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 <dhaj...@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.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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