/usr/lib/R/site-library/DelayedArray/NAMESPACE is in r-bioc-delayedarray 0.4.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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importFrom(stats, setNames,
dbinom, pbinom, qbinom,
dpois, ppois, qpois,
dlogis, plogis, qlogis)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(matrixStats)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClasses(
Array,
ArrayViewport, ArrayGrid, ArrayArbitraryGrid, ArrayRegularGrid,
DelayedArray, DelayedMatrix,
RealizationSink, arrayRealizationSink,
RleArraySeed, SolidRleArraySeed, RleRealizationSink, ChunkedRleArraySeed,
RleArray, RleMatrix
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###
S3method(as.array, DelayedArray)
S3method(as.character, ArrayGrid)
S3method(as.character, DelayedArray)
S3method(as.complex, DelayedArray)
S3method(as.data.frame, DelayedArray)
S3method(as.integer, DelayedArray)
S3method(as.logical, DelayedArray)
S3method(as.matrix, DelayedArray)
S3method(as.numeric, DelayedArray)
S3method(as.raw, DelayedArray)
S3method(as.vector, DelayedArray)
S3method(mean, DelayedArray)
S3method(split, DelayedArray)
### We also export them thru the export() directive so that (a) they can be
### called directly, (b) tab-completion on the name of the generic shows them,
### and (c) methods() doesn't asterisk them.
export(
as.array.DelayedArray,
as.character.ArrayGrid,
as.character.DelayedArray,
as.complex.DelayedArray,
as.data.frame.DelayedArray,
as.integer.DelayedArray,
as.logical.DelayedArray,
as.matrix.DelayedArray,
as.numeric.DelayedArray,
as.raw.DelayedArray,
as.vector.DelayedArray,
mean.DelayedArray,
split.DelayedArray
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in DelayedArray
###
exportMethods(
## Methods for generics defined in the base package:
length, names, "names<-",
dim, "dim<-", dimnames, "dimnames<-",
"[", "[[", "[<-",
lengths,
as.array, as.matrix, as.data.frame, as.vector,
as.logical, as.integer, as.numeric, as.complex, as.character, as.raw,
c, split,
drop, t,
is.na, is.finite, is.infinite, is.nan,
"!",
#"+", "-", "*", "/", "^", "%%", "%/%", # "Arith" group generic
"==", "!=", "<=", ">=", "<", ">", # "Compare" group generic
anyNA, which,
max, min, range, sum, prod, any, all, # "Summary" group generic
mean,
round, signif,
rowSums, colSums, rowMeans, colMeans,
nchar, tolower, toupper,
## Methods for generics defined in the methods package:
coerce, show,
## Methods for generics defined in the stats package:
dbinom, pbinom, qbinom,
dpois, ppois, qpois,
dlogis, plogis, qlogis,
## Methods for generics defined in the BiocGenerics package:
cbind, rbind,
## Methods for generics defined in the S4Vectors package:
isEmpty,
## Methods for generics defined in the IRanges package:
ranges, start, end, width,
splitAsList
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
ArrayViewport, makeNindexFromArrayViewport,
ArrayArbitraryGrid, ArrayRegularGrid,
supportedRealizationBackends, getRealizationBackend, setRealizationBackend,
write_array_to_sink,
RleArray
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in DelayedArray + export corresponding methods
###
export(
arbind, acbind,
refdim, isLinear,
subset_seed_as_array,
matrixClass, DelayedArray, seed, type,
chunk_dim, write_block_to_sink, close,
realize,
pmax2, pmin2, apply,
rowMaxs, colMaxs, rowMins, colMins, rowRanges, colRanges
)
### Exactly the same list as above.
exportMethods(
arbind, acbind,
refdim, isLinear,
subset_seed_as_array,
matrixClass, DelayedArray, seed, type,
chunk_dim, write_block_to_sink, close,
realize,
pmax2, pmin2, apply,
rowMaxs, colMaxs, rowMins, colMins, rowRanges, colRanges
)
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