Re: R and babel on Windows problem

[Nick Dokos <nicholas.dokos@hp.com>]

John Hendy <jw.hendy@gmail.com> wrote:

> 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.
> 

The reason that I sent out that note was that you mentioned pressing M-x
C-M-x (rather than C-u C-M-x) and getting the name of the function
echoed (without the "Edebug: " part), so I wanted to make sure that you
were DTRT here. Could that be what you were doing wrong? or was that a
typo on your part?

> 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))))
> `---
> 

Just fyi and to clarify some basic lisp: the form

     (org-babel-eval org-babel-R-command body)

says: evaluate the org-babel-eval function with arguments
org-babel-R-command and body (actually, those variables are evaluated
first and then the *values* are passed to the function). The evaluation
returns a result (a string in this case) which is assigned to the local
variable output for further processing (local, because this whole thing
is part of a let-form which is not shown in your snippet).

I.e. a function call in lisp always looks like this:

     (<func> <arg1> <arg2> ....)

> 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"
> `---
> 

I presume you just typed "e" when the cursor was after the variable:
that just evaluates the variable. If you press SPACE then the cursor
would advance to after the ``body'' variable (on the closing paren) and
an "e" would evaluate *that* variable.  After another SPACE, the cursor
would be *after* the closing paren and an "e" would evaluate the function
call and you would see the result, i.e. what would be assigned to
``output''.

> 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
> 

OK, at this point I will "exit, stage left, chased by a bear", since
both Windoze and R are within my areas of almost complete ignorance :-)

Nick

> 
> 
> 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
> >> >> >> >
> >> >> >>
> >> >>
> >>
> >
> >
>