/usr/lib/R/site-library/Biobase/NEWS is in r-bioc-biobase 2.38.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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BUG FIXES
o '$' completion on eSet and ExpressionSet works in RStudio.
CHANGES IN VERSION 2.33
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BUG FIXES
o exprs<- enforces value with correct dim, dimnames.
CHANGES IN VERSION 2.31
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NEW FEATURES
o tab completion implemented for eSet classes
o head and tail.AnnotatedDataFrame methods introduced
CHANGES IN VERSION 2.27
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NEW FEATURES
o Add write.AnnotatedDataFrame function; request of
samuel.granjeaud
CHANGES IN VERSION 2.21
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USER VISIBLE CHANGES
o channelNames<-,NChannelSet,*-methods allow re-naming channels
o NChannelSet validity requires all assayDataElementNames() to be
levels in varMetadata()$channel.
BUG FIXES
o Updating an AnnotatedDataFrame no longer duplicates metadata
from partially matching column names.
CHANGES IN VERSION 2.19
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USER VISIBLE CHANGES
o dimnames(), rownames(), colnames() and setters work on
eSet-derived objects
CHANGES IN VERSION 2.17
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USER VISIBLE CHANGES
o l2e(), previously deprecated, has been made defunct.
o All objects made defunct in previous release cycles have been removed.
This includes geneNames, getExpData, eList, reporterNames, getBiocRepos,
read.exprSet, updateOldMiame, df2pD, read.pD, read.phenoData, exprData,
exprList, and phenoData.
CHANGES IN VERSION 2.11
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USER VISIBLE CHANGES
o 'l2e' deprecated, use 'list2env' in base instead
o MIAME class moved to subclass of MIAxE virtual class
NEW FEATURES
o Added MIAxE virtual class to hold experiment meta-data classes
CHANGES IN VERSION 2.7
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USER VISIBLE CHANGES
o 'show,eSet-method' summarizes protocolData, if available.
o 'snpCall' 'snpCallProbability' accessors added for SnpSet.
BUG FIXES
o 'selectSome' returns short factors as character()
CHANGES IN VERSION 2.5
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USER VISIBLE CHANGES
o 'protocolData' slot added to eSet class to store protocol
metadata stored in microarray data files; can be accessed by
protocolData and set by protocolData<-.
o 'sampleNames,NChannelSet-method' returns a vector when the
sample names of each channel are the same.
CHANGES IN VERSION 2.1
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NEW FEATURES
o 'makeDataPacakge' method for ExpressionSet now accepts a
'description' argument for the generated manual page.
BUG FIXES
o combine,matrix,matrix-method would record 'NA' for entries in
the second matrix with niether rows nor columns present in the
first.
o openPDF now checks for NULL or zero-length pdfviewer option
CHANGES IN VERSION 2.0
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SIGNIFICANT USER-VISIBLE CHANGES
o 'combine' on data.frame columns with mismatched levels causes a
warning, rather than error.
o updateObject does not warn about duplicating locked environment,
unlesss verbose=TRUE
NEW FEATURES
o 'combine' now works to combine rows of ExpressionSet
BUG FIXES
o AnnotatedDataFrame 'show' listed additional varMetadata column
names incorrectly when labelDescription was not the first.
NEWLY DEFUNCT CLASSES, METHODS, FUNCTIONS, DATA SETS
o Defunct S4 Classes
1) annotatedDataset - class definition still exits to support
phenoData conversion
2) exprMatrix - removed class definition
3) exprSet - class definition still exists to allow conversion
to ExpressionSet
4) phenoData - class definition still exists to allow
conversion to AnnotatedDataFrame
o Defunct Generics/Methods
1) addVarMetadataEntry - S4 generic definition removed
2) as.data.frame.exprSet - S3 method removed
3) convertVarLabels - S4 generic definition removed
4) eList - S4 methods remain with .Defunct messages
5) "eList<-" - S4 methods remain with .Defunct messages
6) exprs2excel - S4 generic definition removed
7) getExpData - S4 methods remain with .Defunct messages
8) geneNames - S4 methods remain with .Defunct messages
9) "geneNames<-" - S4 methods remain with .Defunct messages
10) getUnits - S4 generic definition removed
11) getVarMetadata - S4 generic definition removed
12) iter - S4 generic definition removed
13) reporterInfo - S4 generic definition removed
14) "reporterInfo<-" - S4 generic definition removed
15) reporterNames - S4 methods remain with .Defunct messages
16) "reporterNames<-" - S4 methods remain with .Defunct messages
17) split (for use with exprSet objects) - S4 generic definition removed
18) update2MIAME - S4 generic definition removed
o Defunct functions
1) df2pD - function stub with .Defunct message
2) read.exprSet - function stub with .Defunct message
3) read.pD - function stub with .Defunct message
4) read.phenoData - function stub with .Defunct message
5) updateOldMiame - function stub with .Defunct message
o Defunct data sets
1) bbsym
2) eset - use sample.ExpressionSet instead
3) golubMergeSub
4) sample.eSet - use sample.MultiSet instead
4) sample.exprSet.1 - use sample.ExpressionSet instead
5) sample.exprSet - use sample.ExpressionSet instead
6) SWPD
7) swrep
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