# This is to allow the use of Sweave with latexmk, and in addition to
#    make synctex work properly with it.  
# SEE THE IMPORTANT NOTES below.
#
# Sweave (http://www.stat.uni-muenchen.de/~leisch/Sweave/) is a tool
# that allows to embed the R code for complete data analyses in latex
# documents.  The user edits a file with an extension like .Rnw, and
# the .tex file is generated from this.
#
# Four problems are solved by the code below:
# 1. Generate the .tex file automatically.
# 2. Arrange not to re-run unmodified chunks of R code.  (A pure
#    optimization.)
# 3. Fix the execution environment for (pdf)latex.
# 4. Deal with synctex: If the user wants to use synctex
#    (www.tug.org/TUGboat/tb29-3/tb93laurens.pdf) to synchronize the
#    pdf file with the source file, by default synctex does the
#    synchronization with the generated .tex file, not the original 
#    source file.  Postprocessing of the .synctex.gz file is necessary
#    to fix this.
#
# The following version was worked out and  tested by a user (thanks
# to Brian Beitzel) on MSWindows.  It will need at least one change to
# work on UNIX-like operating systems (which include Linux and OS-X).

# N.B. ===> IMPORTANT NOTES <===
#
# 1. See the comments in knitr-latexmkrc for an alternative and probably better
#    way of using Sweave with latexmk
#
# 2. The patchDVI package for R needs to be installed from R-Forge, as
#    follows:
#
#  install.packages("patchDVI", repos="http://R-Forge.R-project.org")
#
# 3. In all Sweave (.Rnw) documents, the following lines must be included:
#
#         \usepackage{Sweave}
#         \SweaveOpts{concordance=TRUE}


# Fix the pdflatex command to run Sweave first, and to postprocess the
#  .synctex.gz file:
# !!!!! THIS IS THE VERSION FOR MS-WINDOWS, with && as a command
# separator
$pdflatex = "cmd /c "
       . "Rscript -e \"library(cacheSweave); setCacheDir(getwd()); "
       . "Sweave('%S', driver=cacheSweaveDriver)\""
       . " && R CMD pdflatex -interaction=nonstopmode -synctex=1 %O %B.tex"
       . " && Rscript -e "
       . "\"library('patchDVI');patchSynctex('%B.synctex.gz')\"";
#
# !!!TO FIX THIS FOR Linux/OS-X/UNIX, try uncommenting the following:
#  (this version hasn't been tested).
#$pdflatex = "Rscript -e \"library(cacheSweave); setCacheDir(getwd()); "
#       . "Sweave('%S', driver=cacheSweaveDriver)\""
#       . " ; R CMD pdflatex -interaction=nonstopmode -synctex=1 %O %B.tex"
#       . " ; Rscript -e "
#       . "\"library('patchDVI');patchSynctex('%B.synctex.gz')\"";

