This file is indexed.

/usr/lib/R/site-library/BiocParallel/NAMESPACE is in r-bioc-biocparallel 1.8.1-1.

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
import(methods)

importFrom(stats, setNames, terms)

importFrom(utils, capture.output, find, head, relist,
           setTxtProgressBar, txtProgressBar)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###

exportClass(
    BiocParallelParam,
    MulticoreParam,
    SnowParam,
    DoparParam,
    SerialParam,
    BatchJobsParam
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###

export(
    MulticoreParam, SnowParam, DoparParam, SerialParam, BatchJobsParam,

    ## register
    register, registered, bpparam,

    ## accessor
    bpnworkers,

    ## error handlers
    bpresume, bplasterror, bptry,

    ## helpers
    bploop,                             # worker, manager loops
    multicoreWorkers, snowWorkers, bpvalidate, bpok,
    bprunMPIslave
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics and methods defined in BiocParallel
###

export(
    bplapply, bpvec, bpvectorize, bpmapply, bpaggregate, bpiterate,

    ## bp-controls
    bpworkers, "bpworkers<-", bpbackend, "bpbackend<-",
    bptasks, "bptasks<-", bpjobname, "bpjobname<-",
    bpstart, bpstop, bpisup,
    bpcatchErrors, "bpcatchErrors<-", bpstopOnError, "bpstopOnError<-",
    bpprogressbar, "bpprogressbar<-", bpRNGseed, "bpRNGseed<-",
    bptimeout, "bptimeout<-", bplog, "bplog<-", bplogdir, "bplogdir<-",
    bpthreshold, "bpthreshold<-", bpresultdir, "bpresultdir<-",

    ## schedule
    bpschedule
)

### Same list as above.
exportMethods(
    bplapply, bpvec, bpvectorize, bpmapply, bpaggregate, bpiterate,

    ## bp-controls
    bpworkers, "bpworkers<-", bpbackend, "bpbackend<-",
    bptasks, "bptasks<-", bpjobname, "bpjobname<-",
    bpstart, bpstop, bpisup,
    bpcatchErrors, "bpcatchErrors<-", bpstopOnError, "bpstopOnError<-",
    bpprogressbar, "bpprogressbar<-", bpRNGseed, "bpRNGseed<-",
    bptimeout, "bptimeout<-", bplog, "bplog<-", bplogdir, "bplogdir<-",
    bpthreshold, "bpthreshold<-", bpresultdir, "bpresultdir<-",

    ## schedule
    bpschedule
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in BiocParallel
###

exportMethods(
    show
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###

S3method(print, remote_error)
S3method(print, bplist_error)

S3method(bploop, MPInode)
S3method(bploop, SOCKnode)
S3method(bploop, SOCK0node)
S3method(bploop, lapply)
S3method(bploop, iterate)