Re: [O] accessing source block header arguments from exporters
Robert Klein roklein.de> writes:
>
> Hi,
>
> is there a way, to read header arguments to source blocks in the
> exporters org--src-block funktions?
Not directly. org-babel-exp-code has no provision for headers.
They get dropped.
>
> E.g. is there a way to access :firstline in the example below?
>
Not exactly, but ...
If you precede the code block with
#+attr_firstline: 23
then with point in the src block
(org-element-property :attr_firstline (org-element-context))
will return ("23"). And org-*-src-block functions can use it.
If you really want to use the :firstline idiom, you can add a hook in
`org-export-before-processing-hook' to find :firstline headers and
insert #+attr_firstline lines in the buffer copy that the exporter is using.
> #+begin_src c++ -n :firstline 23
>static struct
> {
> char*entity;
> unsigned char equiv;
> } entities[] =
> {
> { "lt", '<' } ,
> { "gt", '>' } ,
> { "amp", '&' } ,
> { "quot", '"' } ,
> { "trade",153 } , /* trade mark */
> #+end_src
>
> I didn't find it in the `element' structure.
>
> However, if I use
>
> #+begin_src c++ firstline=23
> // random C++
> #+end_src
>
> I could access :parameters from `element' and parse the string.
> However I'm not sure if I'd break some babel stuff or not.
>
C-c C-v C-i on that src block shows that 'firstline=23' is treated as
a switch by babel. So if there is any language that tries to use that
as a switch (or has a regexp that matches it), there could be trouble.
But in C it looks innocuous.
> If I'm trying to implement a firstline feature -- source blocks with
> new line numbering (-n) beginning at a given line number -- I'd prefer
> to use :firstline, but I didn't find anything to suggest `:XXX ZZ'
> header arguments to source blocks are available to the exporters.
>
HTH,
Chuck
Re: [O] Bug: problem when exporting a org-mode file with a lots of code blocks
XIE Yuheng gmail.com> writes: > > > Bug: org-babel-parse-src-block-match reporting "Wrong type argument: > stringp, nil" when exporting a org-mode file with a lots of code blocks > [8.3beta (release_8.3beta-895-g375c83 > /usr/share/emacs/site-lisp/org/)] > > the following is *Messages* buffer >https://www.refheap.com/98243 > the following is the org-mode file with a lot of code blocks >https://github.com/the-little-language-designer/cicada-nymph/blob/ master/cicada-nymph.org Look at the *Messages* buffer and you will see a list of src blocks that were processed without error. The src block *after* the last block in the list (before the error message) caused the error. `org-babel-parse-src-block-match' expects a language for a src block. Specify a language for every src block and it will export. HTH, Chuck
Re: [O] [BUG] on export resulting in endless evaluation
Rainer M Krug krugs.de> writes: > > Sebastien Vauban > writes: > > > Rainer M Krug wrote: > >> Charles Berry writes: > >>> Rainer M Krug krugs.de> writes: > >>>> > >>>> when exporting the fillowing org file, I get an endless loop of > >>>> evaluations. > >>>> > >>>> --8<---cut here---start->8--- > >>>> #+PROPERTY: header-args :exports both > >>>> #+PROPERTY: header-args+ :results output > >>>> * The bug > >>>> This file create an (possibly endless?) loop during export > >>>> * here exports both > >>>> #+begin_src R > >>>> cat(13+14) > >>>> #+end_src > >>>> > >>>> * and here only code > >>>> :PROPERTIES: > >>>> :header-args+: exports code > >>>> :END: > >>>> #+begin_src R > >>>> paste(13+14) > >>>> #+end_src > >>>> --8<---cut here---end--->8--- > >>> [discussion of problem, diagnostic methods, and cures deleted] > 1) I thought that header-args is simply a string, but it already seems > to be a list? Depends on which `header-args' one is discussing: 1. A property, as in `(org-entry-get (point) "header-args" t)' 2. The value of `(nth 2 (org-babel-get-src-block-info))' 3. The value of an elisp variable like `org-babel-default-header-args' 4. The 4th string matched by `org-babel-src-block-regexp' 5. The first string matched by `org-babel-multi-line-header-regexp' 1, 4 and 5 are strings. 2 and 3 are lists. > [more questions deleted] > Exactly what happens and when is a long story, involving a bunch of functions. You might start by reading `org-babel-get-src-block-info' and `org-babel-merge-params'. I think most of what you need to know really is in (info "(org) Using header arguments") and (info "(org) Property syntax") Just remember that a property called `header-args' is a string until Babel starts working on it. > 5) Is there any way in getting, in this function, the same output > (header-args) as from the code block suggested by Charles: > You might try #+BEGIN_SRC emacs-lisp :results pp (cons (org-entry-get (point) "header-args" t) (nth 2 (org-babel-get-src-block-info))) #+END_SRC HTH, Chuck
Re: [O] [BUG] on export resulting in endless evaluation
Rainer M Krug krugs.de> writes: > > > Hi > > when exporting the fillowing org file, I get an endless loop of > evaluations. > > This happens with only orgmode and languages enabled > > , > | GNU Emacs 24.4.1 (x86_64-apple-darwin14.0.0, Carbon Version 157 > | Org-mode version 8.3beta (release_8.3beta-798-g528b90 > ` > > --8<---cut here---start->8--- > #+PROPERTY: header-args :exports both > #+PROPERTY: header-args+ :results output > * The bug > This file create an (possibly endless?) loop during export > * here exports both > #+begin_src R > cat(13+14) > #+end_src > > * and here only code > :PROPERTIES: > :header-args+: exports code > :END: > #+begin_src R > paste(13+14) > #+end_src > --8<---cut here---end--->8--- > Add this to the end of your example and run the src block: --8<---cut here---start->8--- #+BEGIN_SRC emacs-lisp :results pp (org-entry-get (point) "header-args" t) #+END_SRC #+RESULTS: : ":exports both :results output exports code" --8<---cut here---end--->8--- As you see the property API merely adds the `exports code' to the end of the "header-args"value. Babel then ignores the 'exports' and you end up with `:results output code' which creates an executable src block. Since :exports both' is set, that src block is executed. And so on. A bug? I guess Babel could do a better job of screening header-args and barf if invalid args are submitted. I believe that `org-babel-merge-params' is the place where a check could be introduced, but AFAICS there is none such. Of course `:exports code' solves this, but I think you knew that. :-) HTH, Chuck
Re: [O] Custom export backend based on HTML: how to implement own blocks?
Marcin Borkowski wmi.amu.edu.pl> writes: > > Hello, > > I'd like to (ab)use the "underline" syntax for something else. > Basically, I'd like to translate > > _underlined_ > > to > > underlined > > and > > _underlined|with variant_ > > to > > underlinedwith > variant > > but only if the underlining is between > > #+BEGIN_MYBLOCK > ... > #+END_MYBLOCK > > How to achieve this? In particular, I'd like to know: > > 1. How can I know (in org-html-underline, for instance) whether I am in > a MYBLOCK or not? > You do not need to know this directly. See below: > 2. How do I best translate the "|" syntax into "variants"? More > specifically: is it a good idea to do it in org-my-html-underline, by > analysing the "underlined" text (as a string) or maybe it's better to > write a filter? (I guess the former idea is better.) > Define two derived backends: backend 1) Use 'html as the parent. Add 'MYBLOCK' to the `:export-block' list and define your own `org-backend1-export-block' transcoder with a fallback to the parent backend for HTML blocks. You will have access to the :value of MYBLOCK as a string. You can use `org-export-string-as' to process that value according to an arbitrary backend - in this case you use `backend2'. backend 2) Use html as the parent of this backend and define `org-backend2-underline' to use the rules you outline above. You can parse the `contents' arg for the `|' etc. There might be a case for making `backend2' anonymous since you only replace one transcoder of the parent. There is an example in ` org-html--format-toc-headline'. HTH, Chuck
Re: [O] #+CALL get the first row of output table lost when using latex export
gmail.com> writes: > > Hi, > > I encounter a problem when I use #+CALL to create a table with latex > export. The problem is that the first row of the table is missing, if > the table is created with #+CALL. > [deleted - setup info] > The minimal table example is > > #+BEGIN_EXAMPLE > #+NAME: t1 > #+BEGIN_SRC python :exports results > return [['A'],None,[2]] > #+END_SRC > > #+CAPTION: T1 > #+RESULTS: t1 > > #+NAME: t2 > #+CALL: t1() :exports results > > #+CAPTION: T2 > #+RESULTS: t2 > #+END_EXAMPLE > This is not a latex issue per se. If you evaluate t2 with `org-babel-execute-maybe' the same thing will happen. org-babel-execute:python does its own formatting. #+CALL: OTOH passes the results to babel. The workaround is to use #+CALL: t1() :colnames yes HTH, Chuck
Re: [O] Inline code :results replace not working
Sebastien Vauban writes: > > "Charles C. Berry" wrote: > > I find myself writing an inline src block, then typing `C-c C-c C-x u' > > to view > > and then remove the result, then revise, and repeat. I'd be happy to > > just leave > > it in the document. > > What command are you calling with the above? Oops! Make that 'C-c C-c y C-x u' - C-c C-c runs the command org-ctrl-c-ctrl-c. - y confirms code block evaluation - - C-x u runs the command undo. --- saving myself two keystrokes (C-x u) isn't much, but if I wonder off and do something else, then I have to navigate back, find the offending result and edit it out. Best, Chuck
Re: [O] Stack overflow in regexp matcher
Alan Schmitt polytechnique.org> writes: > > Hello, > > I've just got the following backtrace when opening an org > file. Unfortunately I cannot reproduce it reliably, but I was wondering > if others had seen something similar. > I do. Try this. Start emacs 24.4.1. 1) Copy this line: CLOCK: [2013-07-22 Mon 12:29]--[2013-07-22 Mon 15:26] => 2:57 into a new *.org file. 2) Save and close the file and reopen. 3) If no such error, kill the text in the buffer, and yank it twice. 4) Repeat 2 and 3 till the message File mode specification error: (error "Stack overflow in regexp matcher") shows up. 5) prune lines from the file and try step 2 till the error disappears. For me somewhere between 400 and 500 lines is the difference between opening with no error message and opening with the message. Emacs 24.3.1 does not show this behavior - no error message. HTH, Chuck
Re: [O] Text above first headline is being exported, despite :export: tag being used.
Brady Trainor uw.edu> writes: > > I read > > , > | ‘SELECT_TAGS’ > | The tags that select a tree for export (org-export-select-tags). The > | default value is :export:. Within a subtree tagged with :export:, > | you can still exclude entries with :noexport: (see below). When > | headlines are selectively exported with :export: anywhere in a file, > | text before the first headline is ignored. > ` > > But I have trees tagged for export, while text above first headline is > being exported. Can anyone confirm? It works for me. Can you provide an ECM[1]? HTH, Chuck [1] http://orgmode.org/worg/org-faq.html#ecm
Re: [O] [ob-R] table variable passing broken
Andreas Leha med.uni-goettingen.de> writes: > > Hi all, > > There seems to be a bug in table passing as variables now using the > tangle-friendly version of passing variables. > > Here is an example (I get an error also with emacs -Q): > > --8<---cut here---start->8--- > * test > #+name: testtab > | variable | display | unit | > |---+---+---| > | num_cells | Number of Cells in Well | | > | cell_area | Cell Area | μm² | > | nucleus_area | Nucleus Area | μm² | > | roundness | Cell Roundness| | > | ratio_w2l | Cell Width to Length Ratio| | > | inten_nuc_dapi_median | Intensity Nucleus DAPI Median | | > | dapi_median | Intensity Nucleus DAPI Median | | > | edu_median| Intensity edu Median | | > | oct4_median | Intensity oct4 Median | | > | clump_size| Clump Size| cells | > | short_name| Cell Line | | > | p_col | Column| | > | batch | Batch | | > | concentration | Fibronectin Concentration | ugml | > | Residual | Residual | | > | evaluation_guid | Plate | | > | donor | Genotype | | > > #+BEGIN_SRC R :session *test* :var test=testtab > test > #+END_SRC > > #+RESULTS: > --8<---cut here---end--->8--- > > I see this in my R session: > > --8<---cut here---start->8--- > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, > na.strings, (from > testorg.org!917613Wp#22) : > line 17 did not have 3 elements > --8<---cut here---end--->8--- > I think this is the wrong diagnosis. Did you actually revert to the earlier version of ob-R.el to confirm that this would have run correctly? The reason I ask is that I just tried this with org-babel-R-assign-elisp from org-mode-a5686d87786b1d6514ec85959a2188f703346a06/lisp/ob-R.el and got the same error. Note this: --8<---cut here---start->8--- #+name: testtab2 | variable | display | unit | |--+--+--| | donor| Genotype | | #+BEGIN_SRC emacs-lisp :var test=testtab2 (orgtbl-to-tsv test '(:fmt org-babel-R-quote-tsv-field)) #+END_SRC #+RESULTS: : "donor" "Genotype" #+BEGIN_SRC emacs-lisp :var value=testtab2 ;; from org-babel-R-assign-elisp (mapcar 'length (org-remove-if-not 'sequencep value)) #+END_SRC #+RESULTS: | 3 | --8<---cut here---end--->8--- In particular, the empty table cells are omitted even though `value' or `test' has all lengths as 3. This results in calling read.table ( ..., fill=FALSE) implicitly. Not sure if the fix is to retool org-babel-R-assign-elisp or something in org-table.el. HTH, Chuck
Re: [O] left aligned changes to right alignment in table after adding one row - possible bug?
Rainer M Krug krugs.de> writes: > > > #+PROPERTY: header-args :exports both > > * Changing alignment when one row is added > Despite of all values are strings, the alignment changes in the below > example. Is this a bug or am I missing something? > One of these two maybe: ,[ C-h v org-table-number-regexp RET ] | org-table-number-regexp is a variable defined in `org-table.el'. | Its value is | "^\\([<>]?[-+^.0-9]*[0-9][-+^.0-9eEdDx()%:]*\\|[<>]?[-+]?0[xX][0-9a- | [wrapped] fA-F.]+\\|[<>]?[-+]?[0-9]+#[0-9a-zA-Z.]+\\|nan\\|[-+u]?inf\\)$" | | Documentation: | Regular expression for recognizing numbers in table columns. | If a table column contains mostly numbers, it will be aligned to the | right. If not, it will be aligned to the left. | | The default value of this option is a regular expression which allows | anything which looks remotely like a number as used in scientific | context. For example, all of the following will be considered a | number: | 1212.22.4e-082x10^124.034+-0.022.7(10) >3.5 | | Other options offered by the customize interface are more restrictive. | | You can customize this variable. | | [back] ` ,[ C-h v org-table-number-fraction RET ] | org-table-number-fraction is a variable defined in `org-table.el'. | Its value is 0.5 | | Documentation: | Fraction of numbers in a column required to make the column align right. | In a column all non-white fields are considered. If at least | this fraction of fields is matched by `org-table-number-regexp', | alignment to the right border applies. | | You can customize this variable. | | [back] ` With the added row, the fraction is exceeded in the last two columns. HTH, Chuck
[O] debugging export error
I am trying to debug a subtree export. I get member-ignore-case: Wrong type argument: stringp, nil and it seems to come from `org-export-get-environment' but if I instrument that function, the error goes away whether I step thru it or `c' on entry. Likewise, if I M-x debug-on-entry and just `c' on entry, I get no error. Bisecting the file with the subtree I am trying to export, I can find things - like removing an unused src block - that when changed get rid of the error. But I'd really like to know what is going on here and not being able to see the problem thru a debugger is a frustration. Advice appreciated. Chuck
Re: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 /usr/local/share/emacs/site-lisp/org/)]
Ista Zahn gmail.com> writes: > > > > On Oct 7, 2014 3:41 PM, "Henrik Singmann" psychologie.uni-freiburg.de> wrote: > > > > Dear all, > > > > Sorry to resurrect this thread but I still have the issue discussed > > here. I get "Error: could not find function ".ess.eval"" when inside an > > R code block with :session *R* but not without :session *R*. > > [snip] > > > > Can anybody reproduce or solve? > Yes, I can reproduce with emacs 24.3.1, org 8..2.3, and ess 14.09 on org 8.2.3 ?? The last 8.2.3 release I see on git is 2013-11-15 05:58:32 (GMT) The ess 14 patch showed up on 2014-09-18 01:10:40 (GMT). > Archlinux, but only if I don't start the R session first. If I do 'M-x > R' to manually start an R process it works fine, but if there is no R > process already running I get 'Error: could not find function > ".ess.eval"' Yes. (R) starts the session asynchronously, so in programmatic use subsequent commands can jump the queue and confuse the process. This did not seem to matter before ess 14. The 2014-09-18 01:10:40 (GMT) patch forces a wait for (R) to finish before anymore commands are sent to the session. So either update org-mode or downdate ess or replace org-babel-R-initiate-session with the current version and recompile. HTH, Chuck
Re: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 /usr/local/share/emacs/site-lisp/org/)]
Henrik Singmann psychologie.uni-freiburg.de> writes: > > Dear all, > > Sorry to resurrect this thread but I still have the issue discussed here. I get "Error: could not find > function ".ess.eval"" when inside an R code block with :session *R* but > not without :session *R*. > Please confirm that when you do M-x find-function RET org-babel-R-initiate-session RET and scroll down 15 lines: M-1 M-5 you see something like this: (ess-wait-for-process (get-process (or ess-local-process-name ess-current-process-name))) If not, there is something broken in your setup. If you do see that code, please do C-x d and verify that ob-R.el is older than ob-R.elc. If it is not older delete ob-R.elc and restart. Let us know how it goes either way. Chuck
Re: [O] Error Embedding SQL Source from code block into R Source of Another (noweb)
Eric Brown fastmail.fm> writes:
>
> Dear List:
>
> It is possible to embed SQL code as a string to be evaluated in R. I am
> interested in formatting the SQL code in its own source code block, with
> its own syntax highlighting and editing mode (C-c ').
>
> The first time I run the code, I am prompted for R starting directory,
> but I get an error:
>
> ---
> load ESSR: + + + Error: unexpected string constant in:
> source('~/.emacs.d/elpa/ess-20140913.1153/etc/ESSR/R/.load.R',
> local=TRUE) #define load.ESSR
> load.ESSR('"
> ---
>
> and the console locks. I can C-g to get out of it, and then
> re-evaluate, and the code prints what I expect -- the text of the SQL
> command.
[rest deleted]
Hmmm. Maybe the bug that was fixed by commit
0fd29a5ee7d14c3695b22998196373b9a3637413
about two weeks back? Make sure ob-R.el is up to date and compiled (or
that ob-R.elc is deleted).
Anyway, your code works as expected for me - first time.
---
FWIW, I prefer to use :var headers to import strings, but it takes some
setup:
--8<---cut here---start->8---
#+BEGIN_SRC emacs-lisp
(defun grab-src (name)
(save-excursion
(org-babel-goto-named-src-block name)
(nth 1 (org-babel-get-src-block-info 'light
#+END_SRC
#+BEGIN_SRC R :var y=(grab-src "sqlsource") :results output :exports both
y
#+END_SRC
#+RESULTS:
: [1] "select \n * \nfrom \n t \nlimit \n 10"
--8<---cut here---end--->8---
HTH,
Chuck
Re: [O] [ob, bug?] org-sbe
Rasmus gmx.us> writes: > > Hi, > > I used sbe a long time ago. Apparently it has been renamed to > org-spe. > > I was unable get org-spe working as a dumb currency converter, so I > tried the example in the top of ob-table.el. However, I'm also unable > to get this example working, even starting from emacs -q. . . > > This is the suggested test in ob-table.el: > > #+begin_src emacs-lisp :results silent > (defun fibbd (n) (if (< n 2) 1 (+ (fibbd (- n 1)) (fibbd (- n 2) > #+end_src > > #+name: fibbd > #+begin_src emacs-lisp :var n=2 :results silent > (fibbd n) > #+end_src > > | original | fibbd | > |--+| > |0 | #ERROR | > |1 | #ERROR | > |2 | #ERROR | > |3 | #ERROR | > |4 | #ERROR | > |5 | #ERROR | > |6 | #ERROR | > |7 | #ERROR | > |8 | #ERROR | > |9 | #ERROR | > #+TBLFM: $2='(org-sbe 'fibbd (n $1)) > > Did the syntax of org-sbe change or am just missing something obvious here? unquote the fibbd or double quote it --8<---cut here---start->8--- | original | fibbd | |--+---| |0 | 1 | |1 | 1 | |2 | 2 | |3 | 3 | |4 | 5 | |5 | 8 | |6 |13 | |7 |21 | |8 |34 | |9 |55 | #+TBLFM: $2='(org-sbe fibbd (n $1)) --8<---cut here---end--->8--- or --8<---cut here---start->8--- #+TBLFM: $2='(org-sbe "fibbd" (n $1)) --8<---cut here---end--->8--- HTH, Chuck
Re: [O] line numbers in a code block?
John Kitchin andrew.cmu.edu> writes: > > Does anyone know a way to get dedicate line numbers in an org code > block? > > I know how to get buffer code lines, but when we run a code block and > there is an error, the error line number is relative to line 1 of the > code block. Currently, we type C-c ' to get a code buffer, and navigate > to the line. I would like to see code block numbers on the right hand > side of the buffer, and only inside the code block. Any ideas? You mean like (org-add-hook 'org-src-mode-hook 'linum-mode) only with line numbers on the right side? (linum puts them on the left) Or did you mean in the org-mode buffer itself? Maybe (just a guess) hack `linum-update-window' to reset `line' to 0 whenever `(forward-line))'gives you a line that matches `#+begin_src'. HTH, Chuck
Re: [O] meaningfull names for org-src buffers
Andreas Leha med.uni-goettingen.de> writes: > > Hi, > > Grant Rettke wisdomandwonder.com> writes: > > On Thu, Sep 11, 2014 at 5:05 PM, Adriaan Sticker > > gmail.com> wrote: > >> I was wondering if it's somehow possible to give named org src buffer the > >> name they were give in their #+NAME tag? Now there are just called > >> something like: > >> *Org Src test.org[ R ]* > >> > >> But if you have multiple org-src buffers opened at the same time, its > >> hard to find the correct one back. > > > > Excellent idea. I've got so many small source blocks that it is too > > difficult to make sense of > > keeping multiple source block edit buffers open and limit them to one > > at a time eg > > > > , > > | (setq org-src-window-setup 'current-window) > > ` > > > > How have you come upon your workflow of keeping multiple open and what > > are some of the pros and > > cons that you've found with it? > > I'd be interested in this as well. > > Regards, > Andreas > > Maybe I am answering the wrong question, but org-edit-src-code allows you to specify the buffer name: ,[ C-h f org-edit-src-code RET ] | org-edit-src-code is an interactive compiled Lisp function in | `org-src.el'. | | (org-edit-src-code &optional CONTEXT CODE EDIT-BUFFER-NAME) | | ... ` So you can do something like this: #+BEGIN_SRC emacs-lisp (defun org-edit-src-code-plus-name () (interactive) (let* ((eop (org-element-at-point)) (name (or (org-element-property :name (org-element-context eop)) "unnamed")) (lang (org-element-property :language eop)) (buff-name (concat "*Org Src " name "[ " lang " ] *"))) (org-edit-src-code nil nil buff-name))) #+END_SRC which leads to a buffer named like "*Org Src My-block[ R ] *", where 'My-block' is the name of the src block. HTH, Chuck
Re: [O] Exporter dispatcher bug?
Brady Trainor uw.edu> writes: > > > Charles Millar verizon.net> writes: > > > Brady Trainor wrote: > >> Charles Millar verizon.net> writes: > >> > >>> Today, using C-c C-e, the dispatcher shows only the LaTeX and > >>> Publisher options. > >>> > >> What is the result C-h v org-export-backends? > >> > > -- snip -- > > Its value is (ascii html icalendar latex) > > -- snip -- > > > > Charlie > > Looks normal! Wild guess, had to try :) > I think you want to check (mapcar 'org-export-backend-name org-export--registered-backends) to see what backends are actually available to the export dispatcher. and (mapcar 'org-export-backend-menu org-export--registered-backends) to see what menu options should be there. HTH, Chuck
Re: [O] update on missing :parameters in code blocks
John Kitchin andrew.cmu.edu> writes: > > I did some more digging on the missing :parameters during export, and it > seems that the src block itself is different during export than in the > buffer. Below illustrates what I mean. In the buffer, if I look at the > contents of the code block using output from org-element-at-point, it > looks as I expect, with the complete header. But, using the same method > in the export, it is clear that the header args are not there. > > I have not figured out where they disappear yet. > [snip] Instrument org-export-as. Then step thru it. Before this line: (org-export-execute-babel-code) the buffer copy ( my-buffer<2>, say ) will show the parameters/headers. After that line is executed, they are gone. You can work around this by `advicing' various babel functions and inserting things you want to save as attributes, but it would be nice not to need to do that. HTH, Chuck
Re: [O] header arguments, inheritance, and noweb expansion Was: «Macro» expansion in source blocks; code-sharing between blocks
Andreas Kiermeier gmail.com> writes: > > On 19 September 2014 20:29, Rainer M Krug krugs.de> wrote:> [ snip ] > > The alternative mentioned by Chuck Berry is the xtable function (in R) > (https://lists.gnu.org/archive/html/emacs-orgmode/2014-09/msg00519.html). > I just tried it and am happy to share that it does created the whole > output in one go, i.e. it does exactly what I need, including table > float, caption and label. Now I just got to sort out how to created the > tables without the use of tabular ... > I suggested xtable because that is what I often use. But thinking a bit more, I decided to look at tables::tabular() and at Hmisc::latex(), which I think is what you used at first. And it turns out that latex() has args for caption, label, where, and loads of other things. See its help page. So, it looks like you have the control you need and the ability to use latex( tabular(...), caption = <...>, label = <...>, ...) to good effect. HTH, Chuck
Re: [O] [RFC] [PATCH] [babel] read description lists as lists of lists
Aaron Ecay gmail.com> writes:
>
>
> Hello all,
>
> The attached patch makes babel read description lists as lists of the
> following format: (("term" "description") ...). The present default is
> to simply read in the text of each list item, yielding:
> ("term :: description" ...).
>
> Of course, it’s possible to interconvert between the two formats, but I
> think the greater structure of this proposal makes things easier for
> babel authors. (Another way of thinking of the proposal is that it
> treats description lists like two-column tables.)
>
> What do people think?
With that change
#+BEGIN_SRC R :var a=my-desc-list
a
#+END_SRC
returns a data.frame with one column of terms and one of descriptions!
Which, no doubt, is what you were thinking.
This will be handy for creating DESCRIPTION files for R packages.
I love it.
FWIW, rgrep-ing org-babel-\(ref-resolve\)\|\(read-result\) and clicking
on the links, I didn't catch any obvious problem cases.
HTH,
Chuck
Re: [O] «Macro» expansion in source blocks; code-sharing between blocks
Andreas Kiermeier gmail.com> writes:
>
> My two blocks (with some code removed for simplicity) are as follow:
>
> #+NAME: tbl-refyear
> #+BEGIN_SRC R :results silent :exports none
> latex(tabular( ))
> #+END_SRC
>
> #+BEGIN_SRC latex :noweb yes
> \begin{table}[h]
> \label{tbl:refyear}
> \caption{Separation outcomes (death or any type of discharge) by
> reference year.}
> <>
> \end{table}
> #+END_SRC
>
> I've tried :cache yes as part of the tbl-refyear source block, but
> that didn't stop if from being run twice. Am I missing a suitable
> header argument?
>
> This is the only way I could find to wrap the latex table (which has
> some complex formatting and hence why I've used it over just producing
> a table) in a float with a caption (though I still can't properly
> reference the label when I export to a PDF file).
>
> Any thought would be greatly appreciated. TIA!
>
Why not use library(xtable) and do it all in R?
If you are not sure this is the right choice, I suggest you look at the
help page for print.xtable - you have a lot of control over caption,
label, positioning, etc.
HTH,
Chuck
[O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 /usr/local/share/emacs/site-lisp/org/)]
Charles Berry ucsd.edu> writes: > > Rainer M Krug krugs.de> writes: > > > > > Thanks - you came before me. I get the same error but managed to work > > around. > > > > This is likely caused by the upgrade of ess, > > Likely. > > But it may not be an ESS problem per se. > > M-x R starts a process that runs asynchronously. In interactive use there > is no issue (barring something in .First() that slows the startup for > a very long time). > > But, ... > > If the (rename-buffer ...) in org-babel-R-initiate-session > runs before all the setup that ESS performs in the process buffer is > complete, chaos can result. > > Not sure what the best way is to fix this. > OK. Looks like (ess-wait-for-process) fixes this. Here is a patch. Chuck == >From 89472012d80ce9ad4c8722f304c0d29327efa1fc Mon Sep 17 00:00:00 2001 From: chasberry Date: Tue, 16 Sep 2014 19:57:59 -0700 Subject: [PATCH] lisp/ob-R.el: use `ess-wait-for-process' to assure clean session startup * lisp/ob-R.el (org-babel-R-initiate-session): Make sure that (R) has finished before `rename-buffer' is run. TINYCHANGE --- lisp/ob-R.el | 3 +++ 1 file changed, 3 insertions(+) diff --git a/lisp/ob-R.el b/lisp/ob-R.el index 41b943c..7575acf 100644 --- a/lisp/ob-R.el +++ b/lisp/ob-R.el @@ -35,6 +35,8 @@ (declare-function inferior-ess-send-input "ext:ess-inf" ()) (declare-function ess-make-buffer-current "ext:ess-inf" ()) (declare-function ess-eval-buffer "ext:ess-inf" (vis)) +(declare-function ess-wait-for-process "ext:ess-inf" + (&optional proc sec-prompt wait force-redisplay)) (declare-function org-number-sequence "org-compat" (from &optional to inc)) (declare-function org-remove-if-not "org" (predicate seq)) (declare-function org-every "org" (pred seq)) @@ -262,6 +264,7 @@ This function is called by `org-babel-execute-src-block'." ;; Session buffer exists, but with dead process (set-buffer session)) (require 'ess) (R) + (ess-wait-for-process) (rename-buffer (if (bufferp session) (buffer-name session) -- 1.8.5.2 (Apple Git-48)
Re: [O] Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 /usr/local/share/emacs/site-lisp/org/)]
Rainer M Krug krugs.de> writes: > > Thanks - you came before me. I get the same error but managed to work > around. > > This is likely caused by the upgrade of ess, Likely. But it may not be an ESS problem per se. M-x R starts a process that runs asynchronously. In interactive use there is no issue (barring something in .First() that slows the startup for a very long time). But, ... If the (rename-buffer ...) in org-babel-R-initiate-session runs before all the setup that ESS performs in the process buffer is complete, chaos can result. Not sure what the best way is to fix this. A simple hack to temporarily solve the OP's problem is to force a pause before (rename-buffer ...) with (sleep-for 0.1) or something. HTH, Chuck
Re: [O] Format output of org-babel-tangle for exported file
Rainer M Krug krugs.de> writes: > > Hi > > I am calling (org-bable-tangle) in a code block in an org file and I > would show the files resulting from the tangling in a nice format. > > But I do not manage. I have the following at the moment: > > --8<---cut here---start->8--- > #+begin_src emacs-lisp > (replace-regexp-in-string "[)\"]" "" > (replace-regexp-in-string "[(]" "- " > (replace-regexp-in-string " " "\n- " >(prin1-to-string (org-babel-tangle) > #+end_src > [snip] > Which is neither elegant nor short, and I am sure I could do this > easier. Any suggestions? Something like this? Possibly with `(reverse (org-babel-tangle))' #+BEGIN_SRC emacs-lisp :results value (mapconcat (lambda (x) (file-relative-name x "..")) (org-babel-tangle) "\n") #+END_SRC HTH, Chuck
Re: [O] Please help with a filter
Rafael gmail.com> writes: > > > I want that the result of exporting to markdown the following two blocks > be identical: Rafael, You probably want a derived backend taking 'md as the parent. You want to tool up a src-block transcoder. Look at org-html-src-block (which is what markdown uses) and create org-md-sage-src-block (say) based on that. The :language property in `info' - the communication channel - is a human language not a computer language. Confusingly, babel has an `info' variable that has different contents. Filters might be made to work, but it seems like more work than a derived backend. HTH, Chuck
Re: [O] [babel, R] Commands are not copied in the iESS buffer upon evaluation
Sebastien Vauban writes: > > Hi Aaron, > > Aaron Ecay wrote: > > 2014ko abuztuak 29an, Sebastien Vauban-ek idatzi zuen: > > > >> Does it have something to do with `ess-eval-visibly' not being respected > >> (whose default is `t')? > > > > Indeed, babel’s R support let-binds this variable to nil when evaluating > > value-type results in a session. > > OK. Can we put it to `t' by default [1] or, at least, have Org Babel > respect our ESS setting? If you Google `ess-eval-visibly slow' you will get a bunch of hits that show why people prefer `nil' and why that is a good default. But it may be OK to allow a user to override. HTH, Chuck
Re: [O] cannot execute org-mode code from the front page tutorial.
Nick Dokos gmail.com> writes: > > tsd tsdye.com (Thomas S. Dye) writes: > > > Aloha Jenia, > > > > jenia.ivlev gmail.com (jenia.ivlev) writes: > > > >> Hello. > >> > >> I'm trying to go through the org-mode tutorial on its official page. > >> [discussion showing that (if (listp value)...) generates a data.frame deleted] [delete patch turning a data.frame into a vector] > And assuming this is correct, the worg page will need to be corrected > too. > No patch is needed. The point of the code in org-babel-R-assign-elisp is to create a data.frame when `value' is a list. The patch adding `unlist(res)' turns it into an ordinary vector. This will break almost all uses of :var in R scr blocks. I don't think this example could have worked for a long while - turning elisp lists into R data.frames has been a feature for a good while. Also, note the use of `sbe' vs `org-sbe' in the formula. #+TBLFM: @2$1='(sbe "R-mean" (x "tbl-example-data()")) Use `colMeans(x)' to fix the worg page. HTH, Chuck
Re: [O] "#+begin_src R :results output drawer" doesn't work.
Feng Shu gmail.com> writes: > > > #+begin_src R :results output drawer > "1" > "2" > #+end_src > > #+RESULTS: > : 2 > I get: #+RESULTS: :RESULTS: [1] "1" [1] "2" :END: #+BEGIN_SRC emacs-lisp :results drawer (org-version) #+END_SRC #+RESULTS: :RESULTS: 8.3beta :END: HTH, Chuck
Re: [O] R code block produces only partial output
Eric Schulte gmail.com> writes:
>
> Andreas Kiermeier gmail.com> writes:
>
> > On 4 August 2014 21:23, Eric Schulte gmail.com> wrote:
> >> Why are you setting the output type to "graphics" when you are trying to
>
> Hi Andreas,
>
> I can't reproduce your problem. I get the following from your minimal
> example when run in an Org-mode file, and from the command line. They
> are identical. Are you using the latest version of Org-mode?
>
> Best,
> Eric
>
[snip]
>
> [Previously saved workspace restored]
>
> > x <- rnorm(100)
> > y <- quantile(x, probs=seq(0,1,0.1))
> > names(y) <-
as.character(c("0",".1",".2",".3",".4",".5",".6",".7",".8",".9","1"))
> > y
> 0 .1 .2 .3 .4 .5
> -2.53624773 -1.30846042 -0.70659822 -0.43565010 -0.24318346 -0.01034625
> .6 .7 .8 .9 1
> 0.24125644 0.49945059 0.92032314 1.36423669 2.83357915
> >
>
>
>
Eric,
As noted by Andreas and John this is a problem for session output.
org-babel-R-evaluate-session uses
(string-match "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
to find the start of R output in the session.
This does not match the ` 0', but matches the ` .6'
in the output you show above, so if that had been in a session, all the
output up to and including the '.' before the '6' would be clipped
by the following
(substring line (match-end 1))
as Andreas output showed.
Deleting the "\\." fixes Andreas case, but what are the circumstances
requiring the "\\." ?
HTH,
Chuck
Re: [O] proposal to make C-c C-c not remove latex overlays
Bastien gnu.org> writes: > > Hi Nick, > > Nick Dokos gmail.com> writes: > > > getting rid of just latex fragment undoing in > > org-ctrl-c-ctrl-c and toggling with C-c C-x C-l is probably the best > > solution. > > Agreed, this is the case now in master. The docstring for `org-preview-latex-fragment' still says: "The images can be removed again with \\[org-ctrl-c-ctrl-c]." Maybe change that to "\\[org-preview-latex-fragment]"? HTH, Chuck
Re: [O] [patch] [babel] Patches to fix tangling and variable transfer of tables in R
Rainer M Krug krugs.de> writes: > > Nicolas Goaziou nicolasgoaziou.fr> writes: > > > Hello, > > > > Rainer M Krug krugs.de> writes: > > [snip] > > Amended patches attached. AFAICS, these patches are good to go. Can they be applied, please? Chuck
Re: [O] Possible to use src block to generate org headlines for export?
Nick Dokos gmail.com> writes: > > Charles Berry ucsd.edu> writes: > > > Matt Lundin imapmail.org> writes: > > > > [deleted] [more deleted] > > Or wrap the results in a drawer when you type C-c C-c, but render them as > > raw on export (which removes the drawer and replaces with raw results). > > > > Like so: > > > > #+header: :results (if (boundp 'backend) "raw" "drawer") > > #+BEGIN_SRC emacs-lisp :exports both > > > > (format "* headline\n1\n2\n5\n") > > #+END_SRC > > > > That's a very nice tip - one small weakness is that it'll do the wrong > thing if you just happen to have a binding for "backend" outside of the > export mechanism. > Fair enough. But getting assurance that an export process is really up and running looked tricky to me - what with anonymous backends and `info' being let-bound by babel. So this is what I came up with for a more robust test. Hopefully, nobody will bind both `backend' and `org-export-current-backend' to a common backend outside of doing an export... #+BEGIN_SRC emacs-lisp (defun org-export-if-exporting (export-val &optional other-val) "If backend exists, is a backend, and is currently running return EXPORT-VAL otherwise return OTHER-VAL or \"\"." (if (and (boundp 'backend) (equal (car (append backend nil)) 'cl-struct-org-export-backend) (equal org-export-current-backend (org-export-backend-name backend))) export-val (or other-val ""))) #+END_SRC #+header: :results (org-export-if-exporting "raw") #+BEGIN_SRC emacs-lisp :exports both (format "* headline\n1\n2\n6\n") #+END_SRC Chuck
Re: [O] Possible to use src block to generate org headlines for export?
Matt Lundin imapmail.org> writes: [deleted] > Footnotes: > > [fn:1] If one really needs to see the headlines in the original org > buffer, a hook can be used to remove the :RESULTS: drawer. > > --8<---cut here---start->8--- > (defun my-remove-stray-results-drawer (backend) > (when (eq backend 'html) > (while (re-search-forward "^\\s-*:RESULTS:\\s-*\n" nil t) > (replace-match "" > > (add-hook 'org-export-before-parsing-hook 'my-remove-results-drawer) > --8<---cut here---end--->8--- > > Or wrap the results in a drawer when you type C-c C-c, but render them as raw on export (which removes the drawer and replaces with raw results). Like so: #+header: :results (if (boundp 'backend) "raw" "drawer") #+BEGIN_SRC emacs-lisp :exports both (format "* headline\n1\n2\n5\n") #+END_SRC HTH, Chuck
Re: [O] How to show the complete syntax tree
Shiyuan gmail.com> writes: > > Hi, The command I can find in the manual to show the syntax tree is (org-element-parse-buffer). However, when the structure is output to the buffer, by using the commands C-u M-: (org-element-parse-buffer), it seems that only the part up to a certain depth is printed. Yes, as Nick explained there are variables that control this. My eyes sometimes like this approach to viewing lisp objects: #+BEGIN_SRC emacs-lisp (pp-to-string (org-element-parse-buffer)) #+END_SRC HTH, Chuck
Re: [O] passing the contents of a block as an escaped string
Alan Schmitt polytechnique.org> writes: > > Hello, > > I'm trying to write some filters from Pygments, and to record what I'm > doing and make my life simpler, I'm doing it in an orgmode buffer. In > that buffer, I have the code I want to highlight in a source block, and > the python code for the Pygments extension in another block. I'm trying > to find out how to pass the escaped code from the source to highlight to > the python buffer. > > I tried using noweb, but the expansion is verbatim and python complains > about the line breaks. So I'm wondering if there is a way to: > - pass a source block as an escaped string to another source block, or > - save a source block to a temporary file, and pass the file name to > a second source block. > defun a function that formats your src block, then use it in a header :var x=(foo "src-block-name") or maybe wrap (foo ...) in a `format' call or `prin1-to-string' call. An example is below. === Another alternative is to use this idiom (see 14.10 Noweb reference syntax) <> where the code-block-name specifies a formatter (in elisp, say) and the optional argument is the name of the code block you want to format. HTH, Chuck , | #+NAME: prin-block | #+BEGIN_SRC emacs-lisp :var a="abc" | (defun foo (blk) | (save-excursion | (org-babel-goto-named-src-block blk) | (nth 1 (org-babel-get-src-block-info 'light | | #+END_SRC | | #+NAME: weird-text | #+BEGIN_SRC python | just some plain text; | | \\ a double slash | | escape eol \n | | OK?? | #+END_SRC | | | #+BEGIN_SRC python :var a=(foo "weird-text") :results output | print(a); | #+END_SRC | | #+RESULTS: | : just some plain text; | : | : \\ a double slash | : | : escape eol \n | : | : OK?? | | #+header: :var a=(prin1-to-string (foo "weird-text")) | #+BEGIN_SRC python :results output | print(a); | #+END_SRC | | #+RESULTS: | : "just some plain text; | : | : a double slash | : | : escape eol \\n | : | : OK??" `
Re: [O] [Babel] [possible bug] Empty src block prevents other block to expand
Nicolas Girard gmail.com> writes:
>
> The empty src block at the beginning of the following file prevents
> "capture-tmpl" to expand when tangling.
>
I think the diagnosis is incorrect.
The empty source block has no effect.
Adding ':noweb yes' to `capture's header args fixes things.
org-version: 8.3-8-gce2359
Chuck
>
[snip]
> #+name: capture
> #+begin_src emacs-lisp :tangle no
Add `:noweb yes' to the previous line
> ("C" "Capture" entry "
> <>")
> #+end_src
>
> #+begin_src emacs-lisp :noweb yes
> (add-to-list 'org-capture-templates '
> <> 'append)
> #+end_src
> ---8<---
>
[snip]
Re: [O] [PATCH] -for review- Tangling with variable transfer of variables
Aaron Ecay gmail.com> writes:
>
> Hi Rainer,
>
> I have not tested the patch (I rarely use :var), but here are some
> comments from reading the patch.
>
[snip]
>
> > (header (if (or (eq (nth 1 value) 'hline) colnames-p)
> > "TRUE" "FALSE"))
> > (row-names (if rownames-p "1" "NULL")))
> > (if (= max min)
> > - (format "%s <- read.table(\"%s\",
> > + (format "%s <- read.table(textConnection('%s'),
>
> This will fail if ‘file’ contains an apostrophe character. I guess you
> need to escape apostrophes in ‘file’.
>
There are a bunch of issues with the textConnection - the point Aaron
makes, the nasty name (try showConnections() to see), and close()-ing it.
I think you need something more like this:
(header (if (or (eq (nth 1 value) 'hline) colnames-p)
"TRUE" "FALSE"))
(row-names (if rownames-p "1" "NULL")))
(if (= max min)
(format "
%s <-
local({con.object <-
%S
con <- textConnection(con.object)
res <- read.table(con,
header=%s,
row.names=%s,
sep=\"\\t\",
as.is=TRUE)
close(con)
res})"
name file header row-names)
Notes: %S handles Aaron's quoting issue.
local() keeps unwanted objects out of user's way.
This worked on a couple of simple tests
If you have `:session :results output' headers your session
transcript will have `file' dumped into it, which might be an annoyance.
HTH,
Chuck
Re: [O] navigation broken in recent maint
Samuel Wales gmail.com> writes: > > quick and dirty bug report. recent org maint. > > 1: > > jumping from magit (maint) to org using RET always goes > to the wrong location now. > > i don't know that this is org's fault. i have seen it > happen once before, which is when i tried > longlines-mode and similar modes. i think it was only in org, but i > am not sure. > > was there a change in org visibility? > > 2: > > id links always go to the wrong location now. they jump someplace > near the link. > > dunno if 1 and 2 are related. i'd guess not but they > started in the same snapshot. > > can't do ecm at this time. > Here is one I've adapted from the "navigation broken - occur, org-babel-goto-named-src-block, etc fail" thread: http://article.gmane.org/gmane.emacs.orgmode/87575 Before executing the src block in what follows the custom_id links work. After executing the src block the links that are far from their target fail. Anyone who wants to dig into this should see Nicolas Richard's reply at the end of that thread: http://article.gmane.org/gmane.emacs.orgmode/87598 HTH, Chuck == * headline A :PROPERTIES: :CUSTOM_ID: idA :END: [[#idB]] #+NAME: AAA #+BEGIN_SRC x #+END_SRC #+NAME: filler #+BEGIN_SRC emacs-lisp :results output (let ((i ?a)) (while (< i ?z) (princ (format "* %s\n\n\n#+NAME: %s\n\n" (char-to-string i) (char-to-string i))) (setq i (1+ i #+END_SRC [[#idA]] [[#idB]] #+RESULTS: filler [[#idA]] [[#idB]] * headline B :PROPERTIES: :CUSTOM_ID: idB :END: [[#idA]] [[#idB]] #+NAME: BBB #+BEGIN_SRC x #+END_SRC
Re: [O] inclusion of #+RESULTS in a source block
Federico Beffa ieee.org> writes: > > > > Suppose you want to use a program such as Sympy or Maxima to find > the analytic solution of a complicated equation. After this you > want to make use of that solution for numerical evaluation of > various cases. See http://orgmode.org/manual/Noweb-reference-syntax.html#Noweb-reference-syntax You want something like #+BEGIN_SRC python :noweb yes <> #+END_SRC To use in more than one src-block use the `:cache yes' header for `analytic-sol' HTH, Chuck
Re: [O] How do you capture the intent never to tangle or weave a headline or its children?
Grant Rettke wisdomandwonder.com> writes: > > Good evening, > > For both performance and cognitive reasons, sometimes I specifically > never want to tangle or weave a headline or any of > its children. I still value it though, so it belongs in that document, > and it wouldn't make sense for it to be linked as an > external document. For performance reasons, I suspect that it would > speed up tangling, but I need to verify this. > > Thus far I just add something like this, so at least it is obvious to > *me* what is my intent: > > # INTENT: never weave or tangle this headline or its children > :PROPERTIES: > :exports: none > :tangle: no > :END: > You want this: http://orgmode.org/manual/Header-arguments-in-Org-mode-properties.html#Header-arguments-in-Org-mode-properties i.e. :header-args: :exports none :tangle no HTH, Chuck
[O] navigation broken - occur, org-babel-goto-named-src-block, etc fail
Start with emacs -q, then load today's org-mode. Execute the source block in this file: === start of file #+NAME: AAA #+BEGIN_SRC x #+END_SRC #+BEGIN_SRC emacs-lisp :results raw output (let ((i ?a)) (while (< i ?z) (princ (format "* %s\n\n\n#+NAME: %s\n\n" (char-to-string i) (char-to-string i))) (setq i (1+ i #+END_SRC #+NAME: BBB #+BEGIN_SRC x #+END_SRC === end of file Now try C-c C-v g AAA RET C-c C-v g BBB RET C-c C-v n or M-x occur RET \+name RET then try to click on each of the matches in the *Occur* buffer. The first few work, then failure set in. Seems like local moves of a few lines work, but longer jumps fail. I've tried using edebug on org-reveal. When I step through by pressing 'n', occur works fine. When I skip stepping by pressing 'c', it often fails. What gives? Chuck p.s. Org-mode version 8.2.7 (release_8.2.7-1096-g23496c [...] GNU Emacs 24.3.1 [...]
[O] [bug][babel] noweb gotcha
The following , | #+PROPERTY: tangle yes | | #+NAME: print-abc | #+BEGIN_SRC emacs-lisp | (format | "<<%s>>" "abc") | #+END_SRC | | #+NAME: print-def | #+BEGIN_SRC emacs-lisp | (concat | "<<" "def" ">>") | #+END_SRC | | #+BEGIN_SRC emacs-lisp :noweb yes | <> | <> | #+END_SRC ` tangles as , | (format | "<<%s>>" "abc") | | (concat | "<<" "def" ">>") | | (format | "<<%s>>" "abc") | (concat | "") ` Note that ""<<" "def" ">>" disappeared from (concat ...). FWIW, adding quotes inside the constant string in org-babel-noweb-wrap: "\\([^ \"\t\n][^\"]+?[^ \"\t]\\|[^ \"\t\n]\\)" fixes this instance. HTH, Chuck
[O] bug in exporter (org-babel-exp-process-buffer)
The use of `org-confirm-babel-evaluate' as a function breaks inline src blocks just as was described in this thread from last year: http://lists.gnu.org/archive/html/emacs-orgmode/2013-11/msg00669.html I believe that the patch by Eric Schulte in === commit 6a4dfd318296925b3b895ca6ab85e31309acf84d Author: Eric Schulte Date: Sat Nov 23 12:24:34 2013 -0700 fixed export of inline src blocks * lisp/ob-exp.el (org-babel-exp-non-block-elements): Fixed export of inline src blocks. === did the right thing back then, but the function to which it was applied was removed later on, I think org-babel-exp-process-buffer took over the work of the removed function. I believe that Eric's patch or something like it would fix the current problem in org-babel-exp-process-buffer: (inline-src-block - (let* ((info (org-babel-parse-inline-src-block-match)) + (let* ((head (match-beginning 0)) + (info (append (org-babel-parse-inline-src-block-match) +(list nil nil head))) (params (nth 2 info))) (setf (nth 1 info) Can this be fixed, please? Thanks, Chuck
Re: [O] How to create non-inheritable properties?
Thorsten Jolitz gmail.com> writes: > > Grant Rettke wisdomandwonder.com> writes: > > > Hi, > > > > My org file has a lot of text in it. It really needs to be in the same > > file though, so it is a big file. > > > > When I org-babel-tangle, I would like to speed it up as it takes 8 minutes. > > 8 minutes? wow ... > Just guessing at this, but ... I suspect Grant's file has noweb chunks and that `org-babel-use-quick-and-dirty-noweb-expansion' is set to nil. If the :noweb-ref feature is not used, setting that variable to t will make a time difference of a couple of orders of magnitude. HTH, Chuck
Re: [O] Adding export option for babel language
Ken Mankoff gmail.com> writes:
>
>
> I'd like to add support for PythonTeX to Org Babel
> https://github.com/gpoore/pythontex
>
> The motivation is that PythonTeX is a better literate environment than
> just Org + Babel, because it can print results inline just like an
> interactive Python session, instead of all the code followed by all the
> results.
>
> This is just a modification to the existing LaTeX export for python, it
> is not support for a new language. I'm new to Org development and seek
> advice how to begin approaching the solution.
>
> I'd like the python code blocks to behave just as they do now, but if I
> have set (setq org-latex-listings 'pythontex) instead of (setq
> org-latex-listings 'minted), then instead of wrapping python code blocks
> with:
>
> \begin{minted}[]{python}
> x+2
> print x
> \end{minted}
>
> It should wrap them with
>
> \begin{pyconsole}
> x+2
> print x
> \end{pyconsole}
>
A quick-and-dirty approach to do just that much would be to write an export
filter for `src-block' and maybe `inline-src-block', see
(info "(org) Advanced configuration")
http://orgmode.org/worg/dev/org-export-reference.html#filter-system
and
http://orgmode.org/worg/exporters/filter-markup.html
Also, `C-h f org--filter TAB' should give you a buffer of such filter
functions (and a couple of false positives) that you might browse.
HTH,
Chuck
Re: [O] [babel][PATCHES] ob-R patches for review
Eric Schulte gmail.com> writes: > > Rainer M Krug krugs.de> writes: > > > Hi > > > > Attached please find seven patches for review to implement the storing > > of org variables in their own environment and to make the org-issued R > > code look nicer in the R session. > > > > Thanks, > > > > Rainer > > Hi Rainer, > > Thanks for these patches. I don't have the R experience to review or > maintain them, but I'm happy to apply them. > > I missed some previous discussion in this thread. Are these patches > ready to be applied as is? > IMO, the patches hard coded behaviors that would better be customizable and optional. Rainer and I had some back and forth about this -- see the thread. Best, Chuck
Re: [O] [BUG] [babel] in :eval never with :session
Eric Schulte gmail.com> writes:
>
> Rainer M Krug krugs.de> writes:
>
> > The error is back:
> >
>
> You say "back", was this error not present recently? If so could you
> isolate the commit at which this error appeared?
>
The bug seems to be in the use of
(org-link-search heading)
in org-babel-exp-in-export-file which is called in
org-babel-exp-process-buffer.
That search will find the first heading that is a match after
(point-min). So it will mess up other header args, too.
It was there back in 8.0.7 and recent commits did not touch it AFAICS.
HTH,
Chuck
> Thanks,
> Eric
>
> >
> > When one header in a subtree which has the header argument
> > :eval never
> > has the same name as in a following subtree which should be evaluated on
> > export, the second subtree is not exported. When the name of the header
> > is changed, the subtree is exported as expected.
> >
> > --8<---cut here---start->8---
> > #+PROPERTY: exports both
> > #+PROPERTY: session *tmp_R*
> >
> > * Some non-evaluated code
> > :PROPERTIES:
> > :eval: never
> > :END:
> > ** This is the same header
> > #+BEGIN_SRC R
> > cat("\ntwo\n")
> > #+END_SRC
> >
> > * Data Assessment Results
> > ** This is the same header
> > If the name of the header is changed, the subtree is evaluated on export.
> > #+begin_src R
> > cat("\nhere it is
\n")
> > #+end_src
> > --8<---cut here---end--->8---
> >
> > Org-mode version 8.2.6 (release_8.2.6-920-gc6d698
/Users/rainerkrug/.emacs.d/org-mode/lisp/)
> > GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0 AppKit
1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local
> >
> > Cheers,
> >
> > Rainer
>
Re: [O] How to load and use Github Flavored Markdown exporter?
Grant Rettke wisdomandwonder.com> writes: > > Hi, > > Org-mode version 8.2.6. Loaded from MELPA org-2014-04-28. > > The nice github flavored markdown package is in there ox-gfm.el. > > My goal is to use it to do a Markdown export of an org document > instead of the vanilla exporter. > > In an attempt to do so, I ran at startup: > > > (require 'ox-gfm) > > > And did an org dispatch export for Markdown. > > Wondering if this is the correct approach? > > I don't have any expectations for how the file is generated; I just > want to know that I am loading and using it correctly. > If, after loading ox-gfm, this: C-c C-e g G pops up a buffer, then you are on the right track. If the export menu has no [g] Export to Github Flavored Markdown choices, then something is amiss. C- C-e m is the wrong path. HTH, Chuck
Re: [O] Export as ASCII whilst respecting current fill column
Miguel Guedes gmail.com> writes: > > Using org-mode version 7.93f, when exporting to ASCII it doesn't respect > the current fill column. Can this be enforced? > Miguel, Upgrade to current org-mode (version 8.2.6) before you do anything else. Then modify `org-ascii-text-width' to suit your needs. , | | org-ascii-text-width is a variable defined in `ox-ascii.el'. | Its value is 72 | | Automatically becomes buffer-local when set. | | Documentation: | Maximum width of exported text. | This number includes margin size, as set in | `org-ascii-global-margin'. | | You can customize this variable. ` > Also, I've noticed that org doesn't remove verbatim tags (=verbatim=) > but removes BEGIN_EXAMPLE blocks and presumably other BEGIN_xxx blocks; > is this by design? > > Same deal - upgrade. Then =xyz= becomes `xyz' on export. HTH, Chuck
Re: [O] [babel][PATCHES] ob-R patches for review
Rainer M Krug krugs.de> writes: > > Hi > > Attached please find seven patches for review to implement the storing > of org variables in their own environment and to make the org-issued R > code look nicer in the R session. Rainer, I have suggestions and a concern. I suggest that you look at how ESS handles R objects and constructs calls in elisp to be executed in an R session. It uses a package and its NAMESPACE to provide that functionality and store objects. That makes the elisp interface a lot cleaner and keeps ESS variables out of the users way. The package is found at /etc/ESSR/. I also suggest that you introduce a customization variable to allow a user to turn off the functionality you have created. My concern is that you are injecting code into the R user session or script that the user may not want. If I already have an R object named 'org' your code will break my code. Further, all of this is hard coded, so I can't change the variable/file names. HTH, Chuck
Re: [O] Organizing org-mode files: Tree view
David Masterson gmail.com> writes: > > Dotan Cohen gmail.com> writes: > > > Hi all, I am a VIM user enchanted by the power of org-mode. Please > > excuse my apparent naivety! > > > > I am moving from Zim Wiki (excellent GUI program) to either Vimwiki > > (VIM plugin) or org-mode. I was surprised to see that org-mode has all > > the features of several apps that I use, including Task Warrior, Zim > > Wiki, and Tux Cards. However, one feature that is not clear to me is > > how to organize the various org-mode files. Surely I wouldn't leave > > that to the file system! > > > > Is there some Emacs plugin that could present the org-mode files in a > > tree-fashion, such as demonstrated on the left side of this Zim Wiki > > screenshot? [snip] > > If there is a better way to organize the files, then I would love to > > know how the more experienced users do it. > > > > Thank you! > > I guess the answer(s) would be Dired (builtin to Emacs) or External > Links in Org. > Which is pretty much what I use. But I think Dotan might want speedbar. See http://www.emacswiki.org/emacs/SpeedBar Just try it out, open a file -- perhaps a *.org file with multiple headline levels -- and execute M-: (speedbar 1) Browse emacswiki for other possibilities. HTH, Chuck
Re: [O] sharing my firsts, org babel tangle and "init" .org file
Pete Ley gmail.com> writes: > > I've looked at the solution on worg and, though I didn't actually try to > implement, it seems like tangling your init file every time you open > Emacs is a little cumbersome. Please correct me if I'm wrong in this > assumption. OK, here goes: In `org-babel-load-file' the code following the comment ;; tangle if the org-mode file is newer than the elisp file appears to only re-tangle the .el file iff it is older than the .org file HTH, Chuck
Re: [O] How do I chain babel blocks with arguments?
Alan Schmitt polytechnique.org> writes: > > Hello, > > I have several babel blocks that each work well, but I'm now trying to > chain them to build some bigger functionality out of them. I'm having > trouble finding out how to pass arguments between blocks. Here is > a small example: > > --8<---cut here---start->8--- > #+name: test1 > #+begin_src emacs-lisp :var x="foo" > x > #+end_src > > #+name:test2 > #+begin_src emacs-lisp :var z="bar" :var y=test1(x=z) > y > #+end_src > > #+call: test2(z="baz") > --8<---cut here---end--->8--- > > Unfortunately this does not work: the evaluation of block `test2' fails > by telling me `z' does not exist. > > How can I execute block `test1' from block `test2' by passing an > argument that is one from test2? This is not pretty, but it works: #+name:test2 #+begin_src emacs-lisp :var z="bar" (let ((y (org-sbe test1 (x (intern z) y) #+end_src HTH, Chuck
Re: [O] Fwd: Mac OS Alias file links
Ken Mankoff gmail.com> writes:
>
>
> On 2014-04-14 at 12:26, Achim Gratz wrote:
> > Ken Mankoff writes:
> >> Aliases are a type of links ("ln" on linux, "shortcut" on Windows
> >> "alias" on OS X (OS X of course also supports "ln")). The difference
> >> between an OS X alias and "ln" is that if the target is moved, the OS
> >> X alias still points to it, and double-clicking on an alias (or
> >> issuing the "open" command in a terminal) will open the target,
> >> wherever it is.
> >
[...]
> In my fantasy, the link wouldn't be to an alias file, it would *contain
> the alias* the way the BibDesk field does. Therefore C-o on an "alias:"
> link would require extra code: Decode the alias, then pass it off to the
> system.
>
The point of using an alias rather than a filename or the name of a
symbolic link that points to the file is that it inherits the property
of Mac OS X aliases that moving the file does not break the alias ---
it still points to file.
For this to work as you fantasize, you would need to enable the Finder
application to modify the part of the *.org file that encodes the alias
when you change the location of the aliased file just as the Finder
does to the alias when the location of the aliased file is modified in the
Finder.
That is a heavy lift.
OTOH, writing an AppleScript to make an alias in a folder that is never
moved, writing elisp to call that script and then make an org-mode link to
the alias just created might work for you.
HTH,
Chuck
Re: [O] Add-on: Github Flavored Markdown exporter
Lars Tveito student.matnat.uio.no> writes:
>
> Hi, thanks for checking it out!
>
> Thorsten Jolitz writes:
>
> > Thorsten Jolitz gmail.com> writes:
> >
> >> Lars Tveito student.matnat.uio.no> writes:
> >>
> >>> Hi!
> >>>
> >>> I have written an exporter for Github Flavored Markdown, which is a
> >>> derived back-end from the Markdown (vanilla) exporter. It adds
> >>> Github-style src-blocks, strike-through and table of contents.
[snip]
Nice!
>
> Getting it to work with source-blocks was the feature I missed the most
> from the vanilla markdown exporter. If you specify a language in the
> source-block it will be added to the exported version as well; a problem
> occurs if you specify a language not supported by Github. Emacs lisp is
> an example of this, so there is a alist `org-gfm-lang' which by default
> has the value:
>
> (("emacs-lisp" . "lisp") ("elisp" . "lisp"))
>
> So a source block like this:
>
> #+begin_src emacs-lisp
> (defun foo ()
> 'foo)
> #+end_src
>
> exports to this:
>
> ```lisp
> (defun foo ()
> 'foo)
> ```
In
https://github.com/github/linguist/blob/master/lib/linguist/languages.yml
I see this:
,
| Emacs Lisp:
| type: programming
| lexer: Scheme
| color: "#c065db"
| aliases:
| - elisp
| - emacs
| primary_extension: .el
| filenames:
| - .emacs
| extensions:
| - .emacs
`
so doesn't '#+BEGIN_SRC elisp' just work?
And shouldn't '(("emacs-lisp" . "elisp")) be the value of `org-gfm-lang'?
HTH,
Chuck
Re: [O] Help needed - export markdown is it supposed to pre-pend html?
Rick DeNatale gmail.com> writes: > > Hi, I'm a fairly new org mode user. > I'm trying to export to markdown and I can't understand the output: > > For example with the simple org mode buffer > > > Add: #+OPTIONS: toc:nil > * Top level headline > ** Second level > *** Third level > Some text > *** Third level > More text > * Another top level headline > [delete output with table-of-contents at top] > > Is this expected? or is there something wrong with my installation? > Yes. Use the line above to get rid of the table of contents. Grep through the manual for '#+OPTIONS' to get up to speed. HTH, Chuck
Re: [O] Generate a table of contents without exporting
RG Williams gmail.com> writes: > > Hi, > I know you can generate a table of contents when exporting, but can you do > it just within org? For context, I'm uploading an .org file to github and I > don't need to export it to another format because github recognizes and > displays it just fine. It's long so a ToC would be nice. Do I just have to > write it myself? > > AFAIK, you do have to write it yourself, but org-mode provides decent tools for doing it. Here is an example. Run the src-block and a table of contents will appear near the top. Change the content and rerun the src-block and the t-o-c will change accordingly. It doesn't deal with rules for omitting headlines like COMMENT, :noexport:, etc, but if you are simply copying the .org file, maybe it is good enough. --8<---cut here---start->8--- #+RESULTS: Table_of_Contents * h lower H * i lower I * j lower J ** 1 one ** 2 two #+NAME: Table_of_Contents #+BEGIN_SRC emacs-lisp :wrap example (mapconcat 'identity (org-element-map (org-element-parse-buffer 'headline) 'headline (lambda (hl) (let ((lev (org-element-property :level hl)) (htitle (org-element-property :title hl))) (concat (make-string lev ? ) "- " htitle "\n") #+END_SRC --8<---cut here---end--->8--- HTH, Chuck
Re: [O] Controlling example block export?
Heikki Lehvaslaiho gmail.com> writes:
>
>
>
> I am using example blocks as inline notes where I paste snippets of
> (pre-formatted) text. I'd like to be able to control the exporting of
> those block individually (per document would also be useful). I do not
> seem to be able to find documentation about anything along those lines.
>
>
> Here is a mock-up:
>
>
> #+BEGIN_EXAMPLE :exports none
> private notes...
> #+END_EXAMPLE
>
>
Advise or redefine the org--example-block function to use
:switches to decide whether to skip an example block.
Something like this:
#+BEGIN_SRC emacs-lisp
(defvar org-example-block-skip ":skip"
"example block :switch to skip.")
(defun org-latex-example-block (example-block contents info)
"Transcode an EXAMPLE-BLOCK element from Org to LaTeX.
CONTENTS is nil. INFO is a plist holding contextual
information."
(when (and (org-string-nw-p
(org-element-property :value example-block))
(not (string=
org-example-block-skip
(org-element-property :switches example-block
(org-latex--wrap-label
example-block
(format "\\begin{verbatim}\n%s\\end{verbatim}"
(org-export-format-code-default
example-block info)
#+END_SRC
> A bigger question is that while code blocks are well defined and well
> documented, all other blocks are not. Is there somewhere a design
> document the would give a logic of having different blocks and how they
> are controlled? Maybe there is an other type of a block that does what I
> want?
>
>
> The inline documentation in ox*.el files is too low level to be helpful.
>
See also org-element.el and
http://orgmode.org/worg/dev/org-export-reference.html
Looking at what (org-element-at-point) returns often helps.
Special blocks are another possibility, but will require some customization.
HTH,
Chuck
Re: [O] Proposal to replace the prefix repetition with whitespace during expansion of noweb references
Pontus Michael gmail.com> writes: > > I would like to propose a change to the behavior of noweb expansion in > relation to prefix handling. [snip] > I recommend to introduce a change that will replace the inserted prefix > with whitespace of equal length. [snip] The behavior you desire can be obtained by using the <> idiom for noweb. For example, with a suitably crafted block called 'my-noweb', this reference <> would expand just as you want. You can use the functions org-babel-goto-named-src-block and org-babel-get-src-block-info to achieve this. Multiple noweb references might be handled as well by delimiting the second argument, e.g. "foo,bar". --- Revising the behavior of the existing code base might break code that folks have written that depend on the current behavior. HTH, Chuck
Re: [O] Bug: [babel] #+PROPERTY: eval never-export disables interactive evaluation [8.2.5h (release_8.2.5h-806-gb1199e /Users/rainerkrug/.emacs.d/org-mode/lisp/)]
Rainer M Krug krugs.de> writes: > > > The subject says it all - when I set > > #+PROPERTY: eval never-export > > the interactive evaluation of R code blocks is disabled. Message: > > Evaluation of this R code-block is disabled. > [rest deleted] It works as advertised for me. I copy and pasted your PROPERTY line and ran interactively and then exported. Oh yes, I did C-c C-c. I am running Org-mode version 8.2.5h (release_8.2.5h-757-gc444e4 @ ... I tried with and without :session with same results. HTH, Chuck
Re: [O] Out of Order Evaluation
Andreas Leha med.uni-goettingen.de> writes:
>
> Hi Michael,
>
> Michael Weylandt gmail.com> writes:
>
> > Hi,
> >
> > I want to put a summary of my analysis at the beginning of a document
> > using results calculated at the end of the document. Is this possible?
[snip]
> >
> > Is this possible in a single pass?
Not quite. The method suggested by Andreas computes the result twice. If
there is any randomness in the results (as in the example) you will get a
different answer in the summary than when the block is later evaluated.
> > I've played with #+NAME and
> > <> but haven't gotten the out-of-order evaluation quite
> > right.
You can use
#+results: the-mean
before
#+NAME: the-mean
#+begin_src R
mean(x)
#+end_src
which is after 'theanalysis' block.
And if the format is not pleasing add a filter that reformats the result.
> >
> > Michael
> >
>
> How about something along:
>
> --8<---cut here---start->8---
> #+TITLE: Test
> #+AUTHOR: Michael Weylandt
> #+PROPERTY: header-args:R :session *__R__* :exports both
>
> * Summary
> The mean result was src_R[:exports results :var
analysisresults=theanalysis()]{mean(unlist(analysisresults))}
>
> * Analysis,
> We do some complicated calculations:
>
> #+name: theanalysis
> #+BEGIN_SRC R
> x <- rnorm(5)
> #+END_SRC
> --8<---cut here---end--->8---
It might be better to mark all the blocks in the doc ':eval never'
and ':exports code' or ':exports none' and put blocks before the first
headline that do all the calcs from noweb references, and put the #+results
lines (if you need them) wherever you want them in the doc. Like so:
--8<---cut here---start->8---
#+TITLE: Test
#+AUTHOR: Michael Weylandt
#+PROPERTY: header-args:R :session *__R__* :exports both
#+NAME: master
#+BEGIN_SRC R :noweb yes :results silent :exports results
<>
#+END_SRC
* Summary
The mean result was src_R[:exports results]{mean(x)}
* Analysis,
We do some complicated calculations:
#+name: theanalysis
#+BEGIN_SRC R :eval never :exports code
x <- rnorm(5)
#+END_SRC
--8<---cut here---end--->8---
IMO, needing ':exports results' for inline src blocks is a bug not a
feature.
HTH,
Chuck
Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
John Hendy gmail.com> writes: [deleted] > > > > I think the default behavior should be reverted, as tangling and > > exporting are two different things. When I tangle, I want to see the > > code blocks as they are in the org document (with possible variables and > > expansions) but not to create files where I do not put it explicitly > > into a code block. These wrappers have nothing to do with the code, and > > are only there for the exported engine. So I would either revert to the > > original behavior, or, introduce a new header argument, > > e.g. :include-wrappers, which would, if set to t, include the export > > wrappers in the tangled file. This might be useful for debugging > > exporting of code block results, but not for general tangling. > > Thanks for chiming in. This was my gut reaction to the default > behavior. I guess we're still only a sample size of 2, but > intuitively, I would think that tangling would be a separate beast in > most cases from exporting. Just to have it on the record, if I tangle, > it's usually to take the code I've used in something like a Beamer > presentation or document and combine it into a single .R file so > someone can run it without needing Org-mode. ]deleted] Sorry to be late to add my $0.02... I never want the try/catch wrappers. But noweb is indispensable. I use noweb a lot to organize and collect blocks. In some cases, I export them and in others I just tangle them. I hope that the revised code will allow me to turn off try/catch wrapping and still be able to use noweb when tangling or exporting. Best, Chuck
Re: [O] [Patch] don't add indent for empty line when exiting, a code edit
Bastien gnu.org> writes: > > Charles Berry ucsd.edu> writes: > > > Time to failure seems longer. But now I get an infinite loop. > > Er, sorry for the confusion; should be fixed again. > It is not. I am now back to getting the 'End of Buffer' msg Chuck
Re: [O] [Patch] don't add indent for empty line when exiting, a code edit
Bastien gnu.org> writes: > > Hi Charles, > > Charles Berry ucsd.edu> writes: > > > This seems to have broken org-edit-src-exit. > > > > I cannot figure out what triggers it (hence no ECM), but I sometimes > > get an > > 'End of buffer' error from inside the while loop. > > I just pushed a fix. Can you confirm you don't see the error anymore? > Time to failure seems longer. But now I get an infinite loop. The error message is gone. C-g stops the loop, but attempting to exit via C-c ' re-indents the code and the loop starts again. Chuck
Re: [O] Octave/Matlab Code Export Issue?
Phil Regier math.ku.edu> writes: > > I'm having trouble with Octave export, and I am not quite sure where to look. > > In an Org file I have the following: > >#+BEGIN_SRC octave > a = [1;3;5;7;9] > b = [2;4;6;8] > ans=a; >#+END_SRC octave > > Instead try this: --8<---cut here---start->8--- #+NAME: abc #+BEGIN_SRC octave a = [1;3;5;7;9] b = [2;4;6;8] ans=a; #+END_SRC --8<---cut here---end--->8--- Note that the #+END_SRC line has no trailing nor anything else: 14.1 Structure of code blocks = Live code blocks can be specified with a `src' block or inline.(1) The structure of a `src' block is #+NAME: #+BEGIN_SRC #+END_SRC HTH, Chuck
Re: [O] [Patch] don't add indent for empty line when exiting, a code edit
Bastien gnu.org> writes: > > Hi Arun, > > Arun Persaud lbl.gov> writes: > > > I tried to fix this in org. It seems to work over here, but my elisp as > > well as my understanding of org-mode is not perfect ;) Let me know if it > > needs more work. > > Applied, thanks! > Bastien, This seems to have broken org-edit-src-exit. :-( I cannot figure out what triggers it (hence no ECM), but I sometimes get an 'End of buffer' error from inside the while loop. I cannot exit the src edit buffer until I revert org-edit-src-exit to its old version. HTH, Chuck
Re: [O] Proposal/request for input: slidify export for html slides
John Hendy gmail.com> writes:
>
> On Sat, Feb 8, 2014 at 11:18 AM, Charles Berry ucsd.edu> wrote:
>
[snip]
> > But there is some effort and overhead involved, so only the most
> > useful (IMO) have been mapped. Right now, `:noweb yes' will expand the
> > reference(s) in place before export, and `:exports none' will not export
> > the block. Maybe one day ...
>
> Understood, and no worries. I'm making progress. When you say "expand
> references," I'm not sure I follow what that means. References =
> references to variables? So something like :var something=something?
>
'References' refers to noweb references. See
http://orgmode.org/org.html#noweb
> > More a matter of what my workflow is (so the issue doesn't arise). I use
> > the cache=TRUE chunk option on the knitr side to save the results of
> > long
> > running computations. When I start work, I execute a src block that
> > loads
> > knitr and knits the *.Rnw (or *.Rmd, etc), which has the side effect of
> > loading the cached objects. Then I edit the *.org document. If I am
> > working on R code, I run the code interactively either from the src edit
> > buffer or I C-c C-c the src block. Its handy to leave the results in the
> > *.org buffer for reference - they get stripped on export. Maybe I edit
> > a figure caption (knitr option fig.cap=), equations,
> > or text. When I am ready to see the formatted doc, I export via ravel,
> > knit, and view. The cached objects get rebuilt as needed.
>
> Ah. I think I follow this. If you knit the exported .org -> Rmd file
> in the same R session that Org is using, if you change the .org and
> re-export to .Rmd, knitr is smart enough not to re-run the code? Is
> that what you mean?
Almost. ox-ravel does not call knitr. The ravel backends advice
`org-babel-exp-do-export' when a ravel backend runs so R code src blocks
are not run, but are turned into chunks (for knitr, Sweave, or ...) and
exported as such.
When you want to actually process the resulting document, you have to call
on knitr or some other R report generator to do the work.
> That also must imply that export to .Rmd doesn't
> execute any of the Org babel code, right (otherwise there would be no
> benefit to your workflow since you'd be waiting for Org anyway)?
Correct for R src blocks. But emacs-lisp and other languages are treated as
under the parent backends.
>
> If that's the case, I think I could roll with that -- I'd just have
> :eval yes if exporting to .Rmd -> knitr, and do a replace-string to
> :eval no if I was going to export to Beamer.
>
In R scr blocks, :eval is ignored by ravel and so need not change when
ravel is run.
[snip]
> I'm a bit hung up on including non-code-generated images. I'm working
> through one of my presentations to convert to slidify (and may write
> up a Worg tutorial or just one on my blog to add to collective
> knowledge) but am not sure of the right "universal Org syntax" that
> will work with multiple backends. I'm most used to something like
> this:
>
> #+begin_center
> #+attr_backend :height {6cm, 400px, etc.}
> [[./path/to/image.png]]
> #+end_center
>
> That's not seeming to work with ox-ravel thus far. I'd love not to
> have to change the Org image syntax to straight markdown just for my
> occasional use of slidify.
>
It's not related to ox-ravel, which uses the same transcoders as the parent
backends for everything except inline src and src blocks.
I'm not sure how to get what you seem to want.
Maybe use a custom link
http://orgmode.org/org.html#Adding-hyperlink-types
or ask about html/md links in a fresh thread?
HTH,
Chuck
Re: [O] Proposal/request for input: slidify export for html slides
John Hendy gmail.com> writes:
>
> On Fri, Feb 7, 2014 at 11:38 PM, John Hendy gmail.com> wrote:
> > On Fri, Feb 7, 2014 at 7:04 PM, Charles Berry ucsd.edu> wrote:
>
> [snip]
>
> > I'll look into those. I just cloned your repo and loaded ox-ravel.
> > Quite nice! It worked /pretty/ well out of the box. One issue is that
> > it doesn't seem to obey :eval no for babel blocks. I exported to .Rmd
> > successfully, but the presentation has a bunch of errors in the code
> > blocks from trying to actually execute the code. The .Rmd doesn't have
> > any instances of ```{r eval=F}; could this feature be added?
>
> Just kidding. Discovered #+attr_ravel and the proper knitr argument
> for code chunks, which worked as expected with:
>
> #+attr_ravel: eval=F
> #+begin_src R ...
>
> I still think it makes sense to allow :eval no. This seems more
> "Org-ish" since the ideology is to have one set of Org syntax where
> possible, which translates to any number of languages. [...]
In principal, it makes sense to map babel header args to knitr chunk
options. At least when the headers arg and chunk option do about the
same thing.
But there is some effort and overhead involved, so only the most
useful (IMO) have been mapped. Right now, `:noweb yes' will expand the
reference(s) in place before export, and `:exports none' will not export
the block. Maybe one day ...
> I get that we
> have #+attr_latex for latex-only things, #+attr_html for html-only
> things, and so on, but I wouldn't consider :eval to fall into this
> category. Or perhaps I don't understand... would the idea be that I
> don't want to run it in *Org*, but I'd not want all my chunks disabled
> in the .Rmd?
More a matter of what my workflow is (so the issue doesn't arise). I use
the cache=TRUE chunk option on the knitr side to save the results of long
running computations. When I start work, I execute a src block that loads
knitr and knits the *.Rnw (or *.Rmd, etc), which has the side effect of
loading the cached objects. Then I edit the *.org document. If I am
working on R code, I run the code interactively either from the src edit
buffer or I C-c C-c the src block. Its handy to leave the results in the
*.org buffer for reference - they get stripped on export. Maybe I edit
a figure caption (knitr option fig.cap=), equations,
or text. When I am ready to see the formatted doc, I export via ravel,
knit, and view. The cached objects get rebuilt as needed.
>
> My workflow might be odd in that I tend to futz with plot parameters
> once, get the desired image, and then set :eval no for the rest of my
> document work so I don't have to wait for plots on iterative exports.
> I try to put all my setup code (load packages, data
> reading/manipulation, etc.) in it's own block so that I can easily run
> that whenever I first open the document. From there I only need to
> re-run a plot block if necessary and I'll just temporarily change
> :eval no -> yes and then back again after execution.
>
Not odd at all if it saves you time.
But if it takes long to rebuild the objects in that first src block, you
might want to try the cache=TRUE route.
Chuck
p.s. the weird fontification you noted one posting up in this thread seems
like something to raise with the slidify/knitr devs after checking the
*.Rmd to be sure there is no org/ravel induced problem.
Re: [O] Proposal/request for input: slidify export for html slides
John Hendy gmail.com> writes:
>
> On Fri, Feb 7, 2014 at 3:50 PM, Charles Berry ucsd.edu> wrote:
> > John Hendy gmail.com> writes:
> >
> >>
> >> An interesting update on this. Aside from some image and code block
>
[snip - how John turn org to Rmd to md]
> >
> > John,
> >
> > You can put the header code into an MD export block (and ignore
> > index.Rmd).
> > You can add '#+MD: ---' keyword lines to mark new slides.
> >
>
> Awesome! Hadn't thought of that, and sounds great.
>
> > Then you export to my.Rmd directly (using ravel) and run
> > slidify("my.Rmd").
> >
> > Graphics 'just work', but you have to mind the spacing to be sure the
> > slides
> > render nicely.
> >
>
> Hmmm. Could you elaborate on this? I haven't experienced this with R +
> ggplot. The presentation I'm working on for tomorrow is on geo-spatial
> data with R and I generate a lot of maps. I find that something like
> this doesn't produce properly scaled images:
>
> #+header: :file .map.pdf
> #+begin_src R :results output graphics :exports results
>
> # install.packages("maps")
> library(maps)
> world <- map_data("world")
>
> p <- ggplot(world, aes(x = long, y = lat, group = group))
> p <- p + geom_polygon(colour = "white")
> p
>
> #+end_src
>
> I often get something squarish, which makes the map look really
> compressed (see attached). Thus, I seem to need both this (name,
> header)
>
This is a problem that results from rendering in a square rather than
something proportional to what Mercator used: 202cm x 124cm, I think.
slidify wants to have png files for images, so I think you are stuck
having to set up the size of the device as well as the displayed size
to get nice looking results.
> #+name: world-adj
> #+header: :file map-adj.pdf :width 9 :height 6
> #+begin_src R :results output graphics :exports results
>
> # code from above
>
> #+end_src
>
> and this (right height for latex)
>
> #+begin_center
> #+attr_latex: :height 6cm
> #+RESULTS: world-map
> [[file: world-adj.pdf]]
> #+end_center
>
> I guess in this example, the heights are the same, however sometimes
> this isn't the case as to use the right height for the slides can goof
> with how proportionally big the axis, label, and legend text is and it
> requires, in my opinion, wy more work to use the theme() arguments
> in ggplot2 to tailor them correctly vs. just playing with
> :width/:height options and then scaling the final image in the
> #+RESULTS section.
>
> I would love to avoid the above if you have more clarification on "just
work" :)
I wasn't thinking about the case you just demonstrated. I have to use
a line that gives out.width, out.height, fig.width, and fig.height, which
slidify ('knitr' under the hood) uses to render the png and the page as you
did to make something that looks like the Mercator map and still have
the text look OK. See http://yihui.name/knitr/options if the options
listed are not familiar. (knitr chunk options can be put in #+ATTR_RAVEL:
lines for ravel exports to use them.)
[more deleted]
>
> One other question while we're at it... I noticed that
> #+begin/end_center produces this in the output .md file:
>
>
> 
>
>
> This doesn't export with slidify. [snip more details]
Right. IMO, using the knitr tools for dealing with such issues beats
wrestling with the babel and md exporter. i.e. fig.align="center" handles
this. A good part of my motivation for ox-ravel is that I can deal with
fine tuning output from knitr more easily than I can w/ babel exports.
HTH,
Chuck
Re: [O] Proposal/request for input: slidify export for html slides
John Hendy gmail.com> writes:
>
> An interesting update on this. Aside from some image and code block
> stuff, the following works surprisingly well!
> - Export Org -> markdown (md)
> - Start an R session and `setwd("/path/to/file.md")`
> - Run `library(slidify)` and `author("deck")
> - Copy the deck/assets folder into the parent directory
> - Copy the header code from the resultant deck/index.Rmd file into
> exported .md file
> - Add three hyphens before each heading (headings are # Slide title)
> - Save the file as file.Rmd (vs. file.md)
> - From the R session, do `setwd("../")` (running `author("deck")`
> changes the working directory to deck/
> - Run `slidify("file.Rmd")`
>
[much deleted]
John,
You can put the header code into an MD export block (and ignore index.Rmd).
You can add '#+MD: ---' keyword lines to mark new slides.
Then you export to my.Rmd directly (using ravel) and run slidify("my.Rmd").
Graphics 'just work', but you have to mind the spacing to be sure the slides
render nicely.
The file slidify-example.org at
https://github.com/chasberry/orgmode-accessories/
produces a minimal slidify slideshow with code, computed results, and graphics.
And it has some notes on org --> slidify using the md-knitr backend from
ox-ravel.
Ideally, a `md-slidify' backend would get written to automagically
produce the yaml header, separate slides based on headline levels, et
cetera. But that is a low priority right now.
HTH,
Chuck
Re: [O] Name for part of Org mode buffer before first headline
Thomas S. Dye tsdye.com> writes: > > Aloha all, > > Is there a canonical name for the part of the Org mode buffer before the > first headline? > > I checked the manual and probed my failure-prone memory off and on over > the last few days, but didn't come up with anything. > > I'm looking for the Org mode equivalent of LaTeX's preamble. Well, if you want a suggestion how 'bout ante matter which (mixing Latin and English and punning with physics) is the stuff before THE stuff. Or just 'ante' - what you put down before you begin to play. Chuck
Re: [O] Extract source code /with/ captions
James Harkins gmail.com> writes: > > I'm working on a set of Beamer presentations with a bunch of source > code blocks. I would like to collect all the blocks into one text file > per presentation, but I also need the captions and ideally a numeric > index. > [deleted] > So, for instance, where the slideshow and handouts would have a code > block identified like so: > > Listing 3: Compare geometric vs. band-limited waves, aurally. > > ... a student should be able to open up the corresponding code file and find: > > // Listing 3: Compare geometric vs. band-limited waves, aurally. > Can you make the 'caption' into a heading? If so, then ':comments org' will include it in output when you tangle. Or maybe ':comments link' or ':comments both' and some post-processing? HTH, Chuck
Re: [O] Exporting markdown specific string
Nicolas Goaziou gmail.com> writes: > > Hello, > > Bastien gnu.org> writes: > > > Ista Zahn gmail.com> writes: > > > >> I'm trying to figure out how to export a line (say "foo") only when > >> exporting to markdown. > > > > #+BEGIN_MD > > ... > > #+END_MD > > > > will do. > > I added #+begin_markdown...#+end_markdown too, as defined by the > back-end. Doesn't org-md-export-block want (org-export-with-backend 'html export-block contents info) at its end? Chuck
Re: [O] Exporting markdown specific string
Bastien gnu.org> writes: > > Charles Berry ucsd.edu> writes: > > > No it won't. > > > > ox-md.el does not define a transcoder for keyword and falls back to its > > parent: > > Thanks. > > I just added this transcoder to the master branch. > Looking at org-md-export-block shouldn't it export HTML export blocks as well, since markdown allows literal html? HTH, Chuck
Re: [O] Exporting markdown specific string
Charles Berry ucsd.edu> writes: > > Bastien gnu.org> writes: > > > > > Hi Ista, > > > > Ista Zahn gmail.com> writes: > > > > > I'm trying to figure out how to export a line (say "foo") only when > > > exporting to markdown. > > > > #+BEGIN_MD > > ... > > #+END_MD > > > > will do. > > > [snip] > > No it won't. > > ox-md.el does not define a transcoder for keyword and falls back to its > parent: OOPS! I meant 'export-block' --8<---cut here---start->8--- #+BEGIN_SRC emacs-lisp :exports both (assoc 'export-block (org-export-get-all-transcoders 'md)) #+END_SRC #+RESULTS: : (export-block . org-html-export-block) --8<---cut here---end--->8--- Chuck
Re: [O] Exporting markdown specific string
Bastien gnu.org> writes: > > Hi Ista, > > Ista Zahn gmail.com> writes: > > > I'm trying to figure out how to export a line (say "foo") only when > > exporting to markdown. > > #+BEGIN_MD > ... > #+END_MD > > will do. > [snip] No it won't. ox-md.el does not define a transcoder for keyword and falls back to its parent: --8<---cut here---start->8--- #+BEGIN_SRC emacs-lisp :exports both (org-version) #+END_SRC #+RESULTS: : 8.2.4 #+BEGIN_SRC emacs-lisp :exports both (assoc 'keyword (org-export-get-all-transcoders 'md)) #+END_SRC #+RESULTS: : (keyword . org-html-keyword) --8<---cut here---end--->8--- HTH, Chuck
Re: [O] How to use org src functions in other major mode (markdow)?
Shuguang Sun gmail.com> writes:
> Dear all,
> Is it possible to use org src functions in other major mode, e.g.,
> markddown-mode?
> In some extend markdown, source code can be put in to block, for example,
> r-mode for R script```rx <- 1:10```
> Is it possible to highlight the block as org-block "#begion_src R"? How
> to run org-edit-src-code on such markdown blocks?
> Best Regards,
> Shuguang Sun
>
Shuguang,
I cannot tell if you want to move org-mode format to *.Rnd or vice versa.
If you work in org-mode, you can export to markdown.
If you want to go from markdown to org-mode pandoc will do some of the work,
but the org-mode it produces needs further prettying up and the source code
blocks need work.
If you want to use org-mode documents to produce knitr markdown, you can
use ravel.
See https://github.com/chasberry/orgmode-accessories
Here is an example. With a file like this:
--8<---cut here---start->8---
* header 1
#+NAME: markdown-block
#+BEGIN_SRC R
a <- 1
b <- 2
a+b
#+END_SRC
--8<---cut here---end--->8---
Ravel export will produce a *.Rmd file like this:
--8<---cut here---start->8---
Table of Contents
b
1. header 1
# header 1
```{r markdown-block}
a <- 1
b <- 2
a+b
```
--8<---cut here---end--->8---
Which knitr will render as *.md like this:
--8<---cut here---start->8---
Table of Contents
1. header 1
# header 1
```r
a <- 1
b <- 2
a + b
```
```
## [1] 3
```
--8<---cut here---end--->8---
HTH,
Chuck
Re: [O] re-export using same options
Daniel Clemente gmail.com> writes: > > > > > > > Can I re-export using the last settings? > > > > C-u C-c C-e > > Thanks, that makes it faster, but you need to be in the same subtree. Not so. Recent versions of org-mode use this variable to find the subtree: org-export-dispatch-last-position is a variable defined in `ox.el'. Its value is # Documentation: The position where the last export command was created using the dispatcher. This marker will be used with `C-u C-c C-e' to make sure export repetition uses the same subtree if the previous command was restricted to a subtree. and it appears to update during edits so that same the subtree is found in subsequent exports. This If the current buffer hasn't changed and subtree export was activated, the command will affect that same subtree. seems to say that buffer edits will break C-u C-c C-e, but that did not happen in the examples I tried. > Is there something that also remembers which subtree was exported? > If you still think there is a problem, you should produce an ECM[1] to demonstrate it. [1] http://orgmode.org/worg/org-faq.html#ecm
Re: [O] re-export using same options
Daniel Clemente gmail.com> writes: > > > Hi, after exporting a subtree to HTML, I do some change and want to export again. I find that I have to do a long > process to get there: > C-spaceC-c C-u C-c C-e C-s h HC-u space > [snip] > > Can I re-export using the last settings? [snip] C-u C-c C-e See the manual (org) The export dispatcher
Re: [O] escaping org commands
Rustom Mody gmail.com> writes: > > > > On Fri, Dec 20, 2013 at 9:37 PM, Bastien gnu.org> wrote: > > > Hello, > > Rustom Mody gmail.com> writes: > > How does one escape something in a text that is an org-command > > eg > > I wanted to write > > <> > > > > It vanished from the export because its a link-target! > You can customize `org-activate-links' so that radio links are > not activated -- not tested, but my assumption is that the exporter > should handle this fine. > There is also `org-export-filter-radio-target-functions'. > HTH, > > > > > Thanks Bastien that will work in this case > > However I am also looking for something more generic: > [snip] Mark it verbatim or use an export snippet?? Exporting this: * Start Verbatim: : <> Export-snippet: @@ascii:<>@@ * headline to ASCII yields this: 1 Start === Verbatim: , | <> ` Export-snippet: <> 2 headline ==
Re: [O] How do I specify the language for a :results code block
Thomas S. Dye tsdye.com> writes:
>
> Aloha Alan,
>
> Alan Schmitt polytechnique.org> writes:
>
> > Hello,
> >
> > I'm trying to write a block in some language (right now shell, but it
> > will probably be something different) whose output is an org source
> > block is some language (here coq). I keep looking at the documentation
> > and I cannot see how to specify the language. If I try something like:
[example-deleted]
> >
> > How can I have a block with "#+BEGIN_SRC coq" instead?
[snip]
>
> I think this can be accomplished by chaining:
>
[example-deleted]
The problem I see is that the :var x=y() idiom can hand an object to the
src block that is hard to parse and execute -- depending on the language.
If the object is create code in one language and run it in another, it
is sometimes easier to insert results using noweb <> calls.
A simple example: generate code in sh that is run in emacs-lisp
#+name: make-elisp
#+BEGIN_SRC sh :exports none :var fun="+"
echo "(" $fun "1 2)"
#+END_SRC
#+BEGIN_SRC emacs-lisp :noweb yes :exports results
<>
#+END_SRC
#+RESULTS:
: 3
#+BEGIN_SRC emacs-lisp :noweb yes :exports results
<>
#+END_SRC
#+RESULTS:
: -1
#+BEGIN_SRC emacs-lisp :noweb yes :exports results
<>
#+END_SRC
#+RESULTS:
| 1 | 2 |
HTH,
Chuck
Re: [O] Error: (wrong-type-argument integer-or-marker-p nil)
Sebastien Vauban writes: > > Hello Nicolas, > > Nicolas Goaziou wrote: > > "Sebastien Vauban" writes: > > > >> When trying to convert a document which contains R graphics, I get the error: > >> > >> Debugger entered--Lisp error: (wrong-type-argument integer-or-marker-p nil) > >> goto-char(nil) > >> (progn (goto-char link-end) (skip-chars-forward "")) > >> (setq post-blank (progn (goto-char link-end) (skip-chars-forward " ")) end (point)) > > > > Thank you for the report. > > Thank you for your prompt attitude, as always... > > > Could you provide an ECM for it? > > Not easy, no, as it now disappeared after an update to the latest version > of Org. > [rest deleted] There was a problem with org-element-cache-* that Nicolas just fixed recently that was generating issues that seem to me could be causing what you reported. See http://thread.gmane.org/gmane.emacs.orgmode/79160/focus=79377 If you do pursue this, you might try turning off the caching to see if the problems you mention goes away. Or just do M-: (org-element-cache-reset) RET before each export. HTH, Chuck
[O] [bug] [babel] repeated exports w/ inline src blocks yield different results
Consider this code:
,
| * test
|
| #+NAME: block2
| #+BEGIN_SRC emacs-lisp :exports both
| (setf not-yet-bound-a t )
| #+END_SRC
|
| src_emacs-lisp{(+ 1 1)}
|
| end of buffer
|
`
Upon export via
C-c C-e C-b t A y y
yields:
,
| 1 test
| ==
|
| ,
| | (setf not-yet-bound-a t )
| `
|
| ,
| | t
| `
|
| `2'
|
| end of buffer
|
`
just as one would hope.
But trying it again,
C-c C-e C-b t A y y
gives
,
| 1 test
| ==
|
| ,
| | (setf not-yet-bound-a t )
| `
| #+END_SRC
|
| ,
| | t
| `
|
| `2'
|
| end of buffer
|
`
and you see the extra '#+END_SRC' line.
And if you keep repeating those keystrokes, the second result again appears.
However, sometimes a minor change and then an erasure (perhaps 'a a C-x u')
followed by the export keystrokes yields the correct result.
There are some other forms of misbehavior: if I change the header arg
in the src block to ":exports results", then the first export is correct,
but the second export skips execution of the src block and writes the code
in the export as if ':exports code' had been given.
But again 'a a C-x u' seems to clear whatever condition causes the
misbehavior.
Remove the "src_emacs-lisp{...}" and clear with 'a a C-x u' and
everything works fine again through multiple exports. I tagged the
subject line '[babel]' because of that.
Chuck
Re: [O] [BUG] org-confirm-babel-evaluate breaks inline src blocks
Eric Schulte gmail.com> writes: > [delete long discussion of bug] > > I've just pushed up another fix which should fix this for export too. > And it works! Thanks for the fix and for enabling this useful capability! Chuck
Re: [O] [BUG] org-confirm-babel-evaluate breaks inline src blocks
Eric Schulte gmail.com> writes: > > Charles Berry ucsd.edu> writes: > > > Eric Schulte gmail.com> writes: > > > >> > >> Charles Berry ucsd.edu> writes: > >> > > [snip] > Indeed the fix was to set this element of info to point to the front of > the inline src block. I imagine that you probably don't have the > patched version of the relevant function loaded. Please try M-x > describe-function on org-babel-get-src-block-info, then jump to the > definition of said function where you should see the following code > which now sets the location of the inline src block head into the last > element of the info list. > > ;; inline source block > (when (org-babel-get-inline-src-block-matches) > (setq head (match-beginning 0)) > (setq info (org-babel-parse-inline-src-block-match > That _is_ what I had loaded, but ... org-babel-get-src-block-info is *not* *called* for inline src blocks. org-babel-exp-non-block-elements doesn't call org-babel-get-src-block-info. Instead, it has this (let* ((info (org-babel-parse-inline-src-block-match)) for inline src blocks. So changing org-babel-get-src-block-infodoes not fix the inline src block issue. === Juat to be sure that I understood what was happening, I instrumented org-babel-get-src-block-info and ran the ECM I posted at the start of this thread. org-babel-get-src-block-info got called twice for the first src block, then I got prompted "Evaluate this emacs-lisp code block on your system? " If I answer 'n' (skip the block redefining org-confirm-babel-evaluate, then I get prompted for the inline src block _without_ org-babel-get-src-block-info being called again. If I answer 'y' (redefine org-confirm-babel-evaluate as a lambda form), I get the error message. org-babel-exp-results: Wrong type argument: integer-or-marker-p, nil HTH, Chuck
Re: [O] [BUG] org-confirm-babel-evaluate breaks inline src blocks
Eric Schulte gmail.com> writes: > > Charles Berry ucsd.edu> writes: > [snip] > > Thanks for pointing this out, I've just pushed up a fix. > AFAICS, it is still broken. I did a git pull, downloaded the patches, applied them, compiled ob-core.el. I am still getting org-babel-exp-results: Wrong type argument: integer-or-marker-p, nil I suspect that (,head (nth 6 ,info)) ... (goto-char ,head) in the org-babel-check-confirm-evaluate macro is the source of the message. (nth 6 info) is nil for inline src blocks. HTH, Chuck
[O] [BUG] org-confirm-babel-evaluate breaks inline src blocks
Following this thread:
http://thread.gmane.org/gmane.emacs.orgmode/77572/focus=77648
I found that setting org-confirm-babel-evaluate to a lambda form
BREAKS inline src blocks.
Here is an ECM:
#
#+BEGIN_SRC emacs-lisp
(setf org-confirm-babel-evaluate
(lambda (&rest args)
(message "info: %S" (org-babel-get-src-block-info 'light))
nil))
#+END_SRC
#+RESULTS:
src_R{1+1}
#
Re: [O] org babel before excute hook
John Kitchin andrew.cmu.edu> writes: > > > > I have a related kind of problem. When preparing notes > for a class, I may end up with 70 code blocks in an org file, many of > which create graphics. I am always worried about accidentally using the > same filename and overwriting a graphic from an earlier block. A unique, > but reproducible filename would be sufficient for my needs. > Header arg values can be elisp calls. You can use `make-temp-file'. So every time this block is executed, a new file is created and the file link is added to the results. #+BEGIN_SRC R :results output append :file (make-temp-file "temp") cat(date(),"\n") #+END_SRC #+RESULTS: [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fhgn/T/temp302IjV]] [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fhgn/T/temp3028Lu]] See `temporary-file-directory', too, if you want to use this, as the default may not be what you intend. You might want to use this: #+BEGIN_SRC emacs-lisp (defun local-tfile (file) (let ((temporary-file-directory ".")) (make-temp-file file))) #+END_SRC Then the files go in the local directory when this is executed: #+BEGIN_SRC R :file (local-tfile "tfile") :results output append cat(date(),"\n") #+END_SRC You might not want `append' in this case. HTH, Chuck [rest deleted]
Re: [O] LaTeX export with Code
Sam Flint flintfam.org> writes:
>
> I regularly use org-mode for LP, and would like to be able to export the
> name of a code chunk as a caption in LaTeX. I have looked at the
> manual, and don't see any way of doing this, are there?
Yes. Quite a few.
If you want is the src block name to be used as the caption,
you can put this line:
#+CAPTION: use-name-as-caption
before the named src block
and execute this code before you export:
#+BEGIN_SRC emacs-lisp
(defun org-export-use-name-as-caption
(text &optional back-end info)
"Use the block name as the caption."
(replace-regexp-in-string
"label{\\([^}]*\\)}\\(use-name-as-caption\\)"
"label{\\1}\\1"
text))
(add-to-list 'org-export-filter-src-block-functions
'org-export-use-name-as-caption)
#+END_SRC
Then when you export this
#+CAPTION: use-name-as-caption
#+NAME: y-plus-z-becomes-x
#+BEGIN_SRC R
x <- y+z
#+END_SRC
the result is
\begin{figure}[H]
\begin{verbatim}
x <- y+z
\end{verbatim}\caption{\label{y-plus-z-becomes-x}y-plus-z-becomes-x}
\end{figure}
HTH,
Chuck
Re: [O] input data for babel blocks
Alan Schmitt polytechnique.org> writes: > > Hi Charles, > > ccberry ucsd.edu writes: > > > Lacking that, another alternative to the approach you have crafted is to > > use elisp src blocks to set up the commands needed to create the > > objects, > > and then place the results of executing the elisp src block in the src > > block of your favored language using noweb, for example > > > > #+BEGIN_SRC mylang :noweb yes > > <> > > #+END_SRC > > > > might convert 'arg2' to an object of the desired type named 'arg1' in a > > 'mylang' src block. > > This looks like a very powerful approach, but it's a bit beyond my > understanding of babel (which is limited) and noweb (whose existence I > just discovered after reading http://orgmode.org/manual/noweb.html). > Sorry if it was a bit obtuse. The examples given by others seem to have helped. And I will give one more. [deleted] > If you have an example that uses different languages, I'd love to look > at it. I'll then try to write an example for ocaml. > Here is what I use for LaTeX thru elisp to R: * Quote Blocks quote-blks takes two args: - blk :: a string of comma separated src block names - sep :: an optional separator for use when there is more than one block I usually save it in a file and load it in with (org-babel-lob-ingest file). But you can copy and paste and the example below will still work. #+name: quote-blks #+BEGIN_SRC emacs-lisp :var blk="abc" :var sep="\"\n\"" (save-excursion (replace-regexp-in-string "\"\"" "" (mapconcat (lambda (x) (org-babel-goto-named-src-block x) (format "%S" (cadr (org-babel-get-src-block-info t (split-string blk "," t) sep) t t)) #+END_SRC * example of use The LaTeX here can be editted via C-c ' (i.e. org-edit-special --> org-edit-src-code). #+name: lstuff #+BEGIN_SRC latex :eval never :exports none Here is a \backslash. And an unmatched quote: '. #+END_SRC Here is an example using it on the above block. The cat statement prints a formatted version. The str statement shows what R sees (but the outer quotes are not part of the string). #+BEGIN_SRC R :noweb yes :results output some.latex <- <> cat(some.latex,"\n") str(some.latex) #+END_SRC #+RESULTS: : Here is a \backslash. And an unmatched quote: '. : chr "Here is a \\backslash. And an unmatched quote: '." HTH, Chuck
Re: [O] input data for babel blocks
Alan Schmitt polytechnique.org> writes: > > Hello, > > In my quest for analyzing my data in org mode tables, I'm trying to see > if I can use my favorite language (i.e., ocaml). I'm thus looking at how [discussion of revising org-babel-variable-assignments: deleted] > > I have the following questions for the list: > - can I always assume that tables are passed as lists of lists? > - would the patch above be a useful way to deal with this? > - is there a way to specify the :var parsing in a code block or in the table? Alan, Nice description of a problem that has vexed me, too. It would be nice to have more flexibility in passing objects to src blocks in ones favored language via the :var header arg. Lacking that, another alternative to the approach you have crafted is to use elisp src blocks to set up the commands needed to create the objects, and then place the results of executing the elisp src block in the src block of your favored language using noweb, for example #+BEGIN_SRC mylang :noweb yes <> #+END_SRC might convert 'arg2' to an object of the desired type named 'arg1' in a 'mylang' src block. FWIW, my own usage of this approach is to write LaTeX code including backslashes and unmatched quotes, then convert the code to a valid R character string for labelling figures (which undoubled backslashes and unmatched quotes would invalidate). HTH, Chuck
Re: [O] LaTeX export: images subplots
Martin Leduc hotmail.com> writes:
>
>
> Hi all,
> I am using org-mode to write a report with several figures. I would
> like to group some images into a same figure, let say a 2x2 panel. I
> know that I can directly embed latex code in my org file, for
> example by using the subfloats (from the latex subfig package).
> However, I would prefer to use an org-based solution of inserting
> the image links in order to keep the convenient way of previewing
> images right into the buffer with C-c C-x C-v.
> The only solution I found is by using tables such as:
>
> #+CAPTION: Insert caption here.
> #+ATTR_LATEX: :align p{0.5\textwidth}p{0.5\textwidth}
> | [[pathtoimage]] | [[pathtoimage]] |
> | [[pathtoimage]] | [[pathtoimage]] |
>
> where the size of the images is controled by p{} and C-cxv is
> working. However, in the exported TeX file, it is a table, not a
> figure. Is there a cleaner way to make image panels that would
> preserve the figure environment in the exported TeX file ?
I think you are close.
Use
#+BEGIN_SRC org :exports none
#+name: imtable
#+END_SRC
This gives you the images in a form you can view and a way to access the
links so you can export them in a different form.
For example,
#+BEGIN_SRC emacs-lisp :var a=imtable :exports results :results raw
(mapconcat (lambda(y)
(mapconcat
(lambda(x) (org-export-string-as x 'latex t)) y "")) a "")
#+END_SRC
exports as
\includegraphics[width=.9\linewidth]{img3070YH.png}
\includegraphics[width=.9\linewidth]img307BjN.png}
\includegraphics[width=.9\linewidth]img307OtT.png}
\includegraphics[width=.9\linewidth]img307b3Z.png}
when the elements in the table are the image paths img*.png as shown.
HTH,
Chuck
Re: [O] Superscript before character
Roger Mason mun.ca> writes:
>
> Hello,
>
> I'd like to create a superscript that preceeds a letter. I tried
> ^1Fred, ^1 Fred, ^{1}Fred and ^{1} Fred, to no avail.
>
> Can this be done in org (8.0.3)? If so how?
[snip]
\nbsp{}^{1}Fred
exports to ~$^{\text{1}}$Fred in latex and 1Fred in html
HTH,
Chuck
Re: [O] Help proofreading ORG-NEWS for Org 8.1
Bastien gnu.org> writes: > > Hi all, > > I have prepared the changelogs for Org 8.1, see the first > section in this file: > > http://orgmode.org/cgit.cgi/org-mode.git/plain/etc/ORG-NEWS > > I have not documented changes in the contrib/ directory, as > ORG-NEWS is meant to go into the Emacs trunk. > > Please let me know if I missed some important changes or if > some descriptions need some rephrasing/details. Should the changes in the arguments of org-export-to-file/buffer or the move to make the (plist-get info :back-end) return a struct count as 'Incompatible changes'? Or at least be highlighted somewhere as old code may be (and - in my case - was) broken by them. HTH, Chuck
Re: [O] asynchronous code evaluation
Johannes Rainer gmail.com> writes: > > > hi all! > > I have some pretty calculation intense R code in a code block and when I > execute the code (C-c C-c) my emacs freezes and waits for the code to > finish. Is there a way to evaluate the code asynchronously, so that I > could edit the file (obviously not the code block itself) while the code > is being evaluated? > > thanks, jo > Try this: C-c ' in the R src block. Then use C-c C-c (ess-eval-region-or-function-or-paragraph-and-step) to execute the long running code from the ESS edit buffer. You may need to select the region if there are several paragraphs, or delete any blank lines. == Another alternative is to use ravel. https://github.com/chasberry/orgmode-accessories Create a knitr or Sweave doc from the org doc or a suitable subtree of the computationally intensive parts. Then you can knit() the doc from the R session and switch back to the buffer you want to edit. Also, you might want to turn on caching in the knitr doc to enable a quick restart when you log in again.
Re: [O] macro expansion in source code
Johannes Rainer gmail.com> writes:
>
>
> hi,
> I was just wondering if there is a way to use macro expansion also in
> source code blocks or headers. I tried this, but the macro was never
> expanded, but rather the {{{image_width}}} was exported. could the
> expansion be done by calling the macro expansion before export
> (e.g. using a hook)?
>
> something like this:
[snip]
I think the answer is no. But you can accomplish much the same thing with
properties and/or noweb references. Like this
* header
:PROPERTIES:
:image_width: 16
:END:
#+NAME: imwide
#+HEADER: :var iw=(org-entry-get (point) "image_width")
#+BEGIN_SRC R :results value
iw
#+END_SRC
#+RESULTS: imwide
: 16
#+BEGIN_SRC R :noweb yes :results output
image.width <-
<>
image.width
#+END_SRC
#+RESULTS:
: [1] 16
Re: [O] Export attached image files
Johan Ekh gmail.com> writes: [snip] > I would like > to take a series of screenshots, quickly incorporate them into an org > file together with some text without having to rename > the screenshots with suitable names and organize them on my disk etc. I'd > like org-mode to store the images somewhere > in a data directory as an attachment, but of course I'd like the > screenshots to be incorporated in the pdf-file when I export it. > Is this possible? IIUC what you want, yes. There is contrib/lisp/org-screenshot.el for taking screenshots. It needs scrot. Also, some posts showing how to roll your own screenshot during the last six months or so, some of which do not use scrot. If you are on MAC OS X and do not want to install scrot, this might be good enough: http://lists.gnu.org/archive/html/emacs-orgmode//2013-03/msg01843.html If you have * headline text text text [[file:path-to/my-file.jpg]] Then the image gets rolled into your pdf. You might need to mess with the width if you do not want full width for an image. [rest deleted]
Re: [O] Filters not working
Thomas S. Dye tsdye.com> writes: > > Charles Berry ucsd.edu> writes: > [filter to demo extracting back-end name deleted] > > > > , > > | type-of back-end: vector > > | name of back-end: latex > > ` > > Yes, it does. > > > > > Take a look at "(defstruct (org-export-backend..." in ox.el > > OK, I had a look at org-export-backend, but not sure what I'm looking > for in particular. > > I did note that you don't test back-end directly, but instead look at > org-export-backend-name. Perhaps this is what Nicolas means by "Filters > defined here shouldn't make a back-end test, as it may prevent back-ends > derived from this one to behave properly"? That comment was in the context of back-end specific filters and aimed at back-end developers. You are adding to org-export-filter-plain-text-functions, which is for users. So, go ahead and test. > > However, changing my filter so it uses org-export-backend-name doesn't > seem to change anything. > > Or, was I supposed to learn something else from ox.el? > The changes introduced in commit cea0434c4f7f7f1fc1547e6790b96a76bc217e15 ox: Change back-ends internal representation to structures necessitate extracting the name of the back-end from a vector. So, this bit of code (memq backend '(beamer latex)) will never return t, because backend is a vector. Probably what you want is (memq (org-export-backend-name backend) '(latex beamer)) HTH,
