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Revision: 113591
Author: jspidlen
Date: 2016-02-12T20:38:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowUtils/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowUtils/R/writeGatingML.R
Add compensation bug fix based on Mike's suggestion.
Revision: 113589
Author: m.lawrence
Date: 2016-02-12T19:53:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggbio/DESCRIPTION
Modified  /trunk/madman/Rpacks/ggbio/R/GGbio-class.R
correctly evaluate second argument to '+'
Revision: 113588
Author: p.haverty
Date: 2016-02-12T17:42:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Modified  /trunk/madman/Rpacks/genoset/R/plots.R
Modified  /trunk/madman/Rpacks/genoset/R/segments.R
Modified  /trunk/madman/Rpacks/genoset/inst/scripts/make.fake.genoset.data.R
Modified  /trunk/madman/Rpacks/genoset/man/genoset-dataset.Rd
Modified  /trunk/madman/Rpacks/genoset/man/runCBS.Rd
Modified  /trunk/madman/Rpacks/genoset/man/segTable-methods.Rd
Modified  /trunk/madman/Rpacks/genoset/man/segs2Rle.Rd
Modified  /trunk/madman/Rpacks/genoset/man/segs2RleDataFrame.Rd
Modified  /trunk/madman/Rpacks/genoset/vignettes/genoset.Rmd
Version: 1.27.24. data object now just has genoset.ds. Fake data code duplicated in vignette. Vignette modernized a bit to get rid of RangedData and eSet. Some examples got the same treatment.
Revision: 113587
Author: z.skidmore
Date: 2016-02-12T15:52:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenVisR/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenVisR/NEWS
 /trunk/madman/Rpacks/GenVisR/vignettes/GenVisR_intro.Rmd
github sync
Revision: 113584
Author: e.thevenot
Date: 2016-02-12T15:05:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/ropls/DESCRIPTION
Modified  /trunk/madman/Rpacks/ropls/NEWS
Modified  /trunk/madman/Rpacks/ropls/R/plot.opls.R
Modified  /trunk/madman/Rpacks/ropls/inst/unitTests/test_opls.R
Modified  /trunk/madman/Rpacks/ropls/man/ropls-package.Rd
CHANGES IN VERSION 1.3.14
------------------------------

NEW FEATURES

    o plot.opls: when 'parAsColFcVn' is a character vector, it is converted to a factor (thus drawing ellipses by default)

BUG FIXED

    o plot.opls: handling of ellipse display when parEllipseL parameter set to NA (default)
Revision: 113583
Author: m.love
Date: 2016-02-12T12:55:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/tximport/DESCRIPTION
version bump for tximportData
Revision: 113582
Author: hpages
Date: 2016-02-12T11:51:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Improve error handling in "extractROWS" method for GPos objects when subscript
is too big.
Revision: 113581
Author: hpages
Date: 2016-02-12T11:47:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/Vector-class-leftovers.R
speedup "rep.int" method for Vector objects
Revision: 113580
Author: hpages
Date: 2016-02-12T11:22:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/src/vector_utils.c
better error message
Revision: 113579
Author: hpages
Date: 2016-02-12T10:43:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/inter-range-methods.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/intra-range-methods.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/inter-range-methods.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/man/intra-range-methods.Rd
add optimized "shift" and "range" methods for GPos objects
Revision: 113577
Author: hpages
Date: 2016-02-12T10:09:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/src/AEbufs.c
minor cosmetic
Revision: 113575
Author: hpages
Date: 2016-02-12T10:02:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/DESCRIPTION
Deleted  /trunk/madman/Rpacks/Biostrings/R/debug.R
Modified  /trunk/madman/Rpacks/Biostrings/R/needwunsQS.R
Deleted  /trunk/madman/Rpacks/Biostrings/R/test.R
Modified  /trunk/madman/Rpacks/Biostrings/R/zzz.R
Modified  /trunk/madman/Rpacks/Biostrings/inst/extdata/README
Modified  /trunk/madman/Rpacks/Biostrings/inst/unitTests/test_MultipleAlignment.R
Modified  /trunk/madman/Rpacks/Biostrings/inst/unitTests/test_pairwiseAlignment.R
Modified  /trunk/madman/Rpacks/Biostrings/man/AAString-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/AlignedXStringSet-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/BOC_SubjectString-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/Biostrings-internals.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/DNAString-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/GENETIC_CODE.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/IUPAC_CODE_MAP.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/MIndex-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/MaskedXString-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/PDict-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/PairwiseAlignments-io.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/RNAString-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/XString-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringPartialMatches-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringSet-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringSet-comparison.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringSetList-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringViews-class.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/findPalindromes.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/gregexpr2.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/injectHardMask.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/letterFrequency.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/maskMotif.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/matchLRPatterns.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/matchPDict-exact.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/matchPDict-inexact.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/matchPWM.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/matchProbePair.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/needwunsQS.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/nucleotideFrequency.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/padAndClip.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/pairwiseAlignment.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/replaceAt.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/replaceLetterAt.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/substitution_matrices.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/toComplex.Rd
Modified  /trunk/madman/Rpacks/Biostrings/man/xscat.Rd
Modified  /trunk/madman/Rpacks/Biostrings/src/BAB_class.c
Modified  /trunk/madman/Rpacks/Biostrings/src/Biostrings.h
Modified  /trunk/madman/Rpacks/Biostrings/src/BitMatrix.c
Modified  /trunk/madman/Rpacks/Biostrings/src/MIndex_class.c
Modified  /trunk/madman/Rpacks/Biostrings/src/PreprocessedTB_class.c
Modified  /trunk/madman/Rpacks/Biostrings/src/R_init_Biostrings.c
Modified  /trunk/madman/Rpacks/Biostrings/src/RoSeqs_utils.c
Modified  /trunk/madman/Rpacks/Biostrings/src/SparseList_utils.c
Modified  /trunk/madman/Rpacks/Biostrings/src/XStringSetList_class.c
Modified  /trunk/madman/Rpacks/Biostrings/src/XStringSet_class.c
Modified  /trunk/madman/Rpacks/Biostrings/src/XStringSet_io.c
Modified  /trunk/madman/Rpacks/Biostrings/src/XString_class.c
Modified  /trunk/madman/Rpacks/Biostrings/src/align_needwunsQS.c
Modified  /trunk/madman/Rpacks/Biostrings/src/find_palindromes.c
Modified  /trunk/madman/Rpacks/Biostrings/src/lowlevel_matching.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_BOC.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_BOC2.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_PWM.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pattern.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pattern_boyermoore.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pattern_indels.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pattern_shiftor.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pdict.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pdict_ACtree2.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pdict_Twobit.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_pdict_utils.c
Modified  /trunk/madman/Rpacks/Biostrings/src/match_reporting.c
Modified  /trunk/madman/Rpacks/Biostrings/src/utils.c
Added  /trunk/madman/Rpacks/Biostrings/tests
Added  /trunk/madman/Rpacks/Biostrings/tests/run_unitTests.R
- harmonize file names and functions for testing framework
- put the accents on my name :-)
Revision: 113574
Author: r.ivanek
Date: 2016-02-12T09:55:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/Gviz/DESCRIPTION
Modified  /trunk/madman/Rpacks/Gviz/R/Gviz.R
fix for GeneRegioTrack in case of reverseStrand and label position above or below
Revision: 113572
Author: hpages
Date: 2016-02-12T08:42:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/SplicingGraphs/R/zzz.R
Modified  /trunk/madman/Rpacks/SplicingGraphs/tests/run_unitTests.R
harmonize file names and functions for testing framework
Revision: 113571
Author: hpages
Date: 2016-02-12T08:39:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Deleted  /trunk/madman/Rpacks/GenomeInfoDb/R/test_GenomeInfoDb_package.R
Added  /trunk/madman/Rpacks/GenomeInfoDb/R/zzz.R
Deleted  /trunk/madman/Rpacks/GenomeInfoDb/tests/runTests.R
Added  /trunk/madman/Rpacks/GenomeInfoDb/tests/run_unitTests.R
harmonize file names and functions for testing framework
Revision: 113564
Author: hpages
Date: 2016-02-12T06:55:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/man/Ranges-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/Ranges-comparison.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/findOverlaps-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/inter-range-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/intra-range-methods.Rd
Minor formatting improvements in man pages for intra and inter range
transformations.
Revision: 113563
Author: j.java
Date: 2016-02-12T06:53:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocContributions/R/simplify.R
Update 'ManageNewPackagesCredentials()' for multiple maintainers; create draft credentials Gmail; version bump.
Revision: 113562
Author: b.phipson
Date: 2016-02-12T05:41:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/missMethyl/vignettes/missMethyl.Rnw
added gsameth to vignette
Revision: 113560
Author: t.silva
Date: 2016-02-12T04:01:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/DESCRIPTION
Modified  /trunk/madman/Rpacks/TCGAbiolinks/NEWS
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAanalyze.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/sysdata.rda
Modified  /trunk/madman/Rpacks/TCGAbiolinks/README.md
Merge branch 'master' into devel

* master:
  Removing useless white space.
  Version bump
  Bug fix colnames(objectWo) was not needed and it was wrong.
  db update

From: tiago <tiagochst@gmail.com>
Revision: 113559
Author: n.lawlor
Date: 2016-02-12T03:48:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/multiClust/vignettes/multiClust.Rmd
Added explanation for using RNA-seq data with package.
Revision: 113558
Author: n.lawlor
Date: 2016-02-12T03:47:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/multiClust/R/probe_ranking.R
Fixed so code methods and documentation matched.
Revision: 113557
Author: n.lawlor
Date: 2016-02-12T03:44:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/multiClust/NEWS
Added news updates about version 0.99.4
Revision: 113556
Author: n.lawlor
Date: 2016-02-12T03:42:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/multiClust/DESCRIPTION
Pushed package version to 0.99.4 to account for vignette updates.
Revision: 113555
Author: hpages
Date: 2016-02-12T03:39:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/nucleR/DESCRIPTION
Modified  /trunk/madman/Rpacks/nucleR/R/mergeCalls.R
Use 'drop.self' and 'drop.redundant' arguments instead of 'ignoreSelf' and
'ignoreRedundant' when calling findOverlaps() with a query and no subject.
Revision: 113554
Author: hpages
Date: 2016-02-12T03:36:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/exomeCopy/DESCRIPTION
Modified  /trunk/madman/Rpacks/exomeCopy/vignettes/exomeCopy.Rnw
Use 'drop.self' argument instead of 'ignoreSelf' when calling findOverlaps()
with a query and no subject.
Revision: 113553
Author: b.phipson
Date: 2016-02-12T03:35:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/missMethyl/DESCRIPTION
Modified  /trunk/madman/Rpacks/missMethyl/NAMESPACE
Modified  /trunk/madman/Rpacks/missMethyl/R/gometh.R
Added  /trunk/madman/Rpacks/missMethyl/R/gsameth.R
Modified  /trunk/madman/Rpacks/missMethyl/inst/CITATION
Modified  /trunk/madman/Rpacks/missMethyl/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/missMethyl/man/getMappedEntrezIDs.Rd
Modified  /trunk/madman/Rpacks/missMethyl/man/gometh.Rd
Added  /trunk/madman/Rpacks/missMethyl/man/gsameth.Rd
Added  /trunk/madman/Rpacks/missMethyl/man/topGSA.Rd
Added new functions for performing gene set testing with user specified lists of gene sets. Added kegg pathway analysis to gometh. 
Revision: 113552
Author: hpages
Date: 2016-02-12T03:33:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/triform/DESCRIPTION
Modified  /trunk/madman/Rpacks/triform/R/triform.R
Use 'drop.self' and 'drop.redundant' arguments instead of 'ignoreSelf' and
'ignoreRedundant' when calling findOverlaps() with a query and no subject.
Revision: 113551
Author: hpages
Date: 2016-02-12T03:31:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/CAGEr/DESCRIPTION
Modified  /trunk/madman/Rpacks/CAGEr/R/ClusteringFunctions.R
Use 'drop.self' argument instead of 'ignoreSelf' when calling findOverlaps()
with a query and no subject.
Revision: 113550
Author: hpages
Date: 2016-02-12T03:28:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/wavClusteR/DESCRIPTION
Modified  /trunk/madman/Rpacks/wavClusteR/R/getMeta.R
Use 'drop.self' argument instead of 'ignoreSelf' when calling findOverlaps()
with a query and no subject.
Revision: 113549
Author: hpages
Date: 2016-02-12T03:12:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/Genominator/DESCRIPTION
Modified  /trunk/madman/Rpacks/Genominator/R/annotation.R
Use 'drop.self' and 'drop.redundant' arguments instead of 'ignoreSelf' and
'ignoreRedundant' when calling findOverlaps() with a query and no subject.
Revision: 113548
Author: hpages
Date: 2016-02-12T03:09:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/groHMM/DESCRIPTION
Modified  /trunk/madman/Rpacks/groHMM/R/makeConsensusAnnotations.R
Use 'drop.self' and 'drop.redundant' arguments instead of 'ignoreSelf' and
'ignoreRedundant' when calling findOverlaps() with a query and no subject.
Revision: 113547
Author: hpages
Date: 2016-02-12T03:06:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/hiReadsProcessor/DESCRIPTION
Modified  /trunk/madman/Rpacks/hiReadsProcessor/R/hiReadsProcessor.R
Use 'drop.self' and 'drop.redundant' arguments instead of 'ignoreSelf' and
'ignoreRedundant' when calling findOverlaps() with a query and no subject.
Revision: 113546
Author: hpages
Date: 2016-02-12T03:00:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/CNEr/DESCRIPTION
Modified  /trunk/madman/Rpacks/CNEr/R/ceScan.R
Use 'drop.self' and 'drop.redundant' arguments instead of 'ignoreSelf' and
'ignoreRedundant' when calling findOverlaps() with a query and no subject.
Revision: 113545
Author: hpages
Date: 2016-02-12T02:55:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/R/findOverlappingPeaks.R
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/R/privateUtil.R
Use 'drop.self' and 'drop.redundant' arguments instead of 'ignoreSelf' and
'ignoreRedundant' when calling findOverlaps() with a query and no subject.
Revision: 113544
Author: hpages
Date: 2016-02-12T02:49:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-methods.R
Use 'drop.self' and 'drop.redundant' instead of 'ignoreSelf' and
'ignoreRedundant' arguments when calling findOverlaps() with a query and no
subject.
Revision: 113543
Author: hpages
Date: 2016-02-12T02:43:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/nearest-methods.R
Use 'drop.self' instead of 'ignoreSelf' argument when calling findOverlaps()
with only a query and a missing subject.
Revision: 113542
Author: l.zhu
Date: 2016-02-12T02:19:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GUIDEseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/GUIDEseq/R/offTargetAnalysisOfPeakRegions.R
fixed bug when merging
Revision: 113541
Author: hpages
Date: 2016-02-12T02:17:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Deleted  /trunk/madman/Rpacks/IRanges/R/debug.R
Modified  /trunk/madman/Rpacks/IRanges/R/findOverlaps-methods.R
Deleted  /trunk/madman/Rpacks/IRanges/R/mapCoords-methods.R
Modified  /trunk/madman/Rpacks/IRanges/R/nearest-methods.R
Deleted  /trunk/madman/Rpacks/IRanges/R/test_IRanges_package.R
Modified  /trunk/madman/Rpacks/IRanges/R/zzz.R
Modified  /trunk/madman/Rpacks/IRanges/man/GappedRanges-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/Grouping-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/IRanges-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/IRanges-constructor.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/IRanges-utils.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/MaskCollection-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/NCList-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/Ranges-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/Ranges-comparison.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/Views-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/ViewsList-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/coverage-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/extractList.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/findOverlaps-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/inter-range-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/intra-range-methods.Rd
Deleted  /trunk/madman/Rpacks/IRanges/man/mapCoords-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/setops-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/src/Grouping_class.c
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges_class.c
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
Modified  /trunk/madman/Rpacks/IRanges/src/Ranges_class.c
Modified  /trunk/madman/Rpacks/IRanges/src/Ranges_comparison.c
Modified  /trunk/madman/Rpacks/IRanges/src/coverage_methods.c
Modified  /trunk/madman/Rpacks/IRanges/src/inter_range_methods.c
- Rename 'ignoreSelf' and 'ignoreRedundant' argument of the
  findOverlaps,Vector,missing method -> 'drop.self' and 'drop.redundant'.
  The old names are still working but deprecated.
- Remove mapCoords() and pmapCoords() generics (were defunct in BioC 3.2).
- Put the accents on my name :-)
Revision: 113540
Author: l.zhu
Date: 2016-02-12T00:59:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/GUIDEseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/GUIDEseq/R/offTargetAnalysisOfPeakRegions.R
pick one best offtarget per peak
Revision: 113538
Author: l.gatto
Date: 2016-02-11T23:25:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRoloc/R/dynamics.R
fix sample names test in remap

From: Laurent <lg390@cam.ac.uk>
Revision: 113537
Author: l.gatto
Date: 2016-02-11T23:25:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRoloc/NEWS
Modified  /trunk/madman/Rpacks/pRoloc/R/dynamics.R
added error when sampleNames differ in MSnSetList when using remap

From: lmsimp <lisa.m.simp@gmail.com>
Revision: 113536
Author: l.gatto
Date: 2016-02-11T23:25:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRoloc/DESCRIPTION
Modified  /trunk/madman/Rpacks/pRoloc/NEWS
new gh devel version

From: Laurent <lg390@cam.ac.uk>
Revision: 113535
Author: d.tenenbaum
Date: 2016-02-11T23:20:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/fCI/vignettes/fCI.Rmd
replace non-ascii characters
Revision: 113534
Author: hpages
Date: 2016-02-11T22:48:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GenomicRanges-class.R
Fix 2 issues with the ranges() setter for GRanges objects:
- If the supplied value was an IRanges derivative (e.g. NormalIRanges), the
  setter was not turning it into an IRanges *instance* before sticking it
  inside the GRanges object (in its 'ranges' slot).
- If the supplied IRanges object had metadata columns, the setter was not
  dropping them before sticking it inside the GRanges object.
In both case, this resulted in an invalid GRanges object.
Revision: 113533
Author: hpages
Date: 2016-02-11T22:14:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/triplex/DESCRIPTION
Modified  /trunk/madman/Rpacks/triplex/R/TriplexViews-class.R
newViews() was renamed new_Views() in IRanges and is not exported anymore
Revision: 113532
Author: hpages
Date: 2016-02-11T22:09:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/DESCRIPTION
Modified  /trunk/madman/Rpacks/Biostrings/R/XStringViews-class.R
newViews() was renamed new_Views() in IRanges and is not exported anymore
Revision: 113531
Author: hpages
Date: 2016-02-11T21:59:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/IRanges/R/IRanges-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/Ranges-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/RangesList-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/RleViews-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/Views-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/inter-range-methods.R
Modified  /trunk/madman/Rpacks/IRanges/man/IRanges-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/Ranges-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/RangesList-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/Views-class.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/inter-range-methods.Rd
Modified  /trunk/madman/Rpacks/IRanges/man/intra-range-methods.Rd
Modified  /trunk/madman/Rpacks/XVector/DESCRIPTION
Modified  /trunk/madman/Rpacks/XVector/R/XDoubleViews-class.R
Modified  /trunk/madman/Rpacks/XVector/R/XIntegerViews-class.R
- Long time due cleanup of the code and documentation of the inter range
  transformations.
- Deprecate "reduce" method for RangedData objects.
- Rename low-level Views constructor newViews() -> new_Views() and don't
  export it anymore. Also now it propagates the metadata columns of the
  supplied IRanges object to the Views object.
Revision: 113530
Author: d.tenenbaum
Date: 2016-02-11T21:48:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/rpx/tests/runTests.R
use correct pkg name
Revision: 113529
Author: l.zhu
Date: 2016-02-11T21:46:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/GUIDEseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/GUIDEseq/R/offTargetAnalysisOfPeakRegions.R
merge peaks with the same offtarget site
Revision: 113528
Author: j.java
Date: 2016-02-11T20:41:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocContributions/R/simplify.R
Modified  /trunk/madman/Rpacks/BiocContributions/R/utils.R
Created functions to simplify follow-up to adding packages.
Revision: 113522
Author: l.chavez
Date: 2016-02-11T12:09:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/MEDIPS/DESCRIPTION
Modified  /trunk/madman/Rpacks/MEDIPS/R/MEDIPS.correlation.R
Modified  /trunk/madman/Rpacks/MEDIPS/R/MEDIPS.selectROIs.R
Modified  /trunk/madman/Rpacks/MEDIPS/man/MEDIPS.correlation.Rd
Modified  /trunk/madman/Rpacks/MEDIPS/man/MEDIPS.selectROIs.Rd
sum addeded to MEDIPS.selectROI
Revision: 113520
Author: hpages
Date: 2016-02-11T11:13:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/inter-range-methods.R
clean up long-standing messy code in inter-range-methods.R
Revision: 113519
Author: v.kiselev
Date: 2016-02-11T09:58:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/SC3/DESCRIPTION
Modified  /trunk/madman/Rpacks/SC3/R/sc3-funcs.R
Modified  /trunk/madman/Rpacks/SC3/R/sc3.R
Modified  /trunk/madman/Rpacks/SC3/man/sc3.Rd
fix bug when running SC3 on a data.frame, now it coverts it to a matrix first
Revision: 113517
Author: m.choi
Date: 2016-02-11T03:50:09+00:00
Paths:
Deleted  /trunk/madman/Rpacks/MSstats/R/mainfunctions.R
deleting a file
Revision: 113513
Author: smyth
Date: 2016-02-11T01:49:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/R/kegga.R
Modified  /trunk/madman/Rpacks/limma/R/voom.R
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
Modified  /trunk/madman/Rpacks/limma/man/propexpr.Rd
Modified  /trunk/madman/Rpacks/limma/man/voom.Rd
11 February 2016: limma 3.27.12

- new argument 'save.plot' for voom().

- bug fix for kegga() when 'covariate' or 'prior.prob' are not NULL
  and when not all genes in the universe have annotation.
Revision: 113510
Author: a.popa
Date: 2016-02-10T22:14:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/RiboProfiling/DESCRIPTION
Modified  /trunk/madman/Rpacks/RiboProfiling/NEWS
Modified  /trunk/madman/Rpacks/RiboProfiling/R/aroundPromoter.R
Modified  /trunk/madman/Rpacks/RiboProfiling/R/riboSeqFromBAM.R
Modified  /trunk/madman/Rpacks/RiboProfiling/man/riboSeqFromBAM.Rd
SummarizedExperiment::assay
added parameter paramScanBAM (ScanBamParam object) to riboSeqFromBAM function
Revision: 113508
Author: hpages
Date: 2016-02-10T22:07:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/man/extractTranscriptSeqs.Rd
Try to be even more explicit about ordering of exons passed to
extractTranscriptSeqs().
Revision: 113506
Author: j.java
Date: 2016-02-10T20:07:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
Fixed tracker-summary problem; version bump
Revision: 113505
Author: hpages
Date: 2016-02-10T19:38:59+00:00
Paths:
Added  /trunk/madman/Rpacks/HDF5Array
Added  /trunk/madman/Rpacks/HDF5Array/DESCRIPTION
start HDF5Array package
Revision: 113504
Author: hpages
Date: 2016-02-10T19:22:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/SNPlocs-class.R
Modified  /trunk/madman/Rpacks/BSgenome/man/SNPlocs-class.Rd
small code simplification
Revision: 113503
Author: hpages
Date: 2016-02-10T19:04:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
minor rephrasing
Revision: 113502
Author: hpages
Date: 2016-02-10T18:59:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
Coercion from GenomicRanges to GPos now propagates the metadata columns.
Also now it emits a warning when the names on the object to coerce are not
propagated.
Revision: 113501
Author: hpages
Date: 2016-02-10T18:33:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
minor edit
Revision: 113500
Author: hpages
Date: 2016-02-10T18:24:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GPos-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/GPos-class.Rd
add coercion from GenomicRanges to GPos
Revision: 113499
Author: m.mccall
Date: 2016-02-10T18:06:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/spkTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/spkTools/R/spkPair.R
Deleted  /trunk/madman/Rpacks/spkTools/inst
Fix array dimnames error in spkPair function.
Revision: 113496
Author: t.silva
Date: 2016-02-10T17:39:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/NAMESPACE
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAInternal.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAPrepare.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAbiolinks.R
Modified  /trunk/madman/Rpacks/TCGAbiolinks/R/TCGAvisualize.R
Added  /trunk/madman/Rpacks/TCGAbiolinks/man/batch.info.Rd
Deleted  /trunk/madman/Rpacks/TCGAbiolinks/man/batchinfo.Rd
Merge branch 'master' into devel

* master:
  jittrValueLabels was removed from sjplot. Importing grid library was conflicting with cowlplot import.
  This closes #6. It shoud be verified if there are columns with different names but same content.
  Correting the name of the object. This should remove the warning from bioconductor.
  Version bump
  Bug fix: This closes #5

From: tiago <tiagochst@gmail.com>
Revision: 113495
Author: v.obenchain
Date: 2016-02-10T17:17:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/rpx/DESCRIPTION
Modified  /trunk/madman/Rpacks/rpx/vignettes/rpx.Rnw
remove duplicate code in vignette
Revision: 113494
Author: z.skidmore
Date: 2016-02-10T17:15:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenVisR/DESCRIPTION
bump version
Revision: 113493
Author: z.skidmore
Date: 2016-02-10T17:13:00+00:00
Paths:
 /trunk/madman/Rpacks/GenVisR/DESCRIPTION
Deleted  /trunk/madman/Rpacks/GenVisR/Images
 /trunk/madman/Rpacks/GenVisR/LICENSE
 /trunk/madman/Rpacks/GenVisR/NAMESPACE
 /trunk/madman/Rpacks/GenVisR/NEWS
 /trunk/madman/Rpacks/GenVisR/R
Added  /trunk/madman/Rpacks/GenVisR/R/GenVisR.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_alignPlot.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_annoTransTranv.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_calcTransTranvFreq.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_convMaf.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_rmIndel.R
Added  /trunk/madman/Rpacks/GenVisR/R/TvTi_rmMnuc.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnFreq.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnFreq_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnFreq_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnSpec.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnSpec_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnSpec_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView_align.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/cnView_subsetChr.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent_bamRcnt.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent_bamRcnt_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/compIdent_format.R
Added  /trunk/madman/Rpacks/GenVisR/R/covBars.R
Added  /trunk/madman/Rpacks/GenVisR/R/covBars_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/covBars_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_alignPlot.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_assign_ggplotGrob_height.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_assign_ggplotGrob_width.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_buildCov.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_buildTrack.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_extr_ggplotGrob_height.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_extr_ggplotGrob_width.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/genCov_trackViz.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_Granges2dataframe.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_buildGene.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_calcGC.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_cdsFromTXID.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_extrCDS.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_extrUTR.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_formatUTR.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_formatcds.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mapCoordSpace.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mapCovCoordSpace.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mergeRegions.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mergeTypeRegions.R
Added  /trunk/madman/Rpacks/GenVisR/R/geneViz_mergeTypes.R
Added  /trunk/madman/Rpacks/GenVisR/R/ideoView.R
Added  /trunk/madman/Rpacks/GenVisR/R/ideoView_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/ideoView_formatCytobands.R
Added  /trunk/madman/Rpacks/GenVisR/R/ideoView_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_fileGlob.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_lohCalc.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_slidingWindow.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_stepCalc.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_tileCalc.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_tilePosition.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_tileWindow.R
Added  /trunk/madman/Rpacks/GenVisR/R/lohView_windowPosition.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_AA2sidechain.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_Codon2AA.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_DNAconv.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_constructGene.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_dodgeCoordX.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_dodgeCoordY.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_fetchDomain.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_mutationObs.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_reduceLolli.R
Added  /trunk/madman/Rpacks/GenVisR/R/lolliplot_transcriptID2codingSeq.R
Added  /trunk/madman/Rpacks/GenVisR/R/multi_buildClin.R
Added  /trunk/madman/Rpacks/GenVisR/R/multi_chrBound.R
Added  /trunk/madman/Rpacks/GenVisR/R/multi_cytobandRet.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_Custom2anno.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_MAF2anno.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_MGI2anno.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_NA2gene.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_align.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_buildGenePrevelance.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_buildMain.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_buildMutBurden_A.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_buildMutBurden_B.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_calcMutFreq.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_geneAlt.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_geneRecurCutoff.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_geneSort.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_hierarchyTRV.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_qual.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_rmvSilent.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_sampAlt.R
Added  /trunk/madman/Rpacks/GenVisR/R/waterfall_sampSort.R
 /trunk/madman/Rpacks/GenVisR/README.md
Deleted  /trunk/madman/Rpacks/GenVisR/Test_data
 /trunk/madman/Rpacks/GenVisR/data
Added  /trunk/madman/Rpacks/GenVisR/data/HCC1395_Germline.rda
Added  /trunk/madman/Rpacks/GenVisR/data/HCC1395_N.rda
Added  /trunk/madman/Rpacks/GenVisR/data/HCC1395_T.rda
Added  /trunk/madman/Rpacks/GenVisR/data/LucCNseg.rda
Added  /trunk/madman/Rpacks/GenVisR/data/SNPloci.rda
Added  /trunk/madman/Rpacks/GenVisR/data/brcaMAF.rda
Added  /trunk/madman/Rpacks/GenVisR/data/cytoGeno.rda
Added  /trunk/madman/Rpacks/GenVisR/data/hg19chr.rda
Deleted  /trunk/madman/Rpacks/GenVisR/inst
 /trunk/madman/Rpacks/GenVisR/man
Added  /trunk/madman/Rpacks/GenVisR/man/GenVisR.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/HCC1395_Germline.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/HCC1395_N.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/HCC1395_T.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/LucCNseg.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/SNPloci.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_alignPlot.Rd
Added  /trunk/madman/Rpacks/GenVisR/man/TvTi_annoTransTranv.Rd
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Added  /trunk/madman/Rpacks/GenVisR/tests/testthat.R
 /trunk/madman/Rpacks/GenVisR/vignettes
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attempt sync with github

Source Code & Build Reports »

Source code is stored in svn (user: readonly, pass: readonly).

Software packages are built and checked nightly. Build reports:

 

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