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Questions tagged [org-babel]

feature of Org mode that handles source code for multiple languages. It can execute source code from within Org mode documents, making it convenient for producing literate programming documents and managing reproducible research. Note that [tag:org-babel] is now incorporated into [tag:orgmode] as `working with source code` and no longer a separate extension.

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1answer
33 views

Org mode export with R failing

I have an org file with R code in it. When I attempt to export to html or pdf I get an error: For example if my file was: #+begin_src R :exports code square <- function(x) { x * x } square(1:...
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1answer
15 views

Haskell code execution in Org-mode give error but in .hs file the code is good and working

i have this code: qs [] = [] qs [x] = [x] qs (x:xs) = qs [a | a <- xs, a < x] ++ [x] ++ qs [b | b <- xs, b >= x] when i save it to some file .hs and load it to ghci i can execute ...
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0answers
10 views

org-mode/babel and zsh: Getting shell sessions to work

I've been trying to get shell code blocks with sessions to work, but not entirely succeeding. My setup: emacs 26.1 (spacemacs) org-mode 9.2.2 default shell: zsh 5.7.1 Everything seems to work fine ...
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2answers
73 views

Babel + Python function definition with for loop causes IndentationError

I am using orgmode and Babel to run Python source code blocks. I noticed that if I define a function that returns a value, and if this function has a for loop inside it, then evaluating it with Babel ...
8
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4answers
1k views

Org Mode Babel - Interactive code block evaluation in Python

Similarly to this question I would like to evaluate (in org mode) Python source code blocks containing "input" instructions but I can't find a way to have an interactive evaluation (with user input) ...
2
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2answers
109 views

How to find START and END of #+RESULTS region with elisp functions?

I want to call (recode-region) on sh code block results in :post header attribute. So it needs START and END values. Is there a way to define of RESULTS block content boundaries for it ?
47
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6answers
10k views

Can I use org-mode to structure my .emacs or other .el configuration file?

My .emacs configuration file gets bigger and bigger and I'd like to get a better overview and structuring by adding headings, subheadings and being able to hide or show them like I can do with Emacs ...
3
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1answer
73 views

org-export latex pdf output does not render svg

I tried out this section of code from this repo #+LATEX_HEADER_EXTRA: \usepackage{svg} ... #+PROPERTY: header-args :eval never-export :file-ext svg ... #+NAME: sequence12422 #+BEGIN_SRC plantuml :...
4
votes
2answers
74 views

How to copy org-table to postgresql database?

With sqlite one can easily populate a table in a database via a org-table like so: [EDIT](using only one sqlite-scr-block with org-table variable parameter)[/EDIT] #+NAME: A | val1 | val2 | |------+...
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1answer
19 views

org src block php formatting adding commas to phpDoc

In the editing mode (C-c ') I formatted php code using TAB button. But in org mode src block it adds 2 comma to phpDoc.
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1answer
24 views

Unable to run applescript from emacs-lisp

I have the following code block, which I am trying to execute from org-babel: #+BEGIN_SRC emacs-lisp (let ((h (nth 5 (org-heading-components)))) (do-applescript (format "tell application \"...
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1answer
13 views

Grant Applescript via Emacs Lisp permission for UI scripting [closed]

I have a simple applescript, embeded in emacs-lisp, which uses the current org-mode heading to create a calendar event in Apple Calender. However... because scripting Calendar directly is painfully ...
0
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1answer
19 views

How to change org-babel interpreter location

Say I have my ditaa interpreter pointed to at /home/user/.emacs.d/elpa/contrib/scripts/ditaa.jar, how would I set it so it points to a different location?
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0answers
43 views

Print output from org code block immediately

I have an org mode file I use to run some moderately long analyses. Evaluating individual blocks may take 15 minutes to an hour or so. I usually wrap longer bits with calls to date, so I can later ...
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0answers
42 views

tramp gcloud compute ssh not working

I wanted to be able to ssh into my google cloud instances with spacemacs. I found: https://github.com/dustinfreeman/dustinfreeman.emacs.d/blob/master/init.el#L50 which is based off of: https://...
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0answers
15 views

Prevent parsing of text inside verbatim org results block

How do I tell emacs to not not apply treatments to text within a block like this. My issue is that, the * foo at the end causes the export to go bad. I'm using something similar to carl's setup -> ...
4
votes
1answer
336 views

How to generate inline plot result for ob-clojure?

Question: How to generate inline plot image result in Org-mode babel clojure src block? I tried some ways: First way: use :results file :file "clojure-babel-figure-result.png" #+BEGIN_SRC clojure :...
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0answers
13 views

Rmarkdown-like export of Leaflet for R webmap to html from org-mode

With RMarkdown it's easy to embed an interactive webmap. E.g.: --- title: Some title output: rmarkdown::html_document --- ```{r} library(leaflet) leaflet(width = "100%", height = "650px") %>%...
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vote
1answer
33 views

use js2-mode instead of js-mode in org babel source

I want to use js2-mode instead of js-mode inside org-babel sources. Is there a way to define a mode for JavaScript inside those chunks? #+begin_src js console.log(1+1) #+end_src
3
votes
1answer
111 views

How to disable noweb prefix lines?

This says that Noweb insertions now honor prefix characters that appear before <<reference>>. And because of that trying to use #+BEGIN_SRC clojure :noweb-ref dep-cljsbuild [lein-...
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1answer
903 views

Debugging code blocks in org mode

Are there any tools available to make tracing errors in org-mode blocks easier? (I'm working with python specifically) My current workflow is to copy code that works to a source block, and try to ...
1
vote
1answer
163 views

No org-babel execute function for go

#+Begin_SRC go package main import ("fmt") func main(){ fmt.Println("emacs") } #+End_Src ~/.emacs.d/init.el: (when (memq window-system '(mac ns)) (exec-path-from-shell-initialize) (exec-path-...
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votes
1answer
155 views

ledger in org-babel blocks uses incorrect path data in Windows 10

I am trying to include a ledger data file from an org-babel block. I am using Windows10 and the SciMax emacs distribution. #+begin_src ledger :cmdline bal :results output :exports results !include d:/...
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2answers
566 views

Linking to c++ libraries in babel code block

The title says it all, and I've included the relevant sections of my file below. I'm trying to create a src block that uses some functionality of the boost libraries, the first src block sets up the ...
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1answer
183 views

Code block evaluated when exporting, not when publishing

I have this basic org publishing project to test that code blocks evaluation is triggered by publishing in html (org-html-publish-to-html). While exporting through org-mode export dispatcher does ...
0
votes
1answer
47 views

How to prevent org-mode loading babel's major mode stuffs unless entering `org-src-mode`?

I have some Java's scripts in a org file. And I use meghanada-mode in java-mode. Each time I open this org file and do nothing, I get the following error since the mehanada server loaded by java-mode ...
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2answers
292 views

Cannot Execute Org-Babel Haskell Block

In an org-mode file: #+BEGIN_SRC haskell let x = "test" putStrLn x #+END_SRC yields: executing Haskell code block... if: ‘org-babel-script-escape’ expects a string
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0answers
39 views

How to export org-babel document with ox-pandoc?

I want to export an org-babel document to html with bibliographies from a .bib file. The org-file is the following: #+TITLE: Test #+AUTHOR: Your Name #+EMAIL: your-email@server.com #+PANDOC_OPTIONS: ...
3
votes
1answer
85 views

Evaluating `org-babel-clojure` blocks returns all form evaluations

I'm trying to set up babel for use with Clojure according to http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-clojure.html#org85bc1ec and I can evaluate code but when I evaluate a block with ...
4
votes
1answer
34 views

How to display intermediate code block results?

Here is an example to let me explain what I would like to achieve: #+NAME: heavy_computation #+BEGIN_SRC shell :results table echo -e "A\t32\nB\t17" #+END_SRC #+BEGIN_SRC python :var data=...
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vote
1answer
46 views

How to export org-babel document?

In my .emacs file, I have the following variables: (custom-set-variables '(org-babel-load-languages (quote ((emacs-lisp . t) (R . t)))) '(org-confirm-babel-evaluate nil)) I save this example to a ...
0
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1answer
179 views

Tangle only selected src blocks using org-babel on export

I have a document with only several source code blocks that should be tangled. So the structure is: # Some main.org ... #+BEGIN_SRC awk :tangle file1.awk ... #+END_SRC awk ... ...
4
votes
1answer
376 views

Using File Local Variables in org-mode

Is there a way to use file local variables set in an org-mode file in the following contexts: Simply expanding the variable when text is exported (eg: to LaTeX) Passing the value to :var in a babel ...
3
votes
1answer
381 views

ob-ipython error message while evaluating SRC block

I am getting this error when executing any source ipython block such as this one: #+BEGIN_SRC ipython :session :results output drawer # Compute areas and colors import numpy as np import matplotlib....
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vote
1answer
44 views

How to generate the result file for dot source block and include it with another path in org-mode?

I'm starting to write blogs with org-mode and org-static-blog, but now I'm stuck with a problem respecting exporting graphviz dot file to image file. So I have a code block like this with (setq org-...
0
votes
1answer
34 views

eval elisp code to fill org-babel header arguments

I use many org files with figures generated by source code blocks. By example, in an org mode file long/path/document.org I have: #+BEGIN_SRC dot :file my_fig.png :exports results digraph { A->...
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0answers
26 views

How to set a tangled parent directory for each subtree in org mode?

Base on this, one can set a global tangled file. However, I'd like to set one directory for each subtree, e.g. for a * Python subtree, in every code block I can set :tangle a.py or :tangle b.py ...
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vote
0answers
34 views

With org-babel how can I read a result block and pass arguments?

I asked a similar question a few years ago but I never did figure out how to proceed. I ended up aborting my excursion into org-babel. However, I can see how this would be really valuable, to ...
2
votes
1answer
125 views

Org mode elisp in :var in header-args causing max-specpdl-size error

In org mode, :var header arg definitions can actually call other SRC blocks, which is very nice! However I've run into a problem exemplified by the following org file: #+NAME: add3 #+BEGIN_SRC elisp :...
2
votes
1answer
45 views

Setting :stdin with #+call in org-mode shell code block

I've got the following code: #+NAME: example-block1 #+BEGIN_EXAMPLE Lorem ipsum dolor sit amet, consectetur adipisicing elit. #+END_EXAMPLE #+NAME: example-block2 #+BEGIN_EXAMPLE Sed do eiusmod ...
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vote
1answer
47 views

Export an orgmode buffer without expanding noweb references?

Normally, when I use orgmode's export function on a buffer that contains noweb references, they get expanded, resulting in lots of duplicated code throughout the exported HTML document. Is there a ...
0
votes
1answer
263 views

org-babel-execute-src-block: No org-babel-execute function for R!

In org-mode, attempting to execute the following block... #+BEGIN_SRC R 1+2 #+END_SRC ...gives the error message org-babel-execute-src-block: No org-babel-execute function for R!. I have followed ...
7
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1answer
197 views

Converting cURL command to ob-http

I have a whole series of curl commands that I would like convert into ob-http code blocks in a org file (second choice would be to do them in restclient). Here is a simplified sample command: curl -...
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vote
2answers
222 views

Org-babel. :flags in C code blocks dont work correctly anymore

I'm trying to run current code block #+HEADERS: :includes <math.h> <stdio.h> :flags -lm #+HEADERS: :var x=1.0 :var y=4.0 :var z=10.0 #+begin_src C :tangle trying double pi = 4*atan(1); ...
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1answer
21 views

Org babel R: why is 'NA' replaced with 'nil'

When using R in org mode source blocks, any NA (i.e. missing) values in tables get replaced with nil. Why is this? And is there a way to change this (globally, or at the file level)? I regularly ...
0
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1answer
35 views

is there something like org-babel for arbitrary major modes? [duplicate]

org-babel allows editing source code of arbitrary modes inside an .org file. I'd like to do this (with different syntactic markers) inside my major mode, but org-babel is very specific to org. Is ...
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vote
1answer
112 views

org-babel captions on results don't export to LaTeX?

I hope the following complete minimal example is self-explanatory. It contains my question. It should run without error messages in org-babel. I looked at the six related suggested questions on the ...
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votes
2answers
204 views

It is possible to instrument a literate Org-mode configuration file with a backing Emacs Lisp file?

It is a common practice to write Emacs configuration files using literate-programming style in Org mode. Unfortunately, while improving readability, this comes with significant programming ...
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1answer
30 views

Catching warnings from sh source block

I've started on Learn C The Hard Way and want to collect my work in org mode. Executing rm ex1 && CFLAGS="-Wall" make ex1 in the terminal returns cc -Wall ex1.c -o ex1 ex1.c: In ...
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2answers
218 views

org-babel-execute:clojure handle :file result error

-- UPDATE -- Declare what my code is trying to do: I want to let org-babel insert an inline image link which is generated by Clojure code. Here the image is generated by Incanter's function save. ...