[med-svn] [r-bioc-biobase] branch upstream updated (910457e -> d919067)
Andreas Tille
tille at debian.org
Tue Jun 10 11:08:41 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository r-bioc-biobase.
from 910457e Imported Upstream version 2.20.0
new d919067 Imported Upstream version 2.24.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 +-
{inst/doc => vignettes}/BiobaseDevelopment.Rnw | 0
{inst/doc => vignettes}/Bioconductor.Rnw | 0
.../ExpressionSetIntroduction.Rnw | 0
{inst/doc => vignettes}/HowTo.Rnw | 0
{inst/doc => vignettes}/Qviews.Rnw | 0
{inst/doc => vignettes}/esApply.Rnw | 0
{inst/doc => vignettes}/legacy/Biobase.Rnw | 0
123 files changed, 1035 insertions(+), 886 deletions(-)
create mode 100644 build/vignette.rds
delete mode 100644 inst/UnitTests/Makefile
delete mode 100755 inst/UnitTests/runall.sh
delete mode 100644 inst/UnitTests/runalltests.R
delete mode 100755 inst/UnitTests/runfile.sh
rename inst/{UnitTests => unitTests}/VersionedClass_data/1.8/AnnotatedDataFrame.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/1.8/ExpressionSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/1.8/MIAME.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/1.8/exprSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/1.8/phenoData.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/AnnotatedDataFrame.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/ExpressionSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/MIAME.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/MultiSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/ScalarCharacter.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/SnpSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/Versioned.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/VersionedBiobase.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/Versions.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/VersionsNull.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/aggregator.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/container.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/exprSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/2.0/phenoData.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/AnnotatedDataFrame.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/ExpressionSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/MIAME.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/MultiSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/NChannelSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/SWPD.rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/ScalarCharacter.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/ScalarInteger.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/ScalarLogical.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/ScalarNumeric.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/SnpSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/Versioned.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/VersionedBiobase.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/Versions.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/VersionsNull.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/aggregator.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/bbsym.rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/container.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/eset.rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/exprSet.Rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/golubMergeSub.rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/sample.eSet.rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/sample.exprSet.1.rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/sample.exprSet.rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/devel/swrep.rda (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/raw/exprs.tab (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/raw/pData.tab (100%)
rename inst/{UnitTests => unitTests}/VersionedClass_data/raw/varMetadata.tab (100%)
rename inst/{UnitTests/AnnotatedDataFrame_test.R => unitTests/test_AnnotatedDataFrame.R} (87%)
rename inst/{UnitTests/AssayData_test.R => unitTests/test_AssayData.R} (100%)
rename inst/{UnitTests/DataClasses_test.R => unitTests/test_DataClasses.R} (100%)
rename inst/{UnitTests/EsetSubclasses_test.R => unitTests/test_EsetSubclasses.R} (99%)
rename inst/{UnitTests/ExpressionSet_test.R => unitTests/test_ExpressionSet.R} (100%)
rename inst/{UnitTests/NChannelSet_test.R => unitTests/test_NChannelSet.R} (84%)
rename inst/{UnitTests/SnpSet_test.R => unitTests/test_SnpSet.R} (100%)
rename inst/{UnitTests/UpdateObject_test.R => unitTests/test_UpdateObject.R} (94%)
rename inst/{UnitTests/VersionedClass_test.R => unitTests/test_VersionedClass.R} (98%)
rename inst/{UnitTests/cache_test.R => unitTests/test_cache.R} (100%)
rename inst/{UnitTests/checkClass_test.R => unitTests/test_checkClass.R} (100%)
rename inst/{UnitTests/combine_test.R => unitTests/test_combine.R} (100%)
rename inst/{UnitTests/copyEnv_test.R => unitTests/test_copyEnv.R} (100%)
rename inst/{UnitTests/esApply_test.R => unitTests/test_esApply.R} (100%)
rename inst/{UnitTests/subListExtract_test.R => unitTests/test_subListExtract.R} (100%)
rename inst/{UnitTests/unsaveSetSlot_test.R => unitTests/test_unsaveSetSlot.R} (100%)
rename inst/{UnitTests => unitTests}/utilities.R (96%)
delete mode 100644 man/dge.Rd
create mode 100644 src/rowMedians_TYPE-template.h
create mode 100644 src/templates-types.h
create mode 100644 src/templates-types_undef.h
copy {inst/doc => vignettes}/BiobaseDevelopment.Rnw (100%)
copy {inst/doc => vignettes}/Bioconductor.Rnw (100%)
copy {inst/doc => vignettes}/ExpressionSetIntroduction.Rnw (100%)
copy {inst/doc => vignettes}/HowTo.Rnw (100%)
copy {inst/doc => vignettes}/Qviews.Rnw (100%)
copy {inst/doc => vignettes}/esApply.Rnw (100%)
rename {inst/doc => vignettes}/legacy/Biobase.Rnw (100%)
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