From mboxrd@z Thu Jan 1 00:00:00 1970 From: David Hajage Subject: Re: Re: problem with babel and R Date: Thu, 26 Aug 2010 22:20:35 +0200 Message-ID: References: <87tymtnxzi.fsf@gmail.com> <1668ca$1pq4c@mail.curie.net> <87d3tflgc3.fsf@gmail.com> <87k4ndjqxb.fsf@gmail.com> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="===============0495202864==" Return-path: Received: from [140.186.70.92] (port=34154 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1OoiwX-0003V7-Uc for emacs-orgmode@gnu.org; Thu, 26 Aug 2010 16:21:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.69) (envelope-from ) id 1OoiwT-0005SG-IX for emacs-orgmode@gnu.org; Thu, 26 Aug 2010 16:21:01 -0400 Received: from mail-fx0-f41.google.com ([209.85.161.41]:44454) by eggs.gnu.org with esmtp (Exim 4.69) (envelope-from ) id 1OoiwT-0005S7-31 for emacs-orgmode@gnu.org; Thu, 26 Aug 2010 16:20:57 -0400 Received: by fxm3 with SMTP id 3so1879166fxm.0 for ; Thu, 26 Aug 2010 13:20:55 -0700 (PDT) In-Reply-To: <87k4ndjqxb.fsf@gmail.com> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Eric Schulte Cc: emacs-orgmode@gnu.org --===============0495202864== Content-Type: multipart/alternative; boundary=001485f5ce1e433546048ebfbce1 --001485f5ce1e433546048ebfbce1 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I am so sorry to bother you again, but I must miss something. When I write: #+begin_src R :results output org :exports both library(ascii) options(asciiType =3D "org") ascii(head(esoph)) #+end_src The results is: #+results: #+BEGIN_SRC org | | agegp | alcgp | tobgp | ncases | ncontrols | |---+-------+-----------+----------+--------+-----------| | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 | 40.00 | | 2 | 25-34 | 0-39g/day | 10-19 | 0.00 | 10.00 | | 3 | 25-34 | 0-39g/day | 20-29 | 0.00 | 6.00 | | 4 | 25-34 | 0-39g/day | 30+ | 0.00 | 5.00 | | 5 | 25-34 | 40-79 | 0-9g/day | 0.00 | 27.00 | | 6 | 25-34 | 40-79 | 10-19 | 0.00 | 7.00 | #+END_SRC OK, the result is surrounded by BEGIN_SRC org/END_SRC. But when I export this, the results is exported as fontified org code. What should I do to have this result interpreted as org markup? David On Thu, Aug 26, 2010 at 18:10, Eric Schulte wrote: > Hi, > > A fix to this issue has been pushed up to the repository. As can now be > read in the documentation of the `org-babel-insert-result' function [1], > there is now a subtle distinction between ":results org" and ":results > raw", where ":results org" will wrap code block results in a "begin_src > org" block. The block wrapper makes it possible for the entirety of the > results to be located and removed by Babel upon code block > re-evaluation. > > In addition a new ob-org.el file has been added providing support for > evaluation of Org-mode blocks. With this new language support loaded > the above technique becomes a working replacement for ":results raw" > allowing the body of the org code block to be interpreted as inline > org-mode text on export. This is done through some non-standard default > header arguments described in the recent commit message (see [2]) > > Best -- Eric > > "Eric Schulte" writes: > > > Hi David, > > > > "#+end_results: foo" (or some derivative syntax) sounds like a good > > idea, I'll add it to the Babel task list. > > > > Thanks -- Eric > > > > David Hajage writes: > > > >> OK, I understand that using ":results org", the results is not altered= , > >> there is no post processing. But I don't want a post processing, I wou= ld > >> like a way to tell babel where is the begining *and the end* of the > output > >> produces by a particular R source block. I think an "#+end_results: fo= o" > at > >> the end of the output could do the job. Then, the option "replace" cou= ld > >> work in all situation, even if a blank line is inserted somewhere in t= he > org > >> output. No? > >> David > >> > >> > >> On Tue, Aug 17, 2010 at 17:15, Eric Schulte > wrote: > >> > >>> Hi David, > >>> > >>> David Hajage writes: > >>> > >>> > Thank you very much for your answer. > >>> > > >>> > >>> My pleasure > >>> > >>> > > >>> > But when I run the following code directly into R, no extra lines i= s > >>> >added > >>> > by the ascii function: > >>> >> library(ascii) > >>> > Le chargement a n=E9cessit=E9 le package : proto > >>> >> options(asciiType =3D "org") > >>> >> ascii(head(esoph)) # no extra line > >>> > | | agegp | alcgp | tobgp | ncases | ncontrols | > >>> > |---+-------+-----------+----------+--------+-----------| > >>> > | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 | 40.00 | > >>> > | 2 | 25-34 | 0-39g/day | 10-19 | 0.00 | 10.00 | > >>> > | 3 | 25-34 | 0-39g/day | 20-29 | 0.00 | 6.00 | > >>> > | 4 | 25-34 | 0-39g/day | 30+ | 0.00 | 5.00 | > >>> > | 5 | 25-34 | 40-79 | 0-9g/day | 0.00 | 27.00 | > >>> > | 6 | 25-34 | 40-79 | 10-19 | 0.00 | 7.00 | > >>> > > >>> > >>> ah, my fault, this isn't an ascii issue. > >>> > >>> > > >>> > In fact, the solution was to run 'library(ascii)' in another source > >>> block. > >>> > When I run only this: > >>> > > >>> > >>> Thanks for pointing this out, I see what's happening now. > >>> > >>> The :results output header argument (see [1] for information on heade= r > >>> arguments) informs Org-mode to collect all of the output of the sourc= e > >>> code block. This means that when library(ascii) is run, an empty lin= e > >>> is collected and appended to the output. Removing the "output" heade= r > >>> argument should fix this issue. > >>> > >>> My I ask why you are using the ascii package for simple table output? > >>> It seems to me that this would be much simpler using the pure Org-mod= e > >>> solution I suggested in my previous email. > >>> > >>> > > >>> > #+begin_src R :session *R* :results output org replace > >>> > ascii(head(esoph)) > >>> > #+end_src > >>> > > >>> > #+results: foo > >>> > | | agegp | alcgp | tobgp | ncases | ncontrols | > >>> > |---+-------+-----------+----------+--------+-----------| > >>> > | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 | 40.00 | > >>> > | 2 | 25-34 | 0-39g/day | 10-19 | 0.00 | 10.00 | > >>> > | 3 | 25-34 | 0-39g/day | 20-29 | 0.00 | 6.00 | > >>> > | 4 | 25-34 | 0-39g/day | 30+ | 0.00 | 5.00 | > >>> > | 5 | 25-34 | 40-79 | 0-9g/day | 0.00 | 27.00 | > >>> > | 6 | 25-34 | 40-79 | 10-19 | 0.00 | 7.00 | > >>> > > >>> > Everything is then OK. > >>> > I have no idea why "library(ascii)..." generates an extra empty lin= e > in > >>> the > >>> > results. > >>> > > >>> > If I understand, the results is all the text directly under > "#+results:", > >>> > until the first empty line. But what happens if the result contains > empty > >>> > lines? Here an example with ascii and Hmisc package: > >>> > > >>> > >>> This is not quite right, see [2] for a discussion of results handling= . > >>> The "org" option to results is a special case in which no > >>> post-processing of the results takes place, and the raw output is > >>> inserted into the org-mode buffer. > >>> > >>> Under normal usage w/o this header argument, results are either tabul= ar > >>> or are textual. If tabular a single table can easily be recognized a= nd > >>> handled, if textual they are normally enclosed in a block (example, > >>> html, latex, etc...), the block then allows for empty lines while sti= ll > >>> making it clear where the results end. > >>> > >> > >> > >>> > >>> > > >>> >> library(ascii) > >>> >> library(Hmisc) > >>> >> ascii(describe(esoph[, 1:3])) > >>> > #+CAPTION: esoph[, 1:3] > >>> > - 3 Variable > >>> > - 88 Observations > >>> > > >>> > *agegp* > >>> > | n | missing | unique | > >>> > | 88 | 0 | 6 | > >>> > > >>> > | | 25-34 | 35-44 | 45-54 | 55-64 | 65-74 | 75+ | > >>> > | Frequency | 15 | 15 | 16 | 16 | 15 | 11 | > >>> > | % | 17 | 17 | 18 | 18 | 17 | 12 | > >>> > > >>> > *alcgp* > >>> > | n | missing | unique | > >>> > | 88 | 0 | 4 | > >>> > > >>> > 0-39g/day (23, 26%), 40-79 (23, 26%), 80-119 (21, 24%), 120+ (21, > 24%) > >>> > > >>> > *tobgp* > >>> > | n | missing | unique | > >>> > | 88 | 0 | 4 | > >>> > > >>> > 0-9g/day (24, 27%), 10-19 (24, 27%), 20-29 (20, 23%), 30+ (20, 23%= ) > >>> > > >>> > As you can see, describe() generate a description of my data, and > ascii > >>> > generate org-mode markup as result. The result contains empty rows. > Since > >>> > there is no special characters indicating the end of the results in > >>> babel, > >>> > replace option will not work in this case. Is there any workaround? > >>> > > >>> > >>> When using ":results org" there is no workaround, as the explicit > >>> purpose of this setting is for your results to be inserted directly > into > >>> the Org-mode buffer w/o any interpretation or alteration. > >>> > >> > >> > >>> > >>> In general I would recommend keeping a 1-to-1 mapping between code > >>> blocks and result items, which should resolve this issue. > >>> > >>> > > >>> > Of course, ascii is not usefull in this case, but it can coerce int= o > >>> > org-mode markup many other R objects (see my previous example and > >>> > http://orgmode.org/worg/org-contrib/babel/examples/ascii.php) > >>> > > >>> > >>> I see, that answers my question from above. Thanks > >>> > >>> Hope this helps -- Eric > >>> > >>> > > >>> > David > >>> > > >>> > > >>> > On Tue, Aug 17, 2010 at 15:57, Eric Schulte > >>> wrote: > >>> > > >>> >> Hi David, > >>> >> > >>> >> It seems that the problem here is in the ascii package. It is > inserting > >>> >> an empty line at the beginning of your table, so that the table is > not > >>> >> snugly sitting under the #+results foo tag, because of this the > table > >>> >> isn't seen as results and is not replaced -- if you delete that > space > >>> >> then re-run the code block you'll notice that the table is replace= d. > >>> >> > >>> >> Org-mode is very capable of inserting tabular data into Org-mode > >>> >> documents without using the ascii package. For example the > following > >>> >> would be a more idiomatic example of using Org-mode to create a > table > >>> >> from R code. > >>> >> > >>> >> --8<---------------cut here---------------start------------->8--- > >>> >> #+begin_src R > >>> >> numbers <- matrix(c(51,43,22,92,28,21,68,22,9),ncol=3D3,byrow=3DT= RUE) > >>> >> numbers > >>> >> #+end_src > >>> >> > >>> >> #+results: > >>> >> | 51 | 43 | 22 | > >>> >> | 92 | 28 | 21 | > >>> >> | 68 | 22 | 9 | > >>> >> > >>> >> #+begin_src R :colnames yes > >>> >> numbers <- matrix(c(51,43,22,92,28,21,68,22,9),ncol=3D3,byrow=3DT= RUE) > >>> >> numbers > >>> >> #+end_src > >>> >> > >>> >> #+results: > >>> >> | V1 | V2 | V3 | > >>> >> |----+----+----| > >>> >> | 51 | 43 | 22 | > >>> >> | 92 | 28 | 21 | > >>> >> | 68 | 22 | 9 | > >>> >> --8<---------------cut here---------------end--------------->8--- > >>> >> > >>> >> or applied to your example, the following code block should genera= te > the > >>> >> desired results. > >>> >> > >>> >> --8<---------------cut here---------------start------------->8--- > >>> >> #+srcname: foo > >>> >> #+begin_src R :session *R* > >>> >> head(esoph) > >>> >> #+end_src > >>> >> --8<---------------cut here---------------end--------------->8--- > >>> >> > >>> >> One last small note: the "replace" argument to :results is normall= y > the > >>> >> default value, and doesn't need to be explicitly added (although I > can > >>> >> see why you would have added it in this case since it wasn't worki= ng > as > >>> >> expected). > >>> >> > >>> >> Cheers -- Eric > >>> >> > >>> >> David Hajage writes: > >>> >> > >>> >> > I tried the code with the last development version of org-mode: > >>> >> > > >>> >> > #+srcname: foo > >>> >> > #+begin_src R :session *R* :results output org replace > >>> >> > library(ascii) > >>> >> > options(asciiType =3D "org") > >>> >> > ascii(head(esoph)) > >>> >> > #+end_src > >>> >> > > >>> >> > #+results: foo > >>> >> > > >>> >> > | | agegp | alcgp | tobgp | ncases | ncontrols | > >>> >> > |---+-------+-----------+----------+--------+-----------| > >>> >> > | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 | 40.00 | > >>> >> > | 2 | 25-34 | 0-39g/day | 10-19 | 0.00 | 10.00 | > >>> >> > | 3 | 25-34 | 0-39g/day | 20-29 | 0.00 | 6.00 | > >>> >> > | 4 | 25-34 | 0-39g/day | 30+ | 0.00 | 5.00 | > >>> >> > | 5 | 25-34 | 40-79 | 0-9g/day | 0.00 | 27.00 | > >>> >> > | 6 | 25-34 | 40-79 | 10-19 | 0.00 | 7.00 | > >>> >> > > >>> >> > | | agegp | alcgp | tobgp | ncases | ncontrols | > >>> >> > |---+-------+-----------+----------+--------+-----------| > >>> >> > | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 | 40.00 | > >>> >> > | 2 | 25-34 | 0-39g/day | 10-19 | 0.00 | 10.00 | > >>> >> > | 3 | 25-34 | 0-39g/day | 20-29 | 0.00 | 6.00 | > >>> >> > | 4 | 25-34 | 0-39g/day | 30+ | 0.00 | 5.00 | > >>> >> > | 5 | 25-34 | 40-79 | 0-9g/day | 0.00 | 27.00 | > >>> >> > | 6 | 25-34 | 40-79 | 10-19 | 0.00 | 7.00 | > >>> >> > > >>> >> > There is no more ">", but an extra space. > >>> >> > But, the replace option doesn't work: results are still appended= . > I am > >>> >> not > >>> >> > an org-mode guru (far, far away), but I think this is because wh= en > >>> output > >>> >> is > >>> >> > org, there is no indication about the "end" of the results. > >>> >> > > >>> >> > David > >>> >> > > >>> >> > > >>> >> > On Tue, Aug 17, 2010 at 10:17, David Hajage > >>> wrote: > >>> >> > > >>> >> >> Hello, > >>> >> >> > >>> >> >> I am trying to use babel with R. Here the code: > >>> >> >> > >>> >> >> #+srcname: foo > >>> >> >> #+begin_src R :session *R* :results output org replace > >>> >> >> library(ascii) > >>> >> >> options(asciiType =3D "org") > >>> >> >> ascii(head(esoph)) > >>> >> >> #+end_src > >>> >> >> > >>> >> >> #+results: foo > >>> >> >> > >>> >> >> > | | agegp | alcgp | tobgp | ncases | ncontrols | > >>> >> >> |---+-------+-----------+----------+--------+-----------| > >>> >> >> | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 | 40.00 | > >>> >> >> | 2 | 25-34 | 0-39g/day | 10-19 | 0.00 | 10.00 | > >>> >> >> | 3 | 25-34 | 0-39g/day | 20-29 | 0.00 | 6.00 | > >>> >> >> | 4 | 25-34 | 0-39g/day | 30+ | 0.00 | 5.00 | > >>> >> >> | 5 | 25-34 | 40-79 | 0-9g/day | 0.00 | 27.00 | > >>> >> >> | 6 | 25-34 | 40-79 | 10-19 | 0.00 | 7.00 | > >>> >> >> > >>> >> >> > | | agegp | alcgp | tobgp | ncases | ncontrols | > >>> >> >> |---+-------+-----------+----------+--------+-----------| > >>> >> >> | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 | 40.00 | > >>> >> >> | 2 | 25-34 | 0-39g/day | 10-19 | 0.00 | 10.00 | > >>> >> >> | 3 | 25-34 | 0-39g/day | 20-29 | 0.00 | 6.00 | > >>> >> >> | 4 | 25-34 | 0-39g/day | 30+ | 0.00 | 5.00 | > >>> >> >> | 5 | 25-34 | 40-79 | 0-9g/day | 0.00 | 27.00 | > >>> >> >> | 6 | 25-34 | 40-79 | 10-19 | 0.00 | 7.00 | > >>> >> >> > >>> >> >> With org-mode 7.01g in emacs 23, there is two problems: > >>> >> >> - an extra ">" is added in the first line while output is "org= " > >>> >> >> - when I run the code twice, the new results is appended, whil= e > I > >>> have > >>> >> the > >>> >> >> option "replace". > >>> >> >> > >>> >> >> Is there any problem with my header? > >>> >> >> > >>> >> >> Thank you very much for your help. > >>> >> >> David > >>> >> >> > >>> >> > _______________________________________________ > >>> >> > Emacs-orgmode mailing list > >>> >> > Please use `Reply All' to send replies to the list. > >>> >> > Emacs-orgmode@gnu.org > >>> >> > http://lists.gnu.org/mailman/listinfo/emacs-orgmode > >>> >> > >>> > >>> Footnotes: > >>> [1] http://orgmode.org/manual/Header-arguments.html#Header-arguments > >>> > >>> [2] > >>> > http://orgmode.org/manual/Results-of-evaluation.html#Results-of-evaluatio= n > >>> > >>> > >>> L'int=E9grit=E9 de ce message n'=E9tant pas assur=E9e sur Internet, l= 'Institut > >>> Curie ne peut =EAtre tenu responsable de son contenu. > >>> Si vous n'=EAtes pas destinataire de ce message confidentiel, merci d= e le > >>> d=E9truire et d'avertir imm=E9diatement l'exp=E9diteur. > >>> Afin de contribuer au respect de l'environnement, merci de n'imprimer > ce > >>> mail qu'en cas de n=E9cessit=E9. > >>> > > Footnotes: > [1] > ,----[org-babel-insert-result] > | org-babel-insert-result is a Lisp function in `ob.el'. > | > | (org-babel-insert-result RESULT &optional RESULT-PARAMS INFO HASH > | INDENT LANG) > | > | Insert RESULT into the current buffer. > | By default RESULT is inserted after the end of the > | current source block. With optional argument RESULT-PARAMS > | controls insertion of results in the org-mode file. > | RESULT-PARAMS can take the following values... > | > | replace - (default option) insert results after the source block > | replacing any previously inserted results > | > | silent -- no results are inserted > | > | file ---- the results are interpreted as a file path, and are > | inserted into the buffer using the Org-mode file syntax > | > | raw ----- results are added directly to the org-mode file. This > | is a good option if you code block will output org-mode > | formatted text. > | > | org ----- this is the same as the 'raw' option > | > | html ---- results are added inside of a #+BEGIN_HTML block. This > | is a good option if you code block will output html > | formatted text. > | > | latex --- results are added inside of a #+BEGIN_LATEX block. > | This is a good option if you code block will output > | latex formatted text. > | > | code ---- the results are extracted in the syntax of the source > | code of the language being evaluated and are added > | inside of a #+BEGIN_SRC block with the source-code > | language set appropriately. Note this relies on the > | optional LANG argument. > | > | [back] > `---- > > [2] > ,---- > | ob-org has two non-standard header arguments in that it exports it's > | results by default and the result type defaults to raw, this ensures > | that the body of a begin_src org block exports transparently. > | > | This is a breaking change in that if you are currently using org > | code blocks to export org-fontified code you will have to set the > | ":exports" header argument for org-mode blocks to "code" on a block, > | file, language or system-wide basis. > `---- > --001485f5ce1e433546048ebfbce1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I am so sorry to bother you again, but I must miss something.

When I write:

#+begin_src R :results ou= tput org :exports both
library(ascii)
options(asciiType= =3D "org")
ascii(head(esoph))
#+end_src

The re= sults is:

#+results:
#+BEGIN_SRC or= g
| =A0 | agegp | alcgp =A0 =A0 | tobgp =A0 =A0| ncases | ncontro= ls |
|---+-------+-----------+----------+--------+-----------|
| = 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 =A0 | 40.00 =A0 =A0 |
| 2= | 25-34 | 0-39g/day | 10-19 =A0 =A0| 0.00 =A0 | 10.00 =A0 =A0 |
= | 3 | 25-34 | 0-39g/day | 20-29 =A0 =A0| 0.00 =A0 | 6.00 =A0 =A0 =A0|
| 4 | 25-34 | 0-39g/day | 30+ =A0 =A0 =A0| 0.00 =A0 | 5.00 =A0 =A0 =A0= |
| 5 | 25-34 | 40-79 =A0 =A0 | 0-9g/day | 0.00 =A0 | 27.00 =A0 = =A0 |
| 6 | 25-34 | 40-79 =A0 =A0 | 10-19 =A0 =A0| 0.00 =A0 | 7.0= 0 =A0 =A0 =A0|
#+END_SRC

OK, the result is surrounded by BEGIN_SRC org/END= _SRC. But when I export this, the results is exported as fontified org code= . What should I do to have this result interpreted as org markup?
David


On Thu, Aug 26, 2010 at 18:10, Eric Schu= lte <schulte= .eric@gmail.com> wrote:
Hi,

A fix to this issue has been pushed up to the repository. =A0As can now be<= br> read in the documentation of the `org-babel-insert-result' function [1]= ,
there is now a subtle distinction between ":results org" and &quo= t;:results
raw", where ":results org" will wrap code block results in a= "begin_src
org" block. =A0The block wrapper makes it possible for the entirety of= the
results to be located and removed by Babel upon code block
re-evaluation.

In addition a new ob-org.el file has been added providing support for
evaluation of Org-mode blocks. =A0With this new language support loaded
the above technique becomes a working replacement for ":results raw&qu= ot;
allowing the body of the org code block to be interpreted as inline
org-mode text on export. =A0This is done through some non-standard default<= br> header arguments described in the recent commit message (see [2])

Best -- Eric

"Eric Schulte" <schu= lte.eric@gmail.com> writes:

> Hi David,
>
> "#+end_results: foo" (or some derivative syntax) sounds like= a good
> idea, I'll add it to the Babel task list.
>
> Thanks -- Eric
>
> David Hajage <dhajage@gmail.co= m> writes:
>
>> OK, I understand that using ":results org", the results = is not altered,
>> there is no post processing. But I don't want a post processin= g, I would
>> like a way to tell babel where is the begining *and the end* of th= e output
>> produces by a particular R source block. I think an "#+end_re= sults: foo" at
>> the end of the output could do the job. Then, the option "rep= lace" could
>> work in all situation, even if a blank line is inserted somewhere = in the org
>> output. No?
>> David
>>
>>
>> On Tue, Aug 17, 2010 at 17:15, Eric Schulte <schulte.eric@gmail.com> wrote:
>>
>>> Hi David,
>>>
>>> David Hajage <dhajage@= gmail.com> writes:
>>>
>>> > Thank you very much for your answer.
>>> >
>>>
>>> My pleasure
>>>
>>> >
>>> > But when I run the following code directly into R, no ext= ra lines is
>>> >added
>>> > by the ascii function:
>>> >> library(ascii)
>>> > Le chargement a n=E9cessit=E9 le package : proto
>>> >> options(asciiType =3D "org")
>>> >> ascii(head(esoph)) # no extra line
>>> > | =A0 | agegp | alcgp =A0 =A0 | tobgp =A0 =A0| ncases | n= controls |
>>> > |---+-------+-----------+----------+--------+-----------|=
>>> > | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 =A0 | 40.00 =A0= =A0 |
>>> > | 2 | 25-34 | 0-39g/day | 10-19 =A0 =A0| 0.00 =A0 | 10.00= =A0 =A0 |
>>> > | 3 | 25-34 | 0-39g/day | 20-29 =A0 =A0| 0.00 =A0 | 6.00 = =A0 =A0 =A0|
>>> > | 4 | 25-34 | 0-39g/day | 30+ =A0 =A0 =A0| 0.00 =A0 | 5.0= 0 =A0 =A0 =A0|
>>> > | 5 | 25-34 | 40-79 =A0 =A0 | 0-9g/day | 0.00 =A0 | 27.00= =A0 =A0 |
>>> > | 6 | 25-34 | 40-79 =A0 =A0 | 10-19 =A0 =A0| 0.00 =A0 | 7= .00 =A0 =A0 =A0|
>>> >
>>>
>>> ah, my fault, this isn't an ascii issue.
>>>
>>> >
>>> > In fact, the solution was to run 'library(ascii)'= in another source
>>> block.
>>> > When I run only this:
>>> >
>>>
>>> Thanks for pointing this out, I see what's happening now.<= br> >>>
>>> The :results output header argument (see [1] for information o= n header
>>> arguments) informs Org-mode to collect all of the output of th= e source
>>> code block. =A0This means that when library(ascii) is run, an = empty line
>>> is collected and appended to the output. =A0Removing the "= ;output" header
>>> argument should fix this issue.
>>>
>>> My I ask why you are using the ascii package for simple table = output?
>>> It seems to me that this would be much simpler using the pure = Org-mode
>>> solution I suggested in my previous email.
>>>
>>> >
>>> > #+begin_src R :session *R* :results output org replace >>> > =A0 ascii(head(esoph))
>>> > #+end_src
>>> >
>>> > #+results: foo
>>> > | =A0 | agegp | alcgp =A0 =A0 | =A0 =A0tobgp | ncases | n= controls |
>>> > |---+-------+-----------+----------+--------+-----------|=
>>> > | 1 | 25-34 | 0-39g/day | 0-9g/day | =A0 0.00 | =A0 =A0 4= 0.00 |
>>> > | 2 | 25-34 | 0-39g/day | =A0 =A010-19 | =A0 0.00 | =A0 = =A0 10.00 |
>>> > | 3 | 25-34 | 0-39g/day | =A0 =A020-29 | =A0 0.00 | =A0 = =A0 =A06.00 |
>>> > | 4 | 25-34 | 0-39g/day | =A0 =A0 =A030+ | =A0 0.00 | =A0= =A0 =A05.00 |
>>> > | 5 | 25-34 | 40-79 =A0 =A0 | 0-9g/day | =A0 0.00 | =A0 = =A0 27.00 |
>>> > | 6 | 25-34 | 40-79 =A0 =A0 | =A0 =A010-19 | =A0 0.00 | = =A0 =A0 =A07.00 |
>>> >
>>> > Everything is then OK.
>>> > I have no idea why "library(ascii)..." generate= s an extra empty line in
>>> the
>>> > results.
>>> >
>>> > If I understand, the results is all the text directly und= er "#+results:",
>>> > until the first empty line. But what happens if the resul= t contains empty
>>> > lines? Here an example with ascii and Hmisc package:
>>> >
>>>
>>> This is not quite right, see [2] for a discussion of results h= andling.
>>> The "org" option to results is a special case in whi= ch no
>>> post-processing of the results takes place, and the raw output= is
>>> inserted into the org-mode buffer.
>>>
>>> Under normal usage w/o this header argument, results are eithe= r tabular
>>> or are textual. =A0If tabular a single table can easily be rec= ognized and
>>> handled, if textual they are normally enclosed in a block (exa= mple,
>>> html, latex, etc...), the block then allows for empty lines wh= ile still
>>> making it clear where the results end.
>>>
>>
>>
>>>
>>> >
>>> >> library(ascii)
>>> >> library(Hmisc)
>>> >> ascii(describe(esoph[, 1:3]))
>>> > #+CAPTION: esoph[, 1:3]
>>> > - 3 Variable
>>> > - 88 Observations
>>> >
>>> > *agegp*
>>> > | n =A0| missing | unique |
>>> > | 88 | 0 =A0 =A0 =A0 | 6 =A0 =A0 =A0|
>>> >
>>> > | =A0 =A0 =A0 =A0 =A0 | 25-34 | 35-44 | 45-54 | 55-64 | 6= 5-74 | 75+ |
>>> > | Frequency | 15 =A0 =A0| 15 =A0 =A0| 16 =A0 =A0| 16 =A0 = =A0| 15 =A0 =A0| 11 =A0|
>>> > | % =A0 =A0 =A0 =A0 | 17 =A0 =A0| 17 =A0 =A0| 18 =A0 =A0|= 18 =A0 =A0| 17 =A0 =A0| 12 =A0|
>>> >
>>> > *alcgp*
>>> > | n =A0| missing | unique |
>>> > | 88 | 0 =A0 =A0 =A0 | 4 =A0 =A0 =A0|
>>> >
>>> > =A00-39g/day (23, 26%), 40-79 (23, 26%), 80-119 (21, 24%)= , 120+ (21, 24%)
>>> >
>>> > *tobgp*
>>> > | n =A0| missing | unique |
>>> > | 88 | 0 =A0 =A0 =A0 | 4 =A0 =A0 =A0|
>>> >
>>> > =A00-9g/day (24, 27%), 10-19 (24, 27%), 20-29 (20, 23%), = 30+ (20, 23%)
>>> >
>>> > As you can see, describe() generate a description of my d= ata, and ascii
>>> > generate org-mode markup as result. The result contains e= mpty rows. Since
>>> > there is no special characters indicating the end of the = results in
>>> babel,
>>> > replace option will not work in this case. Is there any w= orkaround?
>>> >
>>>
>>> When using ":results org" there is no workaround, as= the explicit
>>> purpose of this setting is for your results to be inserted dir= ectly into
>>> the Org-mode buffer w/o any interpretation or alteration.
>>>
>>
>>
>>>
>>> In general I would recommend keeping a 1-to-1 mapping between = code
>>> blocks and result items, which should resolve this issue.
>>>
>>> >
>>> > Of course, ascii is not usefull in this case, but it can = coerce into
>>> > org-mode markup many other R objects (see my previous exa= mple and
>>> > http://orgmode.org/worg/org-contrib/babel= /examples/ascii.php)
>>> >
>>>
>>> I see, that answers my question from above. Thanks
>>>
>>> Hope this helps -- Eric
>>>
>>> >
>>> > David
>>> >
>>> >
>>> > On Tue, Aug 17, 2010 at 15:57, Eric Schulte <schulte.eric@gmail.com>
>>> wrote:
>>> >
>>> >> Hi David,
>>> >>
>>> >> It seems that the problem here is in the ascii packag= e. =A0It is inserting
>>> >> an empty line at the beginning of your table, so that= the table is not
>>> >> snugly sitting under the #+results foo tag, because o= f this the table
>>> >> isn't seen as results and is not replaced -- if y= ou delete that space
>>> >> then re-run the code block you'll notice that the= table is replaced.
>>> >>
>>> >> Org-mode is very capable of inserting tabular data in= to Org-mode
>>> >> documents without using the ascii package. =A0For exa= mple the following
>>> >> would be a more idiomatic example of using Org-mode t= o create a table
>>> >> from R code.
>>> >>
>>> >> --8<---------------cut here---------------start---= ---------->8---
>>> >> #+begin_src R
>>> >> =A0numbers <- matrix(c(51,43,22,92,28,21,68,22,9),= ncol=3D3,byrow=3DTRUE)
>>> >> =A0numbers
>>> >> #+end_src
>>> >>
>>> >> #+results:
>>> >> | 51 | 43 | 22 |
>>> >> | 92 | 28 | 21 |
>>> >> | 68 | 22 | =A09 |
>>> >>
>>> >> #+begin_src R :colnames yes
>>> >> =A0numbers <- matrix(c(51,43,22,92,28,21,68,22,9),= ncol=3D3,byrow=3DTRUE)
>>> >> =A0numbers
>>> >> #+end_src
>>> >>
>>> >> #+results:
>>> >> | V1 | V2 | V3 |
>>> >> |----+----+----|
>>> >> | 51 | 43 | 22 |
>>> >> | 92 | 28 | 21 |
>>> >> | 68 | 22 | =A09 |
>>> >> --8<---------------cut here---------------end-----= ---------->8---
>>> >>
>>> >> or applied to your example, the following code block = should generate the
>>> >> desired results.
>>> >>
>>> >> --8<---------------cut here---------------start---= ---------->8---
>>> >> #+srcname: foo
>>> >> #+begin_src R :session *R*
>>> >> =A0 head(esoph)
>>> >> #+end_src
>>> >> --8<---------------cut here---------------end-----= ---------->8---
>>> >>
>>> >> One last small note: the "replace" argument= to :results is normally the
>>> >> default value, and doesn't need to be explicitly = added (although I can
>>> >> see why you would have added it in this case since it= wasn't working as
>>> >> expected).
>>> >>
>>> >> Cheers -- Eric
>>> >>
>>> >> David Hajage <dhajage@gmail.com> writes:
>>> >>
>>> >> > I tried the code with the last development versi= on of org-mode:
>>> >> >
>>> >> > #+srcname: foo
>>> >> > #+begin_src R :session *R* :results output org r= eplace
>>> >> > =A0 library(ascii)
>>> >> > =A0 options(asciiType =3D "org")
>>> >> > =A0 ascii(head(esoph))
>>> >> > #+end_src
>>> >> >
>>> >> > #+results: foo
>>> >> >
>>> >> > =A0| =A0 | agegp | alcgp =A0 =A0 | tobgp =A0 =A0= | ncases | ncontrols |
>>> >> > |---+-------+-----------+----------+--------+---= --------|
>>> >> > | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 =A0 | = 40.00 =A0 =A0 |
>>> >> > | 2 | 25-34 | 0-39g/day | 10-19 =A0 =A0| 0.00 = =A0 | 10.00 =A0 =A0 |
>>> >> > | 3 | 25-34 | 0-39g/day | 20-29 =A0 =A0| 0.00 = =A0 | 6.00 =A0 =A0 =A0|
>>> >> > | 4 | 25-34 | 0-39g/day | 30+ =A0 =A0 =A0| 0.00 = =A0 | 5.00 =A0 =A0 =A0|
>>> >> > | 5 | 25-34 | 40-79 =A0 =A0 | 0-9g/day | 0.00 = =A0 | 27.00 =A0 =A0 |
>>> >> > | 6 | 25-34 | 40-79 =A0 =A0 | 10-19 =A0 =A0| 0.0= 0 =A0 | 7.00 =A0 =A0 =A0|
>>> >> >
>>> >> > =A0| =A0 | agegp | alcgp =A0 =A0 | tobgp =A0 =A0= | ncases | ncontrols |
>>> >> > |---+-------+-----------+----------+--------+---= --------|
>>> >> > | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 =A0 | = 40.00 =A0 =A0 |
>>> >> > | 2 | 25-34 | 0-39g/day | 10-19 =A0 =A0| 0.00 = =A0 | 10.00 =A0 =A0 |
>>> >> > | 3 | 25-34 | 0-39g/day | 20-29 =A0 =A0| 0.00 = =A0 | 6.00 =A0 =A0 =A0|
>>> >> > | 4 | 25-34 | 0-39g/day | 30+ =A0 =A0 =A0| 0.00 = =A0 | 5.00 =A0 =A0 =A0|
>>> >> > | 5 | 25-34 | 40-79 =A0 =A0 | 0-9g/day | 0.00 = =A0 | 27.00 =A0 =A0 |
>>> >> > | 6 | 25-34 | 40-79 =A0 =A0 | 10-19 =A0 =A0| 0.0= 0 =A0 | 7.00 =A0 =A0 =A0|
>>> >> >
>>> >> > There is no more ">", but an extra = space.
>>> >> > But, the replace option doesn't work: result= s are still appended. I am
>>> >> not
>>> >> > an org-mode guru (far, far away), but I think th= is is because when
>>> output
>>> >> is
>>> >> > org, there is no indication about the "end&= quot; of the results.
>>> >> >
>>> >> > David
>>> >> >
>>> >> >
>>> >> > On Tue, Aug 17, 2010 at 10:17, David Hajage <= dhajage@gmail.com>
>>> wrote:
>>> >> >
>>> >> >> Hello,
>>> >> >>
>>> >> >> I am trying to use babel with R. Here the co= de:
>>> >> >>
>>> >> >> #+srcname: foo
>>> >> >> #+begin_src R :session *R* :results output o= rg replace
>>> >> >> =A0 library(ascii)
>>> >> >> =A0 options(asciiType =3D "org") >>> >> >> =A0 ascii(head(esoph))
>>> >> >> #+end_src
>>> >> >>
>>> >> >> #+results: foo
>>> >> >>
>>> >> >> > | =A0 | agegp | alcgp =A0 =A0 | tobgp = =A0 =A0| ncases | ncontrols |
>>> >> >> |---+-------+-----------+----------+--------= +-----------|
>>> >> >> | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 = =A0 | 40.00 =A0 =A0 |
>>> >> >> | 2 | 25-34 | 0-39g/day | 10-19 =A0 =A0| 0.0= 0 =A0 | 10.00 =A0 =A0 |
>>> >> >> | 3 | 25-34 | 0-39g/day | 20-29 =A0 =A0| 0.0= 0 =A0 | 6.00 =A0 =A0 =A0|
>>> >> >> | 4 | 25-34 | 0-39g/day | 30+ =A0 =A0 =A0| 0= .00 =A0 | 5.00 =A0 =A0 =A0|
>>> >> >> | 5 | 25-34 | 40-79 =A0 =A0 | 0-9g/day | 0.0= 0 =A0 | 27.00 =A0 =A0 |
>>> >> >> | 6 | 25-34 | 40-79 =A0 =A0 | 10-19 =A0 =A0|= 0.00 =A0 | 7.00 =A0 =A0 =A0|
>>> >> >>
>>> >> >> > | =A0 | agegp | alcgp =A0 =A0 | tobgp = =A0 =A0| ncases | ncontrols |
>>> >> >> |---+-------+-----------+----------+--------= +-----------|
>>> >> >> | 1 | 25-34 | 0-39g/day | 0-9g/day | 0.00 = =A0 | 40.00 =A0 =A0 |
>>> >> >> | 2 | 25-34 | 0-39g/day | 10-19 =A0 =A0| 0.0= 0 =A0 | 10.00 =A0 =A0 |
>>> >> >> | 3 | 25-34 | 0-39g/day | 20-29 =A0 =A0| 0.0= 0 =A0 | 6.00 =A0 =A0 =A0|
>>> >> >> | 4 | 25-34 | 0-39g/day | 30+ =A0 =A0 =A0| 0= .00 =A0 | 5.00 =A0 =A0 =A0|
>>> >> >> | 5 | 25-34 | 40-79 =A0 =A0 | 0-9g/day | 0.0= 0 =A0 | 27.00 =A0 =A0 |
>>> >> >> | 6 | 25-34 | 40-79 =A0 =A0 | 10-19 =A0 =A0|= 0.00 =A0 | 7.00 =A0 =A0 =A0|
>>> >> >>
>>> >> >> With org-mode 7.01g in emacs 23, there is tw= o problems:
>>> >> >> =A0- an extra ">" is added in t= he first line while output is "org"
>>> >> >> =A0- when I run the code twice, the new resu= lts is appended, while I
>>> have
>>> >> the
>>> >> >> option "replace".
>>> >> >>
>>> >> >> Is there any problem with my header?
>>> >> >>
>>> >> >> Thank you very much for your help.
>>> >> >> David
>>> >> >>
>>> >> > _______________________________________________<= br> >>> >> > Emacs-orgmode mailing list
>>> >> > Please use `Reply All' to send replies to th= e list.
>>> >> > Emacs-o= rgmode@gnu.org
>>> >> > http://lists.gnu.org/mailman/listinfo/ema= cs-orgmode
>>> >>
>>>
>>> Footnotes:
>>> [1] =A0http://orgmode.org/manual/Header-ar= guments.html#Header-arguments
>>>
>>> [2]
>>> http://orgmode.org/manual/Result= s-of-evaluation.html#Results-of-evaluation
>>>
>>>
>>> L'int=E9grit=E9 de ce message n'=E9tant pas assur=E9e = sur Internet, l'Institut
>>> Curie ne peut =EAtre tenu responsable de son contenu.
>>> Si vous n'=EAtes pas destinataire de ce message confidenti= el, merci de le
>>> d=E9truire et d'avertir imm=E9diatement l'exp=E9diteur= .
>>> Afin de contribuer au respect de l'environnement, merci de= n'imprimer ce
>>> mail qu'en cas de n=E9cessit=E9.
>>>

Footnotes:
[1]
,----[org-babel-insert-result]
| org-babel-insert-result is a Lisp function in `ob.el'.
|
| (org-babel-insert-result RESULT &optional RESULT-PARAMS INFO HASH
| INDENT LANG)
|
| Insert RESULT into the current buffer.
| By default RESULT is inserted after the end of the
| current source block. =A0With optional argument RESULT-PARAMS
| controls insertion of results in the org-mode file.
| RESULT-PARAMS can take the following values...
|
| replace - (default option) insert results after the source block
| =A0 =A0 =A0 =A0 =A0 replacing any previously inserted results
|
| silent -- no results are inserted
|
| file ---- the results are interpreted as a file path, and are
| =A0 =A0 =A0 =A0 =A0 inserted into the buffer using the Org-mode file synt= ax
|
| raw ----- results are added directly to the org-mode file. =A0This
| =A0 =A0 =A0 =A0 =A0 is a good option if you code block will output org-mo= de
| =A0 =A0 =A0 =A0 =A0 formatted text.
|
| org ----- this is the same as the 'raw' option
|
| html ---- results are added inside of a #+BEGIN_HTML block. =A0This
| =A0 =A0 =A0 =A0 =A0 is a good option if you code block will output html | =A0 =A0 =A0 =A0 =A0 formatted text.
|
| latex --- results are added inside of a #+BEGIN_LATEX block.
| =A0 =A0 =A0 =A0 =A0 This is a good option if you code block will output | =A0 =A0 =A0 =A0 =A0 latex formatted text.
|
| code ---- the results are extracted in the syntax of the source
| =A0 =A0 =A0 =A0 =A0 code of the language being evaluated and are added | =A0 =A0 =A0 =A0 =A0 inside of a #+BEGIN_SRC block with the source-code | =A0 =A0 =A0 =A0 =A0 language set appropriately. =A0Note this relies on th= e
| =A0 =A0 =A0 =A0 =A0 optional LANG argument.
|
| [back]
`----

[2]
,----
| ob-org has two non-standard header arguments in that it exports it's<= br> | results by default and the result type defaults to raw, this ensures
| that the body of a begin_src org block exports transparently.
|
| This is a breaking change in that if you are currently using org
| code blocks to export org-fontified code you will have to set the
| ":exports" header argument for org-mode blocks to "code&qu= ot; on a block,
| file, language or system-wide basis.
`----

--001485f5ce1e433546048ebfbce1-- --===============0495202864== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode --===============0495202864==--