Date: Wednesday, July 30, 2014 @ 12:32:34 Author: ronald Revision: 218370
upgpkg: r 3.1.1-1 update to 3.1.1; remove upstream patch Modified: r/trunk/PKGBUILD Deleted: r/trunk/sweave.patch --------------+ PKGBUILD | 15 - sweave.patch | 500 --------------------------------------------------------- 2 files changed, 5 insertions(+), 510 deletions(-) Modified: PKGBUILD =================================================================== --- PKGBUILD 2014-07-30 09:17:34 UTC (rev 218369) +++ PKGBUILD 2014-07-30 10:32:34 UTC (rev 218370) @@ -4,8 +4,8 @@ # Contributor: K. Piche <[email protected]> pkgname=r -pkgver=3.1.0 -pkgrel=2 +pkgver=3.1.1 +pkgrel=1 pkgdesc="Language and environment for statistical computing and graphics" arch=('i686' 'x86_64') license=('GPL') @@ -21,13 +21,11 @@ source=("http://cran.r-project.org/src/base/R-${pkgver%%.*}/R-${pkgver}.tar.gz"; 'r.desktop' 'r.png' - 'R.conf' - 'sweave.patch') -sha1sums=('a9d13932c739cc12667c6a17fabd9361624a1708' + 'R.conf') +sha1sums=('e974ecc92e49266529e8e791e02a80c75e50b696' 'd7fa521345b230a4187d60d07d06ce4b6d573e3f' 'a69a07ec363440efc18ce0a7f2af103375dea978' - '43668da6cfd1b4455a99f23e79e2059294dddac9' - '7c89c315673406d6f2e08170dbe12f46f9cec1c5') + '43668da6cfd1b4455a99f23e79e2059294dddac9') prepare() { cd R-${pkgver} @@ -35,9 +33,6 @@ sed -i 's|$(rsharedir)/texmf|${datarootdir}/texmf|' share/Makefile.in # 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() { Deleted: sweave.patch =================================================================== --- sweave.patch 2014-07-30 09:17:34 UTC (rev 218369) +++ sweave.patch 2014-07-30 10:32:34 UTC (rev 218370) @@ -1,500 +0,0 @@ -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}
