Allows for communication between .Rnw editor and .pdf viewer.

Description

Utility patching the .synctec(.gz) file resulting from then LaTeXing of a .tex file with the concordance information from the .concordance.tex file resulting from knitting (possibly Sweaving) of the .Rnw source, allowing(for|back)ward searching from the editor to the viewer and back.

Details

Synchronising TeX source and DVI/PDF output considerably eases the editing (and, sometimes, debugging) of such documents, by allowing interaction between source and end-result. Modern DVI/PDF viewers and editors support this synchronization, either directly, by using information embedded in the .dvi or .pdf file, or by using an auxilliary file generated by a LaTeX run with option \synctex=1, teh .synctex(.gz) file.

However, when one uses a tool such as Sweave or knitr to generate a dynamic document (compounding analysis, computations and report), the resulting .tex file is no longer the original source, and the references to the .tex file are of little help in the revision of such a document.

Duncan Murdoch's patchDVI package aims at solving this problem by using a concordance file that can be generated by passing a concordance=TRUE option so Sweave or knit*. This -concordance.tex file contains an RLE encoding of the correspondence between the .Rnw source and the .tex intermediary file.

patchDVI uses this concordance information to patch the DVI pointers to source with the relevant pointers to the .Rnw file.

This package also has a patchSynctex function, attempting t find the relevant information in the .pdf file. However, some (most ?) PDFs happens to be impenetrable to patchDVI's patchSynctex function.

The present package aims at patching the .synctex(.gz) file with pointers to the original .Rnw source(s), using exclusively the .synctex(.gz) file as a source of information. Therefore, the tools (editors and viewers) must support Synctex in such a way that, when a .synctex(.gz) file is present, this information is preffered to the information present in the DVI or PDF document.

This turns out, according to some serious googling and limited testing, to be the case with :

• under Linux: emacs, gedit (editors), evince, okular (viewers), RStudio (IDE);

• under MS-Windows: emacs (editor), Sumatra (viewer), RStudio (IDE).

Furthermore, the .synctex(.gz) file file remains necessary for any synchronization, whereas a patched .dvi file can in principle be used without the .synctex(.gz) file.

This package is mostly aimed at programs (integrated development environments (IDEs), such as RStudio, or programmable editors, such as emacs and gedit) able to get R to execute code: it gives them an easy-to-use interface to a simple function does the ncessary patches for a given document (characterized by its name sans extension).

Its unique function can still be used from an interactive R session for debugging purposes.

Integration in editors and IDEs

This section will be enriched by your contributions.

ESS under emacs

The logical point of insertion of .synctex(.gz) patching is after each PDF compilation. It may be a bit wasteful (when two or more compilations are necessary, in order, for example, to fix references), but there is no standard way to determine if a LaTeX run is final.

This can be achieved by placing an advice on the function used to compile to PDF|DVI. The example shows how to advice PDF compilation.

Up to emacs 24.3

The following elisp snippet can be placed in your emacs initialization file (e. g. ~/.emacs in Unix(-like) systems):

(defadvice ess-swv-PDF (after ess-run-patchKnitr (&optional
						  PDFLATEX-CMD)
			      activate)
  "Patches the .synctex.gz file after PDF compilation"
  (interactive)
  (let* ((fn (buffer-file-name))
	 (fe (file-name-extension fn)))
    (if (string= fe "Rnw")
	(progn
	  (setq RPScmd (concat "patchSynctex('"
			       (file-name-sans-extension fn)
			       "')"))
	  (ess-create-temp-buffer "tampon-ess-execute")
	  (ess-execute "require(patchSynctex)" 'buffer "tampon-ess-execute")
	  (ess-execute RPScmd 'buffer "tampon-ess-execute")
	  (kill-buffer "tampon-ess-execute")))))
(ad-activate 'ess-swv-PDF)
      

From emacs 24.4 onwards

The previous elisp snippet has to be adapted to the newer advice system of elisp:

(defun ess-swv-patch-after-PDF (&optional PDFLATEX-CMD)
  "Patch the synctex file after PDF compilation"
  (let* ((fn (buffer-file-name))
	 (fe (file-name-extension fn)))
    (if (string= fe "Rnw")
	(progn
	  (setq RPScmd (concat "patchSynctex('"
			       (file-name-sans-extension fn)
			       "')"))
	  (ess-create-temp-buffer "tampon-ess-execute")
	  (ess-execute "require(patchSynctex)" 'buffer "tampon-ess-execute")
	  (ess-execute RPScmd 'buffer "tampon-ess-execute")
	  (kill-buffer "tampon-ess-execute")))))
(advice-add 'ess-swv-PDF :after #'ess-swv-patch-after-PDF)
      

AUCTeX under emacs

This is a work in progress : AUCTeX is more sophisticated than ESS about PDF production. There is no single function to advice (and knitting is not yet well integrated, by the way...). In the meantime, ESS functions remain available. Stay tuned...

Eclipse + StatET

Create an external build configuration (Sweave document processing) and place :

require(knitr); 
opts_knit$set(concordance = TRUE); 
texfile <- knit("${resource_loc:${source_file_path}}", encoding="UTF-8")
    

in the sweave tab, and :

syntex <- if (opts_knit$get('concordance'))"-synctex=1" else "-synctex=0";
command=paste("latexmk -pdf", syntex, "-interaction=nonstopmode", shQuote(texfile));
print(paste("Command ",command,"...\n"));
print(shell(command),intern = TRUE);
if (opts_knit$get('concordance')){
    require(patchSynctex);
    patchSynctex(texfile); 
}
print(paste0(substr(texfile,1, nchar(texfile)-3), "pdf"))
      

in the LaTeX tab.

Note

The current (1.8) version of knitr does not yet implement concordance for multifile projects (i. e. children chunks).

Author(s)

Jan Gleixner, Emmanuel Charpentier

Maintainer: Emmanuel Charpentier emm.charpentier@free.fr

References

Duncan Murdoch's excellent patchDVI has a great vignette explaining the basics of the problem.

Create correspondence between .pdf and .Rnw files

Description

patchSynctex(foo) uses the concordance file foo-concordance.tex generated by knitting (possibly Sweaveing) foo.Rnw with the option concordance=TRUE to patch foo.synctex(.gz) with information pointing to foo.Rnw.

Usage

patchSynctex(nwfile, syncfile=NULL, verbose=FALSE, ...)

Arguments

Details

This function reads the information given in the nwfile-concordance.tex file (which must exist) to patch the nwfile.synctex(.gz) file, which originally contains pointers from nwfile.pdf to the source in nwfile.tex with information pointing to the latter's source in nwfile.Rnw.

Editors and viewers supporting Synctex will be able to use this information to allow forward- and backward search between PDF and ists original source, thus easing debugging.

The nwfile will be used sans extension ; this allows your favorite IDE to pass either the name of the noweb file or the name of the .tex file.

The syncfile argument allows to force the addition of the patched references to the main syncfile for a document that uses subfiles. This is a workaround that may or may not be well-supported by knitr and/or your viewer.

The function may raise errors (files not found), warnings (no patch found to be done) or messages (number of patched locations).

This function is principally intended for use by programmable IDEs able to execute R code. It is documented mostly for debugging purposes.

Value

Nothing useful.

Note

The current (1.8) version of knitr does not yet implement concordance for multifile projects (i. e. children chunks).

Author(s)

Jan Gleixner, Emmanuel Charpentier emm.charpentier@free.fr

References

Duncan Murdoch's excellent patchDVI package: https://cran.r-project.org/package=patchDVI.

Examples

if(requireNamespace("tools", quietly=TRUE) &&
   requireNamespace("knitr", quietly=TRUE)) {
    ## Minimal demonstrative knitr example.
    RnwSrc<-"
\\synctex=1
\\documentclass{article}
<<Setup, eval=TRUE, echo=FALSE, results='hide'>>=
opts_knit$set(concordance=TRUE, self.contained=TRUE)##$
require(patchSynctex)
@ 
\\author{A.~U.~Thor}
\\title{A minimal \\textsf{knitr} example}
\\date{Some time}
\\begin{document}
\\maketitle

A first paragraph of text, which offers a target for forward search\\,:
for example, in \\textsf{emacs} with \\textsf{AUCTeX}, typing
``C-c~C-v'' should bring you to your PDF viewer in the corresponding
typeset line.

<<TestFig, echo=FALSE>>=
curve(sin(x), from=-pi, to=pi, main='A curve generated by R',
      sub='back-searching from here should bring you close to the \\'TestFig\\' chunk.')
@ 

This second paragraph of text is also a convenient target for
back-searching. For example, in \\textsf{evince}, a ``<Ctrl>-click''
should bring you to the \\textsf{noweb} source, bypassing the \\LaTeX
intermediate file.
\\end{document}
"
    require(knitr)
    cat(RnwSrc, file="Minimal.Rnw")
    knit2pdf("Minimal.Rnw", quiet=TRUE)
    D1<-file.info("Minimal.synctex.gz")$mtime
    patchSynctex("Minimal", verbose=TRUE)
    ## should print a message telling the number of patches
    D2<-file.info("Minimal.synctex.gz")$mtime
    D1!=D2
    ## should return TRUE
    ## To see the effect, try (example on a Linux system)
    ## Not run: system("evince Minimal.pdf")
}