#' @import methods
#' @importFrom assertthat assert_that is.readable has_extension is.string
#' @importFrom assertthat has_attr "on_failure<-"
NULL
is.empty <- function(x) {
is.null(x) || length(x) == 0L || (length(x) == 1L && !nzchar(x))
}
on_failure(is.empty) <- function(call, env) {
paste0(deparse(call$x), " is not empty.")
}
"%||%" <- function(a, b) {
if (is.empty(a)) force(b) else a
}
"%|na|%" <- function(a, b) {
if (is.null(a) || all(is.na(a))) force(b) else a
}
## Vectorized default operators
"%|%" <- function(a, b) ifelse(nzchar(a), a, b)
"%|NA|%" <- function(a, b) ifelse(is.na(a), b, a)
"%ni%" <- Negate(`%in%`)
compact <- function(x) {
x[!vapply(x, is.empty, FALSE, USE.NAMES=FALSE)]
}
compactChar <- function(x) {
x[vapply(x, nzchar, FALSE, USE.NAMES=FALSE)]
}
compactNA <- function(x) {
x[!is.na(x)]
}
Call <- function(fn, ...) {
fn <- match.fun(fn)
fn(...)
}
Partial <- function(fn, ..., .env = parent.frame()) {
assert_that(is.function(fn))
fcall <- substitute(fn(...))
if (!is.primitive(fn))
fcall <- match.call(fn, fcall)
fcall[[length(fcall) + 1]] <- quote(...)
args <- list("..." = quote(expr = ))
eval(call("function", as.pairlist(args), fcall), .env)
}
Compose <- function (...) {
fns <- lapply(compact(list(...)), match.fun)
len <- length(fns)
function (...) {
res <- Call(fns[[len]], ...)
for (fn in rev(fns[-len]))
res <- fn(res)
res
}
}
usp <- Compose("unlist", "strsplit")
dup <- function (x, n) {
assert_that(is.string(x))
if (any(n < 0)) n[n < 0] <- 0
vapply(.mapply(rep.int, list(rep.int(x, length(n)), n), NULL), paste0, collapse="", "")
}
blanks <- Partial(dup, x = " ")
trim <- function(x, trim = '\\s+') {
assert_that(is.vector(x))
gsub(paste0("^", trim, "|", trim, "$"), '', x)
}
count_re <- function(x, re) {
vapply(gregexpr(re, x), function (x) sum(x > 0L), 1, USE.NAMES=FALSE)
}
ellipsize <- function(obj, width=getOption("width"), ellipsis="...") {
str <- encodeString(obj)
ifelse(nchar(str) > width - 1,
paste0(substring(str, 1, width - nchar(ellipsis) - 1), ellipsis),
str)
}
#' Test if an external executable is available
#'
#' Uses \code{\link{Sys.which}} internally, so it should work
#' on Windows and Unix.alikes.
#'
#' @param cmd The exececutable to test for.
#' @param msg Additional message if the test fails.
#' @keywords internal
has_command <- function (cmd, msg = "") {
assert_that(is.string(cmd))
unname(Sys.which(cmd) != "")
}
on_failure(has_command) <- function(call, env) {
paste0("Dependency ", sQuote(eval(call$cmd, env)), " is not installed\n",
eval(call$msg, env))
}
#' Format paragraphs
#'
#' Similar to \code{\link{strwrap}} but returns a single string with
#' linefeeds inserted
#'
#' @param s a character vector or a list of character vectors
#' @param width a positive integer giving the column for inserting
#' linefeeds
#' @param indent an integer giving the indentation of the first line of
#' the paragraph; negative values of \code{indent} are allowed and reduce
#' the width for the first line by that value.
#' @param offset a non-negative integer giving the indentation of all
#' but the first line
#' @param split regular expression used for splitting. Defaults to
#' a whitespace character.
#' @param FORCE Words are force split if the available width is too small.
#' @param FULL_FORCE Lines are split exactly at the specified width
#' irrespective of whether there is whitespace or not.
#'
#' @return a character vector
#' @keywords internal
linebreak <- function(s, width = getOption("width") - 2,
indent = 0, offset = 0, split = " ",
FORCE = FALSE, FULL_FORCE = FALSE)
{
if (!is.character(s))
s <- as.character(s)
if (length(s) == 0L)
return("")
.first_iteration <- TRUE
# set indent string to "" if a negative value is given
# this lets us shrink the available width for the first line by that value
indent_string <- blanks(indent)
offset_string <- paste0("\n", blanks(offset))
ans <- Map(function(s, width, offset, indent,
indent_string, split, FORCE,
FULL_FORCE)
{
# remove leading and trailing blanks
# convert newlines, tabs, spaces to " "
# find first position where 'split' applies
if (!FULL_FORCE) {
s <- gsub("\\s+", " ", trim(s), perl=TRUE)
}
fws <- regexpr(split, s, perl=TRUE)
if (.first_iteration)
string_width <- indent + nchar(s)
else
string_width <- offset + nchar(s)
if (string_width > width)
{
# if not everything fits on one line
.first_iteration <- FALSE
if(FULL_FORCE ||
((fws == -1 || fws >= (width - string_width)) && FORCE))
{
# if no whitespace or first word too long and force break
# cut through the middle of a word
pat1 <- paste0("^.{", width - offset - indent, "}(?=.+)")
pat2 <- paste0("(?<=^.{", width - offset - indent, "}).+")
leading_string <- regmatches(s, regexpr(pat1, s, perl=TRUE))
trailing_string <- regmatches(s, regexpr(pat2, s, perl=TRUE))
s <- paste0(indent_string, leading_string, offset_string,
linebreak(s=trailing_string, width=width, indent=0,
offset=offset, split=split, FORCE=FORCE,
FULL_FORCE=FULL_FORCE))
}
else if ((fws == -1 || fws >= (width - offset + indent)) && !FORCE)
{
# if no whitespace or first word too long and NO force break
# stop right here
stop("Can't break in the middle of a word. Use the force!")
}
else
{
# break the line
s_split <- unlist(strsplit(s, split))
s_cum <- cumsum(nchar(s_split) + 1)
leading_string <-
paste0(s_split[s_cum < width - offset - indent],
ifelse(split == " ", "", split), collapse=split)
trailing_string <-
paste0(s_split[s_cum >= width - offset - indent], collapse=split)
s <- paste0(indent_string, leading_string, offset_string,
linebreak(s=trailing_string, width=width, indent=0,
offset=offset, split=split, FORCE=FORCE, FULL_FORCE=FULL_FORCE))
}
} else {
# if everything fits on one line go with the string + indent
paste0(indent_string, s)
}
}, s, width, offset, abs(indent), indent_string, split,
FORCE, FULL_FORCE, USE.NAMES=FALSE)
unlist(ans)
}
#' Strip file extensions
#'
#' Strips the extension (or an arbitrary tag) from a file name.
#'
#' @param file The file name(s).
#' @param sep specifies the seperator character (default ".").
#' @param level How many extensions should be stripped.
#' The default (0) strips all, 1 strips the last one, 2 strips the last two,
#' and so on.
#' @keywords internal
strip_ext <- function (file, sep="\\.", level=0) {
assert_that(!missing(file), is.character(file))
if (level == 0L) {
# level 0 ditches everything that comes after a dot
vapply(file, function(x) usp(x, sep)[1L], "", USE.NAMES = FALSE)
} else if (level > 0L) {
# level 1 removes the very last extension: file.xyz.abc > file.xyz
# level 2: file.xyz.abc > file
# and so on
count <- count_re(file, sep) + 1L - level
# to always grab at least the first element after the split
# reset zero counts to 1
count <- ifelse(count < 1, 1, count)
unlist(Map(function(x, lvl) {
paste0(usp(x, sep)[ seq_len(lvl) ], collapse = gsub('\\', '', sep, fixed=TRUE))
}, x=file, lvl=count, USE.NAMES=FALSE))
} else {
stop(sprintf("Level %s is invalid. Must be 0, 1, 2, ...", sQuote(level)))
}
}
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