Re: R and babel on Windows problem

[John Hendy <jw.hendy@gmail.com>]

On Fri, Jul 6, 2012 at 12:12 PM, Nick Dokos <nicholas.dokos@hp.com> wrote:
> John Hendy <jw.hendy@gmail.com> wrote:
>
>> Any updates on this? Could someone provide a minimal example I could
>> try? Or verify that my steps above are correct. I'm not sure why it's
>> not triggering the step by step function execution described.
>>
>
> I had sent out a note about C-u C-M-x and what you should see in the
> echo area after that, but I don't think I've seen a reply: did you try
> that and did it work as expected?
>
> Either gmane is or I am being stupid right now and cannot find the message
> (maybe it never made it, but gmane cannot seem to find the thread at all
> right now), so I append a copy of that message.

Yes. I guess I didn't explicitly say, but I mentioned that I had
triggered something goofy by accident in my earlier hunt for edebug.
I'll walkthrough right now:
- Got to ob-R.el in emacs
- C-s to find org-babel-R-evaluate-external-process
- C-u C-M-x
- Minibuffer: "Edebug: org-babel-R-evaluate-external-process"
- Visit file test.org
- C-c C-c on the src block
- Well... of course it works now. Not sure what I was doing wrong before.

I pressed space continually until failure, then again to verify the
failing line. It's this one (line 313):

,---
| (output (org-babel-eval org-babel-R-command body))))
`---

When I run this line:

,---
| (org-babel-eval org-babel-R-command
`---

I get this in the minibuffer:

,---
| Result: "C:/Progra~1/R/R-2.15.0/bin/R"
`---

Should I be able to run this from the Windows cmd prompt successfully?
I think this is my problem. Even using tab completion to ensure the
path is correct, I get the same error message "The system cannot find
the path specified" when I run this from cmd!

I guess I honed in on my problem. I can run R from my Start Menu shortcut fine.

Update: I'm on 64bit and just now realized there's another set of R
cmds in ../R-2.15.0/bin/x64/. This is what I needed.

Now my problem is that using R along doesn't produce any output. With
the above modification, I get:

,---
| Fatal error: you must specify '--save', '--no-save' or '--vanilla'
`---

I'm quite close! If I add --no-save, I get exported results but they
include all of the R preamble text from when it starts. Here's my
block for reference:

#+begin_src R :results output org :exports results

x <- c(1:10)
summary(x)

#+end_src



Thanks,
John


>
> Nick
>
>
> John Hendy <jw.hendy@gmail.com> wrote:
> ...
>> >
>> > Oh, sorry: edebug is described in
>> >
>> > (info "(elisp) Edebug")
>> >
>> > The basics: visit ob-R.el, go to the org-babel-R-evaluate-external-process
>> > definition and press C-u C-M-x. Then do whatever you were doing to get the
>> > problem. It should stop at the function and you can single-step by pressing
>> > SPACE. At strategic points, you can evaluate things with "e".
>>
>> Eeks. Is the fact that I learned emacs only for org-mode showing. I
>> don't even know how to =(info "(elisp) Edebug")= -- do I put an =M-x=
>> in front of that? =M-x info= seems to bring me to a help page for
>> info!
>>
>
> You have to evaluate it somehow. If you are reading your mail in emacs,
> just place the cursor after the closing paren and press C-x C-e. If not,
> just go to emacs and "C-h i elisp RET i edebug RET" or equivalently,
> type ESC ESC : (info "(elisp) Edebug") RET. Underlying assumption: you
> have the Emacs Lisp info files installed.
>
>> Anyway... I just googled edebug and it says about the same as you did
>> (except for appending "eval-defun with a prefix argument" onto =C-u
>> C-M-x=.
>> - http://www.gnu.org/software/emacs/manual/html_node/elisp/Using-Edebug.html
>>
>> Anyway:
>> - Visited ob-R.el in emacs
>> - Found org-babel-R-evaluate-external-process
>> - Put the cursor on the line =(defun org-babel-R-evaluate-external-process=
>> - Did =M-x C-M-x= and the minibuffer echoed the name of the function
>
> C-u C-M-x please: and the echo area should say "Edebug:
> org-babel-R-evaluate-external-process" afterwards.
>
> Nick
>
>> - Visited my file, test.org and did =C-c C-c= on the R babel block
>> - Nothing different occurred; I just got "The system cannot find the
>> path specified"
>>
>> I tried the above again with regular 'ol org-babel-R-evaluate just in
>> case and had the same results.
>>
>> I'm clearly goofing something but have no idea what it is.
>>
>>
>> John
>>
>>
>> >
>> > If you mess it up (and you probably will a few times), no problem: just try
>> > again. And be patient!
>> >
>> > Good luck,
>> > Nick
>> >
>> >
>> >
>> >>
>> >> John
>> >>
>> >>
>> >> >
>> >> > Nick
>> >> >
>> >> >> Using =M-x R= works find. ESS is finding R. I successfully loaded a
>> >> >> .csv, ggplot2 and plotted.
>> >> >>
>> >> >>
>> >> >> John
>> >> >>
>> >> >> John
>> >> >>
>> >> >> >
>> >> >> > Nick
>> >> >> >
>> >> >>
>> >>
>>
>
>