Re: Re: problem with babel and R

From: David Hajage <dhajage@gmail.com>
To: Eric Schulte <schulte.eric@gmail.com>
Cc: emacs-orgmode@gnu.org
Subject: Re: Re: problem with babel and R
Date: Thu, 26 Aug 2010 22:20:35 +0200	[thread overview]
Message-ID: <AANLkTikenpE76UEGjhr0o_N3G=RjRNW5McsNQKStgN3+@mail.gmail.com> (raw)
In-Reply-To: <87k4ndjqxb.fsf@gmail.com>

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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 = "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 <schulte.eric@gmail.com> 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" <schulte.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.com> 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 would
> >> 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: foo"
> at
> >> the end of the output could do the job. Then, the option "replace" 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 extra lines is
> >>> >added
> >>> > by the ascii function:
> >>> >> library(ascii)
> >>> > Le chargement a nécessité le package : proto
> >>> >> options(asciiType = "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 header
> >>> arguments) informs Org-mode to collect all of the output of the source
> >>> code block.  This means that when library(ascii) is run, an empty line
> >>> is collected and appended to the output.  Removing 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
> >>> >   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 line
> 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 tabular
> >>> or are textual.  If tabular a single table can easily be recognized and
> >>> handled, if textual they are normally enclosed in a block (example,
> >>> html, latex, etc...), the block then allows for empty lines while 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  | 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 into
> >>> > 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 <schulte.eric@gmail.com>
> >>> 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 replaced.
> >>> >>
> >>> >> 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=3,byrow=TRUE)
> >>> >>  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=3,byrow=TRUE)
> >>> >>  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 generate
> 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 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 version of org-mode:
> >>> >> >
> >>> >> > #+srcname: foo
> >>> >> > #+begin_src R :session *R* :results output org replace
> >>> >> >   library(ascii)
> >>> >> >   options(asciiType = "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 when
> >>> output
> >>> >> is
> >>> >> > org, there is no indication about the "end" 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 code:
> >>> >> >>
> >>> >> >> #+srcname: foo
> >>> >> >> #+begin_src R :session *R* :results output org replace
> >>> >> >>   library(ascii)
> >>> >> >>   options(asciiType = "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, while
> 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-evaluation
> >>>
> >>>
> >>> L'intégrité de ce message n'étant pas assurée sur Internet, l'Institut
> >>> Curie ne peut être tenu responsable de son contenu.
> >>> Si vous n'êtes pas destinataire de ce message confidentiel, merci de le
> >>> détruire et d'avertir immédiatement l'expéditeur.
> >>> Afin de contribuer au respect de l'environnement, merci de n'imprimer
> ce
> >>> mail qu'en cas de nécessité.
> >>>
>
> 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.
> `----
>

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