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lyx_mirror/lib/scripts/lyxsweave.R

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# file lyxsweave.R
# This file is part of LyX, the document processor.
# Licence details can be found in the file COPYING.
# author Jean-Marc Lasgouttes
# author Yihui Xie
# Full author contact details are available in file CREDITS
# Wrapper around Sweave that sets up some things for LyX
# argument 1 is the absolute name of the input file
# argument 2 is the absolute name of the output file
# argument 3 is the iconv name for the encoding of the file
# argument 4 is the original document directory
.cmdargs <- commandArgs(trailingOnly=TRUE)
.doc.enc <- .cmdargs[3]
# check whether Sweave.sty is seen by LaTeX. if it is not, we will
# copy it alongside the .tex file (in general in the temporary
# directory). This means that an exported LaTeX file will not work,
# but this is a problem of installation of R on the user's machine.
# The advantage compared to the use of stylepath, is that the exported
# .tex file will be portable to another machine. (JMarc)
if (!length(system("kpsewhich Sweave.sty", intern=TRUE, ignore.stderr=TRUE))) {
.texmf.path <- file.path(R.home("share"), "texmf")
if (!file.exists(.sweave.sty <- file.path(.texmf.path, "Sweave.sty"))) {
.sweave.sty <- file.path(.texmf.path, "tex", "latex", "Sweave.sty")
}
file.copy(.sweave.sty, dirname(.cmdargs[2]), overwrite=TRUE)
rm(list = c('.sweave.sty', '.texmf.path'))
}
# Change current directory to the document directory, so that R can find
# data files.
setwd(.cmdargs[4])
# this is passed as a prefix.string to tell where temporary files should go
# the output file without extension and without '.'
tmpout <- gsub(".", "-", sub("\\.tex$", "", basename(.cmdargs[2])), fixed = TRUE)
# replace
.prefix.str <- paste(dirname(.cmdargs[2]), tmpout, sep="/")
rm(tmpout)
# avoid the default Rplots.pdf
options(device = function(...) {
pdf(file = tempfile())
})
# finally run sweave
# The Sweave version provided with R >= 0.13.1 has proper handling for
# encodings and our workaround for previous versions does not work
# anymore. Therefore, the invocation has to be different.
if (is.null(formals(Sweave)$encoding)) {
# set default encoding for input and output files; .orig.enc is used in
# the sweave module preamble to reset the encoding to what it was.
.orig.enc <- getOption("encoding")
options(encoding=.doc.enc)
Sweave(file=.cmdargs[1], output=.cmdargs[2], syntax="SweaveSyntaxNoweb",
prefix.string=.prefix.str)
} else {
Sweave(file=.cmdargs[1], output=.cmdargs[2], syntax="SweaveSyntaxNoweb",
prefix.string=.prefix.str, encoding=.doc.enc)
}
# remove absolute path from \includegraphics
options(encoding=.doc.enc) # encoding may have been changed in the preamble chunk
ls.doc <- readLines(.cmdargs[2])
ls.cmd <- paste('\\includegraphics{', dirname(.cmdargs[2]), "/", sep = "")
ls.idx <- grep(ls.cmd, ls.doc, fixed = TRUE)
if (length(ls.idx)) {
ls.doc[ls.idx] <- sub(ls.cmd, "\\includegraphics{", ls.doc[ls.idx], fixed = TRUE)
writeLines(ls.doc, .cmdargs[2])
}