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mergedJobs = function(reg, ids, cols) {
if (is.null(ids))
reg$defs[reg$status, cols, on = "def.id", nomatch = 0L, with = missing(cols)]
else
reg$defs[reg$status[ids, nomatch = 0L, on = "job.id"], cols, on = "def.id", nomatch = 0L, with = missing(cols)]
}
auto_increment = function(ids, n = 1L) {
if (length(ids) == 0L) seq_len(n) else max(ids) + seq_len(n)
}
ustamp = function() {
round(as.numeric(Sys.time()), 4L)
}
names2 = function (x, missing.val = NA_character_) {
n = names(x)
if (is.null(n))
return(rep.int(missing.val, length(x)))
replace(n, is.na(n) | !nzchar(n), missing.val)
}
insert = function(x, y) {
x[names2(y)] = y
x[order(names2(x))]
}
makeProgressBar = function(...) {
if (!batchtools$debug && getOption("batchtools.verbose", TRUE) && getOption("batchtools.progress", TRUE) && getOption("width") >= 20L) {
progress_bar$new(...)
} else {
list(tick = function(len = 1, tokens = list()) NULL, update = function(ratio, tokens) NULL)
}
}
seq_row = function(x) {
seq_len(nrow(x))
}
vlapply = function (x, fun, ..., use.names = TRUE) {
vapply(X = x, FUN = fun, ..., FUN.VALUE = NA, USE.NAMES = use.names)
}
viapply = function (x, fun, ..., use.names = TRUE) {
vapply(X = x, FUN = fun, ..., FUN.VALUE = NA_integer_, USE.NAMES = use.names)
}
vnapply = function (x, fun, ..., use.names = TRUE) {
vapply(X = x, FUN = fun, ..., FUN.VALUE = NA_real_, USE.NAMES = use.names)
}
vcapply = function (x, fun, ..., use.names = TRUE) {
vapply(X = x, FUN = fun, ..., FUN.VALUE = NA_character_, USE.NAMES = use.names)
}
is.error = function(x) {
inherits(x, "try-error")
}
# formating info message
info = function(...) {
if (getOption("batchtools.verbose", TRUE))
message(sprintf(...))
}
# formating cat()
catf = function(..., con = "") {
cat(stri_flatten(sprintf(...), "\n"), "\n", sep = "", file = con)
}
# formating message()
messagef = function(..., con = "") {
message(sprintf(...))
}
# formating waring()
warningf = function(...) {
warning(simpleWarning(sprintf(...), call = sys.call(sys.parent())))
}
# formating stop()
stopf = function(...) {
stop(simpleError(sprintf(...), call = NULL))
}
`%nin%` = function(x, y) {
!match(x, y, nomatch = 0L)
}
`%chnin%` = function(x, y) {
!chmatch(x, y, nomatch = 0L)
}
setClasses = function(x, cl) {
setattr(x, "class", cl)
x
}
#' @useDynLib batchtools count_not_missing
count = function(x) {
.Call(count_not_missing, x)
}
filterNull = function(x) {
x[!vlapply(x, is.null)]
}
stri_trunc = function(str, length, append = "") {
if (is.na(str))
return(str)
if (stri_length(str) > length) {
if (is.na(append) || !nzchar(append))
return(stri_sub(str, 1L, length))
return(stri_join(stri_sub(str, 1L, length - stri_length(append)), append))
}
return(str)
}
Rscript = function() {
fs::path(R.home("bin"), ifelse(testOS("windows"), "Rscript.exe", "Rscript"))
}
getSeed = function(start.seed, id) {
if (id > .Machine$integer.max - start.seed)
start.seed - .Machine$integer.max + id
else
start.seed + id
}
chsetdiff = function(x, y) {
# Note: assumes that x has no duplicates
x[chmatch(x, y, 0L) == 0L]
}
chintersect = function(x, y) {
# Note: assumes that x has no duplicates
x[chmatch(y, x, 0L)]
}
rnd_hash = function(prefix = "") {
stri_join(prefix, digest(list(runif(1L), as.numeric(Sys.time()))))
}
now = function() {
if (isTRUE(getOption("batchtools.timestamps", FALSE)))
sprintf(" %s", strftime(Sys.time()))
else
""
}
example_push_temp = function(i = 1L) {
if (identical(Sys.getenv("IN_PKGDOWN"), "true")) {
base = fs::path(dirname(tempdir()), "batchtools-example")
dirs = if (i == 1L) fs::path(base, "reg") else fs::path(base, sprintf("reg%i", seq_len(i)))
fs::dir_delete(dirs[fs::dir_exists(dirs)])
fs::file_temp_push(dirs)
}
}
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