author Name: Hector Corrada Bravo
Commit date: 2014-09-15 12:08:21 -0400
Author date: 2014-09-15 12:08:21 -0400

Commit id: d3cd4d5ab9918df2f35d9ee29d8894b7dfb19d16

    Merge branch 'master' into coverage

    Conflicts:
        DESCRIPTION
        NAMESPACE
        R/EpivizDeviceMgr-class.R
        R/register-methods.R

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-09-11 08:43:01 -0400
Author date: 2014-09-11 08:43:01 -0400

Commit id: cd2f3ea0c308148ffcab985bcc0b14262509f75b

    Merge branch 'coverage' of https://github.com/epiviz/epivizr into coverage

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-07-24 13:18:52 -0400
Author date: 2014-07-24 13:18:52 -0400

Commit id: 524d57e655319d08a8753019e65fb3439a8bc882

    wig using summarize

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-07-24 13:18:30 -0400
Author date: 2014-06-12 13:10:46 -0400

Commit id: e981c75ca56583a9f74da36e56d6a9371cc9976a

    wig using summarize

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-06-12 13:12:59 -0400
Author date: 2014-06-12 13:10:46 -0400

Commit id: 00314a35f2d1320d4288453db88d3918b36d9fe4

    Merge branch 'master' into coverage

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-06-12 08:15:36 -0400
Author date: 2014-06-12 08:15:36 -0400

Commit id: 2dba326d03159f93448a9b28ce8d43dafc5d72e7

    first attempt at wig import

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-05-21 16:58:39 -0400
Author date: 2014-05-21 16:58:39 -0400

Commit id: b9400844eb7a33b4f6794e1a4002087e8c61ed1a

    bamfile coverage viz (all in-mermory version)

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-05-16 09:33:25 -0400
Author date: 2014-05-16 09:33:25 -0400

Commit id: bacea07b79a7bfc573a17f0f1480c13b1d0c4d2b

    plot coverage from GAlignments object (simplest version)

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-05-15 23:34:32 -0400
Author date: 2014-05-15 23:34:32 -0400

Commit id: 357ad4f05d2780d34a5357fb2d7322e922a7219b

    Merge branch 'master' into coverage

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-05-15 23:26:02 -0400
Author date: 2014-05-15 23:26:02 -0400

Commit id: fd5de411e50a98b7327270235911967a4517e55f

    Merge branch 'master' into coverage

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-05-15 23:21:46 -0400
Author date: 2014-05-15 23:21:46 -0400

Commit id: df152f00e26a51ead1c0371e6e978863af2d00de

    register alignments

Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-05-15 23:19:12 -0400
Author date: 2014-05-15 23:19:12 -0400
Revision: 95876
Author: s.aibar
Date: 2014-10-22T16:57:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/vignettes/FGNet.Rmd
3.1.4 Typo: betweenness
Revision: 95875
Author: s.aibar
Date: 2014-10-22T16:44:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/R/3_analyzeNetwork.R
Modified  /trunk/madman/Rpacks/FGNet/R/private_createHtml.R
Modified  /trunk/madman/Rpacks/FGNet/man/analyzeNetwork.Rd
Modified  /trunk/madman/Rpacks/FGNet/vignettes/FGNet.Rmd
3.1.4 Typo: betweenness
Revision: 95874
Author: venkatre
Date: 2014-10-22T15:50:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/DNAcopy/DESCRIPTION
Modified  /trunk/madman/Rpacks/DNAcopy/R/plotSample.R
Modified  /trunk/madman/Rpacks/DNAcopy/inst/CHANGES
add as.numeric to cumsum call in plotSample to address integer overflow

Revision: 95873
Author: l.zhu
Date: 2014-10-22T14:28:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/R/filterOffTarget.R
Modified  /trunk/madman/Rpacks/CRISPRseek/R/offTargetAnalysis.R
Modified  /trunk/madman/Rpacks/CRISPRseek/inst/NEWS
Modified  /trunk/madman/Rpacks/CRISPRseek/man/offTargetAnalysis.Rd
added useEfficacyFromInputSeq parameter in offTargetAnalysis function
Revision: 95872
Author: p.stempor
Date: 2014-10-22T13:21:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: bf7ac3615c3cf6a719846a622e77b2f0aa3d2667

    Update README.md

Committed by: Przemol
Author Name: Przemol
Commit date: 2014-10-22 14:21:12 +0100
Author date: 2014-10-22 14:21:12 +0100
Revision: 95869
Author: d.rossell
Date: 2014-10-22T11:35:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/casper/src/model.cpp
Modified  /trunk/madman/Rpacks/casper/src/model.h
Modified  /trunk/madman/Rpacks/casper/src/seppel.cpp
Modified  /trunk/madman/Rpacks/casper/src/seppel.h
Faster exploreSubmodels that also explores more models
Revision: 95868
Author: f.marini
Date: 2014-10-22T11:17:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowcatchR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 0e2e5deab7e98b5dbc4210459446cf1030a6f188

    fixed url

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-10-22 13:17:09 +0200
Author date: 2014-10-22 13:17:09 +0200
Revision: 95867
Author: f.marini
Date: 2014-10-22T11:05:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowcatchR/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowcatchR/R/auxiliary.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: 44c7bc852ac8a304701817b9ec31a54c0d4bb1a2

    fixed conflicts in description

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-10-22 13:05:11 +0200
Author date: 2014-10-22 13:05:11 +0200

Commit id: 729abbf5b62bfcc2a03621556ea6e7f1032cda0d

    Merge branch 'master' of https://github.com/federicomarini/flowcatchR

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-10-22 13:01:33 +0200
Author date: 2014-10-22 13:01:33 +0200

Commit id: 1cf683832d2c430bc252cc48fbf58488493ec43a

    added additional check on all files for read.Frames

Committed by: Federico Marini
Author Name: Federico Marini
Commit date: 2014-10-22 12:45:50 +0200
Author date: 2014-10-22 12:45:50 +0200
Revision: 95865
Author: m.stadler
Date: 2014-10-22T10:04:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/QuasR/man/qCount.Rd
Modified  /trunk/madman/Rpacks/QuasR/man/qExportWig.Rd
Modified  /trunk/madman/Rpacks/QuasR/man/qMeth.Rd
v1.7.1: fixed typos in documentation and vignette
Revision: 95864
Author: hpages
Date: 2014-10-22T06:48:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/OnDiskLongTable-class.R
add low-level getBlockFromOnDiskLongTable() -- NOT exported
Revision: 95863
Author: m.boenn
Date: 2014-10-22T06:45:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/geecc/DESCRIPTION
Changed GO2list and KEGG2list
Revision: 95861
Author: m.boenn
Date: 2014-10-22T06:42:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/geecc/DESCRIPTION
Modified  /trunk/madman/Rpacks/geecc/R/littlehelpers.R
Changed GO2list and KEGG2list
Revision: 95860
Author: hpages
Date: 2014-10-22T05:31:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/R/OnDiskLongTable-class.R
By default saveAsOnDiskLongTable() now uses 'blocksize=nrow(df)' so only 1
block per column is written on disk.
Revision: 95859
Author: hpages
Date: 2014-10-22T05:26:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/IRanges-utils.R
fix bug in breakInChunks() when 'totalsize=0' and 'chunksize=0'
Revision: 95858
Author: hpages
Date: 2014-10-22T05:16:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/IRanges-utils.R
breakInChunks() now accepts 'chunksize' of 0 if 'totalsize' is 0
Revision: 95857
Author: l.collado-torres
Date: 2014-10-22T03:53:22+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/basicExploration/basicExploration.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 4713befa1a13442feaf281764dacac986073a511

    v1.1.3 -- updated to match changes in derfinder 1.1.5

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-21 23:51:42 -0400
Author date: 2014-10-21 23:51:42 -0400
Revision: 95855
Author: l.collado-torres
Date: 2014-10-22T03:30:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/R/extendedMapSeqlevels.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 19e19c44d87eaa75bfc12ced94df6d51d3613a18

    Fix typo

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-21 23:29:35 -0400
Author date: 2014-10-21 23:29:35 -0400
Revision: 95852
Author: l.collado-torres
Date: 2014-10-22T03:16:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderPlot/DESCRIPTION
Modified  /trunk/madman/Rpacks/derfinderPlot/NAMESPACE
Modified  /trunk/madman/Rpacks/derfinderPlot/NEWS
Modified  /trunk/madman/Rpacks/derfinderPlot/R/plotCluster.R
Modified  /trunk/madman/Rpacks/derfinderPlot/R/plotOverview.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 46f1de7fb9925ce822382ea0999041c4a17db20d

    v1.1.3 -- updated to match bug fixes in derfinder 1.1.5

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-21 23:16:46 -0400
Author date: 2014-10-21 23:16:46 -0400
Revision: 95850
Author: l.collado-torres
Date: 2014-10-22T02:35:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/derfinder/NAMESPACE
Modified  /trunk/madman/Rpacks/derfinder/NEWS
Modified  /trunk/madman/Rpacks/derfinder/R/analyzeChr.R
Modified  /trunk/madman/Rpacks/derfinder/R/annotateRegions.R
Modified  /trunk/madman/Rpacks/derfinder/R/calculatePvalues.R
Modified  /trunk/madman/Rpacks/derfinder/R/coverageToExon.R
Added  /trunk/madman/Rpacks/derfinder/R/extendedMapSeqlevels.R
Modified  /trunk/madman/Rpacks/derfinder/R/findRegions.R
Modified  /trunk/madman/Rpacks/derfinder/R/fullCoverage.R
Modified  /trunk/madman/Rpacks/derfinder/R/getRegionCoverage.R
Modified  /trunk/madman/Rpacks/derfinder/R/loadCoverage.R
Modified  /trunk/madman/Rpacks/derfinder/R/makeGenomicState.R
Modified  /trunk/madman/Rpacks/derfinder/R/mergeResults.R
Modified  /trunk/madman/Rpacks/derfinder/README.md
Modified  /trunk/madman/Rpacks/derfinder/man/analyzeChr.Rd
Added  /trunk/madman/Rpacks/derfinder/man/extendedMapSeqlevels.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/loadCoverage.Rd
Modified  /trunk/madman/Rpacks/derfinder/tests/testthat/test_data.R
Modified  /trunk/madman/Rpacks/derfinder/tests/testthat/test_misc.R
Modified  /trunk/madman/Rpacks/derfinder/vignettes/realVignettes/derfinder.Rmd
Modified  /trunk/madman/Rpacks/derfinder/vignettes/realVignettes/derfinderAdvanced.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 9739f1242d74315a2ce5e91acc63a74911964caa

    v1.1.5 -- adding extendedMapSeqlevels() to add flexibility to derfinder in order to support species currently not supported by GenomeInfoDb (aka, don't crash derfinder) or non-conventional species which are sometimes used in examples of other packages (see ?BamFile in Rsamtools). This solves https://support.bioconductor.org/p/62136. Updated vignettes to reflect changes in 1.1.5 and 1.1.4

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-21 22:34:59 -0400
Author date: 2014-10-21 22:34:59 -0400
Revision: 95849
Author: rscharpf
Date: 2014-10-22T02:11:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/MinimumDistance/DESCRIPTION
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-MinDistExperiment.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 94f7ff00e7a00841a7214bba8db973e15f033209

    version bump

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-10-21 22:11:27 -0400
Author date: 2014-10-21 22:11:27 -0400

Commit id: fbda20ea980574f6cae65ff06a63d7b492356c77

    remove unneeded line in MinDistExperiment constructor

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-10-21 22:10:27 -0400
Author date: 2014-10-21 22:10:27 -0400
Revision: 95848
Author: rscharpf
Date: 2014-10-22T02:09:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/VanillaICE/DESCRIPTION
Modified  /trunk/madman/Rpacks/VanillaICE/inst/unitTests/test_ArrayViews.R
Modified  /trunk/madman/Rpacks/VanillaICE/man/cnvFilter.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 479e87a26c2f6b92be92754d9b4d16d4e1a3f07c

    Fix path for test_ArrayViews

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-10-21 22:07:44 -0400
Author date: 2014-10-21 22:07:44 -0400
Revision: 95847
Author: v.obenchain
Date: 2014-10-22T02:06:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/R/MulticoreParam-class.R
Modified  /trunk/madman/Rpacks/BiocParallel/R/SerialParam-class.R
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpiterate.Rd
add support for iterative REDUCE in .bpiterate_serial()

Revision: 95846
Author: v.obenchain
Date: 2014-10-22T01:59:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/R/unix/bpiterate.R
add check for pre-existing 'res' to .bpiterate_Multicore()
Revision: 95845
Author: hpages
Date: 2014-10-22T01:56:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/R/ExtraSNPlocs-class.R
use an OnDiskLongTable slot in ExtraSNPlocs objects to store the SNP table
Revision: 95844
Author: hpages
Date: 2014-10-22T01:10:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/NAMESPACE
Modified  /trunk/madman/Rpacks/BSgenome/R/OnDiskLongTable-class.R
add support for 'append=TRUE' in saveAsOnDiskLongTable()
Revision: 95843
Author: stvjc
Date: 2014-10-21T23:50:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/ccleWrap/DESCRIPTION
Added  /trunk/madman/Rpacks/ccleWrap/inst/scripts/buildEnv.R
Added  /trunk/madman/Rpacks/ccleWrap/vignettes/ccleWrapLim.Rnw
updating a limited vignette and an environment-aware builder for
expression, CNV and sensitivity data
Revision: 95842
Author: m.carlson
Date: 2014-10-21T23:11:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/scripts/updateToLatestEnsembl.R
notes on how to use S3 and move files back and forth...
Revision: 95841
Author: hpages
Date: 2014-10-21T22:55:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/NAMESPACE
Added  /trunk/madman/Rpacks/BSgenome/R/OnDiskLongTable-class.R
Modified  /trunk/madman/Rpacks/BSgenome/R/utils.R
add OnDiskLongTable container
Revision: 95840
Author: t.backman
Date: 2014-10-21T22:54:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioassayR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e70d2743507c9e955c84c13452c7a858df23f908

    added RSQLite version number

Committed by: Tyler Backman
Author Name: Tyler Backman
Commit date: 2014-10-21 15:54:19 -0700
Author date: 2014-10-21 15:54:19 -0700
Revision: 95839
Author: t.backman
Date: 2014-10-21T22:44:20+00:00
Paths:
Added  /trunk/madman/Rpacks/bioassayR/.gitignore
Modified  /trunk/madman/Rpacks/bioassayR/DESCRIPTION
Modified  /trunk/madman/Rpacks/bioassayR/R/BioassayDB-accessors.R
Modified  /trunk/madman/Rpacks/bioassayR/R/loadingData.R
Modified  /trunk/madman/Rpacks/bioassayR/R/queries.R
Added  /trunk/madman/Rpacks/bioassayR/Vagrantfile
Commit made by the Bioconductor Git-SVN bridge.
Consists of 5 commits.

Commit information:

Commit id: 139674de22cc1dfb7493ec18e5092211166293e0

    Merge pull request #1 from TylerBackman/support-new-RSqlite

    Support new r sqlite
Committed by: Tyler Backman
Author Name: Tyler Backman
Commit date: 2014-10-21 15:44:09 -0700
Author date: 2014-10-21 15:44:09 -0700

Commit id: f4d028c31928a7b99170218555fafce293811679

    RSQLite upgrades work

Committed by: TylerBackman
Author Name: TylerBackman
Commit date: 2014-10-21 15:42:11 -0700
Author date: 2014-10-21 15:42:11 -0700

Commit id: ee5216a789881397a28c6e6fec948fac121f6911

    now ending database transactions

Committed by: TylerBackman
Author Name: TylerBackman
Commit date: 2014-10-14 17:28:50 -0700
Author date: 2014-10-14 17:28:50 -0700

Commit id: 18fa4b23cf8723dc76172f81fc11e5ceaab8123f

    fixed vagrant stuff in gitignore

Committed by: TylerBackman
Author Name: TylerBackman
Commit date: 2014-10-14 11:40:15 -0700
Author date: 2014-10-14 11:40:15 -0700

Commit id: 3a8ee4650b28d7a6d7afb90c7174e1fc54cb8cbd

    updated function calls, vignette still not building

Committed by: TylerBackman
Author Name: TylerBackman
Commit date: 2014-10-14 11:35:12 -0700
Author date: 2014-10-14 11:35:12 -0700
Revision: 95833
Author: b.fischer
Date: 2014-10-21T20:07:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/CHANGES
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
Modified  /trunk/madman/Rpacks/rhdf5/R/H5F.R
Modified  /trunk/madman/Rpacks/rhdf5/R/H5L.R
Modified  /trunk/madman/Rpacks/rhdf5/R/h5checktype.R
Modified  /trunk/madman/Rpacks/rhdf5/R/h5create.R
set mustWork=FALSE in normalizePath to avoid warning for non-existing files
Revision: 95829
Author: p.stempor
Date: 2014-10-21T17:45:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Modified  /trunk/madman/Rpacks/seqplots/man/getPlotSetArray.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 2a80cbf171046e604cca00740f209c72d40137f3

    version bump - 1.1.2

Committed by: przemol
Author Name: przemol
Commit date: 2014-10-21 18:44:05 +0100
Author date: 2014-10-21 18:44:05 +0100

Commit id: 40347bb0f2342aa779dfff6cb0c98899991c2318

    getPlotSetArray documentation update

Committed by: przemol
Author Name: przemol
Commit date: 2014-10-21 18:43:16 +0100
Author date: 2014-10-21 18:43:16 +0100
Revision: 95828
Author: whuber
Date: 2014-10-21T17:08:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGFF.R
I made one warning message a bit more verbose.

Revision: 95821
Author: s.aibar
Date: 2014-10-21T10:01:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/geNetClassifier/DESCRIPTION
Modified  /trunk/madman/Rpacks/geNetClassifier/R/functions.private.R
bugfix (removing DROP=F in PEB)
Revision: 95820
Author: y.chen
Date: 2014-10-21T05:32:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/edgeR/NAMESPACE
Added  /trunk/madman/Rpacks/edgeR/R/romer.DGEList.R
Modified  /trunk/madman/Rpacks/edgeR/man/roast.DGEList.Rd
Added  /trunk/madman/Rpacks/edgeR/man/romer.DGEList.Rd
edgeR 3.9.3: added an S3 romer method for DGEList object.
Revision: 95818
Author: m.lawrence
Date: 2014-10-21T04:01:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VRanges-class.R
missing END header no longer missing in gVCF output
Revision: 95815
Author: bcarvalh
Date: 2014-10-21T00:35:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/oligoClasses/DESCRIPTION
Modified  /trunk/madman/Rpacks/oligoClasses/man/BeadStudioSetList-class.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: c152716a151f992ead2ce068f32c612d9490bc25

    bumped version number

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-10-20 20:35:27 -0400
Author date: 2014-10-20 20:35:27 -0400

Commit id: 738ba1b3d82a3e5cb00372bfbb68426a18a5ebda

    Merge branch 'master' of github.com:benilton/oligoClasses

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-10-20 20:27:47 -0400
Author date: 2014-10-20 20:27:47 -0400

Commit id: 177ac1e5c7d44872a3c9a76eb2f3c800fe8d6f4f

    Change clone to clone2

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-10-20 20:27:16 -0400
Author date: 2014-10-20 20:27:16 -0400
Revision: 95814
Author: m.carlson
Date: 2014-10-20T23:59:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/UniProt.ws/DESCRIPTION
Deleted  /trunk/madman/Rpacks/UniProt.ws/R/makeUPPkg.R
removes code that could have conflicted with changes in RSQLite.
Revision: 95813
Author: jq.sun
Date: 2014-10-20T23:59:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCC/DESCRIPTION
Modified  /trunk/madman/Rpacks/TCC/R/TCC.estimateDE.baySeq.R
fix bugs depends on baySeq changing.
Revision: 95811
Author: hpages
Date: 2014-10-20T20:53:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/SplicingGraphs/vignettes/SplicingGraphs.Rnw
tweak to accomodate addition of all.equal.environment() to R 3.2
Revision: 95810
Author: hpages
Date: 2014-10-20T20:07:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
update dependency on Biostrings
Revision: 95809
Author: hpages
Date: 2014-10-20T20:06:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/DESCRIPTION
Modified  /trunk/madman/Rpacks/Biostrings/NAMESPACE
Modified  /trunk/madman/Rpacks/Biostrings/R/XStringSet-class.R
Modified  /trunk/madman/Rpacks/Biostrings/R/XStringSetList-class.R
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringSetList-class.Rd
Remove stuff that was defunct in BioC 3.0:
  - partitioning() function,
  - "splitAsListReturnedClass" methods (were deprecated in BioC 2.14 but forgot
    to make them defunct in BioC 3.0).
Revision: 95806
Author: hpages
Date: 2014-10-20T19:56:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/XVector/DESCRIPTION
Modified  /trunk/madman/Rpacks/XVector/NAMESPACE
Modified  /trunk/madman/Rpacks/XVector/R/XVectorList-class.R
remove "splitAsListReturnedClass" method (was defunct in BioC 3.0)

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