[med-svn] [r-bioc-biobase] branch master updated (5f2de73 -> df9b2e1)
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 change to branch master
in repository r-bioc-biobase.
from 5f2de73 Move debian/upstream to debian/upstream/metadata
new d919067 Imported Upstream version 2.24.0
new d6ed73d Merge tag 'upstream/2.24.0'
new f80fbd2 New upstream version
new 8d12396 Add myself to Uploaders
new 49e0e0b Remove outdated README.Debian
new 69b325f cme fix dpkg-control
new 901f70d debian/source/format: 3.0 (quilt)
new ff0b4ec Add autopkgtest but http://www.bioconductor.org/packages/release/data/experiment/html/golubEsets.html is needed for the full testsuite
new df9b2e1 Add autopkgtest
The 9 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
debian/README.Debian | 6 -
debian/README.test | 17 ++
debian/changelog | 13 +-
debian/control | 5 +-
debian/docs | 1 +
debian/patches/exclude_testing_golubEsets.patch | 51 ++++
debian/patches/series | 1 +
debian/source/format | 1 +
debian/tests/control | 3 +
debian/tests/run-unit-test | 6 +
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
133 files changed, 1129 insertions(+), 896 deletions(-)
create mode 100644 build/vignette.rds
delete mode 100644 debian/README.Debian
create mode 100644 debian/README.test
create mode 100644 debian/patches/exclude_testing_golubEsets.patch
create mode 100644 debian/patches/series
create mode 100644 debian/source/format
create mode 100644 debian/tests/control
create mode 100644 debian/tests/run-unit-test
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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