/usr/lib/R/site-library/IRanges/unitTests/test_AtomicList.R is in r-bioc-iranges 2.4.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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subclasses <- c(logical="LogicalList",
integer="IntegerList",
#double="NumericList",
numeric="NumericList",
complex="ComplexList",
character="CharacterList",
raw="RawList",
Rle="RleList")
for (elt_type in names(subclasses)) {
subclass <- subclasses[[elt_type]]
constructor <- get(subclass)
vec1 <- get(elt_type)(6)
vec2 <- get(elt_type)(8)
target <- list(A=vec1, B=vec2)
for (compress in c(TRUE, FALSE)) {
current <- constructor(A=vec1, B=vec2, compress=compress)
checkTrue(is(current, subclass))
checkIdentical(compress, is(current, "CompressedList"))
checkIdentical(elt_type, elementType(current))
checkIdentical(target, as.list(current))
checkIdentical(unname(target), as.list(current, use.names=FALSE))
}
}
}
test_AtomicList_GroupGenerics <- function() {
vec1 <- c(1L,2L,3L,5L,2L,8L)
vec2 <- c(15L,45L,20L,1L,15L,100L,80L,5L)
for (compress in c(TRUE, FALSE)) {
for (type in c("IntegerList", "RleList")) {
list1 <- do.call(type, list(one = vec1, vec2, compress = compress))
checkIdentical(as.list(list1 + list1), Map("+", list1, list1))
checkIdentical(as.list(log(list1)), lapply(list1, log))
checkIdentical(as.list(round(sqrt(list1))),
lapply(list1, function(x) round(sqrt(x))))
checkIdentical(sum(list1), sapply(list1, sum))
}
}
}
test_AtomicList_general <- function() {
vec1 <- c(1L,2L,NA,3L,NA,5L,2L,8L)
vec2 <- c(NA,15L,45L,20L,NA,1L,15L,100L,80L,5L,NA)
for (compress in c(TRUE, FALSE)) {
for (type in c("IntegerList", "RleList")) {
list1 <- do.call(type, list(one = vec1, vec2, compress = compress))
checkIdentical(as.list(list1 %in% c(1L, 5L)),
lapply(list1, "%in%", c(1L, 5L)))
checkIdentical(lapply(list1 %in%
IntegerList(one = vec1, vec2,
compress = compress),
as.vector),
mapply("%in%", lapply(list1, as.vector),
list(one = vec1, vec2)))
checkIdentical(as.list(is.na(list1)), lapply(list1, is.na))
checkIdentical(as.list(match(list1, c(1L, 5L))),
lapply(list1, match, c(1L, 5L)))
checkIdentical(lapply(match(list1,
IntegerList(one = vec1, vec2,
compress = compress)),
as.vector),
mapply(match, lapply(list1, as.vector),
list(one = vec1, vec2)))
checkIdentical(as.list(sort(list1)), lapply(list1, sort))
checkIdentical(as.list(unique(list1)), lapply(list1, unique))
}
}
}
test_AtomicList_logical <- function() {
vec1 <- c(TRUE,NA,FALSE, NA)
vec2 <- c(TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,TRUE)
for (compress in c(TRUE, FALSE)) {
for (type in c("LogicalList", "RleList")) {
list1 <- do.call(type, list(one = vec1, vec2, compress = compress))
checkIdentical(as.list(!list1), lapply(list1, "!"))
checkIdentical(as.list(which(list1)), lapply(list1, which))
}
}
}
test_AtomicList_numerical <- function() {
vec1 <- c(1L,2L,NA,3L,NA,5L,2L,8L)
vec2 <- c(NA,15L,45L,20L,NA,1L,15L,100L,80L,5L,NA)
for (compress in c(TRUE, FALSE)) {
for (type in c("IntegerList", "RleList")) {
list1 <- do.call(type, list(one = vec1, vec2, compress = compress))
list2 <- endoapply(list1, rev)
checkIdentical(as.list(diff(list1)), lapply(list1, diff))
checkIdentical(as.list(pmax(list1, list2)),
mapply(pmax, list1, list2))
checkIdentical(as.list(pmin(list1, list2)),
mapply(pmin, list1, list2))
checkIdentical(as.list(pmax.int(list1, list2)),
mapply(pmax.int, list1, list2))
checkIdentical(as.list(pmin.int(list1, list2)),
mapply(pmin.int, list1, list2))
checkIdentical(mean(list1, na.rm=TRUE),
sapply(list1, mean, na.rm=TRUE))
checkIdentical(var(list1, na.rm=TRUE),
sapply(list1, var, na.rm=TRUE))
checkIdentical(cov(list1, list2, use="complete.obs"),
mapply(cov, list1, list2,
MoreArgs = list(use="complete.obs")))
checkIdentical(cor(list1, list2, use="complete.obs"),
mapply(cor, list1, list2,
MoreArgs = list(use="complete.obs")))
checkIdentical(sd(list1, na.rm=TRUE),
sapply(list1, sd, na.rm=TRUE))
checkIdentical(median(list1, na.rm=TRUE),
sapply(list1, median, na.rm=TRUE))
checkIdentical(quantile(list1, na.rm=TRUE),
sapply(list1, quantile, na.rm=TRUE))
checkIdentical(mad(list1, na.rm=TRUE),
sapply(list1, mad, na.rm=TRUE))
checkIdentical(IQR(list1, na.rm=TRUE),
sapply(list1, IQR, na.rm=TRUE))
vec3 <- (-20:20)^2
vec3[c(1,10,21,41)] <- c(100L, 30L, 400L, 470L)
list3 <- do.call(type, list(one = vec3, rev(vec3), compress = compress))
checkIdentical(as.list(smoothEnds(list3)), lapply(list3, smoothEnds))
checkIdentical(as.list(runmed(list3, 7)),
lapply(list3, function(x) {
y <- runmed(x, 7)
if (type != "RleList")
y <- as.vector(y)
y
}))
}
}
}
test_AtomicList_character <- function() {
txt <- c("The", "licenses", "for", "most", "software", "are",
"designed", "to", "take", "away", "your", "freedom",
"to", "share", "and", "change", "it.",
"", "By", "contrast,", "the", "GNU", "General", "Public", "License",
"is", "intended", "to", "guarantee", "your", "freedom", "to",
"share", "and", "change", "free", "software", "--",
"to", "make", "sure", "the", "software", "is",
"free", "for", "all", "its", "users")
for (compress in c(TRUE, FALSE)) {
for (type in c("CharacterList", "RleList")) {
list1 <- do.call(type, list(one = txt, rev(txt), compress = compress))
checkIdentical(as.list(nchar(list1)), lapply(list1, nchar))
checkIdentical(as.list(chartr("@!*", "alo", list1)),
lapply(list1, chartr, old="@!*", new="alo"))
checkIdentical(as.list(tolower(list1)), lapply(list1, tolower))
checkIdentical(as.list(toupper(list1)), lapply(list1, toupper))
checkIdentical(as.list(sub("[b-e]",".", list1)),
lapply(list1, sub, pattern="[b-e]", replacement="."))
checkIdentical(as.list(gsub("[b-e]",".", list1)),
lapply(list1, gsub, pattern="[b-e]", replacement="."))
}
}
}
test_RleList_methods <- function() {
x1 <- RleList(11:15, 15L, integer(0), 15:16, compress=FALSE)
x2 <- RleList(11:15, 15L, integer(0), 15:16, compress=TRUE)
checkIdentical(as(runValue(x1), "CompressedIntegerList"), runValue(x2))
checkIdentical(as(runLength(x1), "CompressedIntegerList"), runLength(x2))
checkIdentical(as(ranges(x1), "CompressedIRangesList"), ranges(x2))
## na.rm
x <- RleList(c(NA,1,1),
c(1L,NA_integer_,1L),
c(1,Inf,1,-Inf),compress=TRUE)
target <- RleList(c(1,2), c(1L,1L), c(Inf,Inf,-Inf))
current <- runsum(x,2, na.rm = TRUE)
checkIdentical(target, current)
target <- RleList(c(NA,2), c(NA_integer_,NA_integer_), c(Inf,Inf,-Inf))
current <- runsum(x,2, na.rm = FALSE)
checkIdentical(target, current)
target <- RleList(c(2,4), c(2,2), c(Inf, Inf, -Inf))
current <- runwtsum(x,2, c(2,2), na.rm = TRUE)
checkIdentical(target, current)
target <- RleList(c(NA,4), c(NA_real_,NA_real_), c(Inf,Inf,-Inf))
current <- runwtsum(x,2, c(2,2), na.rm = FALSE)
checkIdentical(target, current)
target <- RleList(c(1,1), c(1,1), c(Inf,Inf,-Inf))
current <- runmean(x, 2, na.rm = TRUE)
checkIdentical(target, current)
target <- RleList(c(NA,1), c(NA_real_, NA_real_), c(Inf, Inf, -Inf))
current <- runmean(x, 2, na.rm = FALSE)
checkIdentical(target, current)
x <- RleList(c(NA,1,2),
c(2L,NA_integer_,1L),
c(1,Inf,1,-Inf),compress=TRUE)
target <- RleList(c(1,2), c(2L,1L), c(Inf,Inf,1))
current <- runq(x, 2, 2, na.rm = TRUE)
checkIdentical(target, current)
target <- RleList(c(NA,2), c(NA_integer_, NA_integer_), c(Inf, Inf, 1))
current <- runq(x, 2, 2, na.rm = FALSE)
checkIdentical(target, current)
## Binary operations between an RleList and an atomic vector:
a1 <- Rle(1, 999722111)
a2 <- 20 * a1
a <- RleList(a1, a2, compress=TRUE)
b1 <- c(a1, a1)
b2 <- 20 * b1
b <- RleList(b1, b2, compress=FALSE)
## FIXME: 'a1 <= 19:21' is taking forever and eats up all the memory in
## BioC <= 2.12! Seems like 'a1' is expanded to integer vector first, which
## is not good :-/
#for (y in list(8L, 8, 19:21)) {
for (y in list(8L, 8)) {
## With a CompressedRleList
target <- RleList(a1 <= y, a2 <= y, compress=TRUE)
current <- a <= y
checkIdentical(target, current)
target <- RleList(a1 + y, a2 + y, compress=TRUE)
current <- a + y
checkIdentical(target, current)
target <- RleList(a1 * y, a2 * y, compress=TRUE)
current <- a * y
checkIdentical(target, current)
target <- RleList(a1 / y, a2 / y, compress=TRUE)
current <- a / y
checkIdentical(target, current)
## With a SimpleRleList
target <- RleList(b1 <= y, b2 <= y, compress=FALSE)
current <- b <= y
checkIdentical(target, current)
target <- RleList(b1 + y, b2 + y, compress=FALSE)
current <- b + y
checkIdentical(target, current)
target <- RleList(b1 * y, b2 * y, compress=FALSE)
current <- b * y
checkIdentical(target, current)
target <- RleList(b1 / y, b2 / y, compress=FALSE)
current <- b / y
checkIdentical(target, current)
}
}
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