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Revision: 107860
Author: p.shannon
Date: 2015-08-28T04:58:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/MotifDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/MotifDb/NAMESPACE
NAMESPACE now imports Biosrings and methods
MotIV's need go gnu scientific library ("libgsl") prevents use of MotIV in the vignette.
Revision: 107859
Author: c.voichita
Date: 2015-08-28T04:51:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/ROntoTools/DESCRIPTION
Added  /trunk/madman/Rpacks/ROntoTools/LICENSE
updated license information
Revision: 107857
Author: p.shannon
Date: 2015-08-28T04:30:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/MotifDb/inst/unitTests/test_MotifDb.R
disabled references to MotIV: the .so for that (separate) package failed to install
commented out call to tomtom: that is not routinely available
corrected a number of tests for the newly added cisbp database
Revision: 107856
Author: p.shannon
Date: 2015-08-28T03:20:38+00:00
Paths:
Added  /trunk/madman/Rpacks/MotifDb/inst/extdata/cispb.RData
new source of motifs
Revision: 107854
Author: hpages
Date: 2015-08-28T00:08:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/SplicingGraphs/DESCRIPTION
Modified  /trunk/madman/Rpacks/SplicingGraphs/NAMESPACE
Modified  /trunk/madman/Rpacks/SplicingGraphs/R/SplicingGraphs-class.R
Modified  /trunk/madman/Rpacks/SplicingGraphs/man/SplicingGraphs-class.Rd
Modified  /trunk/madman/Rpacks/SplicingGraphs/vignettes/SplicingGraphs.Rnw
fix vignette failure caused by update to TxDb.Hsapiens.UCSC.hg19.knownGene
Revision: 107853
Author: s.arora
Date: 2015-08-27T23:35:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHubResource-class.R
code update

- fix bug for GFF file from Gencode

Revision: 107852
Author: hpages
Date: 2015-08-27T23:34:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicAlignments/vignettes/OverlapEncodings.Rnw
fix "Overlap encodings" vignette
Revision: 107851
Author: s.arora
Date: 2015-08-27T22:23:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEncodeDCC.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeGenecodeGFF.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_recipe.R
code update

- shorten unitTest for EncodeDCC files
- add any() around (grepl("\\w//", url, perl=TRUE)
- fix failing unitTest for Genecode Fasta and GFF files
- fix warning of undocumented object

Revision: 107849
Author: hpages
Date: 2015-08-27T20:48:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
oops, fix another version bump that went wrong...
Revision: 107847
Author: v.obenchain
Date: 2015-08-27T20:02:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/src/BamRangeIterator.h
Modified  /trunk/madman/Rpacks/Rsamtools/src/Template.h
work on pairing out-of-range mates

- move mate pairing up to Templates level
- collect, order all mpos
- group mpos by distances defined by 'bins' in the index
Revision: 107846
Author: hpages
Date: 2015-08-27T19:50:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/src/str_utils.c
Add feature test macro to obtain declaration of tzset() and 'timezone' from
. This should address issue when compiling with -std=c99 instead of
-std=gnu99 (the latter being what's usually used when compiling C code).

    
  
    
Revision: 107845
Author: stvjc
Date: 2015-08-27T18:16:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/gtexLite/data/datalist
datalist thinned
Revision: 107843
Author: c.beauparlant
Date: 2015-08-27T13:46:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagene/DESCRIPTION
Modified  /trunk/madman/Rpacks/metagene/R/parallel_job.R
Modified  /trunk/madman/Rpacks/metagene/inst/unitTests/test_bam_handler.R
Modified  /trunk/madman/Rpacks/metagene/inst/unitTests/test_parallel_job.R
Solved conflicts

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Revision: 107842
Author: a.akalin
Date: 2015-08-27T11:48:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/genomation/DESCRIPTION
Modified  /trunk/madman/Rpacks/genomation/NEWS
Modified  /trunk/madman/Rpacks/genomation/R/scoreMatrix.R
Modified  /trunk/madman/Rpacks/genomation/inst/unitTests/test_ScoreMatrix.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a33a391e3ef3e4ca1f671bd3353b6d98fab24bef

    Merge pull request #118 from katwre/master

    reading paired-end issue in readBam()

Commit id: 7723513b9a5046ef1d944695009d79ca195ab6c4

    paired-end aln issue in readBam()

    ScoreMatrix:
     - removed code that was slowing down reading paired-end alignment. Right now when mates from pair map into two different windows of interest then they are duplicated (counted twice).
     - fixed bug in readBam() in reading single-end reads

Revision: 107841
Author: f.mueller
Date: 2015-08-27T08:47:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/R/RnBSet-class.R
usebigff in mergeSamples for RnBiseqSet
Revision: 107840
Author: g.yu
Date: 2015-08-27T08:02:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/NEWS
Modified  /trunk/madman/Rpacks/ggtree/R/treeIO.R
update rm.singleton.newick
Revision: 107839
Author: g.yu
Date: 2015-08-27T07:00:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/NEWS
Modified  /trunk/madman/Rpacks/ggtree/R/gplot.R
bug fixed in gheatmap
Revision: 107835
Author: ddiez
Date: 2015-08-27T02:37:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/codelink/DESCRIPTION
Modified  /trunk/madman/Rpacks/codelink/R/CodelinkSet-tools.R
Fixed problems caused by using git with svn... sigh. Will have to figure out what am I doing wrong.
Revision: 107833
Author: m.carlson
Date: 2015-08-27T00:55:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeRecentOrgPkgsToDbs.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/scripts/updateToLatestEnsembl.R
Changes the recipe for OrgDbFromPkgsImportPreparer to put resources in versioned rdatapaths.
Revision: 107829
Author: d.tenenbaum
Date: 2015-08-26T18:43:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioc_3.2.manifest
Add AnnotationHubData to the manifest
Revision: 107828
Author: m.lawrence
Date: 2015-08-26T18:29:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/VCF-class.Rd
s/Extended/Expanded
Revision: 107827
Author: hpages
Date: 2015-08-26T17:59:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/src/readGFF.c
increase size of read-in line buffer
Revision: 107825
Author: a.oles
Date: 2015-08-26T16:00:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
Modified  /trunk/madman/Rpacks/EBImage/R/computeFeatures.R
Modified  /trunk/madman/Rpacks/EBImage/src/nativeRaster.c
version 4.11.8
  - minor improvements to 'nativeRaster'
Revision: 107819
Author: k.horan
Date: 2015-08-26T14:52:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/eiR/DESCRIPTION
Modified  /trunk/madman/Rpacks/eiR/vignettes/eiR.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: bcaee2c829f8de82d31b1e7c98fdfafffba61cc2

    some edits

Revision: 107818
Author: j.barry
Date: 2015-08-26T14:14:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/imageHTS/DESCRIPTION
Modified  /trunk/madman/Rpacks/imageHTS/man/fileHTS.Rd
Modified  /trunk/madman/Rpacks/imageHTS/man/makeCellHTS.Rd
Modified  /trunk/madman/Rpacks/imageHTS/man/popCellPicker.Rd
update server URL in examples
Revision: 107813
Author: f.commo
Date: 2015-08-26T11:49:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/rCGH/DESCRIPTION
Modified  /trunk/madman/Rpacks/rCGH/NEWS
Modified  /trunk/madman/Rpacks/rCGH/inst/shinyProfile/helpers.R
Modified  /trunk/madman/Rpacks/rCGH/man/rCGH-package.Rd
v0.99.9
Revision: 107811
Author: hpages
Date: 2015-08-26T08:55:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/R/XStringSet-io.R
fix small typo in comment
Revision: 107810
Author: hpages
Date: 2015-08-26T08:53:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/inst/unitTests/test_gff.R
Small tweak to unit test for GFF import to reflect a minor change (introduced
at revision 107794) in how import() orders the factor levels of the columns in
the returned object. Starting with revision 107794, this order is independent
of the collating sequence of the locale in use.
Revision: 107808
Author: hpages
Date: 2015-08-26T06:52:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/src/gff.c
more work on rtracklayer:::readGFF() (GFF3 and GFF2 supported, GFF1 not yet)
Revision: 107807
Author: g.yu
Date: 2015-08-26T06:12:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/DESCRIPTION
Modified  /trunk/madman/Rpacks/clusterProfiler/NEWS
Modified  /trunk/madman/Rpacks/clusterProfiler/vignettes/clusterProfiler.Rmd
update vignette
Revision: 107803
Author: g.yu
Date: 2015-08-26T03:39:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE/DESCRIPTION
Modified  /trunk/madman/Rpacks/DOSE/NEWS
Modified  /trunk/madman/Rpacks/DOSE/R/utilities.R
bug fixed in EXTID2NAME
Revision: 107799
Author: d.low
Date: 2015-08-26T02:04:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/ssviz/DESCRIPTION
change email address

From: dianalow <lowdiana@gmail.com>
Revision: 107797
Author: hpages
Date: 2015-08-25T23:14:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/makeGRangesFromDataFrame.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/makeGRangesFromDataFrame.Rd
small improvement to makeGRangesFromDataFrame()
Revision: 107795
Author: hpages
Date: 2015-08-25T23:06:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/R/gff.R
some cleaning
Revision: 107794
Author: hpages
Date: 2015-08-25T22:46:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/R/gff.R
Modified  /trunk/madman/Rpacks/rtracklayer/src/R_init_rtracklayer.c
Modified  /trunk/madman/Rpacks/rtracklayer/src/gff.c
Modified  /trunk/madman/Rpacks/rtracklayer/src/gff.h
more work on rtracklayer:::readGFF() (not exported yet)
Revision: 107793
Author: x.zheng
Date: 2015-08-25T22:44:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/SNPRelate/DESCRIPTION
Modified  /trunk/madman/Rpacks/SNPRelate/NEWS
Modified  /trunk/madman/Rpacks/SNPRelate/R/PCA.R
Modified  /trunk/madman/Rpacks/SNPRelate/src/dGenGWAS.cpp
Modified  /trunk/madman/Rpacks/SNPRelate/src/genPCA.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 73b8ceeb98c68ea9d6a969321a1674ec73d7d1d6

    fix #14

    Error in snpgdsPCACorr with SeqArray file

Revision: 107791
Author: v.obenchain
Date: 2015-08-25T21:44:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFiles/man/GenomicFiles-class.Rd
add example to GenomicFiles man page
Revision: 107790
Author: v.obenchain
Date: 2015-08-25T20:23:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensemblVEP/man/ensemblVEP.Rd
edit man page
Revision: 107788
Author: z.gu
Date: 2015-08-25T19:56:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/ComplexHeatmap/DESCRIPTION
Modified  /trunk/madman/Rpacks/ComplexHeatmap/NEWS
Modified  /trunk/madman/Rpacks/ComplexHeatmap/R/Heatmap-class.R
Modified  /trunk/madman/Rpacks/ComplexHeatmap/man/Heatmap.rd
set row_reorder and column_reorder to FALSE
Revision: 107787
Author: v.obenchain
Date: 2015-08-25T19:52:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensemblVEP/DESCRIPTION
add S4Vectors to Suggests
Revision: 107783
Author: v.obenchain
Date: 2015-08-25T18:54:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/grasp2db/DESCRIPTION
Modified  /trunk/madman/Rpacks/grasp2db/R/db_AnnotationHub.R
modify AnnotationHubData recipe to propagate BiocVersion
Revision: 107781
Author: j.hester
Date: 2015-08-25T17:25:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/seq2pathway/DESCRIPTION
Added  /trunk/madman/Rpacks/seq2pathway/R/zzz.R
Deprecate seq2pathway
Revision: 107779
Author: s.pretis
Date: 2015-08-25T16:12:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/LowMACA/inst/NEWS
Fixed the inst/NEWS file

Revision: 107777
Author: s.pretis
Date: 2015-08-25T16:00:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/LowMACA/DESCRIPTION
M simple chage of version number

Revision: 107764
Author: d.sie
Date: 2015-08-25T14:55:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/QDNAseq/.travis.yml
Modified  /trunk/madman/Rpacks/QDNAseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/QDNAseq/NEWS
Modified  /trunk/madman/Rpacks/QDNAseq/R/QDNAseqSignals-accessors.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/createBinAnnotations.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/exportBins.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/getBinAnnotations.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/makeCgh.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/plot-methods.R
Modified  /trunk/madman/Rpacks/QDNAseq/man/createBins.Rd
Modified  /trunk/madman/Rpacks/QDNAseq/man/exportBins.Rd
Modified  /trunk/madman/Rpacks/QDNAseq/man/getBinAnnotations.Rd
Modified  /trunk/madman/Rpacks/QDNAseq/man/makeCgh.Rd
Merge branch 'master' into devel

* master: (300 commits)
  Bump development version number to 1.5.3.
  Update NEWS.
  Change chromosomes() to return a character vector instead of integer. Also remove all hard-coded dependencies on chromosome name conversions between character and integer vectors ("X" -> 23, etc), and instead infers correct sorting order from the order in which chromosomes appear in the bin annotations.
  Run "make Rd".
  Skip loading the dataset if annotation package is not installed.
  Loading of dataset now specificially requests data from annotation package.
  Check availability of annotation package. Suggest installing appropriate package if unavailable.
  Added support for loading bin annotations from local dataset collection. Human bin annotations will be provided by QDNAseq.hg19 annotation package.
  Removed "force" options as it is not yet implemented
  Update .travis.yml
  Update .travis.yml
  Bump development version number to 1.5.2
  Added excludeSeqnames parameter as a generic way of excluding chromosomes
  Check results before filtering mitochondrial chromosomes. Fixes issue #11
  Updared DESCRIPTION
  Update DESCRIPTION
  Update createBinAnnotations.R
  Bump development version number to 1.5.2
  - Check results before filtering mitochondrial chromosomes. Fixes issue #11 - Added excludeSeqnames parameters as a generic way of excluding chromosomes.
  Bump development version number to 1.5.1.
  ...

Conflicts:
	.travis.yml
	DESCRIPTION
	NEWS
	R/createBinAnnotations.R
	R/exportBins.R
	R/getBinAnnotations.R
	man/createBins.Rd
	man/exportBins.Rd
	man/getBinAnnotations.Rd

From: Daoud Sie <daoud.sie@gmail.com>

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