/usr/lib/R/site-library/Biobase/NEWS is in r-bioc-biobase 2.14.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 | 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
----------------------
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
----------------------
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
----------------------
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
----------------------
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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