This file is indexed.

/usr/lib/R/site-library/Rsamtools/NAMESPACE is in r-bioc-rsamtools 1.22.0-1.

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
useDynLib(Rsamtools, .registration=TRUE)

import(methods)

importFrom(bitops, bitAnd)

importFrom(utils, read.table)           # normalizePath --> base in R-2.13

importClassesFrom(BiocGenerics, url, gzfile, unz, pipe)

importFrom(BiocGenerics, cbind, duplicated, eval, Filter, lapply, Map,
           order, paste, rbind, Reduce, rep.int, sapply, setdiff,
           tapply, union, unique)

importFrom(BiocParallel, bplapply)

import(S4Vectors)

import(IRanges)

importClassesFrom(GenomeInfoDb, Seqinfo)

importFrom(GenomeInfoDb, Seqinfo, seqinfo, seqlevels)

importClassesFrom(GenomicRanges, GRanges, GRangesList)

importFrom(GenomicRanges, GRanges, GRangesList)

importMethodsFrom(GenomicRanges, seqnames, strand)

import(XVector)

importClassesFrom(Biostrings, DNAStringSet, BStringSet, PhredQuality)

importFrom(Biostrings, DNA_ALPHABET, readDNAStringSet,
           readRNAStringSet, readAAStringSet,
           DNAStringSet, BStringSet, PhredQuality,
           getSeq, reverseComplement)

exportPattern("^[^\\.]")

export(path)

exportMethods(length, names, "[", "[[", show, getSeq, seqinfo)

S3method(close, BamFile)
S3method(close, BcfFile)
S3method(close, FaFile)
S3method(close, TabixFile)
S3method(close, RsamtoolsFileList)

S3method(open, BamFile)
S3method(open, BcfFile)
S3method(open, FaFile)
S3method(open, TabixFile)
S3method(open, RsamtoolsFileList)