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Revision: 96261
Author: hpages
Date: 2014-10-31T02:07:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/GenomeDataList-class.R
Modified  /trunk/madman/Rpacks/BSgenome/R/gdReduce.R
Modified  /trunk/madman/Rpacks/BSgenome/R/gdapply.R
Modified  /trunk/madman/Rpacks/BSgenome/man/gdReduce.Rd
Modified  /trunk/madman/Rpacks/BSgenome/man/gdapply.Rd
More left overs related to GenomeData and GenomeDataList classes now being
defunct.
Revision: 96260
Author: hpages
Date: 2014-10-31T01:57:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/man/GenomeData-class.Rd
Modified  /trunk/madman/Rpacks/BSgenome/man/GenomeDataList-class.Rd
some left overs related to previous commit
Revision: 96259
Author: hpages
Date: 2014-10-31T01:54:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/GenomeData-class.R
Make GenomeData and GenomeDataList classes defunct (were deprecated in
BioC 3.0).
Revision: 96258
Author: hpages
Date: 2014-10-31T01:49:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/getSeq-methods.R
Remove support for RangedData in "getSeq" method for BSgenome objects (was
defunct since Bioc 2.14).
Revision: 96257
Author: hpages
Date: 2014-10-31T01:43:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/injectSNPs.R
Modified  /trunk/madman/Rpacks/BSgenome/man/injectSNPs.Rd
Modify available.SNPs() and installed.SNPs() to return XtraSNPlocs data
packages in addition to SNPlocs data packages.
Revision: 96256
Author: hpages
Date: 2014-10-31T01:21:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/R/XtraSNPlocs-class.R
Added  /trunk/madman/Rpacks/BSgenome/man/XtraSNPlocs-class.Rd
document XtraSNPlocs API
Revision: 96255
Author: p.shannon
Date: 2014-10-31T00:59:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/MotifDb/DESCRIPTION
bumped version number to track updated LICENSE
Revision: 96254
Author: p.shannon
Date: 2014-10-31T00:58:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/MotifDb/LICENSE
updated permission statements for stamlab and UniPROBE, removing
conditional language.
Revision: 96253
Author: m.carlson
Date: 2014-10-30T22:58:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/EnsemblFastaImportPreparer-class.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/EnsemblImportPreparer-utils.R
Deleted  /trunk/madman/Rpacks/AnnotationHubData/R/ensemblFastaToFaFile.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/scripts/updateToLatestEnsembl.R
Fixes for the ensembl fasta file recipe.

This recipe still cannot be run untill I replace the missing 'getCurrentResources' function.  So that job is next...
Revision: 96252
Author: khansen
Date: 2014-10-30T22:41:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/affxparser/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 55bdf893df33c20118f0afe7f621fb4e8538e6de

    Mini-bumped version

Committed by: hb
Author Name: hb
Commit date: 2014-10-30 15:40:49 -0700
Author date: 2014-10-30 15:40:49 -0700
Revision: 96250
Author: hpages
Date: 2014-10-30T21:36:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/XtraSNPlocs-class.R
improve checking of user-supplied SNP ids in snpsById()
Revision: 96249
Author: v.obenchain
Date: 2014-10-30T21:25:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VCFHeader-class.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/inst/unitTests/test_writeVcf-methods.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/VCFHeader-class.Rd
update fixed(VCFHeader) to return 'ALT' and 'REF' if present
Revision: 96248
Author: khansen
Date: 2014-10-30T21:21:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/affxparser/src/fusion_sdk/file/BPMAPFileData.cpp
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 9db670570e64b1fea42e6c009941c0220880c981

    CLEANUP: Removed another Fusion SDK compilation warning fusion_sdk/file/BPMAPFileData.cpp:371:12: warning: unused variable 'probeBufSize' [-Wunused-variable]         const int probeBufSize=64;

Committed by: hb
Author Name: hb
Commit date: 2014-10-30 14:20:10 -0700
Author date: 2014-10-30 14:20:10 -0700
Revision: 96247
Author: m.carlson
Date: 2014-10-30T20:56:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/interactiveDisplayBase/DESCRIPTION
Modified  /trunk/madman/Rpacks/interactiveDisplayBase/R/dataframe.R
Changes display method for data_frames to use DataTables
Revision: 96246
Author: m.carlson
Date: 2014-10-30T20:55:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/display.R
Fixes problems with display method.
Revision: 96245
Author: hpages
Date: 2014-10-30T20:45:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/NAMESPACE
Modified  /trunk/madman/Rpacks/BSgenome/R/OnDiskLongTable-class.R
Modified  /trunk/madman/Rpacks/BSgenome/R/XtraSNPlocs-class.R
- Rename getDataFromOnDiskLongTable() -> getRowsByIdFromOnDiskLongTable().
- Add getRowsByIndexFromOnDiskLongTable().
- Implement 'ifnotfound' arg in "snpsById" method for XtraSNPlocs objects.
Revision: 96244
Author: v.obenchain
Date: 2014-10-30T20:42:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/AllClasses.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VCFHeader-class.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/VCFHeader-class.Rd
VCFHeader:

- add support for SAMPLE and PEDIGREE header fields
- meta(VCFHeader) now returns DataFrameList instead of DataFrame
- show(VCFHeader) now displays the outer list names in meta
Revision: 96243
Author: v.obenchain
Date: 2014-10-30T20:40:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/R/methods-BcfFile.R
add support for SAMPLE and PEDIGREE in .bcfHeaderAsSimpleList()
Revision: 96238
Author: d.tenenbaum
Date: 2014-10-30T18:44:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocCheck/inst/unitTests/test_BiocCheck.R
Update emails to fredhutch.org domain
Revision: 96235
Author: m.carlson
Date: 2014-10-30T18:40:26+00:00
Paths:
Added  /trunk/madman/Rpacks/AnnotationHub/vignettes
Added  /trunk/madman/Rpacks/AnnotationHub/vignettes/AnnotationHub.Rmd
Added  /trunk/madman/Rpacks/AnnotationHub/vignettes/AnnotationHubRecipes.Rmd
Added  /trunk/madman/Rpacks/AnnotationHub/vignettes/display.png
Adds back the vignettes that we just removed.
Revision: 96234
Author: m.carlson
Date: 2014-10-30T18:39:54+00:00
Paths:
Deleted  /trunk/madman/Rpacks/AnnotationHub/vignettes
removes old vignettes.
Revision: 96233
Author: m.carlson
Date: 2014-10-30T18:36:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
just to bump vignettes dir to ci status
Revision: 96232
Author: m.carlson
Date: 2014-10-30T18:31:10+00:00
Paths:
Added  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Added  /trunk/madman/Rpacks/AnnotationHub/NAMESPACE
Added  /trunk/madman/Rpacks/AnnotationHub/R
Added  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHub-class.R
Added  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHubResource-class.R
Added  /trunk/madman/Rpacks/AnnotationHub/R/cache.R
Added  /trunk/madman/Rpacks/AnnotationHub/R/curl_writer.R
Added  /trunk/madman/Rpacks/AnnotationHub/R/display.R
Added  /trunk/madman/Rpacks/AnnotationHub/R/hub.R
Added  /trunk/madman/Rpacks/AnnotationHub/R/option.R
Added  /trunk/madman/Rpacks/AnnotationHub/R/sql.R
Added  /trunk/madman/Rpacks/AnnotationHub/R/utilities.R
Added  /trunk/madman/Rpacks/AnnotationHub/R/zzz.R
Added  /trunk/madman/Rpacks/AnnotationHub/inst
Added  /trunk/madman/Rpacks/AnnotationHub/inst/scripts
Added  /trunk/madman/Rpacks/AnnotationHub/inst/scripts/shinyTest.R
Added  /trunk/madman/Rpacks/AnnotationHub/inst/scripts/test.R
Added  /trunk/madman/Rpacks/AnnotationHub/man
Added  /trunk/madman/Rpacks/AnnotationHub/man/AnnotationHub-class.Rd
Added  /trunk/madman/Rpacks/AnnotationHub/man/AnnotationHub-package.Rd
Added  /trunk/madman/Rpacks/AnnotationHub/man/hubOption.Rd
Added  /trunk/madman/Rpacks/AnnotationHub/src
Added  /trunk/madman/Rpacks/AnnotationHub/src/AnnotationHub_curl.c
Added  /trunk/madman/Rpacks/AnnotationHub/src/AnnotationHub_curl.h
Added  /trunk/madman/Rpacks/AnnotationHub/src/R_init_AnnotationHub.c
Adds new AnnotationHub.
Revision: 96231
Author: m.carlson
Date: 2014-10-30T18:26:50+00:00
Paths:
Deleted  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Deleted  /trunk/madman/Rpacks/AnnotationHub/NAMESPACE
Deleted  /trunk/madman/Rpacks/AnnotationHub/NEWS
Deleted  /trunk/madman/Rpacks/AnnotationHub/R
Deleted  /trunk/madman/Rpacks/AnnotationHub/inst
Deleted  /trunk/madman/Rpacks/AnnotationHub/man
Deleted  /trunk/madman/Rpacks/AnnotationHub/tests
Removes old AnnotationHub to make room for all new AnnotationHub.
Revision: 96229
Author: p.shannon
Date: 2014-10-30T18:11:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/PSICQUIC/DESCRIPTION
added plyr to Depends, for use of rbind.fill in unitTests
Revision: 96227
Author: r.nicolle
Date: 2014-10-30T17:52:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/CoRegNet/R/display.R
Modified  /trunk/madman/Rpacks/CoRegNet/src/licorn.c
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: fc0602b4e01dbb977dcabb7a4af93bbf7534ffb7

    correcting ward warning

Committed by: RemyNicolle
Author Name: RemyNicolle
Commit date: 2014-10-30 18:51:58 +0100
Author date: 2014-10-30 18:51:58 +0100
Revision: 96226
Author: g.finak
Date: 2014-10-30T17:49:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/MIMOSA/R/helperMethods.R
Modified  /trunk/madman/Rpacks/MIMOSA/man/boxplotMIMOSAResultList.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 5 commits.

Commit information:

Commit id: 1afa49588c164cbbb5e7eeb5c1aade11a00ae6e1

    update docs

Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2014-10-30 10:48:20 -0700
Author date: 2014-10-30 10:48:20 -0700

Commit id: cf8f8059cef6eadb3a64a5bf829957978c9e0415

    Fix documentation

Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2014-10-30 10:47:37 -0700
Author date: 2014-10-30 10:47:37 -0700

Commit id: 0a58c4045ba4d7582787ccb878a0e9e7b95a841c

    fix boxplot names

Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2014-10-30 10:46:41 -0700
Author date: 2014-10-30 10:46:41 -0700

Commit id: bf021a330dcb684ba30199f077b92ec7e02be3e9

    update boxplot code and docs

Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2014-10-30 10:40:07 -0700
Author date: 2014-10-30 10:40:07 -0700

Commit id: e42f7bbfa3eb0c77976c2754959427a2f1750cdc

    Update boxplot code for MIMOSA

Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2014-10-30 10:38:30 -0700
Author date: 2014-10-30 10:38:30 -0700
Revision: 96225
Author: j.meskas
Date: 2014-10-30T17:45:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCL/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowCL/R/flowCL.R
Modified  /trunk/madman/Rpacks/flowCL/R/rQueryFunctions.R
Modified  /trunk/madman/Rpacks/flowCL/R/supportingFunctions.R
Modified  /trunk/madman/Rpacks/flowCL/inst/NEWS
1.5.1: Explanded on one marker queries. Uses sesame to find direct sub classes only.
Revision: 96224
Author: p.shannon
Date: 2014-10-30T17:30:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/PSICQUIC/DESCRIPTION
Modified  /trunk/madman/Rpacks/PSICQUIC/R/PSICQUIC-class.R
Modified  /trunk/madman/Rpacks/PSICQUIC/inst/unitTests/test_IDMapper.R
Modified  /trunk/madman/Rpacks/PSICQUIC/inst/unitTests/test_PSICQUIC.R
removed RefNet dependency in test_IDMapper.R by switching from
RefNet:::smartRbind to plyr's rbind.fill

GeneMANIA test function now included, but since GeneMANIA is still broken, the
results are not actually tested for reasonableness.
Revision: 96222
Author: r.castelo
Date: 2014-10-30T16:21:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/NAMESPACE
Modified  /trunk/madman/Rpacks/VariantFiltering/R/methods-PhastConsDb.R
Modified  /trunk/madman/Rpacks/VariantFiltering/man/PhastConsDb-class.Rd
Adapted the PhastConsDb class to deal with phastCons scores stored in a rda file per chromosome to minimize the memory footprint. Adapted code to deal with newer RSQLite 1.0.0.
Revision: 96215
Author: fhahne
Date: 2014-10-30T15:09:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/Gviz/R/Gviz.R
fixing a bug in the subsetting code
Revision: 96214
Author: a.luna
Date: 2014-10-30T15:07:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/paxtoolsr/DESCRIPTION
Added  /trunk/madman/Rpacks/paxtoolsr/inst/CITATION
Added CITATION file
Revision: 96212
Author: stvjc
Date: 2014-10-30T12:49:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/man/All.cis.Rd
Modified  /trunk/madman/Rpacks/GGtools/man/cisAssoc.Rd
more attacks on warnings
Revision: 96211
Author: hpages
Date: 2014-10-30T12:25:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/NAMESPACE
Modified  /trunk/madman/Rpacks/BSgenome/R/OnDiskLongTable-class.R
Modified  /trunk/madman/Rpacks/BSgenome/R/XtraSNPlocs-class.R
- Add blocksizes() generic with method for OnDiskLongTable objects.
- Fix levels of "batch_label" column returned by getDataFromOnDiskLongTable()
  when the OnDiskLongTable object was created with 'blocksize' set to a value
  < nrow(df) for some batches.
- Add getBatchesFromOnDiskLongTable().
- Refactor and simplifiy implementation of "snpsBySeqname" method for
  XtraSNPlocs objects by using getBatchesFromOnDiskLongTable() internally.
- Switch order of 'ifnotfound' and 'columns' arguments in "snpsById" method for
  XtraSNPlocs objects so 'columns' is in 3rd position like in "snpsBySeqname"
  method.
Revision: 96210
Author: i.scheinin
Date: 2014-10-30T12:24:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/QDNAseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/QDNAseq/NEWS
Modified  /trunk/madman/Rpacks/QDNAseq/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/getBinAnnotations.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/plot-methods.R
Modified  /trunk/madman/Rpacks/QDNAseq/R/segmentBins.R
Added  /trunk/madman/Rpacks/QDNAseq/man/QDNAseq-defunct.Rd
Deleted  /trunk/madman/Rpacks/QDNAseq/man/QDNAseq-deprecated.Rd
Modified  /trunk/madman/Rpacks/QDNAseq/man/QDNAseq-package.Rd
Modified  /trunk/madman/Rpacks/QDNAseq/man/getBinAnnotations.Rd
Modified  /trunk/madman/Rpacks/QDNAseq/man/segmentBins.Rd
Modified  /trunk/madman/Rpacks/QDNAseq/vignettes/QDNAseq.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 7 commits.

Commit information:

Commit id: 41a984dd1ee6bf1dc78c604449293a4da01fc611

    Bump development version number to 1.3.1.

Committed by: Ilari Scheinin
Author Name: Ilari Scheinin
Commit date: 2014-10-30 14:21:41 +0200
Author date: 2014-10-30 14:21:41 +0200

Commit id: 67ee7711f0e8453fdc9c326a38ef5ded8497ff93

    Update NEWS.

Committed by: Ilari Scheinin
Author Name: Ilari Scheinin
Commit date: 2014-10-30 14:16:08 +0200
Author date: 2014-10-30 14:16:08 +0200

Commit id: 107624e3c4c93064f50faa76bc7cdd45dae867fd

    Update vignette for transformation function in segmentBins().

Committed by: Ilari Scheinin
Author Name: Ilari Scheinin
Commit date: 2014-10-30 14:09:11 +0200
Author date: 2014-10-30 14:09:11 +0200

Commit id: 3dfc4586030d228f662c39058e21ca9a7d4a4580

    Add an asterisk to the noise measure symbols to signify that they are not regular standard deviations/variances, but calculated after scaling with the mean.

Committed by: Ilari Scheinin
Author Name: Ilari Scheinin
Commit date: 2014-10-30 13:12:12 +0200
Author date: 2014-10-30 13:12:12 +0200

Commit id: ab95c86c5a69c370e349ab12b94cd0e7a5f8cb22

    Update authors and description.

Committed by: Ilari Scheinin
Author Name: Ilari Scheinin
Commit date: 2014-10-29 19:26:10 +0200
Author date: 2014-10-29 19:26:10 +0200

Commit id: c322325d37cb160f74af27ad560d4c8729dbc214

    Clarify transformFun options in segmentBins().

Committed by: Ilari Scheinin
Author Name: Ilari Scheinin
Commit date: 2014-10-29 19:24:52 +0200
Author date: 2014-10-29 19:24:52 +0200

Commit id: 5603ac6cc5f83326258c4b225c2d4a118c8bb903

    Make downloadBinAnnotations() defunct.

Committed by: Ilari Scheinin
Author Name: Ilari Scheinin
Commit date: 2014-10-29 18:27:29 +0200
Author date: 2014-10-29 18:27:29 +0200
Revision: 96209
Author: stvjc
Date: 2014-10-30T12:22:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/R/cisa.R
drop snfilt from codes
Revision: 96208
Author: stvjc
Date: 2014-10-30T12:04:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GGtools/NAMESPACE
Modified  /trunk/madman/Rpacks/GGtools/R/cisa.R
Modified  /trunk/madman/Rpacks/GGtools/man/cisAssoc.Rd
various cleanup steps
Revision: 96207
Author: r.castelo
Date: 2014-10-30T11:57:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
Modified  /trunk/madman/Rpacks/qpgraph/NAMESPACE
Modified  /trunk/madman/Rpacks/qpgraph/R/AllClass.R
Modified  /trunk/madman/Rpacks/qpgraph/R/eQTLcross-methods.R
Modified  /trunk/madman/Rpacks/qpgraph/R/eQTLnetwork-methods.R
Modified  /trunk/madman/Rpacks/qpgraph/R/eQTLnetworkEstimationParam-methods.R
Modified  /trunk/madman/Rpacks/qpgraph/vignettes/eQTLnetworks.Rnw
Modified  /trunk/madman/Rpacks/qpgraph/vignettes/qpgraph.bib
Modified  /trunk/madman/Rpacks/qpgraph/vignettes/qpgraphSimulate.Rnw
Fixed some bugs on the management of eQTL network data structures, and display of eQTL networks using hive plots. Added documentation.
Revision: 96206
Author: stvjc
Date: 2014-10-30T11:40:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/R/pifdr.R
Modified  /trunk/madman/Rpacks/GGtools/man/cisAssoc.Rd
Modified  /trunk/madman/Rpacks/GGtools/man/pifdr.Rd
fixing up cisAssoc example and trimming pifdr output greater than 1
Revision: 96205
Author: fhahne
Date: 2014-10-30T11:38:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/Gviz/DESCRIPTION
Modified  /trunk/madman/Rpacks/Gviz/NAMESPACE
Modified  /trunk/madman/Rpacks/Gviz/R/AllClasses.R
Modified  /trunk/madman/Rpacks/Gviz/R/Gviz-methods.R
Modified  /trunk/madman/Rpacks/Gviz/R/Gviz.R
Modified  /trunk/madman/Rpacks/Gviz/man/BiomartGeneRegionTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/man/DataTrack-class.Rd
adding some code to better deal with ENSEMBL schema changes
Revision: 96204
Author: stvjc
Date: 2014-10-30T11:22:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/man/cisAssoc.Rd
condition use of scanVcfHeader in cisAssoc man
Revision: 96203
Author: stvjc
Date: 2014-10-30T10:52:36+00:00
Paths:
Added  /trunk/madman/Rpacks/GGtools/man/cisAssoc.Rd
add the man page for cisAssoc
Revision: 96202
Author: stvjc
Date: 2014-10-30T10:52:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/DESCRIPTION
document dropUnivHets
Revision: 96200
Author: l.lahti
Date: 2014-10-30T10:02:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.md
Modified  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse2.png
Added  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse21.png
Added  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse22.png
Modified  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse3.png
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: a083557a66f75f3a5c9cf345c90eeda96f2c49c7

    R

Committed by: antagomir
Author Name: antagomir
Commit date: 2014-10-30 11:01:55 +0100
Author date: 2014-10-30 11:01:55 +0100
Revision: 96199
Author: l.lahti
Date: 2014-10-30T09:55:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/netresponse/DESCRIPTION
Modified  /trunk/madman/Rpacks/netresponse/R/plot-methods.R
Modified  /trunk/madman/Rpacks/netresponse/inst/extras/build.sh
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.Rmd
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.md
Commit made by the Bioconductor Git-SVN bridge.
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Commit information:

Commit id: a488b436c425ec96d9413ce40b11f251602a5a9b

    R

Committed by: antagomir
Author Name: antagomir
Commit date: 2014-10-30 10:55:29 +0100
Author date: 2014-10-30 10:55:29 +0100
Revision: 96198
Author: l.lahti
Date: 2014-10-30T09:48:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.Rmd
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.md
Modified  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse3.png
Commit made by the Bioconductor Git-SVN bridge.
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Commit information:

Commit id: 512b8dbed00a46ad684edae8078aa67e47181bb4

    R

Committed by: antagomir
Author Name: antagomir
Commit date: 2014-10-30 10:48:42 +0100
Author date: 2014-10-30 10:48:42 +0100
Revision: 96197
Author: l.lahti
Date: 2014-10-30T09:47:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.Rmd
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.md
Modified  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse3.png
Commit made by the Bioconductor Git-SVN bridge.
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Commit information:

Commit id: a691c72f878f847a55d4fa24d1aa6f1432b689a7

    R

Committed by: antagomir
Author Name: antagomir
Commit date: 2014-10-30 10:47:27 +0100
Author date: 2014-10-30 10:47:27 +0100
Revision: 96196
Author: l.lahti
Date: 2014-10-30T09:46:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.Rmd
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.md
Added  /trunk/madman/Rpacks/netresponse/vignettes/TODO/TODO.Rmd
Modified  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse2.png
Modified  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse3.png
Modified  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse4.png
Modified  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse5.png
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: d910f4300c5970189961359248818b9aac1d006a

    R

Committed by: antagomir
Author Name: antagomir
Commit date: 2014-10-30 10:46:01 +0100
Author date: 2014-10-30 10:46:01 +0100
Revision: 96195
Author: l.lahti
Date: 2014-10-30T09:33:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/netresponse/R/plot-methods.R
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.Rmd
Modified  /trunk/madman/Rpacks/netresponse/vignettes/NetResponse.md
Modified  /trunk/madman/Rpacks/netresponse/vignettes/figure/NetResponse3.png
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 4ec8299af30967e503848f086a6014452dd4b9ec

    R

Committed by: antagomir
Author Name: antagomir
Commit date: 2014-10-30 10:33:15 +0100
Author date: 2014-10-30 10:33:15 +0100
Revision: 96193
Author: hpages
Date: 2014-10-30T08:15:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/R/OnDiskLongTable-class.R
Modified  /trunk/madman/Rpacks/BSgenome/R/XtraSNPlocs-class.R
- Oops, again please read snplocs() instead of snpcount() in previous commit
  message!
- "snpsById" method for XtraSNPlocs objects almost complete ('ifnotfound' arg
  still not implemented).
Revision: 96192
Author: m.boenn
Date: 2014-10-30T07:25:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/geecc/DESCRIPTION
Modified  /trunk/madman/Rpacks/geecc/NAMESPACE
Modified  /trunk/madman/Rpacks/geecc/R/littlehelpers.R
Modified  /trunk/madman/Rpacks/geecc/man/GO2list.Rd
Added function GO2offspring
Revision: 96190
Author: d.strbenac
Date: 2014-10-30T07:00:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/KolmogorovSmirnovSelection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/KullbackLeiblerSelection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/classes.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/edgeRselection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/errorMap.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/leveneSelection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/likelihoodRatioSelection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/limmaSelection.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/nearestShrunkenCentroidSelectionInterface.R
Added  /trunk/madman/Rpacks/ClassifyR/R/rankStabilityPlot.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/runTest.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/runTests.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/utilities.R
Modified  /trunk/madman/Rpacks/ClassifyR/man/ClassifyResult-class.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/KolmogorovSmirnovSelection.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/KullbackLeiblerSelection.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/calcError.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/distribution.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/edgeRselection.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/errorMap.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/leveneSelection.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/likelihoodRatioSelection.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/limmaSelection.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/nearestShrunkenCentroidSelectionInterface.Rd
Added  /trunk/madman/Rpacks/ClassifyR/man/rankStabilityPlot.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/man/runTests.Rd
Modified  /trunk/madman/Rpacks/ClassifyR/vignettes/ClassifyR.Rmd
- rankStabilityPlot function created.
- Framework updated to keep track of feature rankings from selection.
Revision: 96188
Author: m.carlson
Date: 2014-10-30T00:15:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/EnsemblFastaImportPreparer-class.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/ensemblFastaToFaFile.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeInparanoid8ToDbs.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/scripts/updateToLatestEnsembl.R
update starts us down the path of updating the ensembl fasta recipe.

Still has some bugs I have to squash.
Revision: 96184
Author: sdavis2
Date: 2014-10-29T22:47:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/SRAdb/DESCRIPTION
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Commit information:

Commit id: e25a6c0a7b617aa91626bf4613e4984755974a1b

    Fixes #3

Committed by: Sean Davis
Author Name: Sean Davis
Commit date: 2014-10-29 18:46:59 -0400
Author date: 2014-10-29 18:46:59 -0400
Revision: 96181
Author: m.carlson
Date: 2014-10-29T22:22:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeInparanoid8ToDbs.R
bug fix for inparanoid recipe (a path changed)
Revision: 96178
Author: sdavis2
Date: 2014-10-29T22:13:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/SRAdb/DESCRIPTION
Modified  /trunk/madman/Rpacks/SRAdb/R/getSRA.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 3270ada6fd4e2c867961e4c78afc646d71cbd83e

    Fixes #2

    The changes to RSQLite 1.0 removed the sqliteTableFields() function.  A simple replacement with PRAGMA table_info() did the trick.

Committed by: Sean Davis
Author Name: Sean Davis
Commit date: 2014-10-29 18:12:50 -0400
Author date: 2014-10-29 18:12:50 -0400
Revision: 96177
Author: khansen
Date: 2014-10-29T21:59:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/affxparser/DESCRIPTION
Modified  /trunk/madman/Rpacks/affxparser/src/fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp
Modified  /trunk/madman/Rpacks/affxparser/src/fusion_sdk/calvin_files/data/src/GenericData.cpp
Modified  /trunk/madman/Rpacks/affxparser/src/fusion_sdk/file/BPMAPFileData.cpp
Modified  /trunk/madman/Rpacks/affxparser/src/fusion_sdk/util/TableFile.cpp
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Commit information:

Commit id: fb3057392c3bae7b8ef36fc96cc4a09d68a7e5e0

    CLEANUP: Remove some native-code compile warnings Addressed the following compile warnings (related to Issue #6):

    fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:109:15:
    warning: comparison of unsigned expression < 0 is always false
             [-Wtautological-compare]
       if (groupIdx < 0 || groupIdx >= groupCnt)

    fusion_sdk/calvin_files/data/src/GenericData.cpp:388:18:
    warning: comparison of unsigned expression >= 0 is always true
             [-Wtautological-compare]
       if (dataSetIdx >= 0 && (int32_t)dataSetIdx < dch->GetDataSetCnt())

    fusion_sdk/file/BPMAPFileData.cpp:372:16:
    warning: unused variable 'probeIn' [-Wunused-variable]
       unsigned char
       probeIn[PROBE_STORAGE_BUFFER_LENGTH]="";

    fusion_sdk/file/BPMAPFileData.cpp:373:7:
    warning: unused variable 'probeOut' [-Wunused-variable]
      char probeOut[probeBufSize]="";

Committed by: hb
Author Name: hb
Commit date: 2014-10-29 14:58:39 -0700
Author date: 2014-10-29 14:58:39 -0700
Revision: 96176
Author: m.carlson
Date: 2014-10-29T21:21:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/updateResources.R
makes the default args for updateResources safer.
Revision: 96175
Author: stvjc
Date: 2014-10-29T20:51:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/R/cisa.R
get the catch right
Revision: 96174
Author: stvjc
Date: 2014-10-29T20:36:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/GGtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GGtools/NEWS
Modified  /trunk/madman/Rpacks/GGtools/R/cisa.R
Added  /trunk/madman/Rpacks/GGtools/data/lgeu.rda
Added  /trunk/madman/Rpacks/GGtools/inst/vcf/c20exch.vcf.gz
Added  /trunk/madman/Rpacks/GGtools/inst/vcf/c20exch.vcf.gz.tbi
Modified  /trunk/madman/Rpacks/GGtools/man/All.cis.Rd
deal with universal heterozygosity with option in cisAssoc
Revision: 96173
Author: m.carlson
Date: 2014-10-29T20:24:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/updateResources.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/vignettes/AnnotationHubData.Rmd
Updates the vignette with more information (and better styles it)
Revision: 96171
Author: l.collado-torres
Date: 2014-10-29T18:44:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 85d26515d9325d6dcb176b5a2734867e64b33af8

    Update readme

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-29 14:43:44 -0400
Author date: 2014-10-29 14:43:44 -0400
Revision: 96170
Author: l.collado-torres
Date: 2014-10-29T18:43:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/regionReport/README.md
Modified  /trunk/madman/Rpacks/regionReport/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 3d8886d0d9f7cb27330488fef47b798a577a9e68

    fix citation and README

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-29 14:43:05 -0400
Author date: 2014-10-29 14:43:05 -0400
Revision: 96169
Author: l.collado-torres
Date: 2014-10-29T18:42:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderPlot/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e6c250eec1e31ad3cd49550e667fcd6d18743fcd

    fix citation

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-29 14:42:52 -0400
Author date: 2014-10-29 14:42:52 -0400
Revision: 96168
Author: l.collado-torres
Date: 2014-10-29T18:42:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderHelper/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
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Commit information:

Commit id: 3905619995da03b0898006ce97355f656cf29b75

    fix citation

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-29 14:42:45 -0400
Author date: 2014-10-29 14:42:45 -0400
Revision: 96167
Author: l.collado-torres
Date: 2014-10-29T18:38:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/regionReport/DESCRIPTION
Added  /trunk/madman/Rpacks/regionReport/inst/CITATION
Modified  /trunk/madman/Rpacks/regionReport/vignettes/fakeVignettes/regionReport.Rmd
Modified  /trunk/madman/Rpacks/regionReport/vignettes/realVignettes/regionReport.Rmd
Modified  /trunk/madman/Rpacks/regionReport/vignettes/regionReport.Rmd
Commit made by the Bioconductor Git-SVN bridge.
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Commit information:

Commit id: 6fa254eb930dac6f73e72d2a467fb9676ed935d6

    v1.1.4 -- add CITATION info

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-29 14:38:48 -0400
Author date: 2014-10-29 14:38:48 -0400
Revision: 96166
Author: l.collado-torres
Date: 2014-10-29T18:38:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: dcb29b02e41c4c316f306910c6e776749dfb44a9

    add version

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-29 14:37:53 -0400
Author date: 2014-10-29 14:37:53 -0400
Revision: 96165
Author: l.collado-torres
Date: 2014-10-29T18:37:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderHelper/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 3d0bfa7218db2a8fdf6a2279a4bfc9e616cfe429

    add version

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-29 14:37:43 -0400
Author date: 2014-10-29 14:37:43 -0400
Revision: 96164
Author: l.collado-torres
Date: 2014-10-29T18:37:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinderPlot/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 6b6cd75e17769a501133c3af42c6e039394eea3d

    add version

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-29 14:37:37 -0400
Author date: 2014-10-29 14:37:37 -0400
Revision: 96163
Author: d.mosen-ansorena
Date: 2014-10-29T18:33:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqCNA/DESCRIPTION
Modified  /trunk/madman/Rpacks/seqCNA/R/seqCNA_functions.r
Modified  /trunk/madman/Rpacks/seqCNA/man/seqCNA-package.Rd
Again, trying to commit the previous change.
Revision: 96162
Author: l.collado-torres
Date: 2014-10-29T18:16:13+00:00
Paths:
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: 47d0933e453cd9f659ceb0730b38828903d394e5

    Fix citation, tidy origins

Committed by: lcolladotor
Author Name: lcolladotor
Commit date: 2014-10-29 14:16:05 -0400
Author date: 2014-10-29 14:16:05 -0400

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