One comment: When I execute all the buffer (org-babel-execute-buffer), the result is:
#+begin_src R :results output org :exports both library(ascii) options(asciiType = "org") ascii(head(esoph, 3)) #+end_src #+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 | #+END_SRC #+results: | | 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 | Then, the results is repeated twice in the buffer. I understand why, but perhaps the "silent" option should be turned on by default for org code blocks? David On Thu, Aug 26, 2010 at 23:51, David Hajage <dhaj...@gmail.com> wrote: > 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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