Sweave, Texshop, and sync with included Rnw file
Sweave produces foo-concordance.tex from foo.Rnw, and writes
\input{foo-concordance.tex} in the LaTeX output. You can turn on the
concordance option in knitr as well. Since you do not use RStudio, you
have a couple of more steps to go:
1. borrow \Sconcordance from Sweave.sty;
2. manually \input{foo-concordance.tex};
3. set the option concordance=TRUE in opts_knit;
The rest of steps are the same as Sweave -- you compile the output by
`pdflatex --synctex=1 foo.tex`, and run patchDVI on the results. I do
not use TeXShop, so I'm not sure if it really works.
\documentclass{article}
% from Sweave.sty in R
\newcommand{\Sconcordance}[1]{%
\ifx\pdfoutput\undefined%
\csname newcount\endcsname\pdfoutput\fi%
\ifcase\pdfoutput\special{#1}%
\else%
\begingroup%
\pdfcompresslevel=0%
\immediate\pdfobj stream{#1}%
\pdfcatalog{/SweaveConcordance \the\pdflastobj\space 0 R}%
\endgroup%
\fi}
\input{foo-concordance.tex}
<<setup, include=FALSE>>=
opts_knit$set(concordance=TRUE)
@
\begin{document}
<<>>=
for (i in 1:5) {
print(i)
}
@
\end{document}
Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Thu, Jan 17, 2013 at 7:45 PM, huang min <minhuangr at gmail.com> wrote:
Anybody know if it is possible to use texshop and knitr with the sync working? I add a knitr engine but cannot sync. PS, I am comfortable with texshop but not RStudio. Huang On Fri, Jan 18, 2013 at 7:33 AM, michele caseposta <mic.cipi at gmail.com>wrote:
Hi,
I just updated R and patchDVI (from CRAN).
Now I can reverse search from the pdf to the included.Rnw.
However, I cannot forward search from the included to the pdf. Is this how
it is expected to work?
Forward and inverse search work between main Rnw and pdf.
I am pasting below the code in the two files.
%%%%%%%%% Sweavetest.Rnw %%%%%%%%%%%%
\documentclass{article}
\begin{document}
\SweaveOpts{concordance=TRUE}
\title{an Sweave inclusion test}
\author{Michele}
\maketitle
This is an example for the inclusion of RNW files and forward-inverse
search.
following is a chunk of sweave code:
<<>>=
n <- 5
for(i in 1:n){
print(i)
}
@
\section{text from an included file}
\SweaveInput{included.Rnw}
\end{document}
%%%%%%%%% Included.Rnw %%%%%%%%%%%%
% !Rnw root = Sweavetest.Rnw
this is some text included in an Rnw file
<<>>=
for(i in 1:3){
print('included')
}
@
On Jan 11, 2013, at 5:38 AM, Duncan Murdoch wrote:
On 13-01-10 4:54 PM, michele caseposta wrote:
Hi everybody, thanks for the replies. I might have not explained the problem completely. Duncan Mackay: Yes, I am already having a master file and separate Rnw files. Duncan Murdock: I am using patchDVI in the TexShop Sweave engine. Sync works flawlessly between the master file and the pdf produced by
pdflatex.
My problem is that I don't seem to be able to obtain sync between the
*included* Rnws and the pdf, either way.
The sweave engine is as follows: #!/bin/bash R CMD Sweave "$1" latexmk -pdf -silent -pdflatex=?pdflatex ?shell-escape
?synctex=1?"${1%.*}"
Rscript -e "library(?patchDVI?);patchSynctex(?${1%.*}.synctex.gz?)"
Funny thing is that the sync works in texworks, using the following
Rscript line
patchDVI::SweavePDF('$fullname',stylepath=FALSE)
I tried to mix and match configurations between texshop and texworks
but I had no luck
I just tried a simple example in TeXShop and it worked for me. My
Sweave engine is
#!/bin/tcsh # set path= ($path /usr/local/bin) Rscript -e "patchDVI::SweavePDF( '$1' )" So it seems to be work listing versions: On the Mac, I'm using R 2.15.0
patched, rev 59478, with patchDVI version 1.8.1584 (I just uploaded 1.9 to CRAN, by the way), TeXShop version 2.43.
It also works on Windows, where I have current releases of R and
patchDVI installed.
If you've got current versions of everything installed and it's still
not working, could you try putting together a small reproducible example?
Duncan Murdoch
On Jan 10, 2013, at 11:23 AM, Duncan Murdoch wrote:
On 13-01-09 9:09 PM, Duncan Murdoch wrote:
On 13-01-09 3:25 PM, michele caseposta wrote:
Hello everyone. I am in the process of writing a book in Latex with Texshop, on Mac. This book contains a lot of R code, hence the need to use Sweave. I was able to compile Rnw files, and to sync back and forth from the
pdf to the source Rnw.
My problem now is that the book is divided in Chapters, and every
chapter is in its own Rnw file.
I can compile them from the main one (book.Rnw) using the directive
\SweaveInput{chapter1.Rnw}
The problem stands in the fact that like this I am missing
synchronization between the pdf and the source Rnw. If part of text is in book.Rnw I can synchronize, but if the text is in one of the included files, it just doesn't work.
I am using the sweave engine found in the following webpage:
Has anybody succeeded in synchronizing with included Rnw files?
This is a problem addressed by my patchDVI package, available on R-forge. You have a main file (which can be .tex or .Rnw), and put
code
at the start of each .Rnw file to indicate where to find it. Then you just run Sweave on one of the chapters, and it automatically produces the full document. The sample document here:
includes an appendix describing how to set this up with TeXShop.
I just committed an update to the vignette in patchDVI giving a quick
version of the instructions for basic use. Version 1.8.1585 has the new vignette.
I should get around to pushing it to CRAN one of these days... Duncan Murdoch