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 23:51:45 +0200	[thread overview]
Message-ID: <AANLkTimsYvBrYh63YmB0SdU_A8u-c_3BqoamQZpjVrC0@mail.gmail.com> (raw)
In-Reply-To: <AANLkTikenpE76UEGjhr0o_N3G=RjRNW5McsNQKStgN3+@mail.gmail.com>

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Oups, I forgot ob-org in my .emacs... OK, now, really sorry for this.
David

On Thu, Aug 26, 2010 at 22:20, David Hajage <dhajage@gmail.com> wrote:

> 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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