[arch-commits] Commit in r/trunk (PKGBUILD sweave.patch)
Ronald van Haren
ronald at nymeria.archlinux.org
Wed Jun 4 18:45:22 UTC 2014
Date: Wednesday, June 4, 2014 @ 20:45:22
Author: ronald
Revision: 214263
upgpkg: r 3.1.0-2
upstream fix for https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15752
Added:
r/trunk/sweave.patch
Modified:
r/trunk/PKGBUILD
--------------+
PKGBUILD | 15 +
sweave.patch | 500 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 510 insertions(+), 5 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2014-06-04 17:39:29 UTC (rev 214262)
+++ PKGBUILD 2014-06-04 18:45:22 UTC (rev 214263)
@@ -5,7 +5,7 @@
pkgname=r
pkgver=3.1.0
-pkgrel=1
+pkgrel=2
pkgdesc="Language and environment for statistical computing and graphics"
arch=('i686' 'x86_64')
license=('GPL')
@@ -21,18 +21,23 @@
source=("http://cran.r-project.org/src/base/R-${pkgver%%.*}/R-${pkgver}.tar.gz"
'r.desktop'
'r.png'
- 'R.conf')
+ 'R.conf'
+ 'sweave.patch')
sha1sums=('a9d13932c739cc12667c6a17fabd9361624a1708'
'd7fa521345b230a4187d60d07d06ce4b6d573e3f'
'a69a07ec363440efc18ce0a7f2af103375dea978'
- '43668da6cfd1b4455a99f23e79e2059294dddac9')
+ '43668da6cfd1b4455a99f23e79e2059294dddac9'
+ '7c89c315673406d6f2e08170dbe12f46f9cec1c5')
prepare() {
cd R-${pkgver}
-# set texmf dir correctly in makefile
+ # set texmf dir correctly in makefile
sed -i 's|$(rsharedir)/texmf|${datarootdir}/texmf|' share/Makefile.in
-# fix for texinfo 5.X
+ # fix for texinfo 5.X
sed -i 's|test ${makeinfo_version_min} -lt 7|test ${makeinfo_version_min} -lt 0|' configure
+
+ # upstream fix for https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15752
+ patch -Np0 -i ${srcdir}/sweave.patch
}
build() {
Added: sweave.patch
===================================================================
--- sweave.patch (rev 0)
+++ sweave.patch 2014-06-04 18:45:22 UTC (rev 214263)
@@ -0,0 +1,500 @@
+Index: src/library/utils/R/Sweave.R
+===================================================================
+--- src/library/utils/R/Sweave.R (revision 65431)
++++ src/library/utils/R/Sweave.R (revision 65432)
+@@ -1,7 +1,7 @@
+ # File src/library/utils/R/Sweave.R
+ # Part of the R package, http://www.R-project.org
+ #
+-# Copyright (C) 1995-2012 The R Core Team
++# Copyright (C) 1995-2014 The R Core Team
+ #
+ # This program is free software; you can redistribute it and/or modify
+ # it under the terms of the GNU General Public License as published by
+@@ -30,7 +30,7 @@
+ ### re-encodes the output back to 'encoding': the Rtangle driver
+ ### leaves it in the encoding of the current locale and records what
+ ### that is in a comment. The "UTF-8" encoding is preserved on
+-### both input and output in RweaveLatex, but is handled like
++### both input and output in RweaveLatex, but is handled like
+ ### other encodings in Rtangle.
+ ###
+ ### SweaveReadFile first looks for a call to one of the LaTeX packages
+@@ -202,9 +202,11 @@
+ stop(gettextf("no Sweave file with name %s found",
+ sQuote(file[1L])), domain = NA)
+ else if (length(f) > 1L)
+- stop(paste(gettextf("%d Sweave files for basename %s found",
+- length(f), sQuote(file[1L])),
+- paste(":\n ", f, collapse="")),
++ stop(paste(sprintf(ngettext(length(f), "%d Sweave file for basename %s found",
++ "%d Sweave files for basename %s found",
++
++ domain = "R-utils"),
++ length(f), sQuote(file[1L])), paste(":\n ", f, collapse = "")),
+ domain = NA)
+ }
+
+@@ -228,7 +230,7 @@
+ " declares an encoding that Sweave does not know about",
+ domain = NA, call. = FALSE)
+ }
+- if (enc == "UTF-8")
++ if (enc == "UTF-8")
+ Encoding(text) <- enc
+ else {
+ if (nzchar(enc)) text <- iconv(text, enc, "") else enc <- "ASCII"
+@@ -425,7 +427,7 @@
+ Usage <- function() {
+ cat("Usage: R CMD Sweave [options] file",
+ "",
+- "A front-end for Sweave and other vignette engines",
++ "A front-end for Sweave and other vignette engines, via buildVignette()",
+ "",
+ "Options:",
+ " -h, --help print this help message and exit",
+@@ -433,6 +435,10 @@
+ " --driver=name use named Sweave driver",
+ " --engine=pkg::engine use named vignette engine",
+ " --encoding=enc default encoding 'enc' for file",
++ " --clean corresponds to --clean=default",
++ " --clean= remove some of the created files:",
++ ' "default" removes those the same initial name;',
++ ' "keepOuts" keeps e.g. the *.tex ones even when PDF is produced',
+ " --options= comma-separated list of Sweave/engine options",
+ " --pdf convert to PDF document",
+ " --compact= try to compact PDF document:",
+@@ -454,6 +460,7 @@
+ engine <- NULL
+ toPDF <- FALSE
+ compact <- Sys.getenv("_R_SWEAVE_COMPACT_PDF_", "no")
++ clean <- FALSE ## default!
+ while(length(args)) {
+ a <- args[1L]
+ if (a %in% c("-h", "--help")) {
+@@ -465,7 +472,7 @@
+ R.version[["major"]], ".", R.version[["minor"]],
+ " (r", R.version[["svn rev"]], ")\n", sep = "")
+ cat("",
+- "Copyright (C) 2006-2013 The R Core Team.",
++ "Copyright (C) 2006-2014 The R Core Team.",
+ "This is free software; see the GNU General Public License version 2",
+ "or later for copying conditions. There is NO warranty.",
+ sep = "\n")
+@@ -476,6 +483,18 @@
+ engine <- substr(a, 10, 1000)
+ } else if (substr(a, 1, 11) == "--encoding=") {
+ encoding <- substr(a, 12, 1000)
++ } else if (a == "--clean") {
++ clean <- TRUE
++ } else if (substr(a, 1, 8) == "--clean=") {
++ clean. <- substr(a, 9, 1000)
++ clean <- switch(clean.,
++ "default" = TRUE,
++ "keepOuts" = NA,
++ message(gettextf("Warning: unknown option '--clean='%s",
++ clean.), domain = NA))
++ } else if (a == "--no-clean") { # only exists in 3.1.0
++ message("Warning: '--no-clean' is deprecated; default does not clean, see --clean")
++ clean <- FALSE
+ } else if (substr(a, 1, 10) == "--options=") {
+ options <- substr(a, 11, 1000)
+ } else if (a == "--pdf") {
+@@ -494,7 +513,7 @@
+ Usage()
+ do_exit(1L)
+ }
+- args <- list(file=file, tangle=FALSE, latex=toPDF, engine=engine)
++ args <- list(file=file, tangle=FALSE, latex=toPDF, engine=engine, clean=clean)
+ if(nzchar(driver)) args <- c(args, driver)
+ args <- c(args, encoding = encoding)
+ if(nzchar(options)) {
+@@ -503,7 +522,7 @@
+ }
+ output <- do.call(tools::buildVignette, args)
+ message("Output file: ", output)
+- if (toPDF && compact != "no"
++ if (toPDF && compact != "no"
+ && length(output) == 1 && grepl(".pdf$", output, ignore.case=TRUE)) {
+ ## <NOTE>
+ ## Same code as used for --compact-vignettes in
+@@ -596,7 +615,7 @@
+ Usage()
+ do_exit(1L)
+ }
+- args <- list(file=file, tangle=TRUE, weave=FALSE, engine=engine,
++ args <- list(file=file, tangle=TRUE, weave=FALSE, engine=engine,
+ encoding=encoding)
+ if(nzchar(options)) {
+ opts <- eval(parse(text = paste("list(", options, ")")))
+Index: src/library/tools/R/Vignettes.R
+===================================================================
+--- src/library/tools/R/Vignettes.R (revision 65431)
++++ src/library/tools/R/Vignettes.R (revision 65432)
+@@ -1,7 +1,7 @@
+ # File src/library/tools/R/Vignettes.R
+ # Part of the R package, http://www.R-project.org
+ #
+-# Copyright (C) 1995-2013 The R Core Team
++# Copyright (C) 1995-2014 The R Core Team
+ #
+ # This program is free software; you can redistribute it and/or modify
+ # it under the terms of the GNU General Public License as published by
+@@ -35,7 +35,7 @@
+ # Locates the vignette weave, tangle and texi2pdf product(s) based on the
+ # vignette name. All such products must have the name as their filename
+ # prefix (i.e. "^<name>").
+-# For weave, final = TRUE will look for <name>.pdf and <name>.pdf, whereas
++# For weave, final = TRUE will look for <name>.pdf and <name>.html, whereas
+ # with final = FALSE it also looks for <name>.tex (if <name>.pdf is also
+ # found, it will be returned). For tangle, main = TRUE will look <name>.R,
+ # whereas main = FALSE will look for <name><anything>*.R.
+@@ -44,20 +44,14 @@
+ function(name, by = c("weave", "tangle", "texi2pdf"),
+ final = FALSE, main = TRUE, dir = ".", engine, ...)
+ {
+- stopifnot(length(name) == 1L)
++ stopifnot(length(name) == 1L, file_test("-d", dir))
+ by <- match.arg(by)
+- stopifnot(file_test("-d", dir))
++ exts <- ## (lower case here):
++ switch(by,
++ "weave" = if (final) c("pdf", "html") else c("pdf", "html", "tex"),
++ "tangle" = c("r", "s"),
++ "texi2pdf" = "pdf")
+
+- if (by == "weave") {
+- if (final)
+- exts <- c("pdf", "html")
+- else
+- exts <- c("pdf", "html", "tex")
+- } else if (by == "tangle") {
+- exts <- c("r", "s")
+- } else if (by == "texi2pdf") {
+- exts <- "pdf"
+- }
+ exts <- c(exts, toupper(exts))
+ pattern1 <- sprintf("^%s[.](%s)$", name, paste(exts, collapse = "|"))
+ output0 <- list.files(path = dir, all.files = FALSE, full.names = FALSE, no..=TRUE)
+@@ -113,16 +107,13 @@
+ domain = NA)
+ }
+
++ ## return :
+ if (length(output) > 0L) {
+ if (dir == ".")
+- output <- basename(output)
++ basename(output)
+ else
+- output <- file.path(dir, output)
+- } else {
+- output <- NULL
+- }
+-
+- output
++ file.path(dir, output)
++ } ## else NULL
+ }
+
+
+@@ -382,28 +373,24 @@
+
+ docs <- names <- engines <- patterns <- character()
+ allFiles <- list.files(docdir, all.files = FALSE, full.names = TRUE)
+- matchedPattern <- rep(FALSE, length(allFiles))
++ matchedPattern <- rep.int(FALSE, length(allFiles))
+ msg <- character()
+ if (length(allFiles) > 0L) {
+ for (name in names(engineList)) {
+ engine <- engineList[[name]]
+- patternsT <- engine$pattern
+- for (pattern in patternsT) {
++ for (pattern in engine$pattern) {
+ idxs <- grep(pattern, allFiles)
+- docsT <- allFiles[idxs]
+ matchedPattern[idxs] <- TRUE
+- keep <- logical(length(docsT))
+- for (i in seq_along(docsT))
+- keep[i] <- engineMatches(name, getVignetteEngine(docsT[i]))
+- idxs <- idxs[keep]
+- nidxs <- length(idxs)
+- if (nidxs > 0L) {
++ keep <- vapply(allFiles[idxs], function(.d.)
++ engineMatches(name, getVignetteEngine(.d.)), NA)
++ if (any(keep)) {
++ idxs <- idxs[keep]
+ if (is.function(engine$weave)) {
+ docsT <- allFiles[idxs]
+ docs <- c(docs, docsT)
+ names <- c(names, gsub(pattern, "", basename(docsT)))
+- engines <- c(engines, rep(name, times = nidxs))
+- patterns <- c(patterns, rep(pattern, times = nidxs))
++ engines <- c(engines, rep.int(name, length(idxs)))
++ patterns <- c(patterns, rep.int(pattern, length(idxs)))
+ }
+ matchedPattern <- matchedPattern[-idxs]
+ allFiles <- allFiles[-idxs]
+@@ -421,13 +408,12 @@
+ }
+
+ # Assert
+- stopifnot(length(names) == length(docs))
+- stopifnot(length(engines) == length(docs))
+- stopifnot(length(patterns) == length(docs))
+- stopifnot(!any(duplicated(docs)))
++ stopifnot(length(names) == length(docs),
++ length(engines) == length(docs),
++ length(patterns) == length(docs), !anyDuplicated(docs))
+
+ z <- list(docs=docs, names=names, engines=engines, patterns=patterns,
+- dir=docdir, pkgdir=dir, msg = msg)
++ dir = docdir, pkgdir = dir, msg = msg)
+
+ if (output) {
+ outputs <- character(length(docs))
+@@ -460,7 +446,6 @@
+ ###
+ ### Run a weave and pdflatex on all vignettes of a package and try to
+ ### remove all temporary files that were created.
+-
+ buildVignettes <-
+ function(package, dir, lib.loc = NULL, quiet = TRUE, clean = TRUE, tangle = FALSE)
+ {
+@@ -569,11 +554,11 @@
+ newer <- file_test("-nt", f, ".build.timestamp")
+ ## some packages, e.g. SOAR, create directories
+ unlink(f[newer], recursive = TRUE)
++ f <- setdiff(list.files(all.files = TRUE, no.. = TRUE),
++ c(keep, origfiles))
++ f <- f[file_test("-f", f)]
++ file.remove(f)
+ }
+- f <- setdiff(list.files(all.files = TRUE, no.. = TRUE),
+- c(keep, origfiles))
+- f <- f[file_test("-f", f)]
+- file.remove(f)
+ }
+
+ # Assert
+@@ -592,15 +577,13 @@
+ ###
+ ### Run a weave and/or tangle on one vignette and try to
+ ### remove all temporary files that were created.
+-
+-buildVignette <-
+- function(file, dir = ".", weave = TRUE, latex = TRUE, tangle = TRUE,
+- quiet = TRUE, clean = TRUE, engine = NULL, buildPkg = NULL, ...)
++### Also called from 'R CMD Sweave' via .Sweave() in ../../utils/R/Sweave.R
++buildVignette <- function(file, dir = ".", weave = TRUE, latex = TRUE, tangle = TRUE,
++ quiet = TRUE, clean = TRUE, keep = character(),
++ engine = NULL, buildPkg = NULL, ...)
+ {
+-
+ if (!file_test("-f", file))
+ stop(gettextf("file '%s' not found", file), domain = NA)
+-
+ if (!file_test("-d", dir))
+ stop(gettextf("directory '%s' does not exist", dir), domain = NA)
+
+@@ -628,12 +611,11 @@
+
+ # Set output directory temporarily
+ file <- file_path_as_absolute(file)
+- olddir <- getwd()
++ olddir <- setwd(dir)
+ if (!is.null(olddir)) on.exit(setwd(olddir))
+- setwd(dir)
+
+- # Record existing files
+- origfiles <- list.files(all.files = TRUE)
++ ## # Record existing files
++ ## origfiles <- list.files(all.files = TRUE)
+ if (is.na(clean) || clean) {
+ file.create(".build.timestamp")
+ }
+@@ -662,9 +644,9 @@
+ find_vignette_product(name, by = "tangle", main = FALSE, engine = engine)
+ } # else NULL
+
+- # Cleanup
+- keep <- c(sources, final)
+- if (is.na(clean)) { # Use NA to signal we want .tex files kept.
++ ## Cleanup newly created files unless those in 'keep'
++ keep <- c(sources, final, keep)
++ if (is.na(clean)) { # Use NA to signal we want .tex (or .md) files kept.
+ keep <- c(keep, output)
+ clean <- TRUE
+ }
+@@ -674,10 +656,11 @@
+ ## some packages create directories
+ unlink(f[newer], recursive = TRUE)
+ }
+- f <- setdiff(list.files(all.files = TRUE, no.. = TRUE), c(keep, origfiles))
+- f <- f[file_test("-f", f)]
+- file.remove(f)
+-
++ ### huh? 2nd round of cleaning even if clean is FALSE ??
++ ## f <- setdiff(list.files(all.files = TRUE, no.. = TRUE), c(keep, origfiles))
++ ## f <- f[file_test("-f", f)]
++ ## file.remove(f)
++ ## #}
+ unique(keep)
+ }
+
+@@ -685,18 +668,18 @@
+
+ getVignetteEncoding <- function(file, ...)
+ {
+- # Look for inputen[cx] first, then %\SweaveUTF8. Complain about
++ # Look for inputen[cx] first, then %\SweaveUTF8. Complain about
+ # inconsistencies.
+-
++
+ lines <- readLines(file, warn = FALSE)
+ result1 <- .getVignetteEncoding(lines, ...)
+-
++
+ poss <- grep("^[[:space:]]*%+[[:space:]]*\\\\SweaveUTF8[[:space:]]*$", lines, useBytes = TRUE)
+ if (length(poss)) {
+ result <- "UTF-8"
+ if (!(result1 %in% c("", "non-ASCII", "UTF-8")))
+- stop("Inconsistent encoding specifications: ", result1, " with %\\SweaveUTF8")
+- } else
++ stop(gettextf("Inconsistent encoding specifications: %s with %%\\SweaveUTF8", result1), domain = NA)
++ } else
+ result <- result1
+ result
+ }
+Index: src/library/tools/man/buildVignette.Rd
+===================================================================
+--- src/library/tools/man/buildVignette.Rd (revision 65431)
++++ src/library/tools/man/buildVignette.Rd (revision 65432)
+@@ -4,13 +4,15 @@
+ \description{
+ Run \code{\link{Sweave}} (or other custom weave function)
+ \code{\link{texi2dvi}}, and/or \code{\link{Stangle}}
+- (or other custom tangle function) on one vignette.
++ (or other custom tangle function) on one vignette.
++
++ This is the workhorse of \command{R CMD Sweave}.
+ }
+ \usage{
+ buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, tangle = TRUE,
+- quiet = TRUE, clean = TRUE, engine = NULL, buildPkg = NULL, ...)
++ quiet = TRUE, clean = TRUE, keep = character(),
++ engine = NULL, buildPkg = NULL, ...)
+ }
+-%- maybe also 'usage' for other objects documented here.
+ \arguments{
+ \item{file}{character; the vignette source file}
+ \item{dir}{character; the working directory in which the intermediate and
+@@ -19,9 +21,12 @@
+ \item{latex}{logical; \link{texi2pdf} be run if weaving produces a \file{.tex} file?}
+ \item{tangle}{logical; should tangle be run?}
+ \item{quiet}{logical; run in quiet mode?}
+- \item{clean}{logical; whether to remove intermediate files. See details below.}
+- \item{engine}{\code{NULL} or character; name of vignette engine to use. Overrides
+- any \code{\\VignetteEngine\{\}} markup in the vignette.}
++ \item{clean}{logical; whether to remove some newly created, often
++ intermediate, files. See details below.}
++ \item{keep}{a list of file names to keep in any case when cleaning. Note
++ that \dQuote{target} files are kept anyway.}
++ \item{engine}{\code{NULL} or character; name of vignette engine to
++ use. Overrides any \code{\\VignetteEngine\{\}} markup in the vignette.}
+ \item{buildPkg}{\code{NULL} or character; an optional package in which to find
+ the vignette engine}
+ \item{...}{Additional arguments passed to weave and tangle.}
+@@ -28,26 +33,30 @@
+
+ }
+ \details{
+-This function determines the vignette engine for the vignette (default \code{utils::Sweave}),
+-then weaves and/or tangles the vignette using that engine. Finally, if \code{clean} is \code{TRUE},
+-newly created intermediate files will be deleted. If \code{clean} is \code{NA}, newly created
+-\file{.tex} files will not be deleted even if a \file{.pdf} file has been produced from them.
++ This function determines the vignette engine for the vignette (default
++ \code{utils::Sweave}), then weaves and/or tangles the vignette using
++ that engine. Finally, if \code{clean} is \code{TRUE}, newly created
++ intermediate files (non \dQuote{targets}, where these depend on the engine,
++ etc, and not any in \code{keep}) will be deleted. If \code{clean} is
++ \code{NA}, and \code{weave} is true, newly created intermediate output
++ files (e.g., \file{.tex}) will not be deleted even if a \file{.pdf}
++ file has been produced from them.
+
+-If \code{buildPkg} is specified, it will be loaded before the vignette is processed, and will
+-be used as the default package
+-in the search for a vignette engine, but an explicitly specified package in the vignette source
+-(e.g. using \code{\\VignetteEngine\{utils::Sweave\}} to specify the \code{Sweave}
+-engine in the \pkg{utils} package) will override it. In contrast,
+-if the \code{engine} argument is given, it will override the
+-vignette source.
++ If \code{buildPkg} is specified, it will be loaded before the vignette
++ is processed, and will be used as the default package in the search
++ for a vignette engine, but an explicitly specified package in the
++ vignette source (e.g. using \code{\\VignetteEngine\{utils::Sweave\}}
++ to specify the \code{Sweave} engine in the \pkg{utils} package) will
++ override it. In contrast, if the \code{engine} argument is given, it
++ will override the vignette source.
+ }
+ \value{
+-A character vector naming the files that have been produced.
++ A character vector naming the files that have been produced.
+ }
+ \author{
+-Henrik Bengtsson and Duncan Murdoch
++ Henrik Bengtsson and Duncan Murdoch
+ }
+ \seealso{
+-\code{\link{buildVignettes}} for building all vignettes in a package.
++ \code{\link{buildVignettes}} for building all vignettes in a package.
+ }
+ \keyword{documentation}
+Index: src/library/tools/man/buildVignettes.Rd
+===================================================================
+--- src/library/tools/man/buildVignettes.Rd (revision 65431)
++++ src/library/tools/man/buildVignettes.Rd (revision 65432)
+@@ -39,10 +39,10 @@
+ \item{subdirs}{a character vector of subdirectories of \code{dir} in which
+ to look for vignettes. The first which exists is used. Defaults to
+ \code{"doc"} if \code{package} is supplied, otherwise \code{"vignettes"}.}
+- \item{output}{logical. If \code{TRUE}, the output filename
+- for each vignette in the result.}
+- \item{source}{logical. If \code{TRUE}, include the tangled output filename
+- for each vignette in the result.}
++ \item{output}{logical indicating if the output filenames for each
++ vignette should be returned (in component \code{outputs}).}
++ \item{source}{logical indicating if the \emph{tangled} output
++ filenames for each vignette should be returned (in component \code{sources}).}
+ \item{check}{logical. If \code{TRUE}, check whether all files that
+ have vignette-like filenames have an identifiable vignette engine.
+ This may be a false positive if a file is not a vignette but has a
+@@ -49,7 +49,7 @@
+ filename matching a pattern defined by one of the vignette engines.}
+ }
+ \details{
+- \code{buildVignettes} is used by \code{R CMD build} and \code{R CMD
++ \code{buildVignettes} is used by \command{R CMD build} and \command{R CMD
+ check} to (re-)build vignette PDFs from their sources.
+ }
+ \value{
+@@ -60,5 +60,20 @@
+ \code{pkgVignettes} returns an object of class \code{"pkgVignettes"}
+ if a vignette directory is found, otherwise \code{NULL}.
+ }
++\examples{
++str(gVigns <- pkgVignettes("grid"))
++\dontshow{
++ `\%=f=\%` <- function(a, b) normalizePath(a) == normalizePath(b)
++ with(gVigns,
++ stopifnot(engines == "utils::Sweave",
++ pkgdir \%=f=\% system.file(package="grid"),
++ dir \%=f=\% system.file(package="grid", "doc"),
++ (n. <- length(docs)) >= 12, # have 13
++ n. == length(names), n. == length(engines),
++ length(msg) == 0) ) # as it is a 'base' package
++}
++stopifnot("grid" \%in\% gVigns$names,
++ inherits(gVigns, "pkgVignettes"))
++}
+ \keyword{utilities}
+ \keyword{documentation}
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