From mboxrd@z Thu Jan 1 00:00:00 1970 From: Riccardo Romoli Subject: Generating plot with org-babel-R Date: Sat, 4 Feb 2012 23:52:28 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=f46d041a438ea0094b04b82b48b6 Return-path: Received: from eggs.gnu.org ([140.186.70.92]:38558) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RtoT9-0008JZ-0h for emacs-orgmode@gnu.org; Sat, 04 Feb 2012 17:52:31 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RtoT7-0000ra-NH for emacs-orgmode@gnu.org; Sat, 04 Feb 2012 17:52:30 -0500 Received: from mail-pz0-f41.google.com ([209.85.210.41]:52118) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RtoT7-0000rW-Gg for emacs-orgmode@gnu.org; Sat, 04 Feb 2012 17:52:29 -0500 Received: by dadv6 with SMTP id v6so4232075dad.0 for ; Sat, 04 Feb 2012 14:52:28 -0800 (PST) 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: emacs-orgmode@gnu.org --f46d041a438ea0094b04b82b48b6 Content-Type: text/plain; charset=ISO-8859-1 Hi, I'm trying to generate some figure with R, into an org session. Firstly I use the code in the org site. The problem is that the code do not generate any figure. This is the code: #+TITLE:Test #+AUTHOR: Your Name #+EMAIL: your-email@server.com #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes * Example of Org-Babel for R Literate Programming ** R text output A simple summary. #+begin_src R x <- rnorm(10) summary(x) #+end_src ** R graphics output Note we use the object =x= generated in previous code block, thanks to the header option =:session *R*=. The output graphics file is =a.png=. #+begin_src R :file a.png y <- rnorm(10) plot(x, y) #+end_src Same plot with larger dimension: #+begin_src R :file b.png :width 800 :height 800 plot(x, y) #+end_src Where do I wrong? Best Riccardo --f46d041a438ea0094b04b82b48b6 Content-Type: text/html; charset=ISO-8859-1 Hi, I'm trying to generate some figure with R, into an org session. Firstly I use the code in the org site. The problem is that the code do not generate any figure.

This is the code:

#+TITLE:Test 
#+AUTHOR: Your Name
#+EMAIL: your-email@server.com
#+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes 

* Example of Org-Babel for R Literate Programming
** R text output
A simple summary. 
#+begin_src R 
  x <- rnorm(10)
  summary(x)
#+end_src

** R graphics output
Note we use the object =x= generated in previous code block, thanks to
the header option =:session *R*=.  The output graphics file is
=a.png=. 

#+begin_src R  :file a.png
  y <- rnorm(10)
  plot(x, y)
#+end_src

Same plot with larger dimension:

#+begin_src R  :file b.png :width 800 :height 800
  plot(x, y)
#+end_src

Where do I wrong?

Best
Riccardo
--f46d041a438ea0094b04b82b48b6-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: tsd@tsdye.com (Thomas S. Dye) Subject: Re: Generating plot with org-babel-R Date: Sat, 04 Feb 2012 13:37:01 -1000 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from eggs.gnu.org ([140.186.70.92]:50445) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RtpA6-0004m5-JZ for emacs-orgmode@gnu.org; Sat, 04 Feb 2012 18:36:55 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RtpA5-0000ej-4p for emacs-orgmode@gnu.org; Sat, 04 Feb 2012 18:36:54 -0500 Received: from oproxy8-pub.bluehost.com ([69.89.22.20]:50078) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1RtpA4-0000eb-UP for emacs-orgmode@gnu.org; Sat, 04 Feb 2012 18:36:53 -0500 In-Reply-To: (Riccardo Romoli's message of "Sat, 4 Feb 2012 23:52:28 +0100") 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: Riccardo Romoli Cc: emacs-orgmode@gnu.org Hi Riccardo, This code appears to be outdated. I don't recall this code on the org site. Could you send a URL? All the best, Tom Riccardo Romoli writes: > Hi, I'm trying to generate some figure with R, into an org session. Firstly > I use the code in the org site. The problem is that the code do not > generate any figure. > > This is the code: > > #+TITLE:Test > #+AUTHOR: Your Name > #+EMAIL: your-email@server.com > #+BABEL: :session *R* :cache yes :results output graphics :exports > both :tangle yes > > * Example of Org-Babel for R Literate Programming > ** R text output > A simple summary. > #+begin_src R > x <- rnorm(10) > summary(x) > #+end_src > > ** R graphics output > Note we use the object =x= generated in previous code block, thanks to > the header option =:session *R*=. The output graphics file is > =a.png=. > > #+begin_src R :file a.png > y <- rnorm(10) > plot(x, y) > #+end_src > > Same plot with larger dimension: > > #+begin_src R :file b.png :width 800 :height 800 > plot(x, y) > #+end_src > > > Where do I wrong? > > Best > Riccardo > Hi, I'm trying to generate some figure with R, into an org session. Firstly I use the code in the org site. The problem is that the code do not generate any figure. This is the code: > #+TITLE:Test > #+AUTHOR: Your Name > #+EMAIL: mailto:your-email@server.com > #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes > > * Example of Org-Babel for R Literate Programming > ** R text output > A simple summary. > #+begin_src R > x <- rnorm(10) > summary(x) > #+end_src > > ** R graphics output > Note we use the object =x= generated in previous code block, thanks to > the header option =:session *R*=. The output graphics file is > =a.png=. > > #+begin_src R :file a.png > y <- rnorm(10) > plot(x, y) > #+end_src > > Same plot with larger dimension: > > #+begin_src R :file b.png :width 800 :height 800 > plot(x, y) > #+end_src > Where do I wrong?BestRiccardo -- Thomas S. Dye http://www.tsdye.com From mboxrd@z Thu Jan 1 00:00:00 1970 From: Riccardo Romoli Subject: Re: Generating plot with org-babel-R Date: Sun, 5 Feb 2012 12:08:48 +0100 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=e89a8f503756f3228f04b83591af Return-path: Received: from eggs.gnu.org ([140.186.70.92]:36209) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rtzxj-0003z2-FX for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 06:08:52 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rtzxi-00010U-0r for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 06:08:51 -0500 Received: from mail-pw0-f41.google.com ([209.85.160.41]:51166) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rtzxh-00010H-M0 for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 06:08:49 -0500 Received: by pbaa12 with SMTP id a12so4681537pba.0 for ; Sun, 05 Feb 2012 03:08:48 -0800 (PST) In-Reply-To: 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: "Thomas S. Dye" Cc: emacs-orgmode@gnu.org --e89a8f503756f3228f04b83591af Content-Type: text/plain; charset=ISO-8859-1 Hi, this is the URL: http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html Best R 2012/2/5 Thomas S. Dye > Hi Riccardo, > > This code appears to be outdated. I don't recall this code on the org > site. Could you send a URL? > > All the best, > Tom > > Riccardo Romoli writes: > > > Hi, I'm trying to generate some figure with R, into an org session. > Firstly > > I use the code in the org site. The problem is that the code do not > > generate any figure. > > > > This is the code: > > > > #+TITLE:Test > > #+AUTHOR: Your Name > > #+EMAIL: your-email@server.com > > #+BABEL: :session *R* :cache yes :results output graphics :exports > > both :tangle yes > > > > * Example of Org-Babel for R Literate Programming > > ** R text output > > A simple summary. > > #+begin_src R > > x <- rnorm(10) > > summary(x) > > #+end_src > > > > ** R graphics output > > Note we use the object =x= generated in previous code block, thanks to > > the header option =:session *R*=. The output graphics file is > > =a.png=. > > > > #+begin_src R :file a.png > > y <- rnorm(10) > > plot(x, y) > > #+end_src > > > > Same plot with larger dimension: > > > > #+begin_src R :file b.png :width 800 :height 800 > > plot(x, y) > > #+end_src > > > > > > Where do I wrong? > > > > Best > > Riccardo > > Hi, I'm trying to generate some figure with R, into an org session. > Firstly I use the code in the org site. The problem is that the code do not > generate any figure. This is the code: > > #+TITLE:Test > > #+AUTHOR: Your Name > > #+EMAIL: mailto:your-email@server.com > > #+BABEL: :session *R* :cache yes :results output graphics :exports both > :tangle yes > > > > * Example of Org-Babel for R Literate Programming > > ** R text output > > A simple summary. > > #+begin_src R > > x <- rnorm(10) > > summary(x) > > #+end_src > > > > ** R graphics output > > Note we use the object =x= generated in previous code block, thanks to > > the header option =:session *R*=. The output graphics file is > > =a.png=. > > > > #+begin_src R :file a.png > > y <- rnorm(10) > > plot(x, y) > > #+end_src > > > > Same plot with larger dimension: > > > > #+begin_src R :file b.png :width 800 :height 800 > > plot(x, y) > > #+end_src > > Where do I wrong?BestRiccardo > > -- > Thomas S. Dye > http://www.tsdye.com > --e89a8f503756f3228f04b83591af Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, this is the URL:

http://orgmode.org/worg/org-contrib/= babel/how-to-use-Org-Babel-for-R.html

Best
R

2012/2/5 Thomas S. Dye <tsd@tsdye.com>
Hi Ricca= rdo,

This code appears to be outdated. =A0I don't recall this code on the or= g
site. =A0Could you send a URL?

All the best,
Tom

Riccardo Romoli <ric.romoli@gmai= l.com> writes:

> Hi, I'm trying to generate some figure with R, into an org session= . Firstly
> I use the code in the org site. The problem is that the code do not > generate any figure.
>
> This is the code:
>
> #+TITLE:Test
> #+AUTHOR: Your Name
> #+EMAIL: your-email@server.co= m
> #+BABEL: :session *R* :cache yes :results output graphics :exports
> both :tangle yes
>
> * Example of Org-Babel for R Literate Programming
> ** R text output
> A simple summary.
> #+begin_src R
> =A0 x <- rnorm(10)
> =A0 summary(x)
> #+end_src
>
> ** R graphics output
> Note we use the object =3Dx=3D generated in previous code block, thank= s to
> the header option =3D:session *R*=3D. =A0The output graphics file is > =3Da.png=3D.
>
> #+begin_src R =A0:file a.png
> =A0 y <- rnorm(10)
> =A0 plot(x, y)
> #+end_src
>
> Same plot with larger dimension:
>
> #+begin_src R =A0:file b.png :width 800 :height 800
> =A0 plot(x, y)
> #+end_src
>
>
> Where do I wrong?
>
> Best
> Riccardo
> Hi, I&#39;m trying to generate some figure with R, int= o an org session. Firstly I use the code in the org site. The problem is th= at the code do not generate any figure. This is the code:
> #+TITLE:Test
> #+AUTHOR: Your Name
> #+EMAIL: mailto:your-em= ail@server.com
> #+BABEL: :session *R* :cache y= es :results output graphics :exports both :tangle yes
>
> * Example of Org-Babel for R Literate Programming
> ** R text output
> A simple summary.
> #+begin_src R
> =A0 x <- rnorm(10)
> =A0 summary(x)
> #+end_src
>
> ** R graphics output
> Note we use the object =3Dx=3D generated in previous code block, thank= s to
> the header option =3D:session *R*=3D. =A0The output graphics file is > =3Da.png=3D.
>
> #+begin_src R =A0:file a.png
> =A0 y <- rnorm(10)
> =A0 plot(x, y)
> #+end_src
>
> Same plot with larger dimension:
>
> #+begin_src R =A0:file b.png :width 800 :height 800
> =A0 plot(x, y)
> #+end_src
> Where do I wrong?BestRiccardo

--
Thomas S. Dye
http://www.tsdye.com=

--e89a8f503756f3228f04b83591af-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: tsd@tsdye.com (Thomas S. Dye) Subject: Re: Generating plot with org-babel-R Date: Sun, 05 Feb 2012 06:45:36 -1000 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:36724) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ru5DW-0006qi-8E for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 11:45:33 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Ru5DU-0005Qd-6l for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 11:45:30 -0500 Received: from oproxy8-pub.bluehost.com ([69.89.22.20]:41636) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1Ru5DT-0005QE-Vz for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 11:45:28 -0500 In-Reply-To: (Riccardo Romoli's message of "Sun, 5 Feb 2012 12:08:48 +0100") 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: Riccardo Romoli Cc: emacs-orgmode@gnu.org Hi Riccardo, Thanks for the URL. Org mode has evolved since this article was written. It should probably be revised or taken off Worg. I've copied Eric Schulte, who is better able than me to determine the correct course of action here. In the meantime, an up-to-date description of how Org mode can be used to write literate programs has appeared in the Journal of Statistical Software. You can find it here: http://www.jstatsoft.org/v46/i03 Perhaps you could use the examples in the JSS article to get started? If these don't work for you, or if they raise questions that are difficult to answer, please do come back to the list with your queries. All the best, Tom Riccardo Romoli writes: > Hi, this is the URL: > > http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html > > Best > R > > 2012/2/5 Thomas S. Dye > >> Hi Riccardo, >> >> This code appears to be outdated. I don't recall this code on the org >> site. Could you send a URL? >> >> All the best, >> Tom >> >> Riccardo Romoli writes: >> >> > Hi, I'm trying to generate some figure with R, into an org session. >> Firstly >> > I use the code in the org site. The problem is that the code do not >> > generate any figure. >> > >> > This is the code: >> > >> > #+TITLE:Test >> > #+AUTHOR: Your Name >> > #+EMAIL: your-email@server.com >> > #+BABEL: :session *R* :cache yes :results output graphics :exports >> > both :tangle yes >> > >> > * Example of Org-Babel for R Literate Programming >> > ** R text output >> > A simple summary. >> > #+begin_src R >> > x <- rnorm(10) >> > summary(x) >> > #+end_src >> > >> > ** R graphics output >> > Note we use the object =3Dx=3D generated in previous code block, thank= s to >> > the header option =3D:session *R*=3D. The output graphics file is >> > =3Da.png=3D. >> > >> > #+begin_src R :file a.png >> > y <- rnorm(10) >> > plot(x, y) >> > #+end_src >> > >> > Same plot with larger dimension: >> > >> > #+begin_src R :file b.png :width 800 :height 800 >> > plot(x, y) >> > #+end_src >> > >> > >> > Where do I wrong? >> > >> > Best >> > Riccardo >> > Hi, I'm trying to generate some figure with R, into an org session. >> Firstly I use the code in the org site. The problem is that the code do = not >> generate any figure. This is the code: >> > #+TITLE:Test >> > #+AUTHOR: Your Name >> > #+EMAIL: mailto:your-email@server.com >> > #+BABEL: :session *R* :cache yes :results output graphics :exports both >> :tangle yes >> > >> > * Example of Org-Babel for R Literate Programming >> > ** R text output >> > A simple summary. >> > #+begin_src R >> > x <- rnorm(10) >> > summary(x) >> > #+end_src >> > >> > ** R graphics output >> > Note we use the object =3Dx=3D generated in previous code block, thank= s to >> > the header option =3D:session *R*=3D. The output graphics file is >> > =3Da.png=3D. >> > >> > #+begin_src R :file a.png >> > y <- rnorm(10) >> > plot(x, y) >> > #+end_src >> > >> > Same plot with larger dimension: >> > >> > #+begin_src R :file b.png :width 800 :height 800 >> > plot(x, y) >> > #+end_src >> > Where do I wrong?BestRiccardo >> >> -- >> Thomas S. Dye >> http://www.tsdye.com >> > Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to-use-= Org-Babel-for-R.htmlBestR > 2012/2/5 Thomas S. Dye Hi = Riccardo, > > > This code appears to be outdated. =C2=A0I don't recall this code on t= he org > site. =C2=A0Could you send a URL? > > All the best, > Tom > > Riccardo Romoli writes: > >> Hi, I'm trying to generate some figure with R, into an org session. = Firstly >> I use the code in the org site. The problem is that the code do not >> generate any figure. >> >> This is the code: >> >> #+TITLE:Test >> #+AUTHOR: Your Name >> #+EMAIL: mailto:your-email@server.com >> #+BABEL: :session *R* :cache yes :results output graphics :exports >> both :tangle yes >> >> * Example of Org-Babel for R Literate Programming >> ** R text output >> A simple summary. >> #+begin_src R >> =C2=A0 x <- rnorm(10) >> =C2=A0 summary(x) >> #+end_src >> >> ** R graphics output >> Note we use the object =3Dx=3D generated in previous code block, thanks = to >> the header option =3D:session *R*=3D. =C2=A0The output graphics file is >> =3Da.png=3D. >> >> #+begin_src R =C2=A0:file a.png >> =C2=A0 y <- rnorm(10) >> =C2=A0 plot(x, y) >> #+end_src >> >> Same plot with larger dimension: >> >> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >> =C2=A0 plot(x, y) >> #+end_src >> >> >> Where do I wrong? >> >> Best >> Riccardo >> Hi, I'm trying to generate some figure with R, into an org session. = Firstly I use the code in the org site. The problem is that the code do not= generate any figure. This is the code: >> #+TITLE:Test >> #+AUTHOR: Your Name >> #+EMAIL: mailto:mailto:your-email@server.com >> #+BABEL: :session *R* :cache yes :results output graphics :exports both = :tangle yes >> >> * Example of Org-Babel for R Literate Programming >> ** R text output >> A simple summary. >> #+begin_src R >> =C2=A0 x <- rnorm(10) >> =C2=A0 summary(x) >> #+end_src >> >> ** R graphics output >> Note we use the object =3Dx=3D generated in previous code block, thanks = to >> the header option =3D:session *R*=3D. =C2=A0The output graphics file is >> =3Da.png=3D. >> >> #+begin_src R =C2=A0:file a.png >> =C2=A0 y <- rnorm(10) >> =C2=A0 plot(x, y) >> #+end_src >> >> Same plot with larger dimension: >> >> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >> =C2=A0 plot(x, y) >> #+end_src >> Where do I wrong?BestRiccardo > > -- > Thomas S. Dye > http://www.tsdye.com > --=20 Thomas S. Dye http://www.tsdye.com From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Updating the Babel section of Worg Was: Generating plot with org-babel-R Date: Sun, 05 Feb 2012 12:29:29 -0700 Message-ID: <87mx8xyt7q.fsf_-_@gmx.com> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:41561) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ru7mi-0002Lg-4b for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 14:30:01 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Ru7mg-0006WU-CK for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 14:30:00 -0500 Received: from mailout-us.gmx.com ([74.208.5.67]:49034 helo=mailout-us.mail.com) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1Ru7mg-0006W8-5Z for emacs-orgmode@gnu.org; Sun, 05 Feb 2012 14:29:58 -0500 In-Reply-To: (Thomas S. Dye's message of "Sun, 05 Feb 2012 06:45:36 -1000") 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: "Thomas S. Dye" Cc: emacs-orgmode@gnu.org, Riccardo Romoli Thanks for raising this point. The bulk of the content in the Babel portion of worg is fairly old, predating the syntax standardization efforts this fall. I've just pushed some minor updates to the main babel pages, but updating the language-specific tutorials and the individual use cases will be a much larger effort. I'm not sure how to proceed. One option would be to go through and add a [uses deprecated syntax] tag to the top of each such page, which could be removed after the page has been checked and possibly updated to ensure consistency with the latest syntax. Given that the Babel syntax will not be changing significantly moving forward now would be a good time to do such a review. Ideally this could be completed before the release of Emacs 24 in a couple of months. Any other ideas for update/reorganization or volunteers? Cheers, tsd@tsdye.com (Thomas S. Dye) writes: > Hi Riccardo, > > Thanks for the URL. Org mode has evolved since this article was > written. It should probably be revised or taken off Worg. I've copied > Eric Schulte, who is better able than me to determine the correct course > of action here. > > In the meantime, an up-to-date description of how Org mode can be used > to write literate programs has appeared in the Journal of Statistical > Software. You can find it here: http://www.jstatsoft.org/v46/i03 > > Perhaps you could use the examples in the JSS article to get started? > If these don't work for you, or if they raise questions that are difficult > to answer, please do come back to the list with your queries. > > All the best, > Tom > > Riccardo Romoli writes: > >> Hi, this is the URL: >> >> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html >> >> Best >> R >> >> 2012/2/5 Thomas S. Dye >> >>> Hi Riccardo, >>> >>> This code appears to be outdated. I don't recall this code on the org >>> site. Could you send a URL? >>> >>> All the best, >>> Tom >>> >>> Riccardo Romoli writes: >>> >>> > Hi, I'm trying to generate some figure with R, into an org session. >>> Firstly >>> > I use the code in the org site. The problem is that the code do not >>> > generate any figure. >>> > >>> > This is the code: >>> > >>> > #+TITLE:Test >>> > #+AUTHOR: Your Name >>> > #+EMAIL: your-email@server.com >>> > #+BABEL: :session *R* :cache yes :results output graphics :exports >>> > both :tangle yes >>> > >>> > * Example of Org-Babel for R Literate Programming >>> > ** R text output >>> > A simple summary. >>> > #+begin_src R >>> > x <- rnorm(10) >>> > summary(x) >>> > #+end_src >>> > >>> > ** R graphics output >>> > Note we use the object =3Dx=3D generated in previous code block, than= ks to >>> > the header option =3D:session *R*=3D. The output graphics file is >>> > =3Da.png=3D. >>> > >>> > #+begin_src R :file a.png >>> > y <- rnorm(10) >>> > plot(x, y) >>> > #+end_src >>> > >>> > Same plot with larger dimension: >>> > >>> > #+begin_src R :file b.png :width 800 :height 800 >>> > plot(x, y) >>> > #+end_src >>> > >>> > >>> > Where do I wrong? >>> > >>> > Best >>> > Riccardo >>> > Hi, I'm trying to generate some figure with R, into an org sessio= n. >>> Firstly I use the code in the org site. The problem is that the code do= not >>> generate any figure. This is the code: >>> > #+TITLE:Test >>> > #+AUTHOR: Your Name >>> > #+EMAIL: mailto:your-email@server.com >>> > #+BABEL: :session *R* :cache yes :results output graphics :exports bo= th >>> :tangle yes >>> > >>> > * Example of Org-Babel for R Literate Programming >>> > ** R text output >>> > A simple summary. >>> > #+begin_src R >>> > x <- rnorm(10) >>> > summary(x) >>> > #+end_src >>> > >>> > ** R graphics output >>> > Note we use the object =3Dx=3D generated in previous code block, than= ks to >>> > the header option =3D:session *R*=3D. The output graphics file is >>> > =3Da.png=3D. >>> > >>> > #+begin_src R :file a.png >>> > y <- rnorm(10) >>> > plot(x, y) >>> > #+end_src >>> > >>> > Same plot with larger dimension: >>> > >>> > #+begin_src R :file b.png :width 800 :height 800 >>> > plot(x, y) >>> > #+end_src >>> > Where do I wrong?BestRiccardo >>> >>> -- >>> Thomas S. Dye >>> http://www.tsdye.com >>> >> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to-use= -Org-Babel-for-R.htmlBestR >> 2012/2/5 Thomas S. Dye Hi= Riccardo, >> >> >> This code appears to be outdated. =C2=A0I don't recall this code on = the org >> site. =C2=A0Could you send a URL? >> >> All the best, >> Tom >> >> Riccardo Romoli writes: >> >>> Hi, I'm trying to generate some figure with R, into an org session.= Firstly >>> I use the code in the org site. The problem is that the code do not >>> generate any figure. >>> >>> This is the code: >>> >>> #+TITLE:Test >>> #+AUTHOR: Your Name >>> #+EMAIL: mailto:your-email@server.com >>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>> both :tangle yes >>> >>> * Example of Org-Babel for R Literate Programming >>> ** R text output >>> A simple summary. >>> #+begin_src R >>> =C2=A0 x <- rnorm(10) >>> =C2=A0 summary(x) >>> #+end_src >>> >>> ** R graphics output >>> Note we use the object =3Dx=3D generated in previous code block, thanks= to >>> the header option =3D:session *R*=3D. =C2=A0The output graphics file is >>> =3Da.png=3D. >>> >>> #+begin_src R =C2=A0:file a.png >>> =C2=A0 y <- rnorm(10) >>> =C2=A0 plot(x, y) >>> #+end_src >>> >>> Same plot with larger dimension: >>> >>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>> =C2=A0 plot(x, y) >>> #+end_src >>> >>> >>> Where do I wrong? >>> >>> Best >>> Riccardo >>> Hi, I'm trying to generate some figure with R, into an org >>> session. Firstly I use the code in the org site. The problem is >>> that the code do not generate any figure. This is the code: >>> #+TITLE:Test >>> #+AUTHOR: Your Name >>> #+EMAIL: mailto:mailto:your-email@server.com >>> #+BABEL: :session *R* :cache yes :results output graphics :exports both= :tangle yes >>> >>> * Example of Org-Babel for R Literate Programming >>> ** R text output >>> A simple summary. >>> #+begin_src R >>> =C2=A0 x <- rnorm(10) >>> =C2=A0 summary(x) >>> #+end_src >>> >>> ** R graphics output >>> Note we use the object =3Dx=3D generated in previous code block, thanks= to >>> the header option =3D:session *R*=3D. =C2=A0The output graphics file is >>> =3Da.png=3D. >>> >>> #+begin_src R =C2=A0:file a.png >>> =C2=A0 y <- rnorm(10) >>> =C2=A0 plot(x, y) >>> #+end_src >>> >>> Same plot with larger dimension: >>> >>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>> =C2=A0 plot(x, y) >>> #+end_src >>> Where do I wrong?BestRiccardo >> >> -- >> Thomas S. Dye >> http://www.tsdye.com >> --=20 Eric Schulte http://cs.unm.edu/~eschulte/ From mboxrd@z Thu Jan 1 00:00:00 1970 From: tsd@tsdye.com (Thomas S. Dye) Subject: Re: Updating the Babel section of Worg Was: Generating plot with org-babel-R Date: Sun, 05 Feb 2012 19:43:25 -1000 Message-ID: References: <87mx8xyt7q.fsf_-_@gmx.com> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:59269) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RuHMb-0002ux-Jn for emacs-orgmode@gnu.org; Mon, 06 Feb 2012 00:43:42 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RuHMV-0002tB-Go for emacs-orgmode@gnu.org; Mon, 06 Feb 2012 00:43:41 -0500 Received: from oproxy4-pub.bluehost.com ([69.89.21.11]:48720) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1RuHMU-0002sk-W2 for emacs-orgmode@gnu.org; Mon, 06 Feb 2012 00:43:35 -0500 In-Reply-To: <87mx8xyt7q.fsf_-_@gmx.com> (Eric Schulte's message of "Sun, 05 Feb 2012 12:29:29 -0700") 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: Eric Schulte Cc: emacs-orgmode@gnu.org, Riccardo Romoli Hi Eric, Yes, this is overdue. I think your plan is a good one. Perhaps a few of the individual use cases could be moved to FIXME, instead? I'm thinking here of Feiming Chen's R setup and some of my contributions when I was experimenting writing LaTeX inside source code blocks. The authors could resurrect these as they see fit. Hopefully, others will contribute use examples. My sense from reading the list is there are many interesting ones. I'd like it if Org mode users designed a template for the language specific pages. Currently, these seem to me a mixed bag and it would be good to regularize them. It would also be nice to have one for each of the supported languages. There are 11 language specific pages now, which leaves quite a few languages under-documented. I'll be happy to work on this as I can. All the best, Tom Eric Schulte writes: > Thanks for raising this point. The bulk of the content in the Babel > portion of worg is fairly old, predating the syntax standardization > efforts this fall. I've just pushed some minor updates to the main > babel pages, but updating the language-specific tutorials and the > individual use cases will be a much larger effort. > > I'm not sure how to proceed. One option would be to go through and add > a [uses deprecated syntax] tag to the top of each such page, which could > be removed after the page has been checked and possibly updated to > ensure consistency with the latest syntax. > > Given that the Babel syntax will not be changing significantly moving > forward now would be a good time to do such a review. Ideally this > could be completed before the release of Emacs 24 in a couple of months. > > Any other ideas for update/reorganization or volunteers? > > Cheers, > > tsd@tsdye.com (Thomas S. Dye) writes: > >> Hi Riccardo, >> >> Thanks for the URL. Org mode has evolved since this article was >> written. It should probably be revised or taken off Worg. I've copied >> Eric Schulte, who is better able than me to determine the correct course >> of action here. >> >> In the meantime, an up-to-date description of how Org mode can be used >> to write literate programs has appeared in the Journal of Statistical >> Software. You can find it here: http://www.jstatsoft.org/v46/i03 >> >> Perhaps you could use the examples in the JSS article to get started? >> If these don't work for you, or if they raise questions that are difficu= lt >> to answer, please do come back to the list with your queries. >> >> All the best, >> Tom >> >> Riccardo Romoli writes: >> >>> Hi, this is the URL: >>> >>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.ht= ml >>> >>> Best >>> R >>> >>> 2012/2/5 Thomas S. Dye >>> >>>> Hi Riccardo, >>>> >>>> This code appears to be outdated. I don't recall this code on the org >>>> site. Could you send a URL? >>>> >>>> All the best, >>>> Tom >>>> >>>> Riccardo Romoli writes: >>>> >>>> > Hi, I'm trying to generate some figure with R, into an org session. >>>> Firstly >>>> > I use the code in the org site. The problem is that the code do not >>>> > generate any figure. >>>> > >>>> > This is the code: >>>> > >>>> > #+TITLE:Test >>>> > #+AUTHOR: Your Name >>>> > #+EMAIL: your-email@server.com >>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports >>>> > both :tangle yes >>>> > >>>> > * Example of Org-Babel for R Literate Programming >>>> > ** R text output >>>> > A simple summary. >>>> > #+begin_src R >>>> > x <- rnorm(10) >>>> > summary(x) >>>> > #+end_src >>>> > >>>> > ** R graphics output >>>> > Note we use the object =3Dx=3D generated in previous code block, tha= nks to >>>> > the header option =3D:session *R*=3D. The output graphics file is >>>> > =3Da.png=3D. >>>> > >>>> > #+begin_src R :file a.png >>>> > y <- rnorm(10) >>>> > plot(x, y) >>>> > #+end_src >>>> > >>>> > Same plot with larger dimension: >>>> > >>>> > #+begin_src R :file b.png :width 800 :height 800 >>>> > plot(x, y) >>>> > #+end_src >>>> > >>>> > >>>> > Where do I wrong? >>>> > >>>> > Best >>>> > Riccardo >>>> > Hi, I'm trying to generate some figure with R, into an org sessi= on. >>>> Firstly I use the code in the org site. The problem is that the code d= o not >>>> generate any figure. This is the code: >>>> > #+TITLE:Test >>>> > #+AUTHOR: Your Name >>>> > #+EMAIL: mailto:your-email@server.com >>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports b= oth >>>> :tangle yes >>>> > >>>> > * Example of Org-Babel for R Literate Programming >>>> > ** R text output >>>> > A simple summary. >>>> > #+begin_src R >>>> > x <- rnorm(10) >>>> > summary(x) >>>> > #+end_src >>>> > >>>> > ** R graphics output >>>> > Note we use the object =3Dx=3D generated in previous code block, tha= nks to >>>> > the header option =3D:session *R*=3D. The output graphics file is >>>> > =3Da.png=3D. >>>> > >>>> > #+begin_src R :file a.png >>>> > y <- rnorm(10) >>>> > plot(x, y) >>>> > #+end_src >>>> > >>>> > Same plot with larger dimension: >>>> > >>>> > #+begin_src R :file b.png :width 800 :height 800 >>>> > plot(x, y) >>>> > #+end_src >>>> > Where do I wrong?BestRiccardo >>>> >>>> -- >>>> Thomas S. Dye >>>> http://www.tsdye.com >>>> >>> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to-us= e-Org-Babel-for-R.htmlBestR >>> 2012/2/5 Thomas S. Dye H= i Riccardo, >>> >>> >>> This code appears to be outdated. =C2=A0I don't recall this code on= the org >>> site. =C2=A0Could you send a URL? >>> >>> All the best, >>> Tom >>> >>> Riccardo Romoli writes: >>> >>>> Hi, I'm trying to generate some figure with R, into an org session= . Firstly >>>> I use the code in the org site. The problem is that the code do not >>>> generate any figure. >>>> >>>> This is the code: >>>> >>>> #+TITLE:Test >>>> #+AUTHOR: Your Name >>>> #+EMAIL: mailto:your-email@server.com >>>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>>> both :tangle yes >>>> >>>> * Example of Org-Babel for R Literate Programming >>>> ** R text output >>>> A simple summary. >>>> #+begin_src R >>>> =C2=A0 x <- rnorm(10) >>>> =C2=A0 summary(x) >>>> #+end_src >>>> >>>> ** R graphics output >>>> Note we use the object =3Dx=3D generated in previous code block, thank= s to >>>> the header option =3D:session *R*=3D. =C2=A0The output graphics file is >>>> =3Da.png=3D. >>>> >>>> #+begin_src R =C2=A0:file a.png >>>> =C2=A0 y <- rnorm(10) >>>> =C2=A0 plot(x, y) >>>> #+end_src >>>> >>>> Same plot with larger dimension: >>>> >>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>> =C2=A0 plot(x, y) >>>> #+end_src >>>> >>>> >>>> Where do I wrong? >>>> >>>> Best >>>> Riccardo >>>> Hi, I'm trying to generate some figure with R, into an org >>>> session. Firstly I use the code in the org site. The problem is >>>> that the code do not generate any figure. This is the code: >>>> #+TITLE:Test >>>> #+AUTHOR: Your Name >>>> #+EMAIL: mailto:mailto:your-email@server.com >>>> #+BABEL: :session *R* :cache yes :results output graphics :exports bot= h :tangle yes >>>> >>>> * Example of Org-Babel for R Literate Programming >>>> ** R text output >>>> A simple summary. >>>> #+begin_src R >>>> =C2=A0 x <- rnorm(10) >>>> =C2=A0 summary(x) >>>> #+end_src >>>> >>>> ** R graphics output >>>> Note we use the object =3Dx=3D generated in previous code block, thank= s to >>>> the header option =3D:session *R*=3D. =C2=A0The output graphics file is >>>> =3Da.png=3D. >>>> >>>> #+begin_src R =C2=A0:file a.png >>>> =C2=A0 y <- rnorm(10) >>>> =C2=A0 plot(x, y) >>>> #+end_src >>>> >>>> Same plot with larger dimension: >>>> >>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>> =C2=A0 plot(x, y) >>>> #+end_src >>>> Where do I wrong?BestRiccardo >>> >>> -- >>> Thomas S. Dye >>> http://www.tsdye.com >>> --=20 Thomas S. Dye http://www.tsdye.com From mboxrd@z Thu Jan 1 00:00:00 1970 From: Riccardo Romoli Subject: Re: Generating plot with org-babel-R Date: Mon, 6 Feb 2012 22:12:31 +0100 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=00235452ef54d6ce3f04b8521eb5 Return-path: Received: from eggs.gnu.org ([140.186.70.92]:44686) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RuVrW-00072j-O3 for emacs-orgmode@gnu.org; Mon, 06 Feb 2012 16:12:36 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RuVrU-0006hp-QC for emacs-orgmode@gnu.org; Mon, 06 Feb 2012 16:12:34 -0500 Received: from mail-qy0-f169.google.com ([209.85.216.169]:49376) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RuVrU-0006h5-MW for emacs-orgmode@gnu.org; Mon, 06 Feb 2012 16:12:32 -0500 Received: by qcsd16 with SMTP id d16so4035295qcs.0 for ; Mon, 06 Feb 2012 13:12:31 -0800 (PST) In-Reply-To: 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: "Thomas S. Dye" Cc: emacs-orgmode@gnu.org --00235452ef54d6ce3f04b8521eb5 Content-Type: text/plain; charset=ISO-8859-1 Hi Thomas, thanks a lot for your help!! Using the JSS and the org manual I solved all my problem (....at least for now!! :)) Best Riccardo 2012/2/5 Thomas S. Dye > Hi Riccardo, > > Thanks for the URL. Org mode has evolved since this article was > written. It should probably be revised or taken off Worg. I've copied > Eric Schulte, who is better able than me to determine the correct course > of action here. > > In the meantime, an up-to-date description of how Org mode can be used > to write literate programs has appeared in the Journal of Statistical > Software. You can find it here: http://www.jstatsoft.org/v46/i03 > > Perhaps you could use the examples in the JSS article to get started? > If these don't work for you, or if they raise questions that are difficult > to answer, please do come back to the list with your queries. > > All the best, > Tom > > Riccardo Romoli writes: > > > Hi, this is the URL: > > > > > http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html > > > > Best > > R > > > > 2012/2/5 Thomas S. Dye > > > >> Hi Riccardo, > >> > >> This code appears to be outdated. I don't recall this code on the org > >> site. Could you send a URL? > >> > >> All the best, > >> Tom > >> > >> Riccardo Romoli writes: > >> > >> > Hi, I'm trying to generate some figure with R, into an org session. > >> Firstly > >> > I use the code in the org site. The problem is that the code do not > >> > generate any figure. > >> > > >> > This is the code: > >> > > >> > #+TITLE:Test > >> > #+AUTHOR: Your Name > >> > #+EMAIL: your-email@server.com > >> > #+BABEL: :session *R* :cache yes :results output graphics :exports > >> > both :tangle yes > >> > > >> > * Example of Org-Babel for R Literate Programming > >> > ** R text output > >> > A simple summary. > >> > #+begin_src R > >> > x <- rnorm(10) > >> > summary(x) > >> > #+end_src > >> > > >> > ** R graphics output > >> > Note we use the object =x= generated in previous code block, thanks to > >> > the header option =:session *R*=. The output graphics file is > >> > =a.png=. > >> > > >> > #+begin_src R :file a.png > >> > y <- rnorm(10) > >> > plot(x, y) > >> > #+end_src > >> > > >> > Same plot with larger dimension: > >> > > >> > #+begin_src R :file b.png :width 800 :height 800 > >> > plot(x, y) > >> > #+end_src > >> > > >> > > >> > Where do I wrong? > >> > > >> > Best > >> > Riccardo > >> > Hi, I'm trying to generate some figure with R, into an org > session. > >> Firstly I use the code in the org site. The problem is that the code do > not > >> generate any figure. This is the code: > >> > #+TITLE:Test > >> > #+AUTHOR: Your Name > >> > #+EMAIL: mailto:your-email@server.com > >> > #+BABEL: :session *R* :cache yes :results output graphics :exports > both > >> :tangle yes > >> > > >> > * Example of Org-Babel for R Literate Programming > >> > ** R text output > >> > A simple summary. > >> > #+begin_src R > >> > x <- rnorm(10) > >> > summary(x) > >> > #+end_src > >> > > >> > ** R graphics output > >> > Note we use the object =x= generated in previous code block, thanks to > >> > the header option =:session *R*=. The output graphics file is > >> > =a.png=. > >> > > >> > #+begin_src R :file a.png > >> > y <- rnorm(10) > >> > plot(x, y) > >> > #+end_src > >> > > >> > Same plot with larger dimension: > >> > > >> > #+begin_src R :file b.png :width 800 :height 800 > >> > plot(x, y) > >> > #+end_src > >> > Where do I wrong?BestRiccardo > >> > >> -- > >> Thomas S. Dye > >> http://www.tsdye.com > >> > > Hi, this is the URL: > http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.htmlBestR > > 2012/2/5 Thomas S. Dye Hi > Riccardo, > > > > > > This code appears to be outdated. I don't recall this code on the > org > > site. Could you send a URL? > > > > All the best, > > Tom > > > > Riccardo Romoli writes: > > > >> Hi, I'm trying to generate some figure with R, into an org session. > Firstly > >> I use the code in the org site. The problem is that the code do not > >> generate any figure. > >> > >> This is the code: > >> > >> #+TITLE:Test > >> #+AUTHOR: Your Name > >> #+EMAIL: mailto:your-email@server.com > >> #+BABEL: :session *R* :cache yes :results output graphics :exports > >> both :tangle yes > >> > >> * Example of Org-Babel for R Literate Programming > >> ** R text output > >> A simple summary. > >> #+begin_src R > >> x <- rnorm(10) > >> summary(x) > >> #+end_src > >> > >> ** R graphics output > >> Note we use the object =x= generated in previous code block, thanks to > >> the header option =:session *R*=. The output graphics file is > >> =a.png=. > >> > >> #+begin_src R :file a.png > >> y <- rnorm(10) > >> plot(x, y) > >> #+end_src > >> > >> Same plot with larger dimension: > >> > >> #+begin_src R :file b.png :width 800 :height 800 > >> plot(x, y) > >> #+end_src > >> > >> > >> Where do I wrong? > >> > >> Best > >> Riccardo > >> Hi, I'm trying to generate some figure with R, into an org session. > Firstly I use the code in the org site. The problem is that the code do not > generate any figure. This is the code: > >> #+TITLE:Test > >> #+AUTHOR: Your Name > >> #+EMAIL: mailto:mailto:your-email@server.com > >> #+BABEL: :session *R* :cache yes :results output graphics :exports both > :tangle yes > >> > >> * Example of Org-Babel for R Literate Programming > >> ** R text output > >> A simple summary. > >> #+begin_src R > >> x <- rnorm(10) > >> summary(x) > >> #+end_src > >> > >> ** R graphics output > >> Note we use the object =x= generated in previous code block, thanks to > >> the header option =:session *R*=. The output graphics file is > >> =a.png=. > >> > >> #+begin_src R :file a.png > >> y <- rnorm(10) > >> plot(x, y) > >> #+end_src > >> > >> Same plot with larger dimension: > >> > >> #+begin_src R :file b.png :width 800 :height 800 > >> plot(x, y) > >> #+end_src > >> Where do I wrong?BestRiccardo > > > > -- > > Thomas S. Dye > > http://www.tsdye.com > > > > -- > Thomas S. Dye > http://www.tsdye.com > --00235452ef54d6ce3f04b8521eb5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Thomas,
thanks a lot for your help!! Using the JSS and the org manua= l I solved all my problem (....at least for now!! :))

Best
Riccar= do

2012/2/5 Thomas S. Dye <tsd@tsdye.com>
Hi Riccardo,

Thanks for the URL. =A0Org mode has evolved since this article was
written. =A0It should probably be revised or taken off Worg. =A0I've co= pied
Eric Schulte, who is better able than me to determine the correct course of action here.

In the meantime, an up-to-date description of how Org mode can be used
to write literate programs has appeared in the Journal of Statistical
Software. =A0You can find it here: http://www.jstatsoft.org/v46/i03

Perhaps you could use the examples in the JSS article to get started?
If these don't work for you, or if they raise questions that are diffic= ult
to answer, please do come back to the list with your queries.

All the best,
Tom

Riccardo Romoli <ric.romoli@gmai= l.com> writes:

> Hi, this is the URL:
>
> http://orgmode.org/worg/org-contrib/babel= /how-to-use-Org-Babel-for-R.html
>
> Best
> R
>
> 2012/2/5 Thomas S. Dye <tsd@tsdye.= com>
>
>> Hi Riccardo,
>>
>> This code appears to be outdated. =A0I don't recall this code = on the org
>> site. =A0Could you send a URL?
>>
>> All the best,
>> Tom
>>
>> Riccardo Romoli <ric.ro= moli@gmail.com> writes:
>>
>> > Hi, I'm trying to generate some figure with R, into an or= g session.
>> Firstly
>> > I use the code in the org site. The problem is that the code = do not
>> > generate any figure.
>> >
>> > This is the code:
>> >
>> > #+TITLE:Test
>> > #+AUTHOR: Your Name
>> > #+EMAIL: your-email@= server.com
>> > #+BABEL: :session *R* :cache yes :results output graphics :ex= ports
>> > both :tangle yes
>> >
>> > * Example of Org-Babel for R Literate Programming
>> > ** R text output
>> > A simple summary.
>> > #+begin_src R
>> > =A0 x <- rnorm(10)
>> > =A0 summary(x)
>> > #+end_src
>> >
>> > ** R graphics output
>> > Note we use the object =3Dx=3D generated in previous code blo= ck, thanks to
>> > the header option =3D:session *R*=3D. =A0The output graphics = file is
>> > =3Da.png=3D.
>> >
>> > #+begin_src R =A0:file a.png
>> > =A0 y <- rnorm(10)
>> > =A0 plot(x, y)
>> > #+end_src
>> >
>> > Same plot with larger dimension:
>> >
>> > #+begin_src R =A0:file b.png :width 800 :height 800
>> > =A0 plot(x, y)
>> > #+end_src
>> >
>> >
>> > Where do I wrong?
>> >
>> > Best
>> > Riccardo
>> > Hi, I&#39;m trying to generate some figure with R, into a= n org session.
>> Firstly I use the code in the org site. The problem is that the co= de do not
>> generate any figure. This is the code:
>> > #+TITLE:Test
>> > #+AUTHOR: Your Name
>> > #+EMAIL: mailto:your= -email@server.com
>> > #+BABEL: :session *R* :cache yes :results output graphics :ex= ports both
>> :tangle yes
>> >
>> > * Example of Org-Babel for R Literate Programming
>> > ** R text output
>> > A simple summary.
>> > #+begin_src R
>> > =A0 x <- rnorm(10)
>> > =A0 summary(x)
>> > #+end_src
>> >
>> > ** R graphics output
>> > Note we use the object =3Dx=3D generated in previous code blo= ck, thanks to
>> > the header option =3D:session *R*=3D. =A0The output graphics = file is
>> > =3Da.png=3D.
>> >
>> > #+begin_src R =A0:file a.png
>> > =A0 y <- rnorm(10)
>> > =A0 plot(x, y)
>> > #+end_src
>> >
>> > Same plot with larger dimension:
>> >
>> > #+begin_src R =A0:file b.png :width 800 :height 800
>> > =A0 plot(x, y)
>> > #+end_src
>> > Where do I wrong?BestRiccardo
>>
>> --
>> Thomas S. Dye
>> http://www.tsdy= e.com
>>
> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babe= l-for-R.htmlBestR
> 2012/2/5 Thomas S. Dye <span dir=3D"ltr"><mai= lto:tsd@tsdye.com></span>Hi R= iccardo,
>
>
> This code appears to be outdated. =A0I don&#39;t recall this code = on the org
> site. =A0Could you send a URL?
>
> All the best,
> Tom
>
> Riccardo Romoli <mailto:ric.romoli@gmail.com> writes:
>
>> Hi, I&#39;m trying to generate some figure with R, into an org= session. Firstly
>> I use the code in the org site. The problem is that the code do no= t
>> generate any figure.
>>
>> This is the code:
>>
>> #+TITLE:Test
>> #+AUTHOR: Your Name
>> #+EMAIL: mailto:your-emai= l@server.com
>> #+BABEL: :session *R* :cache yes :results output graphics :exports=
>> both :tangle yes
>>
>> * Example of Org-Babel for R Literate Programming
>> ** R text output
>> A simple summary.
>> #+begin_src R
>> =A0 x <- rnorm(10)
>> =A0 summary(x)
>> #+end_src
>>
>> ** R graphics output
>> Note we use the object =3Dx=3D generated in previous code block, t= hanks to
>> the header option =3D:session *R*=3D. =A0The output graphics file = is
>> =3Da.png=3D.
>>
>> #+begin_src R =A0:file a.png
>> =A0 y <- rnorm(10)
>> =A0 plot(x, y)
>> #+end_src
>>
>> Same plot with larger dimension:
>>
>> #+begin_src R =A0:file b.png :width 800 :height 800
>> =A0 plot(x, y)
>> #+end_src
>>
>>
>> Where do I wrong?
>>
>> Best
>> Riccardo
>> Hi, I&#39;m trying to generate some figure with R, into an org= session. Firstly I use the code in the org site. The problem is that the c= ode do not generate any figure. This is the code:
>> #+TITLE:Test
>> #+AUTHOR: Your Name
>> #+EMAIL: mailto:mailto:<= a href=3D"mailto:your-email@server.com">your-email@server.com
>> #+BABEL: :session *R* :cache yes :results output= graphics :exports both :tangle yes
>>
>> * Example of Org-Babel for R Literate Programming
>> ** R text output
>> A simple summary.
>> #+begin_src R
>> =A0 x <- rnorm(10)
>> =A0 summary(x)
>> #+end_src
>>
>> ** R graphics output
>> Note we use the object =3Dx=3D generated in previous code block, t= hanks to
>> the header option =3D:session *R*=3D. =A0The output graphics file = is
>> =3Da.png=3D.
>>
>> #+begin_src R =A0:file a.png
>> =A0 y <- rnorm(10)
>> =A0 plot(x, y)
>> #+end_src
>>
>> Same plot with larger dimension:
>>
>> #+begin_src R =A0:file b.png :width 800 :height 800
>> =A0 plot(x, y)
>> #+end_src
>> Where do I wrong?BestRiccardo
>
> <span class=3D"HOEnZb">--
> Thomas S. Dye
> http://www.tsdye.co= m
> </span>

--
Thomas S. Dye
http://www.tsdye.com=

--00235452ef54d6ce3f04b8521eb5-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Re: Updating the Babel section of Worg Date: Mon, 06 Feb 2012 14:20:39 -0700 Message-ID: <87pqdrlkuw.fsf_-_@gmx.com> References: <87mx8xyt7q.fsf_-_@gmx.com> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:44287) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RuVzp-0001Eh-V8 for emacs-orgmode@gnu.org; Mon, 06 Feb 2012 16:21:12 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RuVzn-0008GE-Kd for emacs-orgmode@gnu.org; Mon, 06 Feb 2012 16:21:09 -0500 Received: from mailout-us.gmx.com ([74.208.5.67]:41968 helo=mailout-us.mail.com) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1RuVzn-0008G4-Ew for emacs-orgmode@gnu.org; Mon, 06 Feb 2012 16:21:07 -0500 In-Reply-To: (Thomas S. Dye's message of "Sun, 05 Feb 2012 19:43:25 -1000") 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: "Thomas S. Dye" Cc: emacs-orgmode@gnu.org, Eric Schulte , Riccardo Romoli Hi Tom, tsd@tsdye.com (Thomas S. Dye) writes: > Hi Eric, > > Yes, this is overdue. I think your plan is a good one. > > Perhaps a few of the individual use cases could be moved to FIXME, > instead? I'm thinking here of Feiming Chen's R setup and some of my > contributions when I was experimenting writing LaTeX inside source > code blocks. The authors could resurrect these as they see fit. > I don't know what FIXME is, but if there is a way to keep the page in the worg git repository but remove it from the exported HTML then that sounds ideal. > > Hopefully, others will contribute use examples. My sense from reading > the list is there are many interesting ones. > > I'd like it if Org mode users designed a template for the language > specific pages. Currently, these seem to me a mixed bag and it would be > good to regularize them. The below is a modified version of a template which can be found in a couple of the existing language tutorials, I think it serves as a good starting point. - Install and Setup - Instillation and configuration of software (e.g., the language itself) - Configuration of Emacs (e.g., activate language, set command path) - Examples - Common ways to use the language in an Org-mode document - Special cases - are there any language-specific header arguments - does the language support session evaluation - does the language support all result types - is the language different from most babel languages (e.g., C is compiled before execution, ditaa returns files, etc...) > It would also be nice to have one for each of the supported languages. > There are 11 language specific pages now, which leaves quite a few > languages under-documented. (length org-babel-load-languages) ;; =3D> 27 ls org-contrib/babel/languages/ob-doc-*|wc -l # =3D> 11 It looks like we have at least 16 more to go before we hit full language coverage. Perhaps we should use the empty cells in the "documentation" column in the languages table at [1] as a sign up space for volunteers who would be willing to write a brief tutorial demonstrating usage of Org-mode with their favorite language. Moving forward this is likely something we could request of the contributors of new languages. Also, once the template above is finalized it should be posted on worg and linked to through the languages page. > > I'll be happy to work on this as I can. > Great, I don't anticipate having time to put towards this, although I'll be happy to help troubleshoot where I can. Cheers, > > All the best, > Tom > > > Eric Schulte writes: > >> Thanks for raising this point. The bulk of the content in the Babel >> portion of worg is fairly old, predating the syntax standardization >> efforts this fall. I've just pushed some minor updates to the main >> babel pages, but updating the language-specific tutorials and the >> individual use cases will be a much larger effort. >> >> I'm not sure how to proceed. One option would be to go through and add >> a [uses deprecated syntax] tag to the top of each such page, which could >> be removed after the page has been checked and possibly updated to >> ensure consistency with the latest syntax. >> >> Given that the Babel syntax will not be changing significantly moving >> forward now would be a good time to do such a review. Ideally this >> could be completed before the release of Emacs 24 in a couple of months. >> >> Any other ideas for update/reorganization or volunteers? >> >> Cheers, >> >> tsd@tsdye.com (Thomas S. Dye) writes: >> >>> Hi Riccardo, >>> >>> Thanks for the URL. Org mode has evolved since this article was >>> written. It should probably be revised or taken off Worg. I've copied >>> Eric Schulte, who is better able than me to determine the correct course >>> of action here. >>> >>> In the meantime, an up-to-date description of how Org mode can be used >>> to write literate programs has appeared in the Journal of Statistical >>> Software. You can find it here: http://www.jstatsoft.org/v46/i03 >>> >>> Perhaps you could use the examples in the JSS article to get started? >>> If these don't work for you, or if they raise questions that are diffic= ult >>> to answer, please do come back to the list with your queries. >>> >>> All the best, >>> Tom >>> >>> Riccardo Romoli writes: >>> >>>> Hi, this is the URL: >>>> >>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.h= tml >>>> >>>> Best >>>> R >>>> >>>> 2012/2/5 Thomas S. Dye >>>> >>>>> Hi Riccardo, >>>>> >>>>> This code appears to be outdated. I don't recall this code on the org >>>>> site. Could you send a URL? >>>>> >>>>> All the best, >>>>> Tom >>>>> >>>>> Riccardo Romoli writes: >>>>> >>>>> > Hi, I'm trying to generate some figure with R, into an org session. >>>>> Firstly >>>>> > I use the code in the org site. The problem is that the code do not >>>>> > generate any figure. >>>>> > >>>>> > This is the code: >>>>> > >>>>> > #+TITLE:Test >>>>> > #+AUTHOR: Your Name >>>>> > #+EMAIL: your-email@server.com >>>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>> > both :tangle yes >>>>> > >>>>> > * Example of Org-Babel for R Literate Programming >>>>> > ** R text output >>>>> > A simple summary. >>>>> > #+begin_src R >>>>> > x <- rnorm(10) >>>>> > summary(x) >>>>> > #+end_src >>>>> > >>>>> > ** R graphics output >>>>> > Note we use the object =3Dx=3D generated in previous code block, th= anks to >>>>> > the header option =3D:session *R*=3D. The output graphics file is >>>>> > =3Da.png=3D. >>>>> > >>>>> > #+begin_src R :file a.png >>>>> > y <- rnorm(10) >>>>> > plot(x, y) >>>>> > #+end_src >>>>> > >>>>> > Same plot with larger dimension: >>>>> > >>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>> > plot(x, y) >>>>> > #+end_src >>>>> > >>>>> > >>>>> > Where do I wrong? >>>>> > >>>>> > Best >>>>> > Riccardo >>>>> > Hi, I'm trying to generate some figure with R, into an org sess= ion. >>>>> Firstly I use the code in the org site. The problem is that the code = do not >>>>> generate any figure. This is the code: >>>>> > #+TITLE:Test >>>>> > #+AUTHOR: Your Name >>>>> > #+EMAIL: mailto:your-email@server.com >>>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports = both >>>>> :tangle yes >>>>> > >>>>> > * Example of Org-Babel for R Literate Programming >>>>> > ** R text output >>>>> > A simple summary. >>>>> > #+begin_src R >>>>> > x <- rnorm(10) >>>>> > summary(x) >>>>> > #+end_src >>>>> > >>>>> > ** R graphics output >>>>> > Note we use the object =3Dx=3D generated in previous code block, th= anks to >>>>> > the header option =3D:session *R*=3D. The output graphics file is >>>>> > =3Da.png=3D. >>>>> > >>>>> > #+begin_src R :file a.png >>>>> > y <- rnorm(10) >>>>> > plot(x, y) >>>>> > #+end_src >>>>> > >>>>> > Same plot with larger dimension: >>>>> > >>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>> > plot(x, y) >>>>> > #+end_src >>>>> > Where do I wrong?BestRiccardo >>>>> >>>>> -- >>>>> Thomas S. Dye >>>>> http://www.tsdye.com >>>>> >>>> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to-u= se-Org-Babel-for-R.htmlBestR >>>> 2012/2/5 Thomas S. Dye = Hi Riccardo, >>>> >>>> >>>> This code appears to be outdated. =C2=A0I don't recall this code o= n the org >>>> site. =C2=A0Could you send a URL? >>>> >>>> All the best, >>>> Tom >>>> >>>> Riccardo Romoli writes: >>>> >>>>> Hi, I'm trying to generate some figure with R, into an org sessio= n. Firstly >>>>> I use the code in the org site. The problem is that the code do not >>>>> generate any figure. >>>>> >>>>> This is the code: >>>>> >>>>> #+TITLE:Test >>>>> #+AUTHOR: Your Name >>>>> #+EMAIL: mailto:your-email@server.com >>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>> both :tangle yes >>>>> >>>>> * Example of Org-Babel for R Literate Programming >>>>> ** R text output >>>>> A simple summary. >>>>> #+begin_src R >>>>> =C2=A0 x <- rnorm(10) >>>>> =C2=A0 summary(x) >>>>> #+end_src >>>>> >>>>> ** R graphics output >>>>> Note we use the object =3Dx=3D generated in previous code block, than= ks to >>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics file = is >>>>> =3Da.png=3D. >>>>> >>>>> #+begin_src R =C2=A0:file a.png >>>>> =C2=A0 y <- rnorm(10) >>>>> =C2=A0 plot(x, y) >>>>> #+end_src >>>>> >>>>> Same plot with larger dimension: >>>>> >>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>> =C2=A0 plot(x, y) >>>>> #+end_src >>>>> >>>>> >>>>> Where do I wrong? >>>>> >>>>> Best >>>>> Riccardo >>>>> Hi, I'm trying to generate some figure with R, into an org >>>>> session. Firstly I use the code in the org site. The problem is >>>>> that the code do not generate any figure. This is the code: >>>>> #+TITLE:Test >>>>> #+AUTHOR: Your Name >>>>> #+EMAIL: mailto:mailto:your-email@server.com >>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports bo= th :tangle yes >>>>> >>>>> * Example of Org-Babel for R Literate Programming >>>>> ** R text output >>>>> A simple summary. >>>>> #+begin_src R >>>>> =C2=A0 x <- rnorm(10) >>>>> =C2=A0 summary(x) >>>>> #+end_src >>>>> >>>>> ** R graphics output >>>>> Note we use the object =3Dx=3D generated in previous code block, than= ks to >>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics file = is >>>>> =3Da.png=3D. >>>>> >>>>> #+begin_src R =C2=A0:file a.png >>>>> =C2=A0 y <- rnorm(10) >>>>> =C2=A0 plot(x, y) >>>>> #+end_src >>>>> >>>>> Same plot with larger dimension: >>>>> >>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>> =C2=A0 plot(x, y) >>>>> #+end_src >>>>> Where do I wrong?BestRiccardo >>>> >>>> -- >>>> Thomas S. Dye >>>> http://www.tsdye.com >>>> Footnotes:=20 [1] http://orgmode.org/worg/org-contrib/babel/languages.html --=20 Eric Schulte http://cs.unm.edu/~eschulte/ From mboxrd@z Thu Jan 1 00:00:00 1970 From: tsd@tsdye.com (Thomas S. Dye) Subject: Re: Updating the Babel section of Worg Date: Tue, 07 Feb 2012 14:01:51 -1000 Message-ID: References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([140.186.70.92]:60792) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ruuz2-00044Y-Bh for emacs-orgmode@gnu.org; Tue, 07 Feb 2012 19:02:02 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Ruuz0-0004g9-98 for emacs-orgmode@gnu.org; Tue, 07 Feb 2012 19:02:00 -0500 Received: from oproxy6-pub.bluehost.com ([67.222.54.6]:33257) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1Ruuyz-0004fh-TM for emacs-orgmode@gnu.org; Tue, 07 Feb 2012 19:01:58 -0500 In-Reply-To: <87pqdrlkuw.fsf_-_@gmx.com> (Eric Schulte's message of "Mon, 06 Feb 2012 14:20:39 -0700") 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: Eric Schulte Cc: emacs-orgmode@gnu.org, Riccardo Romoli --=-=-= Hi Eric, I've attached a first draft of a template for review and revision. It is heavily influenced by John Hendy's terrific gnuplot page. I believe it incorporates the points in your outline. Feel free to edit as appropriate. All the best, Tom --=-=-= Content-Disposition: attachment; filename=worg-babel-lang.org Content-Description: Language description template #+OPTIONS: H:3 num:nil toc:2 \n:nil @:t ::t |:t ^:{} -:t f:t *:t TeX:t LaTeX:t skip:nil d:(HIDE) tags:not-in-toc #+STARTUP: align fold nodlcheck hidestars oddeven lognotestate hideblocks #+SEQ_TODO: TODO(t) INPROGRESS(i) WAITING(w@) | DONE(d) CANCELED(c@) #+TAGS: Write(w) Update(u) Fix(f) Check(c) noexport(n) #+TITLE: Language Source Code Blocks in Org Mode #+AUTHOR: Your name #+EMAIL: you[at]email[dot]org #+LANGUAGE: en #+STYLE: #+LINK_UP: ../languages.php #+LINK_HOME: http://orgmode.org/worg/ #+EXPORT_EXCLUDE_TAGS: noexport #+name: banner #+begin_html

Org Mode support for Language

#+end_html * Template Checklist [0/13] :noexport: - [ ] Revise #+TITLE: - [ ] Indicate #+AUTHOR: - [ ] Add #+EMAIL: - [ ] Revise banner source block [0/3] - [ ] Add link to a useful language web site - [ ] Replace "Language" with language name - [ ] Find a suitable graphic and use it to link to the language web site - [ ] Write an [[Introduction]] - [ ] Describe [[Requirements%20and%20Setup][Requirements and Setup]] - [ ] Replace "Language" with language name in [[Org%20Mode%20Features%20for%20Language%20Source%20Code%20Blocks][Org Mode Features for Language Source Code Blocks]] - [ ] Specify [[Org%20Mode%20Configuration][Org Mode Configuration]] - [ ] Describe [[Header%20Arguments][Header Arguments]] - [ ] Describe support for [[Sessions]] - [ ] Describe [[Result%20Types][Result Types]] - [ ] Describe [[Other]] differences from supported languages - [ ] Provide brief [[Examples%20of%20Use][Examples of Use]] * Introduction - Brief description of language. - Range of typical uses within Org Mode. - Link to this Org Mode file. * Requirements and Setup - Installation and configuration of language software - Emacs configuration * Org Mode Features for Language Source Code Blocks ** Org Mode Configuration - org-babel-do-load-languages ** Header Arguments - Language-specific default values - Language-specific header arguments ** Sessions - Support or not - Typical use for sessions ** Result Types - Which result types are supported? ** Other - Differences from other supported languages * Examples of Use - Hello World! - Common uses - Links to tutorials and other resources --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Eric Schulte writes: > Hi Tom, > > tsd@tsdye.com (Thomas S. Dye) writes: > >> Hi Eric, >> >> Yes, this is overdue. I think your plan is a good one. >> >> Perhaps a few of the individual use cases could be moved to FIXME, >> instead? I'm thinking here of Feiming Chen's R setup and some of my >> contributions when I was experimenting writing LaTeX inside source >> code blocks. The authors could resurrect these as they see fit. >> > > I don't know what FIXME is, but if there is a way to keep the page in > the worg git repository but remove it from the exported HTML then that > sounds ideal. > >> >> Hopefully, others will contribute use examples. My sense from reading >> the list is there are many interesting ones. >> >> I'd like it if Org mode users designed a template for the language >> specific pages. Currently, these seem to me a mixed bag and it would be >> good to regularize them. > > The below is a modified version of a template which can be found in a > couple of the existing language tutorials, I think it serves as a good > starting point. > > - Install and Setup > - Instillation and configuration of software (e.g., the language itself) > - Configuration of Emacs (e.g., activate language, set command path) > - Examples > - Common ways to use the language in an Org-mode document > - Special cases > - are there any language-specific header arguments > - does the language support session evaluation > - does the language support all result types > - is the language different from most babel languages > (e.g., C is compiled before execution, ditaa returns files, etc...) > >> It would also be nice to have one for each of the supported languages. >> There are 11 language specific pages now, which leaves quite a few >> languages under-documented. > > (length org-babel-load-languages) ;; =3D> 27 > > ls org-contrib/babel/languages/ob-doc-*|wc -l # =3D> 11 > > It looks like we have at least 16 more to go before we hit full language > coverage. Perhaps we should use the empty cells in the "documentation" > column in the languages table at [1] as a sign up space for volunteers > who would be willing to write a brief tutorial demonstrating usage of > Org-mode with their favorite language. > > Moving forward this is likely something we could request of the > contributors of new languages. > > Also, once the template above is finalized it should be posted on worg > and linked to through the languages page. > >> >> I'll be happy to work on this as I can. >> > > Great, I don't anticipate having time to put towards this, although I'll > be happy to help troubleshoot where I can. > > Cheers, > >> >> All the best, >> Tom >> >> >> Eric Schulte writes: >> >>> Thanks for raising this point. The bulk of the content in the Babel >>> portion of worg is fairly old, predating the syntax standardization >>> efforts this fall. I've just pushed some minor updates to the main >>> babel pages, but updating the language-specific tutorials and the >>> individual use cases will be a much larger effort. >>> >>> I'm not sure how to proceed. One option would be to go through and add >>> a [uses deprecated syntax] tag to the top of each such page, which could >>> be removed after the page has been checked and possibly updated to >>> ensure consistency with the latest syntax. >>> >>> Given that the Babel syntax will not be changing significantly moving >>> forward now would be a good time to do such a review. Ideally this >>> could be completed before the release of Emacs 24 in a couple of months. >>> >>> Any other ideas for update/reorganization or volunteers? >>> >>> Cheers, >>> >>> tsd@tsdye.com (Thomas S. Dye) writes: >>> >>>> Hi Riccardo, >>>> >>>> Thanks for the URL. Org mode has evolved since this article was >>>> written. It should probably be revised or taken off Worg. I've copied >>>> Eric Schulte, who is better able than me to determine the correct cour= se >>>> of action here. >>>> >>>> In the meantime, an up-to-date description of how Org mode can be used >>>> to write literate programs has appeared in the Journal of Statistical >>>> Software. You can find it here: http://www.jstatsoft.org/v46/i03 >>>> >>>> Perhaps you could use the examples in the JSS article to get started? >>>> If these don't work for you, or if they raise questions that are diffi= cult >>>> to answer, please do come back to the list with your queries. >>>> >>>> All the best, >>>> Tom >>>> >>>> Riccardo Romoli writes: >>>> >>>>> Hi, this is the URL: >>>>> >>>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.= html >>>>> >>>>> Best >>>>> R >>>>> >>>>> 2012/2/5 Thomas S. Dye >>>>> >>>>>> Hi Riccardo, >>>>>> >>>>>> This code appears to be outdated. I don't recall this code on the o= rg >>>>>> site. Could you send a URL? >>>>>> >>>>>> All the best, >>>>>> Tom >>>>>> >>>>>> Riccardo Romoli writes: >>>>>> >>>>>> > Hi, I'm trying to generate some figure with R, into an org session. >>>>>> Firstly >>>>>> > I use the code in the org site. The problem is that the code do not >>>>>> > generate any figure. >>>>>> > >>>>>> > This is the code: >>>>>> > >>>>>> > #+TITLE:Test >>>>>> > #+AUTHOR: Your Name >>>>>> > #+EMAIL: your-email@server.com >>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>> > both :tangle yes >>>>>> > >>>>>> > * Example of Org-Babel for R Literate Programming >>>>>> > ** R text output >>>>>> > A simple summary. >>>>>> > #+begin_src R >>>>>> > x <- rnorm(10) >>>>>> > summary(x) >>>>>> > #+end_src >>>>>> > >>>>>> > ** R graphics output >>>>>> > Note we use the object =3Dx=3D generated in previous code block, t= hanks to >>>>>> > the header option =3D:session *R*=3D. The output graphics file is >>>>>> > =3Da.png=3D. >>>>>> > >>>>>> > #+begin_src R :file a.png >>>>>> > y <- rnorm(10) >>>>>> > plot(x, y) >>>>>> > #+end_src >>>>>> > >>>>>> > Same plot with larger dimension: >>>>>> > >>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>> > plot(x, y) >>>>>> > #+end_src >>>>>> > >>>>>> > >>>>>> > Where do I wrong? >>>>>> > >>>>>> > Best >>>>>> > Riccardo >>>>>> > Hi, I'm trying to generate some figure with R, into an org ses= sion. >>>>>> Firstly I use the code in the org site. The problem is that the code= do not >>>>>> generate any figure. This is the code: >>>>>> > #+TITLE:Test >>>>>> > #+AUTHOR: Your Name >>>>>> > #+EMAIL: mailto:your-email@server.com >>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports= both >>>>>> :tangle yes >>>>>> > >>>>>> > * Example of Org-Babel for R Literate Programming >>>>>> > ** R text output >>>>>> > A simple summary. >>>>>> > #+begin_src R >>>>>> > x <- rnorm(10) >>>>>> > summary(x) >>>>>> > #+end_src >>>>>> > >>>>>> > ** R graphics output >>>>>> > Note we use the object =3Dx=3D generated in previous code block, t= hanks to >>>>>> > the header option =3D:session *R*=3D. The output graphics file is >>>>>> > =3Da.png=3D. >>>>>> > >>>>>> > #+begin_src R :file a.png >>>>>> > y <- rnorm(10) >>>>>> > plot(x, y) >>>>>> > #+end_src >>>>>> > >>>>>> > Same plot with larger dimension: >>>>>> > >>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>> > plot(x, y) >>>>>> > #+end_src >>>>>> > Where do I wrong?BestRiccardo >>>>>> >>>>>> -- >>>>>> Thomas S. Dye >>>>>> http://www.tsdye.com >>>>>> >>>>> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to-= use-Org-Babel-for-R.htmlBestR >>>>> 2012/2/5 Thomas S. Dye Hi Riccardo, >>>>> >>>>> >>>>> This code appears to be outdated. =C2=A0I don't recall this code = on the org >>>>> site. =C2=A0Could you send a URL? >>>>> >>>>> All the best, >>>>> Tom >>>>> >>>>> Riccardo Romoli writes: >>>>> >>>>>> Hi, I'm trying to generate some figure with R, into an org sessi= on. Firstly >>>>>> I use the code in the org site. The problem is that the code do not >>>>>> generate any figure. >>>>>> >>>>>> This is the code: >>>>>> >>>>>> #+TITLE:Test >>>>>> #+AUTHOR: Your Name >>>>>> #+EMAIL: mailto:your-email@server.com >>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>> both :tangle yes >>>>>> >>>>>> * Example of Org-Babel for R Literate Programming >>>>>> ** R text output >>>>>> A simple summary. >>>>>> #+begin_src R >>>>>> =C2=A0 x <- rnorm(10) >>>>>> =C2=A0 summary(x) >>>>>> #+end_src >>>>>> >>>>>> ** R graphics output >>>>>> Note we use the object =3Dx=3D generated in previous code block, tha= nks to >>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics file= is >>>>>> =3Da.png=3D. >>>>>> >>>>>> #+begin_src R =C2=A0:file a.png >>>>>> =C2=A0 y <- rnorm(10) >>>>>> =C2=A0 plot(x, y) >>>>>> #+end_src >>>>>> >>>>>> Same plot with larger dimension: >>>>>> >>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>> =C2=A0 plot(x, y) >>>>>> #+end_src >>>>>> >>>>>> >>>>>> Where do I wrong? >>>>>> >>>>>> Best >>>>>> Riccardo >>>>>> Hi, I'm trying to generate some figure with R, into an org >>>>>> session. Firstly I use the code in the org site. The problem is >>>>>> that the code do not generate any figure. This is the code: >>>>>> #+TITLE:Test >>>>>> #+AUTHOR: Your Name >>>>>> #+EMAIL: mailto:mailto:your-email@server.com >>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports b= oth :tangle yes >>>>>> >>>>>> * Example of Org-Babel for R Literate Programming >>>>>> ** R text output >>>>>> A simple summary. >>>>>> #+begin_src R >>>>>> =C2=A0 x <- rnorm(10) >>>>>> =C2=A0 summary(x) >>>>>> #+end_src >>>>>> >>>>>> ** R graphics output >>>>>> Note we use the object =3Dx=3D generated in previous code block, tha= nks to >>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics file= is >>>>>> =3Da.png=3D. >>>>>> >>>>>> #+begin_src R =C2=A0:file a.png >>>>>> =C2=A0 y <- rnorm(10) >>>>>> =C2=A0 plot(x, y) >>>>>> #+end_src >>>>>> >>>>>> Same plot with larger dimension: >>>>>> >>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>> =C2=A0 plot(x, y) >>>>>> #+end_src >>>>>> Where do I wrong?BestRiccardo >>>>> >>>>> -- >>>>> Thomas S. Dye >>>>> http://www.tsdye.com >>>>> > > > Footnotes:=20 > [1] http://orgmode.org/worg/org-contrib/babel/languages.html --=20 Thomas S. Dye http://www.tsdye.com --=-=-=-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: Martyn Jago Subject: Re: Updating the Babel section of Worg Date: Wed, 08 Feb 2012 01:04:39 +0000 Message-ID: References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([140.186.70.92]:54623) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ruvxw-0005cU-6e for emacs-orgmode@gnu.org; Tue, 07 Feb 2012 20:04:58 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Ruvxt-0002kT-UY for emacs-orgmode@gnu.org; Tue, 07 Feb 2012 20:04:56 -0500 Received: from plane.gmane.org ([80.91.229.3]:55454) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ruvxt-0002kK-HR for emacs-orgmode@gnu.org; Tue, 07 Feb 2012 20:04:53 -0500 Received: from list by plane.gmane.org with local (Exim 4.69) (envelope-from ) id 1Ruvxs-0002Dv-5D for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 02:04:52 +0100 Received: from 88-96-171-142.dsl.zen.co.uk ([88.96.171.142]) by main.gmane.org with esmtp (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Wed, 08 Feb 2012 02:04:52 +0100 Received: from martyn.jago by 88-96-171-142.dsl.zen.co.uk with local (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Wed, 08 Feb 2012 02:04:52 +0100 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: emacs-orgmode@gnu.org Hi Thomas and Eric Love it. I will try to help! Worg is a great resource that is getting better and better. The template looks good (Babel wise) and should be up there as a check-sheet, although maybe not as a requirement. Eric - perhaps mark good pages as good rather than bad pages. They're not necessarily bad? It would be cool to say [Tested 2 days ago] at the top of the page (in a nice green) or something like that. (or validation link in green / yellow / red) I also think that [Under development] should be removed from index.html. Worg is always under development, that's what it is? For anybody that is not that familiar with Worg, you can contribute to it right now - it's pure community. Best, Martyn tsd@tsdye.com (Thomas S. Dye) writes: > Hi Eric, > > I've attached a first draft of a template for review and revision. It > is heavily influenced by John Hendy's terrific gnuplot page. I > believe it incorporates the points in your outline. Feel free to > edit as appropriate. > > All the best, > Tom > > > #+OPTIONS: H:3 num:nil toc:2 \n:nil @:t ::t |:t ^:{} -:t f:t *:t TeX:t LaTeX:t skip:nil d:(HIDE) tags:not-in-toc > #+STARTUP: align fold nodlcheck hidestars oddeven lognotestate hideblocks > #+SEQ_TODO: TODO(t) INPROGRESS(i) WAITING(w@) | DONE(d) CANCELED(c@) > #+TAGS: Write(w) Update(u) Fix(f) Check(c) noexport(n) > #+TITLE: Language Source Code Blocks in Org Mode > #+AUTHOR: Your name > #+EMAIL: you[at]email[dot]org > #+LANGUAGE: en > #+STYLE: > #+LINK_UP: ../languages.php > #+LINK_HOME: http://orgmode.org/worg/ > #+EXPORT_EXCLUDE_TAGS: noexport > > #+name: banner > #+begin_html >
>

> Org Mode support for Language >

>

> > > >

>
> #+end_html > > * Template Checklist [0/13] :noexport: > - [ ] Revise #+TITLE: > - [ ] Indicate #+AUTHOR: > - [ ] Add #+EMAIL: > - [ ] Revise banner source block [0/3] > - [ ] Add link to a useful language web site > - [ ] Replace "Language" with language name > - [ ] Find a suitable graphic and use it to link to the language > web site > - [ ] Write an [[Introduction]] > - [ ] Describe [[Requirements%20and%20Setup][Requirements and Setup]] > - [ ] Replace "Language" with language name in [[Org%20Mode%20Features%20for%20Language%20Source%20Code%20Blocks][Org Mode Features for Language Source Code Blocks]] > - [ ] Specify [[Org%20Mode%20Configuration][Org Mode Configuration]] > - [ ] Describe [[Header%20Arguments][Header Arguments]] > - [ ] Describe support for [[Sessions]] > - [ ] Describe [[Result%20Types][Result Types]] > - [ ] Describe [[Other]] differences from supported languages > - [ ] Provide brief [[Examples%20of%20Use][Examples of Use]] > * Introduction > - Brief description of language. > - Range of typical uses within Org Mode. > - Link to this Org Mode file. > * Requirements and Setup > - Installation and configuration of language software > - Emacs configuration > * Org Mode Features for Language Source Code Blocks > ** Org Mode Configuration > - org-babel-do-load-languages > ** Header Arguments > - Language-specific default values > - Language-specific header arguments > ** Sessions > - Support or not > - Typical use for sessions > ** Result Types > - Which result types are supported? > ** Other > - Differences from other supported languages > * Examples of Use > - Hello World! > - Common uses > - Links to tutorials and other resources > > > Eric Schulte writes: > >> Hi Tom, >> >> tsd@tsdye.com (Thomas S. Dye) writes: >> >>> Hi Eric, >>> >>> Yes, this is overdue. I think your plan is a good one. >>> >>> Perhaps a few of the individual use cases could be moved to FIXME, >>> instead? I'm thinking here of Feiming Chen's R setup and some of my >>> contributions when I was experimenting writing LaTeX inside source >>> code blocks. The authors could resurrect these as they see fit. >>> >> >> I don't know what FIXME is, but if there is a way to keep the page in >> the worg git repository but remove it from the exported HTML then that >> sounds ideal. >> >>> >>> Hopefully, others will contribute use examples. My sense from reading >>> the list is there are many interesting ones. >>> >>> I'd like it if Org mode users designed a template for the language >>> specific pages. Currently, these seem to me a mixed bag and it would be >>> good to regularize them. >> >> The below is a modified version of a template which can be found in a >> couple of the existing language tutorials, I think it serves as a good >> starting point. >> >> - Install and Setup >> - Instillation and configuration of software (e.g., the language itself) >> - Configuration of Emacs (e.g., activate language, set command path) >> - Examples >> - Common ways to use the language in an Org-mode document >> - Special cases >> - are there any language-specific header arguments >> - does the language support session evaluation >> - does the language support all result types >> - is the language different from most babel languages >> (e.g., C is compiled before execution, ditaa returns files, etc...) >> >>> It would also be nice to have one for each of the supported languages. >>> There are 11 language specific pages now, which leaves quite a few >>> languages under-documented. >> >> (length org-babel-load-languages) ;; => 27 >> >> ls org-contrib/babel/languages/ob-doc-*|wc -l # => 11 >> >> It looks like we have at least 16 more to go before we hit full language >> coverage. Perhaps we should use the empty cells in the "documentation" >> column in the languages table at [1] as a sign up space for volunteers >> who would be willing to write a brief tutorial demonstrating usage of >> Org-mode with their favorite language. >> >> Moving forward this is likely something we could request of the >> contributors of new languages. >> >> Also, once the template above is finalized it should be posted on worg >> and linked to through the languages page. >> >>> >>> I'll be happy to work on this as I can. >>> >> >> Great, I don't anticipate having time to put towards this, although I'll >> be happy to help troubleshoot where I can. >> >> Cheers, >> >>> >>> All the best, >>> Tom >>> >>> >>> Eric Schulte writes: >>> >>>> Thanks for raising this point. The bulk of the content in the Babel >>>> portion of worg is fairly old, predating the syntax standardization >>>> efforts this fall. I've just pushed some minor updates to the main >>>> babel pages, but updating the language-specific tutorials and the >>>> individual use cases will be a much larger effort. >>>> >>>> I'm not sure how to proceed. One option would be to go through and add >>>> a [uses deprecated syntax] tag to the top of each such page, which could >>>> be removed after the page has been checked and possibly updated to >>>> ensure consistency with the latest syntax. >>>> >>>> Given that the Babel syntax will not be changing significantly moving >>>> forward now would be a good time to do such a review. Ideally this >>>> could be completed before the release of Emacs 24 in a couple of months. >>>> >>>> Any other ideas for update/reorganization or volunteers? >>>> >>>> Cheers, >>>> >>>> tsd@tsdye.com (Thomas S. Dye) writes: >>>> >>>>> Hi Riccardo, >>>>> >>>>> Thanks for the URL. Org mode has evolved since this article was >>>>> written. It should probably be revised or taken off Worg. I've copied >>>>> Eric Schulte, who is better able than me to determine the correct course >>>>> of action here. >>>>> >>>>> In the meantime, an up-to-date description of how Org mode can be used >>>>> to write literate programs has appeared in the Journal of Statistical >>>>> Software. You can find it here: http://www.jstatsoft.org/v46/i03 >>>>> >>>>> Perhaps you could use the examples in the JSS article to get started? >>>>> If these don't work for you, or if they raise questions that are difficult >>>>> to answer, please do come back to the list with your queries. >>>>> >>>>> All the best, >>>>> Tom >>>>> >>>>> Riccardo Romoli writes: >>>>> >>>>>> Hi, this is the URL: >>>>>> >>>>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html >>>>>> >>>>>> Best >>>>>> R >>>>>> >>>>>> 2012/2/5 Thomas S. Dye >>>>>> >>>>>>> Hi Riccardo, >>>>>>> >>>>>>> This code appears to be outdated. I don't recall this code on the org >>>>>>> site. Could you send a URL? >>>>>>> >>>>>>> All the best, >>>>>>> Tom >>>>>>> >>>>>>> Riccardo Romoli writes: >>>>>>> >>>>>>> > Hi, I'm trying to generate some figure with R, into an org session. >>>>>>> Firstly >>>>>>> > I use the code in the org site. The problem is that the code do not >>>>>>> > generate any figure. >>>>>>> > >>>>>>> > This is the code: >>>>>>> > >>>>>>> > #+TITLE:Test >>>>>>> > #+AUTHOR: Your Name >>>>>>> > #+EMAIL: your-email@server.com >>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>>> > both :tangle yes >>>>>>> > >>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>> > ** R text output >>>>>>> > A simple summary. >>>>>>> > #+begin_src R >>>>>>> > x <- rnorm(10) >>>>>>> > summary(x) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > ** R graphics output >>>>>>> > Note we use the object =x= generated in previous code block, thanks to >>>>>>> > the header option =:session *R*=. The output graphics file is >>>>>>> > =a.png=. >>>>>>> > >>>>>>> > #+begin_src R :file a.png >>>>>>> > y <- rnorm(10) >>>>>>> > plot(x, y) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > Same plot with larger dimension: >>>>>>> > >>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>> > plot(x, y) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > >>>>>>> > Where do I wrong? >>>>>>> > >>>>>>> > Best >>>>>>> > Riccardo >>>>>>> > Hi, I'm trying to generate some figure with R, into an org session. >>>>>>> Firstly I use the code in the org site. The problem is that the code do not >>>>>>> generate any figure. This is the code: >>>>>>> > #+TITLE:Test >>>>>>> > #+AUTHOR: Your Name >>>>>>> > #+EMAIL: mailto:your-email@server.com >>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports both >>>>>>> :tangle yes >>>>>>> > >>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>> > ** R text output >>>>>>> > A simple summary. >>>>>>> > #+begin_src R >>>>>>> > x <- rnorm(10) >>>>>>> > summary(x) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > ** R graphics output >>>>>>> > Note we use the object =x= generated in previous code block, thanks to >>>>>>> > the header option =:session *R*=. The output graphics file is >>>>>>> > =a.png=. >>>>>>> > >>>>>>> > #+begin_src R :file a.png >>>>>>> > y <- rnorm(10) >>>>>>> > plot(x, y) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > Same plot with larger dimension: >>>>>>> > >>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>> > plot(x, y) >>>>>>> > #+end_src >>>>>>> > Where do I wrong?BestRiccardo >>>>>>> >>>>>>> -- >>>>>>> Thomas S. Dye >>>>>>> http://www.tsdye.com >>>>>>> >>>>>> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.htmlBestR >>>>>> 2012/2/5 Thomas S. Dye Hi Riccardo, >>>>>> >>>>>> >>>>>> This code appears to be outdated.  I don't recall this code on the org >>>>>> site.  Could you send a URL? >>>>>> >>>>>> All the best, >>>>>> Tom >>>>>> >>>>>> Riccardo Romoli writes: >>>>>> >>>>>>> Hi, I'm trying to generate some figure with R, into an org session. Firstly >>>>>>> I use the code in the org site. The problem is that the code do not >>>>>>> generate any figure. >>>>>>> >>>>>>> This is the code: >>>>>>> >>>>>>> #+TITLE:Test >>>>>>> #+AUTHOR: Your Name >>>>>>> #+EMAIL: mailto:your-email@server.com >>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>>> both :tangle yes >>>>>>> >>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>> ** R text output >>>>>>> A simple summary. >>>>>>> #+begin_src R >>>>>>>   x <- rnorm(10) >>>>>>>   summary(x) >>>>>>> #+end_src >>>>>>> >>>>>>> ** R graphics output >>>>>>> Note we use the object =x= generated in previous code block, thanks to >>>>>>> the header option =:session *R*=.  The output graphics file is >>>>>>> =a.png=. >>>>>>> >>>>>>> #+begin_src R  :file a.png >>>>>>>   y <- rnorm(10) >>>>>>>   plot(x, y) >>>>>>> #+end_src >>>>>>> >>>>>>> Same plot with larger dimension: >>>>>>> >>>>>>> #+begin_src R  :file b.png :width 800 :height 800 >>>>>>>   plot(x, y) >>>>>>> #+end_src >>>>>>> >>>>>>> >>>>>>> Where do I wrong? >>>>>>> >>>>>>> Best >>>>>>> Riccardo >>>>>>> Hi, I'm trying to generate some figure with R, into an org >>>>>>> session. Firstly I use the code in the org site. The problem is >>>>>>> that the code do not generate any figure. This is the code: >>>>>>> #+TITLE:Test >>>>>>> #+AUTHOR: Your Name >>>>>>> #+EMAIL: mailto:mailto:your-email@server.com >>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes >>>>>>> >>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>> ** R text output >>>>>>> A simple summary. >>>>>>> #+begin_src R >>>>>>>   x <- rnorm(10) >>>>>>>   summary(x) >>>>>>> #+end_src >>>>>>> >>>>>>> ** R graphics output >>>>>>> Note we use the object =x= generated in previous code block, thanks to >>>>>>> the header option =:session *R*=.  The output graphics file is >>>>>>> =a.png=. >>>>>>> >>>>>>> #+begin_src R  :file a.png >>>>>>>   y <- rnorm(10) >>>>>>>   plot(x, y) >>>>>>> #+end_src >>>>>>> >>>>>>> Same plot with larger dimension: >>>>>>> >>>>>>> #+begin_src R  :file b.png :width 800 :height 800 >>>>>>>   plot(x, y) >>>>>>> #+end_src >>>>>>> Where do I wrong?BestRiccardo >>>>>> >>>>>> -- >>>>>> Thomas S. Dye >>>>>> http://www.tsdye.com >>>>>> >> >> >> Footnotes: >> [1] http://orgmode.org/worg/org-contrib/babel/languages.html From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Re: Updating the Babel section of Worg Date: Wed, 08 Feb 2012 07:14:15 -0700 Message-ID: <8762fhe76u.fsf@gmx.com> References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:54593) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rv8Q9-0000El-4s for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:22:59 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rv8Q3-0002pH-CP for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:22:53 -0500 Received: from mailout-us.gmx.com ([74.208.5.67]:49690) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1Rv8Q3-0002p0-5u for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:22:47 -0500 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: "Thomas S. Dye" Cc: emacs-orgmode@gnu.org, Riccardo Romoli tsd@tsdye.com (Thomas S. Dye) writes: > Hi Eric, > > I've attached a first draft of a template for review and revision. It > is heavily influenced by John Hendy's terrific gnuplot page. I > believe it incorporates the points in your outline. Feel free to > edit as appropriate. > Looks great to me. I made a small change, and I've just pushed it up to worg and linked to it from the languages page. We can continue to improve this template as needed on worg although I think it is already in very good shape and ready for use. Thanks, > > All the best, > Tom > > > > > Eric Schulte writes: > >> Hi Tom, >> >> tsd@tsdye.com (Thomas S. Dye) writes: >> >>> Hi Eric, >>> >>> Yes, this is overdue. I think your plan is a good one. >>> >>> Perhaps a few of the individual use cases could be moved to FIXME, >>> instead? I'm thinking here of Feiming Chen's R setup and some of my >>> contributions when I was experimenting writing LaTeX inside source >>> code blocks. The authors could resurrect these as they see fit. >>> >> >> I don't know what FIXME is, but if there is a way to keep the page in >> the worg git repository but remove it from the exported HTML then that >> sounds ideal. >> >>> >>> Hopefully, others will contribute use examples. My sense from reading >>> the list is there are many interesting ones. >>> >>> I'd like it if Org mode users designed a template for the language >>> specific pages. Currently, these seem to me a mixed bag and it would be >>> good to regularize them. >> >> The below is a modified version of a template which can be found in a >> couple of the existing language tutorials, I think it serves as a good >> starting point. >> >> - Install and Setup >> - Instillation and configuration of software (e.g., the language itsel= f) >> - Configuration of Emacs (e.g., activate language, set command path) >> - Examples >> - Common ways to use the language in an Org-mode document >> - Special cases >> - are there any language-specific header arguments >> - does the language support session evaluation >> - does the language support all result types >> - is the language different from most babel languages >> (e.g., C is compiled before execution, ditaa returns files, etc...) >> >>> It would also be nice to have one for each of the supported languages. >>> There are 11 language specific pages now, which leaves quite a few >>> languages under-documented. >> >> (length org-babel-load-languages) ;; =3D> 27 >> >> ls org-contrib/babel/languages/ob-doc-*|wc -l # =3D> 11 >> >> It looks like we have at least 16 more to go before we hit full language >> coverage. Perhaps we should use the empty cells in the "documentation" >> column in the languages table at [1] as a sign up space for volunteers >> who would be willing to write a brief tutorial demonstrating usage of >> Org-mode with their favorite language. >> >> Moving forward this is likely something we could request of the >> contributors of new languages. >> >> Also, once the template above is finalized it should be posted on worg >> and linked to through the languages page. >> >>> >>> I'll be happy to work on this as I can. >>> >> >> Great, I don't anticipate having time to put towards this, although I'll >> be happy to help troubleshoot where I can. >> >> Cheers, >> >>> >>> All the best, >>> Tom >>> >>> >>> Eric Schulte writes: >>> >>>> Thanks for raising this point. The bulk of the content in the Babel >>>> portion of worg is fairly old, predating the syntax standardization >>>> efforts this fall. I've just pushed some minor updates to the main >>>> babel pages, but updating the language-specific tutorials and the >>>> individual use cases will be a much larger effort. >>>> >>>> I'm not sure how to proceed. One option would be to go through and add >>>> a [uses deprecated syntax] tag to the top of each such page, which cou= ld >>>> be removed after the page has been checked and possibly updated to >>>> ensure consistency with the latest syntax. >>>> >>>> Given that the Babel syntax will not be changing significantly moving >>>> forward now would be a good time to do such a review. Ideally this >>>> could be completed before the release of Emacs 24 in a couple of month= s. >>>> >>>> Any other ideas for update/reorganization or volunteers? >>>> >>>> Cheers, >>>> >>>> tsd@tsdye.com (Thomas S. Dye) writes: >>>> >>>>> Hi Riccardo, >>>>> >>>>> Thanks for the URL. Org mode has evolved since this article was >>>>> written. It should probably be revised or taken off Worg. I've copi= ed >>>>> Eric Schulte, who is better able than me to determine the correct cou= rse >>>>> of action here. >>>>> >>>>> In the meantime, an up-to-date description of how Org mode can be used >>>>> to write literate programs has appeared in the Journal of Statistical >>>>> Software. You can find it here: http://www.jstatsoft.org/v46/i03 >>>>> >>>>> Perhaps you could use the examples in the JSS article to get started? >>>>> If these don't work for you, or if they raise questions that are diff= icult >>>>> to answer, please do come back to the list with your queries. >>>>> >>>>> All the best, >>>>> Tom >>>>> >>>>> Riccardo Romoli writes: >>>>> >>>>>> Hi, this is the URL: >>>>>> >>>>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R= .html >>>>>> >>>>>> Best >>>>>> R >>>>>> >>>>>> 2012/2/5 Thomas S. Dye >>>>>> >>>>>>> Hi Riccardo, >>>>>>> >>>>>>> This code appears to be outdated. I don't recall this code on the = org >>>>>>> site. Could you send a URL? >>>>>>> >>>>>>> All the best, >>>>>>> Tom >>>>>>> >>>>>>> Riccardo Romoli writes: >>>>>>> >>>>>>> > Hi, I'm trying to generate some figure with R, into an org sessio= n. >>>>>>> Firstly >>>>>>> > I use the code in the org site. The problem is that the code do n= ot >>>>>>> > generate any figure. >>>>>>> > >>>>>>> > This is the code: >>>>>>> > >>>>>>> > #+TITLE:Test >>>>>>> > #+AUTHOR: Your Name >>>>>>> > #+EMAIL: your-email@server.com >>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>>> > both :tangle yes >>>>>>> > >>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>> > ** R text output >>>>>>> > A simple summary. >>>>>>> > #+begin_src R >>>>>>> > x <- rnorm(10) >>>>>>> > summary(x) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > ** R graphics output >>>>>>> > Note we use the object =3Dx=3D generated in previous code block, = thanks to >>>>>>> > the header option =3D:session *R*=3D. The output graphics file is >>>>>>> > =3Da.png=3D. >>>>>>> > >>>>>>> > #+begin_src R :file a.png >>>>>>> > y <- rnorm(10) >>>>>>> > plot(x, y) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > Same plot with larger dimension: >>>>>>> > >>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>> > plot(x, y) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > >>>>>>> > Where do I wrong? >>>>>>> > >>>>>>> > Best >>>>>>> > Riccardo >>>>>>> > Hi, I'm trying to generate some figure with R, into an org se= ssion. >>>>>>> Firstly I use the code in the org site. The problem is that the cod= e do not >>>>>>> generate any figure. This is the code: >>>>>>> > #+TITLE:Test >>>>>>> > #+AUTHOR: Your Name >>>>>>> > #+EMAIL: mailto:your-email@server.com >>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :export= s both >>>>>>> :tangle yes >>>>>>> > >>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>> > ** R text output >>>>>>> > A simple summary. >>>>>>> > #+begin_src R >>>>>>> > x <- rnorm(10) >>>>>>> > summary(x) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > ** R graphics output >>>>>>> > Note we use the object =3Dx=3D generated in previous code block, = thanks to >>>>>>> > the header option =3D:session *R*=3D. The output graphics file is >>>>>>> > =3Da.png=3D. >>>>>>> > >>>>>>> > #+begin_src R :file a.png >>>>>>> > y <- rnorm(10) >>>>>>> > plot(x, y) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > Same plot with larger dimension: >>>>>>> > >>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>> > plot(x, y) >>>>>>> > #+end_src >>>>>>> > Where do I wrong?BestRiccardo >>>>>>> >>>>>>> -- >>>>>>> Thomas S. Dye >>>>>>> http://www.tsdye.com >>>>>>> >>>>>> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to= -use-Org-Babel-for-R.htmlBestR >>>>>> 2012/2/5 Thomas S. Dye Hi Riccardo, >>>>>> >>>>>> >>>>>> This code appears to be outdated. =C2=A0I don't recall this code= on the org >>>>>> site. =C2=A0Could you send a URL? >>>>>> >>>>>> All the best, >>>>>> Tom >>>>>> >>>>>> Riccardo Romoli writes: >>>>>> >>>>>>> Hi, I'm trying to generate some figure with R, into an org sess= ion. Firstly >>>>>>> I use the code in the org site. The problem is that the code do not >>>>>>> generate any figure. >>>>>>> >>>>>>> This is the code: >>>>>>> >>>>>>> #+TITLE:Test >>>>>>> #+AUTHOR: Your Name >>>>>>> #+EMAIL: mailto:your-email@server.com >>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>>> both :tangle yes >>>>>>> >>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>> ** R text output >>>>>>> A simple summary. >>>>>>> #+begin_src R >>>>>>> =C2=A0 x <- rnorm(10) >>>>>>> =C2=A0 summary(x) >>>>>>> #+end_src >>>>>>> >>>>>>> ** R graphics output >>>>>>> Note we use the object =3Dx=3D generated in previous code block, th= anks to >>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics fil= e is >>>>>>> =3Da.png=3D. >>>>>>> >>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>> =C2=A0 y <- rnorm(10) >>>>>>> =C2=A0 plot(x, y) >>>>>>> #+end_src >>>>>>> >>>>>>> Same plot with larger dimension: >>>>>>> >>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>> =C2=A0 plot(x, y) >>>>>>> #+end_src >>>>>>> >>>>>>> >>>>>>> Where do I wrong? >>>>>>> >>>>>>> Best >>>>>>> Riccardo >>>>>>> Hi, I'm trying to generate some figure with R, into an org >>>>>>> session. Firstly I use the code in the org site. The problem is >>>>>>> that the code do not generate any figure. This is the code: >>>>>>> #+TITLE:Test >>>>>>> #+AUTHOR: Your Name >>>>>>> #+EMAIL: mailto:mailto:your-email@server.com >>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports = both :tangle yes >>>>>>> >>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>> ** R text output >>>>>>> A simple summary. >>>>>>> #+begin_src R >>>>>>> =C2=A0 x <- rnorm(10) >>>>>>> =C2=A0 summary(x) >>>>>>> #+end_src >>>>>>> >>>>>>> ** R graphics output >>>>>>> Note we use the object =3Dx=3D generated in previous code block, th= anks to >>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics fil= e is >>>>>>> =3Da.png=3D. >>>>>>> >>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>> =C2=A0 y <- rnorm(10) >>>>>>> =C2=A0 plot(x, y) >>>>>>> #+end_src >>>>>>> >>>>>>> Same plot with larger dimension: >>>>>>> >>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>> =C2=A0 plot(x, y) >>>>>>> #+end_src >>>>>>> Where do I wrong?BestRiccardo >>>>>> >>>>>> -- >>>>>> Thomas S. Dye >>>>>> http://www.tsdye.com >>>>>> >> >> >> Footnotes:=20 >> [1] http://orgmode.org/worg/org-contrib/babel/languages.html --=20 Eric Schulte http://cs.unm.edu/~eschulte/ From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Re: Updating the Babel section of Worg Date: Wed, 08 Feb 2012 07:21:50 -0700 Message-ID: <87zkctcsma.fsf@gmx.com> References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:54601) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rv8QA-0000G0-H3 for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:23:01 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rv8Q5-0002pa-Du for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:22:54 -0500 Received: from mailout-us.gmx.com ([74.208.5.67]:43995) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1Rv8Q5-0002pU-4G for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:22:49 -0500 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: Martyn Jago Cc: emacs-orgmode@gnu.org Martyn Jago writes: > Hi Thomas and Eric > > Love it. I will try to help! > > Worg is a great resource that is getting better and better. > > The template looks good (Babel wise) and should be up there as a > check-sheet, although maybe not as a requirement. > I agree, I've just linked to it from the languages page [1] with the following statement. Please feel free to edit this directly on worg if it sounds too strong. Note: Many languages in this table still require documentation. A template is provided in the worg git repository for the addition of language documentation. > > Eric - perhaps mark good pages as good rather than bad pages. They're > not necessarily bad? > I agree, I don't think any of the pages are "bad". Rather some pages simply need to be updated to use the new standard syntax. In this case I would find it better to simply flag those pages which need to be updated, rather than litter all pages with tags. > > It would be cool to say [Tested 2 days ago] at the top of the page > (in a nice green) or something like that. (or validation link in green / > yellow / red) > I see you point, but the plan is that after this falls syntax standardization we should not be making any breaking changes moving forward, so a page from Dec 2011 should be as valid as a page from Jan 2013. > > I also think that [Under development] should be removed from > index.html. Worg is always under development, that's what it is? > I agree. > > For anybody that is not that familiar with Worg, you can contribute to > it right now - it's pure community. > ^ well said! | Cheers, > > Best, Martyn > > tsd@tsdye.com (Thomas S. Dye) writes: > >> Hi Eric, >> >> I've attached a first draft of a template for review and revision. It >> is heavily influenced by John Hendy's terrific gnuplot page. I >> believe it incorporates the points in your outline. Feel free to >> edit as appropriate. >> >> All the best, >> Tom >> >> >> #+OPTIONS: H:3 num:nil toc:2 \n:nil @:t ::t |:t ^:{} -:t f:t *:t TeX:= t LaTeX:t skip:nil d:(HIDE) tags:not-in-toc >> #+STARTUP: align fold nodlcheck hidestars oddeven lognotestate hidebl= ocks >> #+SEQ_TODO: TODO(t) INPROGRESS(i) WAITING(w@) | DONE(d) CANCELED(c@) >> #+TAGS: Write(w) Update(u) Fix(f) Check(c) noexport(n) >> #+TITLE: Language Source Code Blocks in Org Mode >> #+AUTHOR: Your name >> #+EMAIL: you[at]email[dot]org >> #+LANGUAGE: en >> #+STYLE: >> #+LINK_UP: ../languages.php >> #+LINK_HOME: http://orgmode.org/worg/ >> #+EXPORT_EXCLUDE_TAGS: noexport >> >> #+name: banner >> #+begin_html >>
>>

>> Org Mode support for Language >>

>>

>> >> >> >>

>>
>> #+end_html >> >> * Template Checklist [0/13] :noex= port: >> - [ ] Revise #+TITLE: >> - [ ] Indicate #+AUTHOR: >> - [ ] Add #+EMAIL: >> - [ ] Revise banner source block [0/3] >> - [ ] Add link to a useful language web site >> - [ ] Replace "Language" with language name >> - [ ] Find a suitable graphic and use it to link to the language >> web site >> - [ ] Write an [[Introduction]] >> - [ ] Describe [[Requirements%20and%20Setup][Requirements and Setup]] >> - [ ] Replace "Language" with language name in [[Org%20Mode%20Features= %20for%20Language%20Source%20Code%20Blocks][Org Mode Features for Language = Source Code Blocks]] >> - [ ] Specify [[Org%20Mode%20Configuration][Org Mode Configuration]] >> - [ ] Describe [[Header%20Arguments][Header Arguments]] >> - [ ] Describe support for [[Sessions]] >> - [ ] Describe [[Result%20Types][Result Types]] >> - [ ] Describe [[Other]] differences from supported languages >> - [ ] Provide brief [[Examples%20of%20Use][Examples of Use]] >> * Introduction >> - Brief description of language. >> - Range of typical uses within Org Mode. >> - Link to this Org Mode file. >> * Requirements and Setup >> - Installation and configuration of language software >> - Emacs configuration >> * Org Mode Features for Language Source Code Blocks >> ** Org Mode Configuration >> - org-babel-do-load-languages >> ** Header Arguments >> - Language-specific default values >> - Language-specific header arguments >> ** Sessions >> - Support or not >> - Typical use for sessions >> ** Result Types >> - Which result types are supported? >> ** Other >> - Differences from other supported languages >> * Examples of Use >> - Hello World! >> - Common uses >> - Links to tutorials and other resources >> >> >> Eric Schulte writes: >> >>> Hi Tom, >>> >>> tsd@tsdye.com (Thomas S. Dye) writes: >>> >>>> Hi Eric, >>>> >>>> Yes, this is overdue. I think your plan is a good one. >>>> >>>> Perhaps a few of the individual use cases could be moved to FIXME, >>>> instead? I'm thinking here of Feiming Chen's R setup and some of my >>>> contributions when I was experimenting writing LaTeX inside source >>>> code blocks. The authors could resurrect these as they see fit. >>>> >>> >>> I don't know what FIXME is, but if there is a way to keep the page in >>> the worg git repository but remove it from the exported HTML then that >>> sounds ideal. >>> >>>> >>>> Hopefully, others will contribute use examples. My sense from reading >>>> the list is there are many interesting ones. >>>> >>>> I'd like it if Org mode users designed a template for the language >>>> specific pages. Currently, these seem to me a mixed bag and it would = be >>>> good to regularize them. >>> >>> The below is a modified version of a template which can be found in a >>> couple of the existing language tutorials, I think it serves as a good >>> starting point. >>> >>> - Install and Setup >>> - Instillation and configuration of software (e.g., the language itse= lf) >>> - Configuration of Emacs (e.g., activate language, set command path) >>> - Examples >>> - Common ways to use the language in an Org-mode document >>> - Special cases >>> - are there any language-specific header arguments >>> - does the language support session evaluation >>> - does the language support all result types >>> - is the language different from most babel languages >>> (e.g., C is compiled before execution, ditaa returns files, etc...) >>> >>>> It would also be nice to have one for each of the supported languages. >>>> There are 11 language specific pages now, which leaves quite a few >>>> languages under-documented. >>> >>> (length org-babel-load-languages) ;; =3D> 27 >>> >>> ls org-contrib/babel/languages/ob-doc-*|wc -l # =3D> 11 >>> >>> It looks like we have at least 16 more to go before we hit full language >>> coverage. Perhaps we should use the empty cells in the "documentation" >>> column in the languages table at [1] as a sign up space for volunteers >>> who would be willing to write a brief tutorial demonstrating usage of >>> Org-mode with their favorite language. >>> >>> Moving forward this is likely something we could request of the >>> contributors of new languages. >>> >>> Also, once the template above is finalized it should be posted on worg >>> and linked to through the languages page. >>> >>>> >>>> I'll be happy to work on this as I can. >>>> >>> >>> Great, I don't anticipate having time to put towards this, although I'll >>> be happy to help troubleshoot where I can. >>> >>> Cheers, >>> >>>> >>>> All the best, >>>> Tom >>>> >>>> >>>> Eric Schulte writes: >>>> >>>>> Thanks for raising this point. The bulk of the content in the Babel >>>>> portion of worg is fairly old, predating the syntax standardization >>>>> efforts this fall. I've just pushed some minor updates to the main >>>>> babel pages, but updating the language-specific tutorials and the >>>>> individual use cases will be a much larger effort. >>>>> >>>>> I'm not sure how to proceed. One option would be to go through and a= dd >>>>> a [uses deprecated syntax] tag to the top of each such page, which co= uld >>>>> be removed after the page has been checked and possibly updated to >>>>> ensure consistency with the latest syntax. >>>>> >>>>> Given that the Babel syntax will not be changing significantly moving >>>>> forward now would be a good time to do such a review. Ideally this >>>>> could be completed before the release of Emacs 24 in a couple of mont= hs. >>>>> >>>>> Any other ideas for update/reorganization or volunteers? >>>>> >>>>> Cheers, >>>>> >>>>> tsd@tsdye.com (Thomas S. Dye) writes: >>>>> >>>>>> Hi Riccardo, >>>>>> >>>>>> Thanks for the URL. Org mode has evolved since this article was >>>>>> written. It should probably be revised or taken off Worg. I've cop= ied >>>>>> Eric Schulte, who is better able than me to determine the correct co= urse >>>>>> of action here. >>>>>> >>>>>> In the meantime, an up-to-date description of how Org mode can be us= ed >>>>>> to write literate programs has appeared in the Journal of Statistical >>>>>> Software. You can find it here: http://www.jstatsoft.org/v46/i03 >>>>>> >>>>>> Perhaps you could use the examples in the JSS article to get started? >>>>>> If these don't work for you, or if they raise questions that are dif= ficult >>>>>> to answer, please do come back to the list with your queries. >>>>>> >>>>>> All the best, >>>>>> Tom >>>>>> >>>>>> Riccardo Romoli writes: >>>>>> >>>>>>> Hi, this is the URL: >>>>>>> >>>>>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-= R.html >>>>>>> >>>>>>> Best >>>>>>> R >>>>>>> >>>>>>> 2012/2/5 Thomas S. Dye >>>>>>> >>>>>>>> Hi Riccardo, >>>>>>>> >>>>>>>> This code appears to be outdated. I don't recall this code on the= org >>>>>>>> site. Could you send a URL? >>>>>>>> >>>>>>>> All the best, >>>>>>>> Tom >>>>>>>> >>>>>>>> Riccardo Romoli writes: >>>>>>>> >>>>>>>> > Hi, I'm trying to generate some figure with R, into an org sessi= on. >>>>>>>> Firstly >>>>>>>> > I use the code in the org site. The problem is that the code do = not >>>>>>>> > generate any figure. >>>>>>>> > >>>>>>>> > This is the code: >>>>>>>> > >>>>>>>> > #+TITLE:Test >>>>>>>> > #+AUTHOR: Your Name >>>>>>>> > #+EMAIL: your-email@server.com >>>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :expor= ts >>>>>>>> > both :tangle yes >>>>>>>> > >>>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>>> > ** R text output >>>>>>>> > A simple summary. >>>>>>>> > #+begin_src R >>>>>>>> > x <- rnorm(10) >>>>>>>> > summary(x) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > ** R graphics output >>>>>>>> > Note we use the object =3Dx=3D generated in previous code block,= thanks to >>>>>>>> > the header option =3D:session *R*=3D. The output graphics file = is >>>>>>>> > =3Da.png=3D. >>>>>>>> > >>>>>>>> > #+begin_src R :file a.png >>>>>>>> > y <- rnorm(10) >>>>>>>> > plot(x, y) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > Same plot with larger dimension: >>>>>>>> > >>>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>>> > plot(x, y) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > >>>>>>>> > Where do I wrong? >>>>>>>> > >>>>>>>> > Best >>>>>>>> > Riccardo >>>>>>>> > Hi, I'm trying to generate some figure with R, into an org s= ession. >>>>>>>> Firstly I use the code in the org site. The problem is that the co= de do not >>>>>>>> generate any figure. This is the code: >>>>>>>> > #+TITLE:Test >>>>>>>> > #+AUTHOR: Your Name >>>>>>>> > #+EMAIL: mailto:your-email@server.com >>>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :expor= ts both >>>>>>>> :tangle yes >>>>>>>> > >>>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>>> > ** R text output >>>>>>>> > A simple summary. >>>>>>>> > #+begin_src R >>>>>>>> > x <- rnorm(10) >>>>>>>> > summary(x) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > ** R graphics output >>>>>>>> > Note we use the object =3Dx=3D generated in previous code block,= thanks to >>>>>>>> > the header option =3D:session *R*=3D. The output graphics file = is >>>>>>>> > =3Da.png=3D. >>>>>>>> > >>>>>>>> > #+begin_src R :file a.png >>>>>>>> > y <- rnorm(10) >>>>>>>> > plot(x, y) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > Same plot with larger dimension: >>>>>>>> > >>>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>>> > plot(x, y) >>>>>>>> > #+end_src >>>>>>>> > Where do I wrong?BestRiccardo >>>>>>>> >>>>>>>> -- >>>>>>>> Thomas S. Dye >>>>>>>> http://www.tsdye.com >>>>>>>> >>>>>>> Hi, this is the >>>>>>> URL:http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-= for-R.htmlBestR >>>>>>> 2012/2/5 Thomas S. Dye Hi Riccardo, >>>>>>> >>>>>>> >>>>>>> This code appears to be outdated. =C2=A0I don't recall this cod= e on the org >>>>>>> site. =C2=A0Could you send a URL? >>>>>>> >>>>>>> All the best, >>>>>>> Tom >>>>>>> >>>>>>> Riccardo Romoli writes: >>>>>>> >>>>>>>> Hi, I'm trying to generate some figure with R, into an org ses= sion. Firstly >>>>>>>> I use the code in the org site. The problem is that the code do not >>>>>>>> generate any figure. >>>>>>>> >>>>>>>> This is the code: >>>>>>>> >>>>>>>> #+TITLE:Test >>>>>>>> #+AUTHOR: Your Name >>>>>>>> #+EMAIL: mailto:your-email@server.com >>>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>>>> both :tangle yes >>>>>>>> >>>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>>> ** R text output >>>>>>>> A simple summary. >>>>>>>> #+begin_src R >>>>>>>> =C2=A0 x <- rnorm(10) >>>>>>>> =C2=A0 summary(x) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> ** R graphics output >>>>>>>> Note we use the object =3Dx=3D generated in previous code block, t= hanks to >>>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics fi= le is >>>>>>>> =3Da.png=3D. >>>>>>>> >>>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>>> =C2=A0 y <- rnorm(10) >>>>>>>> =C2=A0 plot(x, y) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> Same plot with larger dimension: >>>>>>>> >>>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>>> =C2=A0 plot(x, y) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> >>>>>>>> Where do I wrong? >>>>>>>> >>>>>>>> Best >>>>>>>> Riccardo >>>>>>>> Hi, I'm trying to generate some figure with R, into an org >>>>>>>> session. Firstly I use the code in the org site. The problem is >>>>>>>> that the code do not generate any figure. This is the code: >>>>>>>> #+TITLE:Test >>>>>>>> #+AUTHOR: Your Name >>>>>>>> #+EMAIL: mailto:mailto:your-email@server.com >>>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports= both :tangle yes >>>>>>>> >>>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>>> ** R text output >>>>>>>> A simple summary. >>>>>>>> #+begin_src R >>>>>>>> =C2=A0 x <- rnorm(10) >>>>>>>> =C2=A0 summary(x) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> ** R graphics output >>>>>>>> Note we use the object =3Dx=3D generated in previous code block, t= hanks to >>>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics fi= le is >>>>>>>> =3Da.png=3D. >>>>>>>> >>>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>>> =C2=A0 y <- rnorm(10) >>>>>>>> =C2=A0 plot(x, y) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> Same plot with larger dimension: >>>>>>>> >>>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>>> =C2=A0 plot(x, y) >>>>>>>> #+end_src >>>>>>>> Where do I wrong?BestRiccardo >>>>>>> >>>>>>> -- >>>>>>> Thomas S. Dye >>>>>>> http://www.tsdye.com >>>>>>> >>> >>> >>> Footnotes:=20 >>> [1] http://orgmode.org/worg/org-contrib/babel/languages.html > > Footnotes:=20 [1] http://orgmode.org/worg/org-contrib/babel/languages.html --=20 Eric Schulte http://cs.unm.edu/~eschulte/ From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rainer M Krug Subject: Re: Updating the Babel section of Worg Date: Wed, 08 Feb 2012 15:44:06 +0100 Message-ID: <4F328A36.9010501@gmail.com> References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> <87zkctcsma.fsf@gmx.com> Reply-To: R.M.Krug@gmail.com Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([140.186.70.92]:40390) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rv8ks-0008OM-CE for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:44:25 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rv8kl-00083k-Cn for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:44:18 -0500 Received: from mail-we0-f169.google.com ([74.125.82.169]:34966) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rv8kl-00083U-1d for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:44:11 -0500 Received: by wera13 with SMTP id a13so551190wer.0 for ; Wed, 08 Feb 2012 06:44:10 -0800 (PST) In-Reply-To: <87zkctcsma.fsf@gmx.com> 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: Eric Schulte Cc: Martyn Jago , emacs-orgmode@gnu.org -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 08/02/12 15:21, Eric Schulte wrote: > Martyn Jago writes: > >> Hi Thomas and Eric >> >> Love it. I will try to help! >> >> Worg is a great resource that is getting better and better. >> >> The template looks good (Babel wise) and should be up there as a >> check-sheet, although maybe not as a requirement. >> > > I agree, I've just linked to it from the languages page [1] with > the following statement. Please feel free to edit this directly on > worg if it sounds too strong. Nice - I will take a look at it. Just to make it easier for non-regular worg contributors: I would suggest to give an email where one can send the completed template to to be submitted to worg. Rainer > > Note: Many languages in this table still require documentation. A > template is provided in the worg git repository for the addition > of language documentation. > >> >> Eric - perhaps mark good pages as good rather than bad pages. >> They're not necessarily bad? >> > > I agree, I don't think any of the pages are "bad". Rather some > pages simply need to be updated to use the new standard syntax. In > this case I would find it better to simply flag those pages which > need to be updated, rather than litter all pages with tags. > >> >> It would be cool to say [Tested 2 days ago] at the top of the >> page (in a nice green) or something like that. (or validation >> link in green / yellow / red) >> > > I see you point, but the plan is that after this falls syntax > standardization we should not be making any breaking changes > moving forward, so a page from Dec 2011 should be as valid as a > page from Jan 2013. > >> >> I also think that [Under development] should be removed from >> index.html. Worg is always under development, that's what it is? >> > > I agree. > >> >> For anybody that is not that familiar with Worg, you can >> contribute to it right now - it's pure community. >> > ^ well said! | > > Cheers, > >> >> Best, Martyn >> >> tsd@tsdye.com (Thomas S. Dye) writes: >> >>> Hi Eric, >>> >>> I've attached a first draft of a template for review and >>> revision. It is heavily influenced by John Hendy's terrific >>> gnuplot page. I believe it incorporates the points in your >>> outline. Feel free to edit as appropriate. >>> >>> All the best, Tom >>> >>> >>> #+OPTIONS: H:3 num:nil toc:2 \n:nil @:t ::t |:t ^:{} -:t f:t >>> *:t TeX:t LaTeX:t skip:nil d:(HIDE) tags:not-in-toc #+STARTUP: >>> align fold nodlcheck hidestars oddeven lognotestate hideblocks >>> #+SEQ_TODO: TODO(t) INPROGRESS(i) WAITING(w@) | DONE(d) >>> CANCELED(c@) #+TAGS: Write(w) Update(u) Fix(f) Check(c) >>> noexport(n) #+TITLE: Language Source Code Blocks in Org >>> Mode #+AUTHOR: Your name #+EMAIL: >>> you[at]email[dot]org #+LANGUAGE: en #+STYLE: #+LINK_UP: ../languages.php #+LINK_HOME: >>> http://orgmode.org/worg/ #+EXPORT_EXCLUDE_TAGS: noexport >>> >>> #+name: banner #+begin_html >>> #+end_html >>> >>> * Template Checklist [0/13] >>> :noexport: - [ ] Revise #+TITLE: - [ ] Indicate #+AUTHOR: - [ ] >>> Add #+EMAIL: - [ ] Revise banner source block [0/3] - [ ] Add >>> link to a useful language web site - [ ] Replace "Language" >>> with language name - [ ] Find a suitable graphic and use it to >>> link to the language web site - [ ] Write an [[Introduction]] - >>> [ ] Describe [[Requirements%20and%20Setup][Requirements and >>> Setup]] - [ ] Replace "Language" with language name in >>> [[Org%20Mode%20Features%20for%20Language%20Source%20Code%20Blocks][Org >>> Mode Features for Language Source Code Blocks]] - [ ] Specify >>> [[Org%20Mode%20Configuration][Org Mode Configuration]] - [ ] >>> Describe [[Header%20Arguments][Header Arguments]] - [ ] >>> Describe support for [[Sessions]] - [ ] Describe >>> [[Result%20Types][Result Types]] - [ ] Describe [[Other]] >>> differences from supported languages - [ ] Provide brief >>> [[Examples%20of%20Use][Examples of Use]] * Introduction - Brief >>> description of language. - Range of typical uses within Org >>> Mode. - Link to this Org Mode file. * Requirements and Setup - >>> Installation and configuration of language software - Emacs >>> configuration * Org Mode Features for Language Source Code >>> Blocks ** Org Mode Configuration - org-babel-do-load-languages >>> ** Header Arguments - Language-specific default values - >>> Language-specific header arguments ** Sessions - Support or >>> not - Typical use for sessions ** Result Types - Which result >>> types are supported? ** Other - Differences from other >>> supported languages * Examples of Use - Hello World! - Common >>> uses - Links to tutorials and other resources >>> >>> >>> Eric Schulte writes: >>> >>>> Hi Tom, >>>> >>>> tsd@tsdye.com (Thomas S. Dye) writes: >>>> >>>>> Hi Eric, >>>>> >>>>> Yes, this is overdue. I think your plan is a good one. >>>>> >>>>> Perhaps a few of the individual use cases could be moved to >>>>> FIXME, instead? I'm thinking here of Feiming Chen's R >>>>> setup and some of my contributions when I was experimenting >>>>> writing LaTeX inside source code blocks. The authors could >>>>> resurrect these as they see fit. >>>>> >>>> >>>> I don't know what FIXME is, but if there is a way to keep the >>>> page in the worg git repository but remove it from the >>>> exported HTML then that sounds ideal. >>>> >>>>> >>>>> Hopefully, others will contribute use examples. My sense >>>>> from reading the list is there are many interesting ones. >>>>> >>>>> I'd like it if Org mode users designed a template for the >>>>> language specific pages. Currently, these seem to me a >>>>> mixed bag and it would be good to regularize them. >>>> >>>> The below is a modified version of a template which can be >>>> found in a couple of the existing language tutorials, I think >>>> it serves as a good starting point. >>>> >>>> - Install and Setup - Instillation and configuration of >>>> software (e.g., the language itself) - Configuration of Emacs >>>> (e.g., activate language, set command path) - Examples - >>>> Common ways to use the language in an Org-mode document - >>>> Special cases - are there any language-specific header >>>> arguments - does the language support session evaluation - >>>> does the language support all result types - is the language >>>> different from most babel languages (e.g., C is compiled >>>> before execution, ditaa returns files, etc...) >>>> >>>>> It would also be nice to have one for each of the supported >>>>> languages. There are 11 language specific pages now, which >>>>> leaves quite a few languages under-documented. >>>> >>>> (length org-babel-load-languages) ;; => 27 >>>> >>>> ls org-contrib/babel/languages/ob-doc-*|wc -l # => 11 >>>> >>>> It looks like we have at least 16 more to go before we hit >>>> full language coverage. Perhaps we should use the empty >>>> cells in the "documentation" column in the languages table at >>>> [1] as a sign up space for volunteers who would be willing to >>>> write a brief tutorial demonstrating usage of Org-mode with >>>> their favorite language. >>>> >>>> Moving forward this is likely something we could request of >>>> the contributors of new languages. >>>> >>>> Also, once the template above is finalized it should be >>>> posted on worg and linked to through the languages page. >>>> >>>>> >>>>> I'll be happy to work on this as I can. >>>>> >>>> >>>> Great, I don't anticipate having time to put towards this, >>>> although I'll be happy to help troubleshoot where I can. >>>> >>>> Cheers, >>>> >>>>> >>>>> All the best, Tom >>>>> >>>>> >>>>> Eric Schulte writes: >>>>> >>>>>> Thanks for raising this point. The bulk of the content >>>>>> in the Babel portion of worg is fairly old, predating the >>>>>> syntax standardization efforts this fall. I've just >>>>>> pushed some minor updates to the main babel pages, but >>>>>> updating the language-specific tutorials and the >>>>>> individual use cases will be a much larger effort. >>>>>> >>>>>> I'm not sure how to proceed. One option would be to go >>>>>> through and add a [uses deprecated syntax] tag to the top >>>>>> of each such page, which could be removed after the page >>>>>> has been checked and possibly updated to ensure >>>>>> consistency with the latest syntax. >>>>>> >>>>>> Given that the Babel syntax will not be changing >>>>>> significantly moving forward now would be a good time to >>>>>> do such a review. Ideally this could be completed before >>>>>> the release of Emacs 24 in a couple of months. >>>>>> >>>>>> Any other ideas for update/reorganization or volunteers? >>>>>> >>>>>> Cheers, >>>>>> >>>>>> tsd@tsdye.com (Thomas S. Dye) writes: >>>>>> >>>>>>> Hi Riccardo, >>>>>>> >>>>>>> Thanks for the URL. Org mode has evolved since this >>>>>>> article was written. It should probably be revised or >>>>>>> taken off Worg. I've copied Eric Schulte, who is >>>>>>> better able than me to determine the correct course of >>>>>>> action here. >>>>>>> >>>>>>> In the meantime, an up-to-date description of how Org >>>>>>> mode can be used to write literate programs has >>>>>>> appeared in the Journal of Statistical Software. You >>>>>>> can find it here: http://www.jstatsoft.org/v46/i03 >>>>>>> >>>>>>> Perhaps you could use the examples in the JSS article >>>>>>> to get started? If these don't work for you, or if they >>>>>>> raise questions that are difficult to answer, please do >>>>>>> come back to the list with your queries. >>>>>>> >>>>>>> All the best, Tom >>>>>>> >>>>>>> Riccardo Romoli writes: >>>>>>> >>>>>>>> Hi, this is the URL: >>>>>>>> >>>>>>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html >>>>>>>> >>>>>>>> >>>>>>>> Best >>>>>>>> R >>>>>>>> >>>>>>>> 2012/2/5 Thomas S. Dye >>>>>>>> >>>>>>>>> Hi Riccardo, >>>>>>>>> >>>>>>>>> This code appears to be outdated. I don't recall >>>>>>>>> this code on the org site. Could you send a URL? >>>>>>>>> >>>>>>>>> All the best, Tom >>>>>>>>> >>>>>>>>> Riccardo Romoli writes: >>>>>>>>> >>>>>>>>>> Hi, I'm trying to generate some figure with R, >>>>>>>>>> into an org session. >>>>>>>>> Firstly >>>>>>>>>> I use the code in the org site. The problem is >>>>>>>>>> that the code do not generate any figure. >>>>>>>>>> >>>>>>>>>> This is the code: >>>>>>>>>> >>>>>>>>>> #+TITLE:Test #+AUTHOR: Your Name #+EMAIL: >>>>>>>>>> your-email@server.com #+BABEL: :session *R* >>>>>>>>>> :cache yes :results output graphics :exports both >>>>>>>>>> :tangle yes >>>>>>>>>> >>>>>>>>>> * Example of Org-Babel for R Literate >>>>>>>>>> Programming ** R text output A simple summary. >>>>>>>>>> #+begin_src R x <- rnorm(10) summary(x) >>>>>>>>>> #+end_src >>>>>>>>>> >>>>>>>>>> ** R graphics output Note we use the object =x= >>>>>>>>>> generated in previous code block, thanks to the >>>>>>>>>> header option =:session *R*=. The output >>>>>>>>>> graphics file is =a.png=. >>>>>>>>>> >>>>>>>>>> #+begin_src R :file a.png y <- rnorm(10) plot(x, >>>>>>>>>> y) #+end_src >>>>>>>>>> >>>>>>>>>> Same plot with larger dimension: >>>>>>>>>> >>>>>>>>>> #+begin_src R :file b.png :width 800 :height >>>>>>>>>> 800 plot(x, y) #+end_src >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Where do I wrong? >>>>>>>>>> >>>>>>>>>> Best Riccardo Hi, I'm trying to generate some >>>>>>>>>> figure with R, into an org session. >>>>>>>>> Firstly I use the code in the org site. The problem >>>>>>>>> is that the code do not generate any figure. This >>>>>>>>> is the code: >>>>>>>>>> #+TITLE:Test #+AUTHOR: Your Name #+EMAIL: >>>>>>>>>> mailto:your-email@server.com #+BABEL: :session >>>>>>>>>> *R* :cache yes :results output graphics :exports >>>>>>>>>> both >>>>>>>>> :tangle yes >>>>>>>>>> >>>>>>>>>> * Example of Org-Babel for R Literate >>>>>>>>>> Programming ** R text output A simple summary. >>>>>>>>>> #+begin_src R x <- rnorm(10) summary(x) >>>>>>>>>> #+end_src >>>>>>>>>> >>>>>>>>>> ** R graphics output Note we use the object =x= >>>>>>>>>> generated in previous code block, thanks to the >>>>>>>>>> header option =:session *R*=. The output >>>>>>>>>> graphics file is =a.png=. >>>>>>>>>> >>>>>>>>>> #+begin_src R :file a.png y <- rnorm(10) plot(x, >>>>>>>>>> y) #+end_src >>>>>>>>>> >>>>>>>>>> Same plot with larger dimension: >>>>>>>>>> >>>>>>>>>> #+begin_src R :file b.png :width 800 :height >>>>>>>>>> 800 plot(x, y) #+end_src Where do I >>>>>>>>>> wrong?BestRiccardo >>>>>>>>> >>>>>>>>> -- Thomas S. Dye http://www.tsdye.com >>>>>>>>> >>>>>>>> Hi, this is the >>>>>>>> URL:http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.htmlBestR >>>>>>>> >>>>>>>> 2012/2/5 Thomas S. Dye Hi Riccardo, >>>>>>>> >>>>>>>> >>>>>>>> This code appears to be outdated. I don't recall >>>>>>>> this code on the org site. Could you send a URL? >>>>>>>> >>>>>>>> All the best, Tom >>>>>>>> >>>>>>>> Riccardo Romoli >>>>>>>> writes: >>>>>>>> >>>>>>>>> Hi, I'm trying to generate some figure with R, >>>>>>>>> into an org session. Firstly I use the code in the >>>>>>>>> org site. The problem is that the code do not >>>>>>>>> generate any figure. >>>>>>>>> >>>>>>>>> This is the code: >>>>>>>>> >>>>>>>>> #+TITLE:Test #+AUTHOR: Your Name #+EMAIL: >>>>>>>>> mailto:your-email@server.com #+BABEL: :session *R* >>>>>>>>> :cache yes :results output graphics :exports both >>>>>>>>> :tangle yes >>>>>>>>> >>>>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>>>> ** R text output A simple summary. #+begin_src R x >>>>>>>>> <- rnorm(10) summary(x) #+end_src >>>>>>>>> >>>>>>>>> ** R graphics output Note we use the object =x= >>>>>>>>> generated in previous code block, thanks to the >>>>>>>>> header option =:session *R*=. The output graphics >>>>>>>>> file is =a.png=. >>>>>>>>> >>>>>>>>> #+begin_src R :file a.png y <- rnorm(10) plot(x, >>>>>>>>> y) #+end_src >>>>>>>>> >>>>>>>>> Same plot with larger dimension: >>>>>>>>> >>>>>>>>> #+begin_src R :file b.png :width 800 :height 800 >>>>>>>>> plot(x, y) #+end_src >>>>>>>>> >>>>>>>>> >>>>>>>>> Where do I wrong? >>>>>>>>> >>>>>>>>> Best Riccardo Hi, I'm trying to generate some >>>>>>>>> figure with R, into an org session. Firstly I use >>>>>>>>> the code in the org site. The problem is that the >>>>>>>>> code do not generate any figure. This is the code: >>>>>>>>> #+TITLE:Test #+AUTHOR: Your Name #+EMAIL: >>>>>>>>> mailto:mailto:your-email@server.com #+BABEL: >>>>>>>>> :session *R* :cache yes :results output graphics >>>>>>>>> :exports both :tangle yes >>>>>>>>> >>>>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>>>> ** R text output A simple summary. #+begin_src R x >>>>>>>>> <- rnorm(10) summary(x) #+end_src >>>>>>>>> >>>>>>>>> ** R graphics output Note we use the object =x= >>>>>>>>> generated in previous code block, thanks to the >>>>>>>>> header option =:session *R*=. The output graphics >>>>>>>>> file is =a.png=. >>>>>>>>> >>>>>>>>> #+begin_src R :file a.png y <- rnorm(10) plot(x, >>>>>>>>> y) #+end_src >>>>>>>>> >>>>>>>>> Same plot with larger dimension: >>>>>>>>> >>>>>>>>> #+begin_src R :file b.png :width 800 :height 800 >>>>>>>>> plot(x, y) #+end_src Where do I wrong?BestRiccardo >>>>>>>> >>>>>>>> -- Thomas S. Dye >>>>>>>> http://www.tsdye.com >>>> >>>> >>>> Footnotes: [1] >>>> http://orgmode.org/worg/org-contrib/babel/languages.html >> >> > > > Footnotes: [1] > http://orgmode.org/worg/org-contrib/babel/languages.html > - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: Rainer@krugs.de Skype: RMkrug -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk8yijYACgkQoYgNqgF2egrYOgCePUalLt/aey4qysCIwfXsJC3i Z7oAni4fmMDJbQpnEiHcu7KwQ3/eo14I =hls7 -----END PGP SIGNATURE----- From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Hendy Subject: Re: Updating the Babel section of Worg Date: Wed, 8 Feb 2012 09:41:11 -0600 Message-ID: References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:33154) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rv9e5-0002pP-IE for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 10:41:27 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rv9dz-0002Z6-0z for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 10:41:21 -0500 Received: from mail-bk0-f41.google.com ([209.85.214.41]:33463) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rv9dy-0002Yt-Lz for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 10:41:14 -0500 Received: by bkty12 with SMTP id y12so742224bkt.0 for ; Wed, 08 Feb 2012 07:41:13 -0800 (PST) In-Reply-To: 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: "Thomas S. Dye" Cc: emacs-orgmode@gnu.org, Eric Schulte , Riccardo Romoli On Tue, Feb 7, 2012 at 6:01 PM, Thomas S. Dye wrote: > Hi Eric, > > I've attached a first draft of a template for review and revision. =C2=A0= It > is heavily influenced by John Hendy's terrific gnuplot page. =C2=A0I > believe it incorporates the points in your outline. =C2=A0Feel free to > edit as appropriate. > Thanks for the kind words. I give the credit to Nick Dokos and Eric Schulte for encouraging me to post my solution on Worg once I found it. -- http://www.mail-archive.com/emacs-orgmode@gnu.org/msg28995.html I hate to say it, but without that nudge I might have "dined and dashed" -- gotten help from the list, solved the issue, and then returned to my cave :) Glad it proved useful! Best regards, John > All the best, > Tom > > > > > Eric Schulte writes: > >> Hi Tom, >> >> tsd@tsdye.com (Thomas S. Dye) writes: >> >>> Hi Eric, >>> >>> Yes, this is overdue. =C2=A0I think your plan is a good one. >>> >>> Perhaps a few of the individual use cases could be moved to FIXME, >>> instead? =C2=A0I'm thinking here of Feiming Chen's R setup and some of = my >>> contributions when I was experimenting writing LaTeX inside source >>> code blocks. =C2=A0The authors could resurrect these as they see fit. >>> >> >> I don't know what FIXME is, but if there is a way to keep the page in >> the worg git repository but remove it from the exported HTML then that >> sounds ideal. >> >>> >>> Hopefully, others will contribute use examples. =C2=A0My sense from rea= ding >>> the list is there are many interesting ones. >>> >>> I'd like it if Org mode users designed a template for the language >>> specific pages. =C2=A0Currently, these seem to me a mixed bag and it wo= uld be >>> good to regularize them. >> >> The below is a modified version of a template which can be found in a >> couple of the existing language tutorials, I think it serves as a good >> starting point. >> >> - Install and Setup >> =C2=A0 - Instillation and configuration of software (e.g., the language = itself) >> =C2=A0 - Configuration of Emacs (e.g., activate language, set command pa= th) >> - Examples >> =C2=A0 - Common ways to use the language in an Org-mode document >> - Special cases >> =C2=A0 - are there any language-specific header arguments >> =C2=A0 - does the language support session evaluation >> =C2=A0 - does the language support all result types >> =C2=A0 - is the language different from most babel languages >> =C2=A0 =C2=A0 (e.g., C is compiled before execution, ditaa returns files= , etc...) >> >>> It would also be nice to have one for each of the supported languages. >>> There are 11 language specific pages now, which leaves quite a few >>> languages under-documented. >> >> (length org-babel-load-languages) ;; =3D> 27 >> >> ls org-contrib/babel/languages/ob-doc-*|wc -l # =3D> 11 >> >> It looks like we have at least 16 more to go before we hit full language >> coverage. =C2=A0Perhaps we should use the empty cells in the "documentat= ion" >> column in the languages table at [1] as a sign up space for volunteers >> who would be willing to write a brief tutorial demonstrating usage of >> Org-mode with their favorite language. >> >> Moving forward this is likely something we could request of the >> contributors of new languages. >> >> Also, once the template above is finalized it should be posted on worg >> and linked to through the languages page. >> >>> >>> I'll be happy to work on this as I can. >>> >> >> Great, I don't anticipate having time to put towards this, although I'll >> be happy to help troubleshoot where I can. >> >> Cheers, >> >>> >>> All the best, >>> Tom >>> >>> >>> Eric Schulte writes: >>> >>>> Thanks for raising this point. =C2=A0The bulk of the content in the Ba= bel >>>> portion of worg is fairly old, predating the syntax standardization >>>> efforts this fall. =C2=A0I've just pushed some minor updates to the ma= in >>>> babel pages, but updating the language-specific tutorials and the >>>> individual use cases will be a much larger effort. >>>> >>>> I'm not sure how to proceed. =C2=A0One option would be to go through a= nd add >>>> a [uses deprecated syntax] tag to the top of each such page, which cou= ld >>>> be removed after the page has been checked and possibly updated to >>>> ensure consistency with the latest syntax. >>>> >>>> Given that the Babel syntax will not be changing significantly moving >>>> forward now would be a good time to do such a review. =C2=A0Ideally th= is >>>> could be completed before the release of Emacs 24 in a couple of month= s. >>>> >>>> Any other ideas for update/reorganization or volunteers? >>>> >>>> Cheers, >>>> >>>> tsd@tsdye.com (Thomas S. Dye) writes: >>>> >>>>> Hi Riccardo, >>>>> >>>>> Thanks for the URL. =C2=A0Org mode has evolved since this article was >>>>> written. =C2=A0It should probably be revised or taken off Worg. =C2= =A0I've copied >>>>> Eric Schulte, who is better able than me to determine the correct cou= rse >>>>> of action here. >>>>> >>>>> In the meantime, an up-to-date description of how Org mode can be use= d >>>>> to write literate programs has appeared in the Journal of Statistical >>>>> Software. =C2=A0You can find it here: http://www.jstatsoft.org/v46/i0= 3 >>>>> >>>>> Perhaps you could use the examples in the JSS article to get started? >>>>> If these don't work for you, or if they raise questions that are diff= icult >>>>> to answer, please do come back to the list with your queries. >>>>> >>>>> All the best, >>>>> Tom >>>>> >>>>> Riccardo Romoli writes: >>>>> >>>>>> Hi, this is the URL: >>>>>> >>>>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R= .html >>>>>> >>>>>> Best >>>>>> R >>>>>> >>>>>> 2012/2/5 Thomas S. Dye >>>>>> >>>>>>> Hi Riccardo, >>>>>>> >>>>>>> This code appears to be outdated. =C2=A0I don't recall this code on= the org >>>>>>> site. =C2=A0Could you send a URL? >>>>>>> >>>>>>> All the best, >>>>>>> Tom >>>>>>> >>>>>>> Riccardo Romoli writes: >>>>>>> >>>>>>> > Hi, I'm trying to generate some figure with R, into an org sessio= n. >>>>>>> Firstly >>>>>>> > I use the code in the org site. The problem is that the code do n= ot >>>>>>> > generate any figure. >>>>>>> > >>>>>>> > This is the code: >>>>>>> > >>>>>>> > #+TITLE:Test >>>>>>> > #+AUTHOR: Your Name >>>>>>> > #+EMAIL: your-email@server.com >>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :export= s >>>>>>> > both :tangle yes >>>>>>> > >>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>> > ** R text output >>>>>>> > A simple summary. >>>>>>> > #+begin_src R >>>>>>> > =C2=A0 x <- rnorm(10) >>>>>>> > =C2=A0 summary(x) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > ** R graphics output >>>>>>> > Note we use the object =3Dx=3D generated in previous code block, = thanks to >>>>>>> > the header option =3D:session *R*=3D. =C2=A0The output graphics f= ile is >>>>>>> > =3Da.png=3D. >>>>>>> > >>>>>>> > #+begin_src R =C2=A0:file a.png >>>>>>> > =C2=A0 y <- rnorm(10) >>>>>>> > =C2=A0 plot(x, y) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > Same plot with larger dimension: >>>>>>> > >>>>>>> > #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>> > =C2=A0 plot(x, y) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > >>>>>>> > Where do I wrong? >>>>>>> > >>>>>>> > Best >>>>>>> > Riccardo >>>>>>> > Hi, I'm trying to generate some figure with R, into an org se= ssion. >>>>>>> Firstly I use the code in the org site. The problem is that the cod= e do not >>>>>>> generate any figure. This is the code: >>>>>>> > #+TITLE:Test >>>>>>> > #+AUTHOR: Your Name >>>>>>> > #+EMAIL: mailto:your-email@server.com >>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :export= s both >>>>>>> :tangle yes >>>>>>> > >>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>> > ** R text output >>>>>>> > A simple summary. >>>>>>> > #+begin_src R >>>>>>> > =C2=A0 x <- rnorm(10) >>>>>>> > =C2=A0 summary(x) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > ** R graphics output >>>>>>> > Note we use the object =3Dx=3D generated in previous code block, = thanks to >>>>>>> > the header option =3D:session *R*=3D. =C2=A0The output graphics f= ile is >>>>>>> > =3Da.png=3D. >>>>>>> > >>>>>>> > #+begin_src R =C2=A0:file a.png >>>>>>> > =C2=A0 y <- rnorm(10) >>>>>>> > =C2=A0 plot(x, y) >>>>>>> > #+end_src >>>>>>> > >>>>>>> > Same plot with larger dimension: >>>>>>> > >>>>>>> > #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>> > =C2=A0 plot(x, y) >>>>>>> > #+end_src >>>>>>> > Where do I wrong?BestRiccardo >>>>>>> >>>>>>> -- >>>>>>> Thomas S. Dye >>>>>>> http://www.tsdye.com >>>>>>> >>>>>> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-to= -use-Org-Babel-for-R.htmlBestR >>>>>> 2012/2/5 Thomas S. Dye Hi Riccardo, >>>>>> >>>>>> >>>>>> This code appears to be outdated. =C2=A0I don't recall this code= on the org >>>>>> site. =C2=A0Could you send a URL? >>>>>> >>>>>> All the best, >>>>>> Tom >>>>>> >>>>>> Riccardo Romoli writes: >>>>>> >>>>>>> Hi, I'm trying to generate some figure with R, into an org sess= ion. Firstly >>>>>>> I use the code in the org site. The problem is that the code do not >>>>>>> generate any figure. >>>>>>> >>>>>>> This is the code: >>>>>>> >>>>>>> #+TITLE:Test >>>>>>> #+AUTHOR: Your Name >>>>>>> #+EMAIL: mailto:your-email@server.com >>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>>> both :tangle yes >>>>>>> >>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>> ** R text output >>>>>>> A simple summary. >>>>>>> #+begin_src R >>>>>>> =C2=A0 x <- rnorm(10) >>>>>>> =C2=A0 summary(x) >>>>>>> #+end_src >>>>>>> >>>>>>> ** R graphics output >>>>>>> Note we use the object =3Dx=3D generated in previous code block, th= anks to >>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics fil= e is >>>>>>> =3Da.png=3D. >>>>>>> >>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>> =C2=A0 y <- rnorm(10) >>>>>>> =C2=A0 plot(x, y) >>>>>>> #+end_src >>>>>>> >>>>>>> Same plot with larger dimension: >>>>>>> >>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>> =C2=A0 plot(x, y) >>>>>>> #+end_src >>>>>>> >>>>>>> >>>>>>> Where do I wrong? >>>>>>> >>>>>>> Best >>>>>>> Riccardo >>>>>>> Hi, I'm trying to generate some figure with R, into an org >>>>>>> session. Firstly I use the code in the org site. The problem is >>>>>>> that the code do not generate any figure. This is the code: >>>>>>> #+TITLE:Test >>>>>>> #+AUTHOR: Your Name >>>>>>> #+EMAIL: mailto:mailto:your-email@server.com >>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports = both :tangle yes >>>>>>> >>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>> ** R text output >>>>>>> A simple summary. >>>>>>> #+begin_src R >>>>>>> =C2=A0 x <- rnorm(10) >>>>>>> =C2=A0 summary(x) >>>>>>> #+end_src >>>>>>> >>>>>>> ** R graphics output >>>>>>> Note we use the object =3Dx=3D generated in previous code block, th= anks to >>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics fil= e is >>>>>>> =3Da.png=3D. >>>>>>> >>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>> =C2=A0 y <- rnorm(10) >>>>>>> =C2=A0 plot(x, y) >>>>>>> #+end_src >>>>>>> >>>>>>> Same plot with larger dimension: >>>>>>> >>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>> =C2=A0 plot(x, y) >>>>>>> #+end_src >>>>>>> Where do I wrong?BestRiccardo >>>>>> >>>>>> -- >>>>>> Thomas S. Dye >>>>>> http://www.tsdye.com >>>>>> >> >> >> Footnotes: >> [1] =C2=A0http://orgmode.org/worg/org-contrib/babel/languages.html > > -- > Thomas S. Dye > http://www.tsdye.com > From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Re: Updating the Babel section of Worg Date: Wed, 08 Feb 2012 08:27:20 -0700 Message-ID: <87fwelny5j.fsf@gmx.com> References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> <87zkctcsma.fsf@gmx.com> <4F328A36.9010501@gmail.com> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([140.186.70.92]:34636) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rv9TS-0007B1-F3 for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 10:30:30 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rv9TH-0000fL-EV for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 10:30:22 -0500 Received: from mailout-us.gmx.com ([74.208.5.67]:47904 helo=mailout-us.mail.com) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1Rv9TH-0000e7-6d for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 10:30:11 -0500 In-Reply-To: <4F328A36.9010501@gmail.com> (Rainer M. Krug's message of "Wed, 08 Feb 2012 15:44:06 +0100") 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: R.M.Krug@gmail.com Cc: Martyn Jago , emacs-orgmode@gnu.org Rainer M Krug writes: > On 08/02/12 15:21, Eric Schulte wrote: >> Martyn Jago writes: >> >>> Hi Thomas and Eric >>> >>> Love it. I will try to help! >>> >>> Worg is a great resource that is getting better and better. >>> >>> The template looks good (Babel wise) and should be up there as a >>> check-sheet, although maybe not as a requirement. >>> >> >> I agree, I've just linked to it from the languages page [1] with >> the following statement. Please feel free to edit this directly on >> worg if it sounds too strong. > > Nice - I will take a look at it. > > Just to make it easier for non-regular worg contributors: I would > suggest to give an email where one can send the completed template to > to be submitted to worg. > I will be happy to apply any language documentation sent to this list. Best, -- Eric Schulte http://cs.unm.edu/~eschulte/ From mboxrd@z Thu Jan 1 00:00:00 1970 From: tsd@tsdye.com (Thomas S. Dye) Subject: Re: Updating the Babel section of Worg Date: Thu, 09 Feb 2012 07:20:11 -1000 Message-ID: References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> <8762fhe76u.fsf@gmx.com> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:57182) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RvXfa-0005Zd-SM for emacs-orgmode@gnu.org; Thu, 09 Feb 2012 12:20:35 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RvXfQ-0006Oy-4Y for emacs-orgmode@gnu.org; Thu, 09 Feb 2012 12:20:30 -0500 Received: from oproxy9.bluehost.com ([69.89.24.6]:35356) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1RvXfP-0006OS-NQ for emacs-orgmode@gnu.org; Thu, 09 Feb 2012 12:20:20 -0500 In-Reply-To: <8762fhe76u.fsf@gmx.com> (Eric Schulte's message of "Wed, 08 Feb 2012 07:14:15 -0700") 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: Eric Schulte Cc: emacs-orgmode@gnu.org Hi Eric, I pushed a draft of the revised LaTeX language section to Worg (http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.html). Please take a look and edit as necessary. Too often I understand these things partially! If Andreas Leha is reading this it would be good to take a look at my description of the ImageMagick facility. I tried to stick closely to the sources, but might have strayed. All the best, Tom Eric Schulte writes: > tsd@tsdye.com (Thomas S. Dye) writes: > >> Hi Eric, >> >> I've attached a first draft of a template for review and revision. It >> is heavily influenced by John Hendy's terrific gnuplot page. I >> believe it incorporates the points in your outline. Feel free to >> edit as appropriate. >> > > Looks great to me. I made a small change, and I've just pushed it up to > worg and linked to it from the languages page. We can continue to > improve this template as needed on worg although I think it is already > in very good shape and ready for use. > > Thanks, > >> >> All the best, >> Tom >> >> >> >> >> Eric Schulte writes: >> >>> Hi Tom, >>> >>> tsd@tsdye.com (Thomas S. Dye) writes: >>> >>>> Hi Eric, >>>> >>>> Yes, this is overdue. I think your plan is a good one. >>>> >>>> Perhaps a few of the individual use cases could be moved to FIXME, >>>> instead? I'm thinking here of Feiming Chen's R setup and some of my >>>> contributions when I was experimenting writing LaTeX inside source >>>> code blocks. The authors could resurrect these as they see fit. >>>> >>> >>> I don't know what FIXME is, but if there is a way to keep the page in >>> the worg git repository but remove it from the exported HTML then that >>> sounds ideal. >>> >>>> >>>> Hopefully, others will contribute use examples. My sense from reading >>>> the list is there are many interesting ones. >>>> >>>> I'd like it if Org mode users designed a template for the language >>>> specific pages. Currently, these seem to me a mixed bag and it would = be >>>> good to regularize them. >>> >>> The below is a modified version of a template which can be found in a >>> couple of the existing language tutorials, I think it serves as a good >>> starting point. >>> >>> - Install and Setup >>> - Instillation and configuration of software (e.g., the language itse= lf) >>> - Configuration of Emacs (e.g., activate language, set command path) >>> - Examples >>> - Common ways to use the language in an Org-mode document >>> - Special cases >>> - are there any language-specific header arguments >>> - does the language support session evaluation >>> - does the language support all result types >>> - is the language different from most babel languages >>> (e.g., C is compiled before execution, ditaa returns files, etc...) >>> >>>> It would also be nice to have one for each of the supported languages. >>>> There are 11 language specific pages now, which leaves quite a few >>>> languages under-documented. >>> >>> (length org-babel-load-languages) ;; =3D> 27 >>> >>> ls org-contrib/babel/languages/ob-doc-*|wc -l # =3D> 11 >>> >>> It looks like we have at least 16 more to go before we hit full language >>> coverage. Perhaps we should use the empty cells in the "documentation" >>> column in the languages table at [1] as a sign up space for volunteers >>> who would be willing to write a brief tutorial demonstrating usage of >>> Org-mode with their favorite language. >>> >>> Moving forward this is likely something we could request of the >>> contributors of new languages. >>> >>> Also, once the template above is finalized it should be posted on worg >>> and linked to through the languages page. >>> >>>> >>>> I'll be happy to work on this as I can. >>>> >>> >>> Great, I don't anticipate having time to put towards this, although I'll >>> be happy to help troubleshoot where I can. >>> >>> Cheers, >>> >>>> >>>> All the best, >>>> Tom >>>> >>>> >>>> Eric Schulte writes: >>>> >>>>> Thanks for raising this point. The bulk of the content in the Babel >>>>> portion of worg is fairly old, predating the syntax standardization >>>>> efforts this fall. I've just pushed some minor updates to the main >>>>> babel pages, but updating the language-specific tutorials and the >>>>> individual use cases will be a much larger effort. >>>>> >>>>> I'm not sure how to proceed. One option would be to go through and a= dd >>>>> a [uses deprecated syntax] tag to the top of each such page, which co= uld >>>>> be removed after the page has been checked and possibly updated to >>>>> ensure consistency with the latest syntax. >>>>> >>>>> Given that the Babel syntax will not be changing significantly moving >>>>> forward now would be a good time to do such a review. Ideally this >>>>> could be completed before the release of Emacs 24 in a couple of mont= hs. >>>>> >>>>> Any other ideas for update/reorganization or volunteers? >>>>> >>>>> Cheers, >>>>> >>>>> tsd@tsdye.com (Thomas S. Dye) writes: >>>>> >>>>>> Hi Riccardo, >>>>>> >>>>>> Thanks for the URL. Org mode has evolved since this article was >>>>>> written. It should probably be revised or taken off Worg. I've cop= ied >>>>>> Eric Schulte, who is better able than me to determine the correct co= urse >>>>>> of action here. >>>>>> >>>>>> In the meantime, an up-to-date description of how Org mode can be us= ed >>>>>> to write literate programs has appeared in the Journal of Statistical >>>>>> Software. You can find it here: http://www.jstatsoft.org/v46/i03 >>>>>> >>>>>> Perhaps you could use the examples in the JSS article to get started? >>>>>> If these don't work for you, or if they raise questions that are dif= ficult >>>>>> to answer, please do come back to the list with your queries. >>>>>> >>>>>> All the best, >>>>>> Tom >>>>>> >>>>>> Riccardo Romoli writes: >>>>>> >>>>>>> Hi, this is the URL: >>>>>>> >>>>>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-= R.html >>>>>>> >>>>>>> Best >>>>>>> R >>>>>>> >>>>>>> 2012/2/5 Thomas S. Dye >>>>>>> >>>>>>>> Hi Riccardo, >>>>>>>> >>>>>>>> This code appears to be outdated. I don't recall this code on the= org >>>>>>>> site. Could you send a URL? >>>>>>>> >>>>>>>> All the best, >>>>>>>> Tom >>>>>>>> >>>>>>>> Riccardo Romoli writes: >>>>>>>> >>>>>>>> > Hi, I'm trying to generate some figure with R, into an org sessi= on. >>>>>>>> Firstly >>>>>>>> > I use the code in the org site. The problem is that the code do = not >>>>>>>> > generate any figure. >>>>>>>> > >>>>>>>> > This is the code: >>>>>>>> > >>>>>>>> > #+TITLE:Test >>>>>>>> > #+AUTHOR: Your Name >>>>>>>> > #+EMAIL: your-email@server.com >>>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :expor= ts >>>>>>>> > both :tangle yes >>>>>>>> > >>>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>>> > ** R text output >>>>>>>> > A simple summary. >>>>>>>> > #+begin_src R >>>>>>>> > x <- rnorm(10) >>>>>>>> > summary(x) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > ** R graphics output >>>>>>>> > Note we use the object =3Dx=3D generated in previous code block,= thanks to >>>>>>>> > the header option =3D:session *R*=3D. The output graphics file = is >>>>>>>> > =3Da.png=3D. >>>>>>>> > >>>>>>>> > #+begin_src R :file a.png >>>>>>>> > y <- rnorm(10) >>>>>>>> > plot(x, y) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > Same plot with larger dimension: >>>>>>>> > >>>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>>> > plot(x, y) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > >>>>>>>> > Where do I wrong? >>>>>>>> > >>>>>>>> > Best >>>>>>>> > Riccardo >>>>>>>> > Hi, I'm trying to generate some figure with R, into an org s= ession. >>>>>>>> Firstly I use the code in the org site. The problem is that the co= de do not >>>>>>>> generate any figure. This is the code: >>>>>>>> > #+TITLE:Test >>>>>>>> > #+AUTHOR: Your Name >>>>>>>> > #+EMAIL: mailto:your-email@server.com >>>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :expor= ts both >>>>>>>> :tangle yes >>>>>>>> > >>>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>>> > ** R text output >>>>>>>> > A simple summary. >>>>>>>> > #+begin_src R >>>>>>>> > x <- rnorm(10) >>>>>>>> > summary(x) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > ** R graphics output >>>>>>>> > Note we use the object =3Dx=3D generated in previous code block,= thanks to >>>>>>>> > the header option =3D:session *R*=3D. The output graphics file = is >>>>>>>> > =3Da.png=3D. >>>>>>>> > >>>>>>>> > #+begin_src R :file a.png >>>>>>>> > y <- rnorm(10) >>>>>>>> > plot(x, y) >>>>>>>> > #+end_src >>>>>>>> > >>>>>>>> > Same plot with larger dimension: >>>>>>>> > >>>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>>> > plot(x, y) >>>>>>>> > #+end_src >>>>>>>> > Where do I wrong?BestRiccardo >>>>>>>> >>>>>>>> -- >>>>>>>> Thomas S. Dye >>>>>>>> http://www.tsdye.com >>>>>>>> >>>>>>> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-t= o-use-Org-Babel-for-R.htmlBestR >>>>>>> 2012/2/5 Thomas S. Dye Hi Riccardo, >>>>>>> >>>>>>> >>>>>>> This code appears to be outdated. =C2=A0I don't recall this cod= e on the org >>>>>>> site. =C2=A0Could you send a URL? >>>>>>> >>>>>>> All the best, >>>>>>> Tom >>>>>>> >>>>>>> Riccardo Romoli writes: >>>>>>> >>>>>>>> Hi, I'm trying to generate some figure with R, into an org ses= sion. Firstly >>>>>>>> I use the code in the org site. The problem is that the code do not >>>>>>>> generate any figure. >>>>>>>> >>>>>>>> This is the code: >>>>>>>> >>>>>>>> #+TITLE:Test >>>>>>>> #+AUTHOR: Your Name >>>>>>>> #+EMAIL: mailto:your-email@server.com >>>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>>>> both :tangle yes >>>>>>>> >>>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>>> ** R text output >>>>>>>> A simple summary. >>>>>>>> #+begin_src R >>>>>>>> =C2=A0 x <- rnorm(10) >>>>>>>> =C2=A0 summary(x) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> ** R graphics output >>>>>>>> Note we use the object =3Dx=3D generated in previous code block, t= hanks to >>>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics fi= le is >>>>>>>> =3Da.png=3D. >>>>>>>> >>>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>>> =C2=A0 y <- rnorm(10) >>>>>>>> =C2=A0 plot(x, y) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> Same plot with larger dimension: >>>>>>>> >>>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>>> =C2=A0 plot(x, y) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> >>>>>>>> Where do I wrong? >>>>>>>> >>>>>>>> Best >>>>>>>> Riccardo >>>>>>>> Hi, I'm trying to generate some figure with R, into an org >>>>>>>> session. Firstly I use the code in the org site. The problem is >>>>>>>> that the code do not generate any figure. This is the code: >>>>>>>> #+TITLE:Test >>>>>>>> #+AUTHOR: Your Name >>>>>>>> #+EMAIL: mailto:mailto:your-email@server.com >>>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports= both :tangle yes >>>>>>>> >>>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>>> ** R text output >>>>>>>> A simple summary. >>>>>>>> #+begin_src R >>>>>>>> =C2=A0 x <- rnorm(10) >>>>>>>> =C2=A0 summary(x) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> ** R graphics output >>>>>>>> Note we use the object =3Dx=3D generated in previous code block, t= hanks to >>>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics fi= le is >>>>>>>> =3Da.png=3D. >>>>>>>> >>>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>>> =C2=A0 y <- rnorm(10) >>>>>>>> =C2=A0 plot(x, y) >>>>>>>> #+end_src >>>>>>>> >>>>>>>> Same plot with larger dimension: >>>>>>>> >>>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>>> =C2=A0 plot(x, y) >>>>>>>> #+end_src >>>>>>>> Where do I wrong?BestRiccardo >>>>>>> >>>>>>> -- >>>>>>> Thomas S. Dye >>>>>>> http://www.tsdye.com >>>>>>> >>> >>> >>> Footnotes:=20 >>> [1] http://orgmode.org/worg/org-contrib/babel/languages.html --=20 Thomas S. Dye http://www.tsdye.com From mboxrd@z Thu Jan 1 00:00:00 1970 From: Eric Schulte Subject: Re: Updating the Babel section of Worg Date: Sat, 18 Feb 2012 14:53:17 -0700 Message-ID: <871uprn702.fsf@gmx.com> References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> <8762fhe76u.fsf@gmx.com> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:49733) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RysDi-00064f-5I for emacs-orgmode@gnu.org; Sat, 18 Feb 2012 16:53:32 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RysDg-0008S5-4U for emacs-orgmode@gnu.org; Sat, 18 Feb 2012 16:53:30 -0500 Received: from mailout-us.gmx.com ([74.208.5.67]:37788 helo=mailout-us.mail.com) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1RysDf-0008S1-Sk for emacs-orgmode@gnu.org; Sat, 18 Feb 2012 16:53:28 -0500 In-Reply-To: (Thomas S. Dye's message of "Thu, 09 Feb 2012 07:20:11 -1000") 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: "Thomas S. Dye" Cc: emacs-orgmode@gnu.org tsd@tsdye.com (Thomas S. Dye) writes: > Hi Eric, > > I pushed a draft of the revised LaTeX language section to Worg > (http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.html). > > Please take a look and edit as necessary. Too often I understand > these things partially! > Everything looks great to me. Thanks for the contribution! > > If Andreas Leha is reading this it would be good to take a look at my > description of the ImageMagick facility. I tried to stick closely to > the sources, but might have strayed. > > All the best, > Tom > > Eric Schulte writes: > >> tsd@tsdye.com (Thomas S. Dye) writes: >> >>> Hi Eric, >>> >>> I've attached a first draft of a template for review and revision. It >>> is heavily influenced by John Hendy's terrific gnuplot page. I >>> believe it incorporates the points in your outline. Feel free to >>> edit as appropriate. >>> >> >> Looks great to me. I made a small change, and I've just pushed it up to >> worg and linked to it from the languages page. We can continue to >> improve this template as needed on worg although I think it is already >> in very good shape and ready for use. >> >> Thanks, >> >>> >>> All the best, >>> Tom >>> >>> >>> >>> >>> Eric Schulte writes: >>> >>>> Hi Tom, >>>> >>>> tsd@tsdye.com (Thomas S. Dye) writes: >>>> >>>>> Hi Eric, >>>>> >>>>> Yes, this is overdue. I think your plan is a good one. >>>>> >>>>> Perhaps a few of the individual use cases could be moved to FIXME, >>>>> instead? I'm thinking here of Feiming Chen's R setup and some of my >>>>> contributions when I was experimenting writing LaTeX inside source >>>>> code blocks. The authors could resurrect these as they see fit. >>>>> >>>> >>>> I don't know what FIXME is, but if there is a way to keep the page in >>>> the worg git repository but remove it from the exported HTML then that >>>> sounds ideal. >>>> >>>>> >>>>> Hopefully, others will contribute use examples. My sense from reading >>>>> the list is there are many interesting ones. >>>>> >>>>> I'd like it if Org mode users designed a template for the language >>>>> specific pages. Currently, these seem to me a mixed bag and it would= be >>>>> good to regularize them. >>>> >>>> The below is a modified version of a template which can be found in a >>>> couple of the existing language tutorials, I think it serves as a good >>>> starting point. >>>> >>>> - Install and Setup >>>> - Instillation and configuration of software (e.g., the language its= elf) >>>> - Configuration of Emacs (e.g., activate language, set command path) >>>> - Examples >>>> - Common ways to use the language in an Org-mode document >>>> - Special cases >>>> - are there any language-specific header arguments >>>> - does the language support session evaluation >>>> - does the language support all result types >>>> - is the language different from most babel languages >>>> (e.g., C is compiled before execution, ditaa returns files, etc...) >>>> >>>>> It would also be nice to have one for each of the supported languages. >>>>> There are 11 language specific pages now, which leaves quite a few >>>>> languages under-documented. >>>> >>>> (length org-babel-load-languages) ;; =3D> 27 >>>> >>>> ls org-contrib/babel/languages/ob-doc-*|wc -l # =3D> 11 >>>> >>>> It looks like we have at least 16 more to go before we hit full langua= ge >>>> coverage. Perhaps we should use the empty cells in the "documentation" >>>> column in the languages table at [1] as a sign up space for volunteers >>>> who would be willing to write a brief tutorial demonstrating usage of >>>> Org-mode with their favorite language. >>>> >>>> Moving forward this is likely something we could request of the >>>> contributors of new languages. >>>> >>>> Also, once the template above is finalized it should be posted on worg >>>> and linked to through the languages page. >>>> >>>>> >>>>> I'll be happy to work on this as I can. >>>>> >>>> >>>> Great, I don't anticipate having time to put towards this, although I'= ll >>>> be happy to help troubleshoot where I can. >>>> >>>> Cheers, >>>> >>>>> >>>>> All the best, >>>>> Tom >>>>> >>>>> >>>>> Eric Schulte writes: >>>>> >>>>>> Thanks for raising this point. The bulk of the content in the Babel >>>>>> portion of worg is fairly old, predating the syntax standardization >>>>>> efforts this fall. I've just pushed some minor updates to the main >>>>>> babel pages, but updating the language-specific tutorials and the >>>>>> individual use cases will be a much larger effort. >>>>>> >>>>>> I'm not sure how to proceed. One option would be to go through and = add >>>>>> a [uses deprecated syntax] tag to the top of each such page, which c= ould >>>>>> be removed after the page has been checked and possibly updated to >>>>>> ensure consistency with the latest syntax. >>>>>> >>>>>> Given that the Babel syntax will not be changing significantly moving >>>>>> forward now would be a good time to do such a review. Ideally this >>>>>> could be completed before the release of Emacs 24 in a couple of mon= ths. >>>>>> >>>>>> Any other ideas for update/reorganization or volunteers? >>>>>> >>>>>> Cheers, >>>>>> >>>>>> tsd@tsdye.com (Thomas S. Dye) writes: >>>>>> >>>>>>> Hi Riccardo, >>>>>>> >>>>>>> Thanks for the URL. Org mode has evolved since this article was >>>>>>> written. It should probably be revised or taken off Worg. I've co= pied >>>>>>> Eric Schulte, who is better able than me to determine the correct c= ourse >>>>>>> of action here. >>>>>>> >>>>>>> In the meantime, an up-to-date description of how Org mode can be u= sed >>>>>>> to write literate programs has appeared in the Journal of Statistic= al >>>>>>> Software. You can find it here: http://www.jstatsoft.org/v46/i03 >>>>>>> >>>>>>> Perhaps you could use the examples in the JSS article to get starte= d? >>>>>>> If these don't work for you, or if they raise questions that are di= fficult >>>>>>> to answer, please do come back to the list with your queries. >>>>>>> >>>>>>> All the best, >>>>>>> Tom >>>>>>> >>>>>>> Riccardo Romoli writes: >>>>>>> >>>>>>>> Hi, this is the URL: >>>>>>>> >>>>>>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for= -R.html >>>>>>>> >>>>>>>> Best >>>>>>>> R >>>>>>>> >>>>>>>> 2012/2/5 Thomas S. Dye >>>>>>>> >>>>>>>>> Hi Riccardo, >>>>>>>>> >>>>>>>>> This code appears to be outdated. I don't recall this code on th= e org >>>>>>>>> site. Could you send a URL? >>>>>>>>> >>>>>>>>> All the best, >>>>>>>>> Tom >>>>>>>>> >>>>>>>>> Riccardo Romoli writes: >>>>>>>>> >>>>>>>>> > Hi, I'm trying to generate some figure with R, into an org sess= ion. >>>>>>>>> Firstly >>>>>>>>> > I use the code in the org site. The problem is that the code do= not >>>>>>>>> > generate any figure. >>>>>>>>> > >>>>>>>>> > This is the code: >>>>>>>>> > >>>>>>>>> > #+TITLE:Test >>>>>>>>> > #+AUTHOR: Your Name >>>>>>>>> > #+EMAIL: your-email@server.com >>>>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :expo= rts >>>>>>>>> > both :tangle yes >>>>>>>>> > >>>>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>>>> > ** R text output >>>>>>>>> > A simple summary. >>>>>>>>> > #+begin_src R >>>>>>>>> > x <- rnorm(10) >>>>>>>>> > summary(x) >>>>>>>>> > #+end_src >>>>>>>>> > >>>>>>>>> > ** R graphics output >>>>>>>>> > Note we use the object =3Dx=3D generated in previous code block= , thanks to >>>>>>>>> > the header option =3D:session *R*=3D. The output graphics file= is >>>>>>>>> > =3Da.png=3D. >>>>>>>>> > >>>>>>>>> > #+begin_src R :file a.png >>>>>>>>> > y <- rnorm(10) >>>>>>>>> > plot(x, y) >>>>>>>>> > #+end_src >>>>>>>>> > >>>>>>>>> > Same plot with larger dimension: >>>>>>>>> > >>>>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>>>> > plot(x, y) >>>>>>>>> > #+end_src >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > Where do I wrong? >>>>>>>>> > >>>>>>>>> > Best >>>>>>>>> > Riccardo >>>>>>>>> > Hi, I'm trying to generate some figure with R, into an org = session. >>>>>>>>> Firstly I use the code in the org site. The problem is that the c= ode do not >>>>>>>>> generate any figure. This is the code: >>>>>>>>> > #+TITLE:Test >>>>>>>>> > #+AUTHOR: Your Name >>>>>>>>> > #+EMAIL: mailto:your-email@server.com >>>>>>>>> > #+BABEL: :session *R* :cache yes :results output graphics :expo= rts both >>>>>>>>> :tangle yes >>>>>>>>> > >>>>>>>>> > * Example of Org-Babel for R Literate Programming >>>>>>>>> > ** R text output >>>>>>>>> > A simple summary. >>>>>>>>> > #+begin_src R >>>>>>>>> > x <- rnorm(10) >>>>>>>>> > summary(x) >>>>>>>>> > #+end_src >>>>>>>>> > >>>>>>>>> > ** R graphics output >>>>>>>>> > Note we use the object =3Dx=3D generated in previous code block= , thanks to >>>>>>>>> > the header option =3D:session *R*=3D. The output graphics file= is >>>>>>>>> > =3Da.png=3D. >>>>>>>>> > >>>>>>>>> > #+begin_src R :file a.png >>>>>>>>> > y <- rnorm(10) >>>>>>>>> > plot(x, y) >>>>>>>>> > #+end_src >>>>>>>>> > >>>>>>>>> > Same plot with larger dimension: >>>>>>>>> > >>>>>>>>> > #+begin_src R :file b.png :width 800 :height 800 >>>>>>>>> > plot(x, y) >>>>>>>>> > #+end_src >>>>>>>>> > Where do I wrong?BestRiccardo >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Thomas S. Dye >>>>>>>>> http://www.tsdye.com >>>>>>>>> >>>>>>>> Hi, this is the URL:http://orgmode.org/worg/org-contrib/babel/how-= to-use-Org-Babel-for-R.htmlBestR >>>>>>>> 2012/2/5 Thomas S. Dye Hi Riccardo, >>>>>>>> >>>>>>>> >>>>>>>> This code appears to be outdated. =C2=A0I don't recall this co= de on the org >>>>>>>> site. =C2=A0Could you send a URL? >>>>>>>> >>>>>>>> All the best, >>>>>>>> Tom >>>>>>>> >>>>>>>> Riccardo Romoli writes: >>>>>>>> >>>>>>>>> Hi, I'm trying to generate some figure with R, into an org se= ssion. Firstly >>>>>>>>> I use the code in the org site. The problem is that the code do n= ot >>>>>>>>> generate any figure. >>>>>>>>> >>>>>>>>> This is the code: >>>>>>>>> >>>>>>>>> #+TITLE:Test >>>>>>>>> #+AUTHOR: Your Name >>>>>>>>> #+EMAIL: mailto:your-email@server.com >>>>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :exports >>>>>>>>> both :tangle yes >>>>>>>>> >>>>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>>>> ** R text output >>>>>>>>> A simple summary. >>>>>>>>> #+begin_src R >>>>>>>>> =C2=A0 x <- rnorm(10) >>>>>>>>> =C2=A0 summary(x) >>>>>>>>> #+end_src >>>>>>>>> >>>>>>>>> ** R graphics output >>>>>>>>> Note we use the object =3Dx=3D generated in previous code block, = thanks to >>>>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics f= ile is >>>>>>>>> =3Da.png=3D. >>>>>>>>> >>>>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>>>> =C2=A0 y <- rnorm(10) >>>>>>>>> =C2=A0 plot(x, y) >>>>>>>>> #+end_src >>>>>>>>> >>>>>>>>> Same plot with larger dimension: >>>>>>>>> >>>>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>>>> =C2=A0 plot(x, y) >>>>>>>>> #+end_src >>>>>>>>> >>>>>>>>> >>>>>>>>> Where do I wrong? >>>>>>>>> >>>>>>>>> Best >>>>>>>>> Riccardo >>>>>>>>> Hi, I'm trying to generate some figure with R, into an org >>>>>>>>> session. Firstly I use the code in the org site. The problem is >>>>>>>>> that the code do not generate any figure. This is the code: >>>>>>>>> #+TITLE:Test >>>>>>>>> #+AUTHOR: Your Name >>>>>>>>> #+EMAIL: mailto:mailto:your-email@server.com >>>>>>>>> #+BABEL: :session *R* :cache yes :results output graphics :export= s both :tangle yes >>>>>>>>> >>>>>>>>> * Example of Org-Babel for R Literate Programming >>>>>>>>> ** R text output >>>>>>>>> A simple summary. >>>>>>>>> #+begin_src R >>>>>>>>> =C2=A0 x <- rnorm(10) >>>>>>>>> =C2=A0 summary(x) >>>>>>>>> #+end_src >>>>>>>>> >>>>>>>>> ** R graphics output >>>>>>>>> Note we use the object =3Dx=3D generated in previous code block, = thanks to >>>>>>>>> the header option =3D:session *R*=3D. =C2=A0The output graphics f= ile is >>>>>>>>> =3Da.png=3D. >>>>>>>>> >>>>>>>>> #+begin_src R =C2=A0:file a.png >>>>>>>>> =C2=A0 y <- rnorm(10) >>>>>>>>> =C2=A0 plot(x, y) >>>>>>>>> #+end_src >>>>>>>>> >>>>>>>>> Same plot with larger dimension: >>>>>>>>> >>>>>>>>> #+begin_src R =C2=A0:file b.png :width 800 :height 800 >>>>>>>>> =C2=A0 plot(x, y) >>>>>>>>> #+end_src >>>>>>>>> Where do I wrong?BestRiccardo >>>>>>>> >>>>>>>> -- >>>>>>>> Thomas S. Dye >>>>>>>> http://www.tsdye.com >>>>>>>> >>>> >>>> >>>> Footnotes:=20 >>>> [1] http://orgmode.org/worg/org-contrib/babel/languages.html --=20 Eric Schulte http://cs.unm.edu/~eschulte/