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.e...@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.e...@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 <dhaj...@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.e...@gmail.com> > wrote: > >> > >>> Hi David, > >>> > >>> David Hajage <dhaj...@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.e...@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 <dhaj...@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 <dhaj...@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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