SVN: Bioconductor (trunk)

Revision 77702 by s.balcome

s.balcome — Wed, 19 Jun 2013 09:13:43 GMT

Initial work with unit testing.  Not there yet.

(Wed, 19 Jun 2013 09:13:43 GMT)

Modified	/trunk/madman/Rpacks/displayR/R/displayR.R
Added	/trunk/madman/Rpacks/displayR/tests/displayR_test.R
Added	/trunk/madman/Rpacks/displayR/tests/run-all.R
Added	/trunk/madman/Rpacks/displayR/inst/tests
Added	/trunk/madman/Rpacks/displayR/inst/tests/displayR_test.R

Revision 77698 by s.balcome

s.balcome — Wed, 19 Jun 2013 07:17:39 GMT

Committing to SVN in unfinished state just as a precaution.  Added Marc Carlson's summarized experiment example as method skeleton.  Added SummExp.Rda and testing.Rda data files.  

(Wed, 19 Jun 2013 07:17:39 GMT)

Modified	/trunk/madman/Rpacks/displayR/R/displayR.R
Added	/trunk/madman/Rpacks/displayR/data/testing.Rda
Added	/trunk/madman/Rpacks/displayR/data/SummExp.Rda

Revision 77696 by c.zuo

c.zuo — Wed, 19 Jun 2013 06:56:58 GMT

existing functions

(Wed, 19 Jun 2013 06:56:58 GMT)

Modified

/trunk/madman/Rpacks/ExperimentHub/R/supplement.R

Revision 77695 by c.zuo

c.zuo — Wed, 19 Jun 2013 06:46:23 GMT

existing functions

(Wed, 19 Jun 2013 06:46:23 GMT)

Added	/trunk/madman/Rpacks/ExperimentHub/R/ExperimentHub.R
Added	/trunk/madman/Rpacks/ExperimentHub/R/test.R
Added	/trunk/madman/Rpacks/ExperimentHub/R
Added	/trunk/madman/Rpacks/ExperimentHub/DESCRIPTION
Added	/trunk/madman/Rpacks/ExperimentHub/man/run.Rd
Added	/trunk/madman/Rpacks/ExperimentHub/man
Added	/trunk/madman/Rpacks/ExperimentHub/NAMESPACE
Added	/trunk/madman/Rpacks/ExperimentHub/inst
Added	/trunk/madman/Rpacks/ExperimentHub/R/supplement.R

Revision 77694 by hpages

hpages — Wed, 19 Jun 2013 06:12:35 GMT

Complete sequenceLayer().

(Wed, 19 Jun 2013 06:12:35 GMT)

Modified	/trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified	/trunk/madman/Rpacks/Rsamtools/R/sequenceLayer.R

Revision 77693 by n.pavelka

n.pavelka — Wed, 19 Jun 2013 03:58:59 GMT

version 1.33.1:

* minor changes:
--removed unnecessary calls to `which' within subsetting operations, to avoid
  potential unintended consequences pointed out by Wolfgang Huber:
  

(Wed, 19 Jun 2013 03:58:59 GMT)

Modified	/trunk/madman/Rpacks/plgem/NEWS
Modified	/trunk/madman/Rpacks/plgem/R/plgem.obsStn.R
Modified	/trunk/madman/Rpacks/plgem/DESCRIPTION
Modified	/trunk/madman/Rpacks/plgem/R/plgem.deg.R
Modified	/trunk/madman/Rpacks/plgem/R/plgem.resampledStn.R
Modified	/trunk/madman/Rpacks/plgem/R/plgem.fit.R
Modified	/trunk/madman/Rpacks/plgem/R/run.plgem.R

Revision 77692 by mtmorgan

mtmorgan — Wed, 19 Jun 2013 03:56:03 GMT

parse only requested fixed, info, geno fields

(Wed, 19 Jun 2013 03:56:03 GMT)

Modified	/trunk/madman/Rpacks/VariantAnnotation/inst/unitTests/test_scanVcf.R
Modified	/trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified	/trunk/madman/Rpacks/VariantAnnotation/src/utilities.c
Modified	/trunk/madman/Rpacks/VariantAnnotation/R/methods-scanVcf.R
Modified	/trunk/madman/Rpacks/VariantAnnotation/src/vcffile.c
Modified	/trunk/madman/Rpacks/VariantAnnotation/src/utilities.h
Modified	/trunk/madman/Rpacks/VariantAnnotation/src/vcftype.c

Revision 77687 by v.obenchain

v.obenchain — Tue, 18 Jun 2013 22:27:34 GMT

readGT() now retains genotype phasing.

(Tue, 18 Jun 2013 22:27:34 GMT)

Modified	/trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified	/trunk/madman/Rpacks/VariantAnnotation/inst/unitTests/test_readVcf-methods.R
Modified	/trunk/madman/Rpacks/VariantAnnotation/R/methods-readVcf.R

Revision 77686 by hpages

hpages — Tue, 18 Jun 2013 00:00:00 GMT

Rename 'remove.N.regions' arg -> 'N.regions.removed'.

(Tue, 18 Jun 2013 00:00:00 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/src/cigar_utils.c
Modified	/trunk/madman/Rpacks/GenomicRanges/man/cigar-utils.Rd
Modified	/trunk/madman/Rpacks/GenomicRanges/R/cigar-utils.R

Revision 77684 by hpages

hpages — Tue, 18 Jun 2013 21:43:26 GMT

split sequenceLayer.R from stackStringsFromBam.R

(Tue, 18 Jun 2013 21:43:26 GMT)

Modified	/trunk/madman/Rpacks/Rsamtools/R/stackStringsFromBam.R
Added	/trunk/madman/Rpacks/Rsamtools/R/sequenceLayer.R

Revision 77682 by hpages

hpages — Tue, 18 Jun 2013 21:20:31 GMT

Add extractAlignmentRangesOnReference() as a replacement for now deprecated
cigarToIRangesListByAlignment() and cigarToIRangesListByRName().

(Tue, 18 Jun 2013 21:20:31 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/NAMESPACE
Modified	/trunk/madman/Rpacks/GenomicRanges/R/GAlignments-class.R
Modified	/trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_cigar-utils.R
Modified	/trunk/madman/Rpacks/GenomicRanges/man/cigar-utils.Rd
Modified	/trunk/madman/Rpacks/GenomicRanges/R/cigar-utils.R

Revision 77679 by hpages

hpages — Tue, 18 Jun 2013 20:03:54 GMT

- Add 'remove.N.regions' argument to cigarRangesOnReferenceSpace(),
  cigarRangesOnPairwiseSpace(), cigarWidthOnReferenceSpace(), and
  cigarWidthOnPairwiseSpace().
- Add 'before.hard.clipping' and 'after.soft.clipping' arguments to
  cigarRangesOnQuerySpace().
- Add 'after.soft.clipping' argument to cigarWidthOnQuerySpace().
- Add 'flag' argument to cigarWidthOnReferenceSpace(), cigarWidthOnQuerySpace(),
  and cigarWidthOnPairwiseSpace().

(Tue, 18 Jun 2013 20:03:54 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/src/R_init_GenomicRanges.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/cigar_utils.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/GenomicRanges.h
Modified	/trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_cigar-utils.R
Modified	/trunk/madman/Rpacks/GenomicRanges/man/cigar-utils.Rd
Modified	/trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified	/trunk/madman/Rpacks/GenomicRanges/R/cigar-utils.R

Revision 77678 by t.yin

t.yin — Tue, 18 Jun 2013 19:57:15 GMT

support subseting tracks by '[' method

(Tue, 18 Jun 2013 19:57:15 GMT)

Modified	/trunk/madman/Rpacks/ggbio/R/AllGenerics.R
Modified	/trunk/madman/Rpacks/ggbio/R/Tracks-class.R
Modified	/trunk/madman/Rpacks/ggbio/R/Plot-class.R

Revision 77676 by s.balcome

s.balcome — Tue, 18 Jun 2013 18:43:47 GMT

Combined two sliders into one UI element.

(Tue, 18 Jun 2013 18:43:47 GMT)

Modified

/trunk/madman/Rpacks/displayR/R/displayR.R

Revision 77670 by p.haverty

p.haverty — Tue, 18 Jun 2013 17:33:42 GMT

Version 1.4.0. Added updatedObject with import from BiocGenerics

(Tue, 18 Jun 2013 17:33:42 GMT)

Modified	/trunk/madman/Rpacks/bigmemoryExtras/DESCRIPTION
Modified	/trunk/madman/Rpacks/bigmemoryExtras/R/BigMatrix2.R

Revision 77669 by s.balcome

s.balcome — Tue, 18 Jun 2013 17:32:51 GMT

Fixed the range slider.  Now the range window is dynamically determined by max/min ranges from a single chromosome selected from dropdown UI element.

(Tue, 18 Jun 2013 17:32:51 GMT)

Modified

/trunk/madman/Rpacks/displayR/R/displayR.R

Revision 77667 by p.haverty

p.haverty — Tue, 18 Jun 2013 17:11:49 GMT

adding dimnames, optionally, works in BigMatrix2 now

(Tue, 18 Jun 2013 17:11:49 GMT)

Modified

/trunk/madman/Rpacks/bigmemoryExtras/R/BigMatrix2.R

Revision 77666 by s.balcome

s.balcome — Tue, 18 Jun 2013 16:44:38 GMT

Reduced size of sample GRange data.

(Tue, 18 Jun 2013 16:44:38 GMT)

Modified

/trunk/madman/Rpacks/displayR/data/mmgrsubren.rda

Revision 77665 by s.balcome

s.balcome — Tue, 18 Jun 2013 16:33:53 GMT

Added expressionSet and GRange sample data to package.

(Tue, 18 Jun 2013 16:33:53 GMT)

Modified	/trunk/madman/Rpacks/displayR/R/displayR.R
Added	/trunk/madman/Rpacks/displayR/data/expr.rda
Added	/trunk/madman/Rpacks/displayR/data/mmgrsubren.rda

Revision 77655 by j.barry

j.barry — Tue, 18 Jun 2013 07:46:34 GMT

remove export of getAlphaNumeric

(Tue, 18 Jun 2013 07:46:34 GMT)

Modified

/trunk/madman/Rpacks/cellHTS2/NAMESPACE

Revision 77654 by hpages

hpages — Tue, 18 Jun 2013 06:49:17 GMT

- Add 'f' argument to cigarRangesOnReferenceSpace().
- More code simplifications.

(Tue, 18 Jun 2013 06:49:17 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/src/R_init_GenomicRanges.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/cigar_utils.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/GenomicRanges.h
Modified	/trunk/madman/Rpacks/GenomicRanges/man/cigar-utils.Rd
Modified	/trunk/madman/Rpacks/GenomicRanges/R/cigar-utils.R

Revision 77653 by t.yin

t.yin — Tue, 18 Jun 2013 05:26:42 GMT

hack for command list, support many data structure in tracks, support bamfile, bamfilelist, etc

(Tue, 18 Jun 2013 05:26:42 GMT)

Modified	/trunk/madman/Rpacks/ggbio/R/autoplot-method.R
Modified	/trunk/madman/Rpacks/ggbio/R/Cache-class.R
Deleted	/trunk/madman/Rpacks/ggbio/R/tracks.R
Added	/trunk/madman/Rpacks/ggbio/R/Tracks-class.R
Modified	/trunk/madman/Rpacks/ggbio/R/GGbio-class.R
Modified	/trunk/madman/Rpacks/ggbio/R/Grob-class.R
Modified	/trunk/madman/Rpacks/ggbio/R/stat_mismatch-method.R
Modified	/trunk/madman/Rpacks/ggbio/R/utils.R
Modified	/trunk/madman/Rpacks/ggbio/R/Plot-class.R
Modified	/trunk/madman/Rpacks/ggbio/inst/example/GGbio-class.R
Modified	/trunk/madman/Rpacks/ggbio/DESCRIPTION
Modified	/trunk/madman/Rpacks/ggbio/R/geom_alignment-method.R
Modified	/trunk/madman/Rpacks/ggbio/R/stat_coverage-method.R

Revision 77652 by hpages

hpages — Tue, 18 Jun 2013 00:00:00 GMT

Some code simplifications.

(Tue, 18 Jun 2013 00:00:00 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/src/R_init_GenomicRanges.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/cigar_utils.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/GenomicRanges.h
Modified	/trunk/madman/Rpacks/GenomicRanges/R/cigar-utils.R

Revision 77647 by w.shi

w.shi — Mon, 17 Jun 2013 23:16:35 GMT

version 1.11.6

(Mon, 17 Jun 2013 23:16:35 GMT)

Modified	/trunk/madman/Rpacks/Rsubread/CHANGELOG
Modified	/trunk/madman/Rpacks/Rsubread/inst/doc/SubreadUsersGuide.pdf
Modified	/trunk/madman/Rpacks/Rsubread/DESCRIPTION

Revision 77645 by hpages

hpages — Mon, 17 Jun 2013 22:46:56 GMT

Deprecate cigarToIRanges().

(Mon, 17 Jun 2013 22:46:56 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/NAMESPACE
Modified	/trunk/madman/Rpacks/GenomicRanges/src/R_init_GenomicRanges.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/cigar_utils.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/GenomicRanges.h
Modified	/trunk/madman/Rpacks/GenomicRanges/man/cigar-utils.Rd
Modified	/trunk/madman/Rpacks/GenomicRanges/R/cigar-utils.R

Revision 77644 by j.kaminker

j.kaminker — Mon, 17 Jun 2013 22:35:07 GMT

fixed height of search and input boxes so that txt is centered on safari

(Mon, 17 Jun 2013 22:35:07 GMT)

Modified

/trunk/madman/Rpacks/ReportingTools/inst/extdata/csslib/reprise.table.bootstrap.css

Revision 77643 by hpages

hpages — Mon, 17 Jun 2013 22:24:40 GMT

- Rename cigarToWidth() -> cigarWidthOnReferenceSpace(), and cigarToQWidth() ->
  cigarWidthOnQuerySpace(). Make the old names aliases for the new names and
  deprecate them.
- Add cigarWidthOnPairwiseSpace().

(Mon, 17 Jun 2013 22:24:40 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/NAMESPACE
Modified	/trunk/madman/Rpacks/GenomicRanges/R/GAlignments-class.R
Modified	/trunk/madman/Rpacks/GenomicRanges/src/R_init_GenomicRanges.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/cigar_utils.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/GenomicRanges.h
Modified	/trunk/madman/Rpacks/GenomicRanges/man/cigar-utils.Rd
Modified	/trunk/madman/Rpacks/GenomicRanges/R/cigar-utils.R
Modified	/trunk/madman/Rpacks/GenomicRanges/R/GAlignmentsList-class.R

Revision 77642 by j.kaminker

j.kaminker — Mon, 17 Jun 2013 22:09:27 GMT

fixed width of the search boxes

(Mon, 17 Jun 2013 22:09:27 GMT)

Modified

/trunk/madman/Rpacks/ReportingTools/inst/extdata/csslib/reprise.table.bootstrap.css

Revision 77641 by j.kaminker

j.kaminker — Mon, 17 Jun 2013 21:32:46 GMT

added line to make sure that no sorting content was styled

(Mon, 17 Jun 2013 21:32:46 GMT)

Modified

/trunk/madman/Rpacks/ReportingTools/inst/extdata/csslib/reprise.table.bootstrap.css

Revision 77640 by w.luo

w.luo — Mon, 17 Jun 2013 20:31:57 GMT

version 2.11.1

(Mon, 17 Jun 2013 20:31:57 GMT)

Modified	/trunk/madman/Rpacks/gage/inst/doc/dataPrep.pdf
Modified	/trunk/madman/Rpacks/gage/inst/doc/gage.pdf
Modified	/trunk/madman/Rpacks/gage/R/sigGeneSet.R
Modified	/trunk/madman/Rpacks/gage/inst/doc/gage.bib
Modified	/trunk/madman/Rpacks/gage/DESCRIPTION

Revision 77639 by j.hackney

j.hackney — Mon, 17 Jun 2013 20:18:15 GMT

Now allowing manual setting of column classes for tabular output.
Defaults have been set for most objects, and modified data.frames should
still get some coherent default behavior.

(Mon, 17 Jun 2013 20:18:15 GMT)

Modified	/trunk/madman/Rpacks/ReportingTools/DESCRIPTION
Modified	/trunk/madman/Rpacks/ReportingTools/vignettes/microarrayAnalysis.Rnw
Modified	/trunk/madman/Rpacks/ReportingTools/R/HyperGResult-methods.R
Modified	/trunk/madman/Rpacks/ReportingTools/R/objectToHTML-methods.R
Added	/trunk/madman/Rpacks/ReportingTools/R/getDefaultColumnClasses-methods.R

Revision 77638 by m.carlson

m.carlson — Mon, 17 Jun 2013 18:49:05 GMT

Adds code to support bioc style unit testing.

(Mon, 17 Jun 2013 18:49:05 GMT)

Added	/trunk/madman/Rpacks/displayR/tests/displayR_unit_tests.R
Added	/trunk/madman/Rpacks/displayR/inst/unitTests
Added	/trunk/madman/Rpacks/displayR/R/test_displayR_package.R
Modified	/trunk/madman/Rpacks/displayR/DESCRIPTION
Added	/trunk/madman/Rpacks/displayR/inst/unitTests/test_display.R

Revision 77637 by mtmorgan

mtmorgan — Mon, 17 Jun 2013 18:31:12 GMT

seman nmuloc tRamoib ni egnahc etadomocca

(Mon, 17 Jun 2013 18:31:12 GMT)

Modified	/trunk/madman/Rpacks/GenomicFeatures/R/makeTranscriptDbFromBiomart.R
Modified	/trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION

Revision 77635 by w.luo

w.luo — Mon, 17 Jun 2013 18:18:15 GMT

vignette 1.1.4

(Mon, 17 Jun 2013 18:18:15 GMT)

Modified	/trunk/madman/Rpacks/pathview/inst/CITATION
Modified	/trunk/madman/Rpacks/pathview/inst/doc/pathview.pdf
Modified	/trunk/madman/Rpacks/pathview/DESCRIPTION
Modified	/trunk/madman/Rpacks/pathview/inst/doc/pathview.bib

Revision 77634 by v.obenchain

v.obenchain — Mon, 17 Jun 2013 18:11:60 GMT

Make 'showHeadLines' and 'showTailLines' robust to NA, Inf and numeric.

(Mon, 17 Jun 2013 18:11:60 GMT)

Modified	/trunk/madman/Rpacks/IRanges/R/DataTable-API.R
Modified	/trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified	/trunk/madman/Rpacks/IRanges/R/Ranges-class.R

Revision 77633 by v.obenchain

v.obenchain — Mon, 17 Jun 2013 00:00:00 GMT

Make 'showHeadLines' and 'showTailLines' robust to NA, Inf and numeric.

(Mon, 17 Jun 2013 00:00:00 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/R/utils.R
Modified	/trunk/madman/Rpacks/GenomicRanges/R/Seqinfo-class.R

Revision 77632 by l.chavez

l.chavez — Mon, 17 Jun 2013 17:58:17 GMT

paired-end update

(Mon, 17 Jun 2013 17:58:17 GMT)

Modified	/trunk/madman/Rpacks/MEDIPS/DESCRIPTION
Modified	/trunk/madman/Rpacks/MEDIPS/R/MEDIPS.readRegionsFile.R

Revision 77631 by d.tenenbaum

d.tenenbaum — Mon, 17 Jun 2013 17:41:50 GMT

add vtpnet to devel manifest per Vince

(Mon, 17 Jun 2013 17:41:50 GMT)

Modified

/trunk/madman/Rpacks/bioc_2.13.manifest

Revision 77630 by mtmorgan

mtmorgan — Mon, 17 Jun 2013 17:21:13 GMT

sync with github

- 4512f42 :Martin Morgan: Acknowledge Ryan's contributions

(Mon, 17 Jun 2013 17:21:13 GMT)

Modified

/trunk/madman/Rpacks/BiocParallel/DESCRIPTION

Revision 77628 by w.luo

w.luo — Mon, 17 Jun 2013 16:52:38 GMT

vignette 1.1.3

(Mon, 17 Jun 2013 16:52:38 GMT)

Modified	/trunk/madman/Rpacks/pathview/inst/CITATION
Modified	/trunk/madman/Rpacks/pathview/NEWS
Modified	/trunk/madman/Rpacks/pathview/inst/doc/pathview.pdf
Modified	/trunk/madman/Rpacks/pathview/DESCRIPTION
Modified	/trunk/madman/Rpacks/pathview/inst/doc/pathview.bib

Revision 77627 by r.uriarte

r.uriarte — Mon, 17 Jun 2013 16:45:23 GMT

 minor cosmetic changes to vignette

(Mon, 17 Jun 2013 16:45:23 GMT)

Modified	/trunk/madman/Rpacks/ADaCGH2/vignettes/ADaCGH2.Rnw
Modified	/trunk/madman/Rpacks/ADaCGH2/DESCRIPTION

Revision 77626 by r.uriarte

r.uriarte — Mon, 17 Jun 2013 16:04:60 GMT

up to v.2.1.2; Trying to get it to wrok on mac, added benchmarks, and fixed ordering of output in long vignette

(Mon, 17 Jun 2013 16:04:60 GMT)

Modified	/trunk/madman/Rpacks/ADaCGH2/vignettes/ADaCGH2.Rnw
Modified	/trunk/madman/Rpacks/ADaCGH2/inst/NEWS
Modified	/trunk/madman/Rpacks/ADaCGH2/inst/doc/ADaCGH2-long-examples.Rnw
Modified	/trunk/madman/Rpacks/ADaCGH2/man/cutFile.Rd
Modified	/trunk/madman/Rpacks/ADaCGH2/inst/doc/ADaCGH2-long-examples.pdf
Added	/trunk/madman/Rpacks/ADaCGH2/inst/imagemap-example/README-usage-Python-for-HTML-with-maps.txt
Modified	/trunk/madman/Rpacks/ADaCGH2/DESCRIPTION

Revision 77625 by p.haverty

p.haverty — Mon, 17 Jun 2013 15:28:23 GMT

Experimenting with BigMatrix2 class that ditches the descriptor file
and keeps the description as a list internally and stores rownames and
colnames internally too to avoid the conversion cost from C++ to R.

(Mon, 17 Jun 2013 15:28:23 GMT)

Added

/trunk/madman/Rpacks/bigmemoryExtras/R/BigMatrix2.R

Revision 77623 by j.paulson

j.paulson — Mon, 17 Jun 2013 14:54:16 GMT

allows colors for plotGenus now

(Mon, 17 Jun 2013 14:54:16 GMT)

Modified

/trunk/madman/Rpacks/metagenomeSeq/R/plotGenus.R

Revision 77621 by r.stojnic

r.stojnic — Mon, 17 Jun 2013 13:52:02 GMT

Clarify help for group.only

(Mon, 17 Jun 2013 13:52:02 GMT)

Modified	/trunk/madman/Rpacks/PWMEnrich/R/pwm.R
Modified	/trunk/madman/Rpacks/PWMEnrich/man/motifEnrichment.Rd

Revision 77620 by r.stojnic

r.stojnic — Mon, 17 Jun 2013 10:50:41 GMT

Bump version to 2.3.1:
 o Don't ignore group.only for most backgrounds in motifEnrichment()
 o Fixed unknown function call in plotTopMotifsSequence()
 o Different defaults for margins in plotMultipleMotifs() for nicer graphs

(Mon, 17 Jun 2013 10:50:41 GMT)

Modified	/trunk/madman/Rpacks/PWMEnrich/DESCRIPTION
Modified	/trunk/madman/Rpacks/PWMEnrich/inst/doc/PWMEnrich.Rnw
Modified	/trunk/madman/Rpacks/PWMEnrich/R/pwm.R
Modified	/trunk/madman/Rpacks/PWMEnrich/inst/NEWS
Modified	/trunk/madman/Rpacks/PWMEnrich/man/plotMultipleMotifs.Rd
Modified	/trunk/madman/Rpacks/PWMEnrich/inst/doc/references.bib
Modified	/trunk/madman/Rpacks/PWMEnrich/R/MotifEnrichmentResults-methods.R
Modified	/trunk/madman/Rpacks/PWMEnrich/R/plot.R

Revision 77619 by s.balcome

s.balcome — Mon, 17 Jun 2013 07:27:03 GMT

More work with S4 and Roxygen2.

(Mon, 17 Jun 2013 07:27:03 GMT)

Modified	/trunk/madman/Rpacks/displayR/man/displayR.Rd
Added	/trunk/madman/Rpacks/displayR/man/displayR-methods.Rd
Modified	/trunk/madman/Rpacks/displayR/R/displayR.R
Modified	/trunk/madman/Rpacks/displayR/NAMESPACE
Deleted	/trunk/madman/Rpacks/displayR/man/displayR-package.Rd
Modified	/trunk/madman/Rpacks/displayR/DESCRIPTION

Revision 77616 by hpages

hpages — Mon, 17 Jun 2013 06:41:12 GMT

sequenceLayer() now allows to lay sequences belonging to 1 of the 3 supported
spaces (query/reference/pairwise) to any of the other 3 spaces.

(Mon, 17 Jun 2013 06:41:12 GMT)

Modified	/trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified	/trunk/madman/Rpacks/Rsamtools/R/stackStringsFromBam.R

Revision 77615 by y.liao

y.liao — Mon, 17 Jun 2013 05:29:40 GMT

Output format and -u issues

(Mon, 17 Jun 2013 05:29:40 GMT)

Modified

/trunk/madman/Rpacks/Rsubread/src/sorted-hashtable.c

Revision 77614 by y.liao

y.liao — Mon, 17 Jun 2013 05:29:10 GMT

Output format and -u issues

(Mon, 17 Jun 2013 05:29:10 GMT)

Modified

/trunk/madman/Rpacks/Rsubread/src/index-builder.c

Revision 77613 by y.liao

y.liao — Mon, 17 Jun 2013 05:20:41 GMT

Output format and -u issues

(Mon, 17 Jun 2013 05:20:41 GMT)

Modified	/trunk/madman/Rpacks/Rsubread/src/aligner.c
Modified	/trunk/madman/Rpacks/Rsubread/src/exon-align.c
Modified	/trunk/madman/Rpacks/Rsubread/src/gene-algorithms.c
Modified	/trunk/madman/Rpacks/Rsubread/src/sorted-hashtable.c

Revision 77612 by hpages

hpages — Mon, 17 Jun 2013 04:29:10 GMT

Add low-level CIGAR utility cigarRangesOnPairwiseSpace().

(Mon, 17 Jun 2013 04:29:10 GMT)

Modified	/trunk/madman/Rpacks/GenomicRanges/NAMESPACE
Modified	/trunk/madman/Rpacks/GenomicRanges/src/R_init_GenomicRanges.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/cigar_utils.c
Modified	/trunk/madman/Rpacks/GenomicRanges/src/GenomicRanges.h
Modified	/trunk/madman/Rpacks/GenomicRanges/man/cigar-utils.Rd
Modified	/trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified	/trunk/madman/Rpacks/GenomicRanges/R/cigar-utils.R

Revision 77611 by j.paulson

j.paulson — Mon, 17 Jun 2013 03:28:45 GMT

fix taxa names in fitZig output

(Mon, 17 Jun 2013 03:28:45 GMT)

Modified	/trunk/madman/Rpacks/metagenomeSeq/DESCRIPTION
Modified	/trunk/madman/Rpacks/metagenomeSeq/R/fitZig.R
Modified	/trunk/madman/Rpacks/metagenomeSeq/vignettes/metagenomeSeq.synctex.gz
Modified	/trunk/madman/Rpacks/metagenomeSeq/vignettes/metagenomeSeq.log

Revision 77610 by y.liao

y.liao — Mon, 17 Jun 2013 02:47:44 GMT

Updated index-builder output messages and logs

(Mon, 17 Jun 2013 02:47:44 GMT)

Modified	/trunk/madman/Rpacks/Rsubread/src/readSummary.c
Modified	/trunk/madman/Rpacks/Rsubread/src/index-builder.c

Revision 77609 by y.liao

y.liao — Mon, 17 Jun 2013 02:04:41 GMT

Updated featureCounts output messages

(Mon, 17 Jun 2013 02:04:41 GMT)

Modified

/trunk/madman/Rpacks/Rsubread/src/readSummary.c

Revision 77608 by y.liao

y.liao — Mon, 17 Jun 2013 02:01:39 GMT

Updated featureCounts output messages

(Mon, 17 Jun 2013 02:01:39 GMT)

Modified

/trunk/madman/Rpacks/Rsubread/src/readSummary.c

Revision 77607 by g.ryslik

g.ryslik — Mon, 17 Jun 2013 01:29:34 GMT

Slightly changed the description file for the get.Positions function to better explain "Failure" status.

(Mon, 17 Jun 2013 01:29:34 GMT)

Modified

/trunk/madman/Rpacks/iPAC/man/get.Positions.Rd

Revision 77606 by g.ryslik

g.ryslik — Mon, 17 Jun 2013 01:22:23 GMT

Allows iPAC to continue to correctly process FASTA sequences from an appropriate COSMIC URL.

(Mon, 17 Jun 2013 01:22:23 GMT)

Modified

/trunk/madman/Rpacks/iPAC/R/get.AASeq.R

Revision 77605 by g.ryslik

g.ryslik — Sun, 16 Jun 2013 23:57:30 GMT

No Longer Needed.

(Sun, 16 Jun 2013 23:57:30 GMT)

Deleted

/trunk/madman/Rpacks/GraphPAC/inst/unitTests/.Rapp.history

Revision 77604 by g.ryslik

g.ryslik — Sun, 16 Jun 2013 23:54:51 GMT

COSMIC changed the way it displays FASTA files. Reworked examples to use Uniprot for FASTA sequence.

(Sun, 16 Jun 2013 23:54:51 GMT)

Modified	/trunk/madman/Rpacks/GraphPAC/man/GraphClust.Rd
Modified	/trunk/madman/Rpacks/GraphPAC/man/Plot.Protein.Rd
Modified	/trunk/madman/Rpacks/GraphPAC/inst/NEWS.Rd
Modified	/trunk/madman/Rpacks/GraphPAC/man/graphPAC-package.Rd
Modified	/trunk/madman/Rpacks/GraphPAC/man/Find.TSP.Path.Rd
Modified	/trunk/madman/Rpacks/GraphPAC/vignettes/GraphPAC.Rnw
Modified	/trunk/madman/Rpacks/GraphPAC/DESCRIPTION

Revision 77603 by g.ryslik

g.ryslik — Sun, 16 Jun 2013 22:13:52 GMT

Changed package to pull data from Uniprot as opposed to COSMIC as COSMIC changed their data set up.

(Sun, 16 Jun 2013 22:13:52 GMT)

Modified	/trunk/madman/Rpacks/iPAC/man/ClusterFind.Rd
Deleted	/trunk/madman/Rpacks/iPAC/inst/doc
Modified	/trunk/madman/Rpacks/iPAC/man/get.Positions.Rd
Modified	/trunk/madman/Rpacks/iPAC/man/get.Remapped.Order.Rd
Modified	/trunk/madman/Rpacks/iPAC/man/iPAC-package.Rd
Modified	/trunk/madman/Rpacks/iPAC/man/Plot.Protein.Linear.Rd
Modified	/trunk/madman/Rpacks/iPAC/man/get.AASeq.Rd
Modified	/trunk/madman/Rpacks/iPAC/man/get.AlignedPositions.Rd
Modified	/trunk/madman/Rpacks/iPAC/R/get.AASeq.R
Modified	/trunk/madman/Rpacks/iPAC/vignettes/iPAC.Rnw
Modified	/trunk/madman/Rpacks/iPAC/inst/NEWS.Rd