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This is a terribly simple request, and I can't believe I haven't found the solution to this yet, but I've been searching for it far and wide without luck.

I have an .Rnw file loaded up in Emacs, I use M-n s to compile it. Everything works well, and it even opens an R buffer. Great. But that buffer is entirely useless: it doesn't contain the objects that I just sourced!

Example minimal .Rnw file:

\documentclass{article}
\begin{document}
<<>>=
  foo <- "bar"
@
\end{document}

Using M-n s, I now have a new R-buffer with a session loaded up, but:

> foo
Error: object 'foo' not found

That is disappointing. I would like to play around with the data interactively. How do I achieve that? I don't want to be sourcing the file line-by-line, or region-by-region with C-c C-c or something similar every time I change my code. Ideally, it should be just like RStudio's source function, that leaves me with a fully prepared R session.

I haven't tried this with sweave yet, only with knitr.

EDIT: the eval=TRUE chunk option does not seem to result in the correct behaviour.

Aleksandar Dimitrov
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2 Answers2

6

Open an interactive R session, and then call Sweave directly, I believe like this (untested though). knitr works in the same way, though you need to load the knitr library first.

> Sweave("yourfile.Rnw")

There is some potential for peril here, though. If you call Sweave in a session after doing other things, your code can use things previously in the workspace, thus making your results unreproducible.

Aaron left Stack Overflow
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  • That's a bit of a kludge, but at least it works. The correct knitr way to do it seems to be knitr::knit("file.Rnw"). For the sake of reproducibility, one should probably use `rm(list=ls())` first, so that old objects don't interfere. So I guess my only option is to bind this to some shortcut somehow… – Aleksandar Dimitrov Sep 07 '13 at 12:53
  • I see, didn't realize you were looking for an ESS key-binding for this. Glad to hear you found another answer that works for you. – Aaron left Stack Overflow Sep 08 '13 at 01:38
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This behaviour was recently changed in ESS. Now sweave and knitr are executed directly in the global environment, as if when you write it yourself at command line. So wait for a couple of more weeks till ESSv13.09 is out or use the development version.

Alternatively, you can also set ess-swv-processing-command to "%s(%s)" and you will get the same result, except automatic library loading.

For the record, knitr (in contrast to sweave) evaluates everything in it's own environment unless you instruct it otherwise.

[edit: Something went wrong. I don't see the correct .ess_weave any more. Probably some git commit messup again. So it is not fixed in 13.09. Fixing it now. Sorry.]

VitoshKa
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  • specifically, `knitr` evaluates code in `parent.frame()` by default, unless you `knit(..., envir = globalenv())` (sometimes `parent.frame()` is just `globalenv()`, and sometimes it is not) – Yihui Xie Sep 07 '13 at 18:28
  • Nice to hear that you've fixed this. Thanks! Along the lines of @Yihui's comment, I had a while ago fixed this for myself by editing `.ess_weave()` in `"$EMACS_HOME/site-lisp/ess/etc/ESSR.R"` to use `envir=parent.frame(2)` (as in `command(file, envir = parent.frame(2))`), rather than the `knit()`'s default `envir=parent.frame()`. (I'm just a **knitr** user these days, so am not sure how that edit plays with Sweave.) – Josh O'Brien Sep 07 '13 at 18:57
  • Thank you for your response! Setting `ess-swv-processing-command` didn't do the trick for me, but I'm looking into using `envir=globalenv()` right now. I don't think I want to switch to the development version, but I'll watch upstream ESS like a hawk :-) – Aleksandar Dimitrov Sep 07 '13 at 20:05