[med-svn] [r-bioc-biobase] 02/09: Merge tag 'upstream/2.24.0'
Andreas Tille
tille at debian.org
Tue Jun 10 11:08:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-biobase.
commit d6ed73dc58c7403a4d6cf94ae41112a1c33c52bf
Merge: 5f2de73 d919067
Author: Andreas Tille <tille at debian.org>
Date: Tue Jun 10 11:01:22 2014 +0200
Merge tag 'upstream/2.24.0'
Upstream version 2.24.0
DESCRIPTION | 14 +-
NAMESPACE | 39 +-
NEWS | 18 +
R/AllGenerics.R | 20 +-
R/DataClasses.R | 72 ++-
R/VersionedClasses.R | 17 +-
R/VersionsClass.R | 2 +-
R/methods-AnnotatedDataFrame.R | 49 +-
R/methods-AssayData.R | 173 +++---
R/methods-ExpressionSet.R | 109 ++--
R/methods-MIAME.R | 32 +-
R/methods-NChannelSet.R | 227 ++++---
R/methods-ScalarObject.R | 8 +-
R/methods-SnpSet.R | 2 +-
R/methods-VersionedClass.R | 2 +-
R/methods-VersionsNull.R | 2 +-
R/methods-container.R | 2 +-
R/methods-eSet.R | 135 ++--
R/rowOp-methods.R | 18 +-
build/vignette.rds | Bin 0 -> 481 bytes
inst/UnitTests/Makefile | 19 -
inst/UnitTests/runall.sh | 3 -
inst/UnitTests/runalltests.R | 18 -
inst/UnitTests/runfile.sh | 10 -
inst/doc/BiobaseDevelopment.pdf | Bin 246476 -> 246481 bytes
inst/doc/Bioconductor.pdf | Bin 71296 -> 71100 bytes
inst/doc/ExpressionSetIntroduction.pdf | Bin 174950 -> 174953 bytes
inst/doc/HowTo.pdf | Bin 54522 -> 54524 bytes
inst/doc/Qviews.pdf | Bin 77432 -> 77433 bytes
inst/doc/esApply.pdf | Bin 93275 -> 93274 bytes
.../VersionedClass_data/1.8/AnnotatedDataFrame.Rda | Bin
.../VersionedClass_data/1.8/ExpressionSet.Rda | Bin
.../VersionedClass_data/1.8/MIAME.Rda | Bin
.../VersionedClass_data/1.8/exprSet.Rda | Bin
.../VersionedClass_data/1.8/phenoData.Rda | Bin
.../VersionedClass_data/2.0/AnnotatedDataFrame.Rda | Bin
.../VersionedClass_data/2.0/ExpressionSet.Rda | Bin
.../VersionedClass_data/2.0/MIAME.Rda | Bin
.../VersionedClass_data/2.0/MultiSet.Rda | Bin
.../VersionedClass_data/2.0/ScalarCharacter.Rda | Bin
.../VersionedClass_data/2.0/SnpSet.Rda | Bin
.../VersionedClass_data/2.0/Versioned.Rda | Bin
.../VersionedClass_data/2.0/VersionedBiobase.Rda | Bin
.../VersionedClass_data/2.0/Versions.Rda | Bin
.../VersionedClass_data/2.0/VersionsNull.Rda | Bin
.../VersionedClass_data/2.0/aggregator.Rda | Bin
.../VersionedClass_data/2.0/container.Rda | Bin
.../VersionedClass_data/2.0/exprSet.Rda | Bin
.../VersionedClass_data/2.0/phenoData.Rda | Bin
.../devel/AnnotatedDataFrame.Rda | Bin
.../VersionedClass_data/devel/ExpressionSet.Rda | Bin
.../VersionedClass_data/devel/MIAME.Rda | Bin
.../VersionedClass_data/devel/MultiSet.Rda | Bin
.../VersionedClass_data/devel/NChannelSet.Rda | Bin
.../VersionedClass_data/devel/SWPD.rda | Bin
.../VersionedClass_data/devel/ScalarCharacter.Rda | Bin
.../VersionedClass_data/devel/ScalarInteger.Rda | Bin
.../VersionedClass_data/devel/ScalarLogical.Rda | Bin
.../VersionedClass_data/devel/ScalarNumeric.Rda | Bin
.../VersionedClass_data/devel/SnpSet.Rda | Bin
.../VersionedClass_data/devel/Versioned.Rda | Bin
.../VersionedClass_data/devel/VersionedBiobase.Rda | Bin
.../VersionedClass_data/devel/Versions.Rda | Bin
.../VersionedClass_data/devel/VersionsNull.Rda | Bin
.../VersionedClass_data/devel/aggregator.Rda | Bin
.../VersionedClass_data/devel/bbsym.rda | Bin
.../VersionedClass_data/devel/container.Rda | Bin
.../VersionedClass_data/devel/eset.rda | Bin
.../VersionedClass_data/devel/exprSet.Rda | Bin
.../VersionedClass_data/devel/golubMergeSub.rda | Bin
.../VersionedClass_data/devel/sample.eSet.rda | Bin
.../VersionedClass_data/devel/sample.exprSet.1.rda | Bin
.../VersionedClass_data/devel/sample.exprSet.rda | Bin
.../VersionedClass_data/devel/swrep.rda | Bin
.../VersionedClass_data/raw/exprs.tab | 0
.../VersionedClass_data/raw/pData.tab | 0
.../VersionedClass_data/raw/varMetadata.tab | 0
.../test_AnnotatedDataFrame.R} | 44 +-
.../test_AssayData.R} | 0
.../test_DataClasses.R} | 0
.../test_EsetSubclasses.R} | 4 +-
.../test_ExpressionSet.R} | 0
.../test_NChannelSet.R} | 41 +-
.../SnpSet_test.R => unitTests/test_SnpSet.R} | 0
.../test_UpdateObject.R} | 10 +-
.../test_VersionedClass.R} | 2 +-
.../cache_test.R => unitTests/test_cache.R} | 0
.../test_checkClass.R} | 0
.../combine_test.R => unitTests/test_combine.R} | 0
.../copyEnv_test.R => unitTests/test_copyEnv.R} | 0
.../esApply_test.R => unitTests/test_esApply.R} | 0
.../test_subListExtract.R} | 0
.../test_unsaveSetSlot.R} | 0
inst/{UnitTests => unitTests}/utilities.R | 2 +-
man/channel.Rd | 4 +-
man/channelNames.Rd | 35 +-
man/class.AnnotatedDataFrame.Rd | 5 +
man/class.ExpressionSet.Rd | 24 +-
man/class.MIAxE.Rd | 4 +-
man/class.NChannelSet.Rd | 25 +-
man/class.Versioned.Rd | 14 +-
man/class.VersionedBiobase.Rd | 9 +-
man/class.eSet.Rd | 36 +-
man/copySubstitute.Rd | 3 +-
man/dge.Rd | 49 --
man/isCurrent.Rd | 4 +-
man/isVersioned.Rd | 4 +-
man/rowMedians.Rd | 25 +-
man/selectChannels.Rd | 4 +-
src/Rinit.c | 4 +-
src/envir.c | 3 +-
src/rowMedians.c | 302 ++-------
src/rowMedians_TYPE-template.h | 206 +++++++
src/templates-types.h | 46 ++
src/templates-types_undef.h | 18 +
tests/test-all.R | 3 +-
vignettes/BiobaseDevelopment.Rnw | 684 +++++++++++++++++++++
vignettes/Bioconductor.Rnw | 96 +++
vignettes/ExpressionSetIntroduction.Rnw | 493 +++++++++++++++
vignettes/HowTo.Rnw | 91 +++
vignettes/Qviews.Rnw | 176 ++++++
vignettes/esApply.Rnw | 132 ++++
{inst/doc => vignettes}/legacy/Biobase.Rnw | 0
123 files changed, 2707 insertions(+), 886 deletions(-)
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