From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Hendy Subject: Re: R and babel on Windows problem Date: Fri, 6 Jul 2012 12:46:44 -0500 Message-ID: References: <87ipea3rfq.fsf@Rainer.invalid> <18442.1340998640@alphaville> <18840.1341001001@alphaville> <31262.1341264369@alphaville> <21447.1341594758@alphaville> Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Return-path: Received: from eggs.gnu.org ([208.118.235.92]:51914) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1SnCcD-0003jS-Si for emacs-orgmode@gnu.org; Fri, 06 Jul 2012 13:46:51 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1SnCcB-0005Ha-G9 for emacs-orgmode@gnu.org; Fri, 06 Jul 2012 13:46:49 -0400 Received: from mail-bk0-f41.google.com ([209.85.214.41]:51110) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1SnCcB-0005HJ-3H for emacs-orgmode@gnu.org; Fri, 06 Jul 2012 13:46:47 -0400 Received: by bkcjc3 with SMTP id jc3so6286500bkc.0 for ; Fri, 06 Jul 2012 10:46:44 -0700 (PDT) In-Reply-To: <21447.1341594758@alphaville> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: nicholas.dokos@hp.com Cc: Achim Gratz , emacs-orgmode@gnu.org On Fri, Jul 6, 2012 at 12:12 PM, Nick Dokos wrote: > John Hendy 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 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 >> >> >> > >> >> >> >> >> >> > >