This file is indexed.

/usr/lib/R/site-library/IRanges/INDEX is in r-bioc-iranges 1.20.4-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

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Annotated-class         Annotated class
AtomicList              Lists of Atomic Vectors in Natural and Rle Form
DataFrame-class         External Data Frame
DataFrameList-class     List of DataFrames
DataTable-API           The DataTable API
DataTable-stats         Statistical modeling with DataTable
FilterMatrix-class      Matrix for Filter Results
FilterRules-class       Collection of Filter Rules
GappedRanges-class      GappedRanges objects
Grouping-class          Grouping objects
Hits-class              Set of hits between 2 vector-like objects
HitsList-class          List of Hits objects
IRanges-class           IRanges and NormalIRanges objects
IRanges-constructor     The IRanges constructor and supporting
                        functions
IRanges-utils           IRanges utility functions
IRangesList-class       List of IRanges and NormalIRanges
IntervalForest-class    Interval Search Forests
IntervalTree-class      Interval Search Trees
List-class              List objects
MaskCollection-class    MaskCollection objects
OverlapEncodings-class
                        OverlapEncodings objects
RangedData-class        Data on ranges
RangedDataList-class    Lists of RangedData
RangedSelection-class   Selection of ranges and columns
Ranges-class            Ranges objects
Ranges-comparison       Comparing and ordering ranges
RangesList-class        List of Ranges
RangesMapping-class     Mapping of ranges to another sequence
Rle-class               Rle objects
RleViews-class          The RleViews class
RleViewsList-class      List of RleViews
SimpleList-class        Simple and Compressed List Classes
Vector-class            Vector objects
Vector-comparison       Compare, order, tabulate vector-like objects
Views-class             Views objects
ViewsList-class         List of Views
classNameForDisplay     Provide a class name for displaying to users
coverage-methods        Coverage across a set of ranges
encodeOverlaps          Compute overlap encodings
endoapply               Endomorphisms via application of a function
                        over an object's elements
expand                  The expand method for uncompressing compressed
                        data columns
findOverlaps-methods    Finding overlapping ranges
funprog-methods         Functional programming methods for List objects
inter-range-methods     Inter range transformations of a Ranges, Views,
                        RangesList, MaskCollection, or RangedData
                        object
intra-range-methods     Intra range transformations of a Ranges, Views,
                        RangesList, or MaskCollection object
isConstant              Test if an atomic vector or array is constant
multisplit              Split elements belonging to multiple groups
nearest-methods         Finding the nearest range neighbor
rdapply                 Applying over spaces
read.Mask               Read a mask from a file
reverse                 reverse
runstat                 Fixed width running window summaries across
                        vector-like objects
safeExplode             Low-level string utilities
score                   Score accessor and setter
seqapply                Apply function and cast to Vector
setops-methods          Set operations on IRanges, RangesList, and Hits
                        objects
slice-methods           Slice a vector-like or list-like object
updateObject-methods    Update an object of a class defined in the
                        IRanges package to its current class definition
view-summarization-methods
                        Summarize views on a vector-like object with
                        numeric values