* Org-mode and ESS
@ 2008-11-11 18:00 Graham Smith
2008-11-11 18:30 ` Detlef Steuer
2008-11-12 19:42 ` Austin Frank
0 siblings, 2 replies; 10+ messages in thread
From: Graham Smith @ 2008-11-11 18:00 UTC (permalink / raw)
To: emacs-orgmode
Is any one using Org-mode with ESS. ESS seems to need a file with a
*.R name to work, but it would be really useful to use Org-mode
features to keep notes of comments and code, before sending to R, and
of course to copy results back into an Org-Mode file from R.
As a search here and a google hasn't thrown up anything obvious, I
assume not, but I thought I would ask.
Thanks,
Graham
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Org-mode and ESS
2008-11-11 18:00 Org-mode and ESS Graham Smith
@ 2008-11-11 18:30 ` Detlef Steuer
2008-11-11 19:13 ` Graham Smith
2008-11-12 19:42 ` Austin Frank
1 sibling, 1 reply; 10+ messages in thread
From: Detlef Steuer @ 2008-11-11 18:30 UTC (permalink / raw)
To: emacs-orgmode
Hi Graham,
if you have ess loaded and you are working on a file test.org:
* test
ls()
and you have an R process running in another buffer, then
you can i.e. put the cursor on the line with ls() in test.org
and execute M-x ess-eval-line.
The command is then executed in your running R session.
Hth
detlef
On Tue, 11 Nov 2008 18:00:01 +0000
"Graham Smith" <myotisone@gmail.com> wrote:
> Is any one using Org-mode with ESS. ESS seems to need a file with a
> *.R name to work, but it would be really useful to use Org-mode
> features to keep notes of comments and code, before sending to R, and
> of course to copy results back into an Org-Mode file from R.
>
> As a search here and a google hasn't thrown up anything obvious, I
> assume not, but I thought I would ask.
>
> Thanks,
>
> Graham
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Remember: use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>
--
Wisely, and slow. They stumble that run fast. - Shakespeare
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Re: Org-mode and ESS
2008-11-11 18:30 ` Detlef Steuer
@ 2008-11-11 19:13 ` Graham Smith
0 siblings, 0 replies; 10+ messages in thread
From: Graham Smith @ 2008-11-11 19:13 UTC (permalink / raw)
To: emacs-orgmode
Detlef,
Ah thanks, I should probably worked that out myself.
> if you have ess loaded and you are working on a file test.org:
>
> * test
> ls()
>
> and you have an R process running in another buffer, then
> you can i.e. put the cursor on the line with ls() in test.org
> and execute M-x ess-eval-line.
> The command is then executed in your running R session.
Graham
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Org-mode and ESS
2008-11-11 18:00 Org-mode and ESS Graham Smith
2008-11-11 18:30 ` Detlef Steuer
@ 2008-11-12 19:42 ` Austin Frank
2008-11-12 19:51 ` Graham Smith
` (2 more replies)
1 sibling, 3 replies; 10+ messages in thread
From: Austin Frank @ 2008-11-12 19:42 UTC (permalink / raw)
To: emacs-orgmode
[-- Attachment #1.1: Type: text/plain, Size: 3300 bytes --]
On Tue, Nov 11 2008, Graham Smith wrote:
> Is any one using Org-mode with ESS. ESS seems to need a file with a
> *.R name to work, but it would be really useful to use Org-mode
> features to keep notes of comments and code, before sending to R, and
> of course to copy results back into an Org-Mode file from R.
>
> As a search here and a google hasn't thrown up anything obvious, I
> assume not, but I thought I would ask.
In my local git repo of the org sources I have a pretty nice setup for
using R or S inside org-mode. I liked the in-file native editing of
source code so much that I decided that I wanted to use org files as
source files with Sweave (instead of using .Rtex or .Rnw files). My
goal was to export documents with embedded R code, rather than to use
org within the comments of R files. I can certainly see a use for the
latter approach (which seems to be what you have in mind), as well.
There was recently a thread where someone created a preprocessing system
for specific types of blocks. That would be another possible strategy
for evaluating blocks of R code before export. Since that facility
didn't exist yet and there was already the extensible Sweave
pre-processor, I took the route of making Sweave org-aware.
Basically, in the workflow I've developed, I create a file with the
extension .Rorg, say homework_key.Rorg. Within that file, I can embed
blocks of R code, and can refer to variables defined in the R code
contained in the document.
--8<---------------cut here---------------start------------->8---
#+BEGIN_R
a <- 3
a
#+END_R
* the value of a is \R{a}
* the value of a + 3 is \R{a + 3}
--8<---------------cut here---------------end--------------->8---
Executing C-c ' inside the block takes you into a temporary buffer
that's in ESS mode, with full support for interactive evaluation.
When I'm ready to export, I run the R command
Sweave("homework_key.Rorg", driver=RweaveOrgLatex, syntax=SweaveSyntaxOrg).
(I've defined those driver and syntax functions locally). This creates
a new file, homework_key.org. In the new file, the above text would be
translated into
--8<---------------cut here---------------start------------->8---
#+BEGIN_LATEX
\begin{Schunk}
\begin{Sinput}
> a <- 3
> a
\end{Sinput}
\begin{Soutput}
[1] 3
\end{Soutput}
\end{Schunk}
#+END_LATEX
* the value of a is 3
* the value of a + 3 is 6
--8<---------------cut here---------------end--------------->8---
The plain homework_key.org file could then be exported into \LaTeX. It
even works with the new pdf export.
I haven't put the code anywhere public because there are several things
I still need to do:
- test graphic creation and export
- improve generation of latex headers
- automate processing from .Rorg to .tex (or .pdf) (currently at least 3
steps, should be 1)
- come up with suggested keybindings for inserting the #+BEGIN/END_R
blocks
- create a driver to generate HTML instead of \LaTeX
Still, it is in a works-for-me state at the moment, and I could send a
pull request to Carsten or could push it worg if folks were interested.
Let me know,
/au
--
Austin Frank
http://aufrank.net
GPG Public Key (D7398C2F): http://aufrank.net/personal.asc
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Emacs-orgmode mailing list
Remember: use `Reply All' to send replies to the list.
Emacs-orgmode@gnu.org
http://lists.gnu.org/mailman/listinfo/emacs-orgmode
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Re: Org-mode and ESS
2008-11-12 19:42 ` Austin Frank
@ 2008-11-12 19:51 ` Graham Smith
2008-11-12 20:45 ` Detlef Steuer
2008-11-13 3:22 ` Eric Schulte
2 siblings, 0 replies; 10+ messages in thread
From: Graham Smith @ 2008-11-12 19:51 UTC (permalink / raw)
To: Austin Frank; +Cc: emacs-orgmode
Austin
> In my local git repo of the org sources I have a pretty nice setup for
> using R or S inside org-mode.
I did see the original posts on this, and was interested in what you
were doing, but its a bit beyond me at the moment while I am still
trying to grasp how Emacs/org works.
At the moment, as you surmised I am just looking to add a bit of
structure to the notes I make while working on an analysis. But I may
well come back to what you are doing, as I become more comfortable
with Emacs.
Thanks,
Graham
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Org-mode and ESS
2008-11-12 19:42 ` Austin Frank
2008-11-12 19:51 ` Graham Smith
@ 2008-11-12 20:45 ` Detlef Steuer
2008-11-13 3:22 ` Eric Schulte
2 siblings, 0 replies; 10+ messages in thread
From: Detlef Steuer @ 2008-11-12 20:45 UTC (permalink / raw)
To: emacs-orgmode
This looks just quite cool.
:-)
I am certainly interested, just starting to prepare a lecture I'll
have to give next term and looking for right tool.
So, where to grab it? It would be great to collaborate on this, but I fear
my emacs skills are _very_ limited. (My only excuse: I converted from VIM to
emacs after 15 years ... ESS and org made the difference!)
detlef
On Wed, 12 Nov 2008 14:42:24 -0500
Austin Frank <austin.frank@gmail.com> wrote:
> On Tue, Nov 11 2008, Graham Smith wrote:
>
> > Is any one using Org-mode with ESS. ESS seems to need a file with a
> > *.R name to work, but it would be really useful to use Org-mode
> > features to keep notes of comments and code, before sending to R, and
> > of course to copy results back into an Org-Mode file from R.
> >
> > As a search here and a google hasn't thrown up anything obvious, I
> > assume not, but I thought I would ask.
>
> In my local git repo of the org sources I have a pretty nice setup for
> using R or S inside org-mode. I liked the in-file native editing of
> source code so much that I decided that I wanted to use org files as
> source files with Sweave (instead of using .Rtex or .Rnw files). My
> goal was to export documents with embedded R code, rather than to use
> org within the comments of R files. I can certainly see a use for the
> latter approach (which seems to be what you have in mind), as well.
>
> There was recently a thread where someone created a preprocessing system
> for specific types of blocks. That would be another possible strategy
> for evaluating blocks of R code before export. Since that facility
> didn't exist yet and there was already the extensible Sweave
> pre-processor, I took the route of making Sweave org-aware.
>
>
> Basically, in the workflow I've developed, I create a file with the
> extension .Rorg, say homework_key.Rorg. Within that file, I can embed
> blocks of R code, and can refer to variables defined in the R code
> contained in the document.
>
> --8<---------------cut here---------------start------------->8---
> #+BEGIN_R
> a <- 3
> a
> #+END_R
>
> * the value of a is \R{a}
> * the value of a + 3 is \R{a + 3}
> --8<---------------cut here---------------end--------------->8---
>
> Executing C-c ' inside the block takes you into a temporary buffer
> that's in ESS mode, with full support for interactive evaluation.
>
>
> When I'm ready to export, I run the R command
>
> Sweave("homework_key.Rorg", driver=RweaveOrgLatex, syntax=SweaveSyntaxOrg).
>
> (I've defined those driver and syntax functions locally). This creates
> a new file, homework_key.org. In the new file, the above text would be
> translated into
>
> --8<---------------cut here---------------start------------->8---
> #+BEGIN_LATEX
> \begin{Schunk}
> \begin{Sinput}
> > a <- 3
> > a
> \end{Sinput}
> \begin{Soutput}
> [1] 3
> \end{Soutput}
> \end{Schunk}
> #+END_LATEX
>
> * the value of a is 3
> * the value of a + 3 is 6
> --8<---------------cut here---------------end--------------->8---
>
> The plain homework_key.org file could then be exported into \LaTeX. It
> even works with the new pdf export.
>
>
> I haven't put the code anywhere public because there are several things
> I still need to do:
>
> - test graphic creation and export
> - improve generation of latex headers
> - automate processing from .Rorg to .tex (or .pdf) (currently at least 3
> steps, should be 1)
> - come up with suggested keybindings for inserting the #+BEGIN/END_R
> blocks
> - create a driver to generate HTML instead of \LaTeX
>
> Still, it is in a works-for-me state at the moment, and I could send a
> pull request to Carsten or could push it worg if folks were interested.
>
> Let me know,
> /au
>
>
> --
> Austin Frank
> http://aufrank.net
> GPG Public Key (D7398C2F): http://aufrank.net/personal.asc
>
--
Wisely, and slow. They stumble that run fast. - Shakespeare
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Re: Org-mode and ESS
2008-11-12 19:42 ` Austin Frank
2008-11-12 19:51 ` Graham Smith
2008-11-12 20:45 ` Detlef Steuer
@ 2008-11-13 3:22 ` Eric Schulte
2008-11-13 5:40 ` Austin Frank
2 siblings, 1 reply; 10+ messages in thread
From: Eric Schulte @ 2008-11-13 3:22 UTC (permalink / raw)
To: Austin Frank; +Cc: emacs-orgmode
Austin Frank <austin.frank@gmail.com> writes:
> On Tue, Nov 11 2008, Graham Smith wrote:
>
>> Is any one using Org-mode with ESS. ESS seems to need a file with a
>> *.R name to work, but it would be really useful to use Org-mode
>> features to keep notes of comments and code, before sending to R, and
>> of course to copy results back into an Org-Mode file from R.
>>
>> As a search here and a google hasn't thrown up anything obvious, I
>> assume not, but I thought I would ask.
>
> In my local git repo of the org sources I have a pretty nice setup for
> using R or S inside org-mode. I liked the in-file native editing of
> source code so much that I decided that I wanted to use org files as
> source files with Sweave (instead of using .Rtex or .Rnw files). My
> goal was to export documents with embedded R code, rather than to use
> org within the comments of R files. I can certainly see a use for the
> latter approach (which seems to be what you have in mind), as well.
>
> There was recently a thread where someone created a preprocessing system
> for specific types of blocks.
Hi Austin,
I would be interested to help extend the block prepreocessing system to
handle cases like the one you mention here.
>
> Basically, in the workflow I've developed, I create a file with the
> extension .Rorg, say homework_key.Rorg. Within that file, I can embed
> blocks of R code, and can refer to variables defined in the R code
> contained in the document.
>
> #+BEGIN_R
> a <- 3
> a
> #+END_R
>
> * the value of a is \R{a}
> * the value of a + 3 is \R{a + 3}
>
In the above example how would you/Sweave handle the case where there
are multiple R blocks in the same file? For example
#+BEGIN_R
a <- 3
a
#+END_R
- the value of a is \R{a}
- the value of a + 3 is \R{a + 3}
#+BEGIN_R
a <- 8
a
#+END_R
- the value of a is \R{a}
- the value of a + 3 is \R{a + 3}
With that questions answered it should be relatively straightforward to
implement exporting as you described using only org-mode's block
processing, and letting ESS do the actual calculations all without any
dependence on Sweave.
> I haven't put the code anywhere public because there are several things
> I still need to do:
>
> - test graphic creation and export
if you have examples of graphic creation, I'd be interested to see how
they work, and relatedly how difficult it would be to move that
functionality into org-mode.
However I think the rest of the point you make immediately below would
be easily addressed through using an org-mode only approach.
> - improve generation of latex headers
> - automate processing from .Rorg to .tex (or .pdf) (currently at least 3
> steps, should be 1)
> - come up with suggested keybindings for inserting the #+BEGIN/END_R
> blocks
If you happen to use yasnippets, I find it makes the creation of blocks
in org files a very quick/easy experience. See
http://legito.net/worg/org-configs/index.php#sec-2.1 for details.
>
> - create a driver to generate HTML instead of \LaTeX
>
Cheers -- Eric
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Org-mode and ESS
2008-11-13 3:22 ` Eric Schulte
@ 2008-11-13 5:40 ` Austin Frank
2008-11-14 1:22 ` Eric Schulte
0 siblings, 1 reply; 10+ messages in thread
From: Austin Frank @ 2008-11-13 5:40 UTC (permalink / raw)
To: Eric Schulte; +Cc: emacs-orgmode
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On Wed, Nov 12 2008, Eric Schulte wrote:
> In the above example how would you/Sweave handle the case where there
> are multiple R blocks in the same file? For example
Sweave puts all variables defined in a document into the same
environment. So assigning to a twice overwrites the first assignment.
,----[ tmp2.Rorg ]
| #+BEGIN_R
| a <- 3
| a
| #+END_R
|
| - the value of a is \R{a}
| - the value of a + 3 is \R{a + 3}
|
| #+BEGIN_R
| a <- 8
| a
| #+END_R
|
| - the value of a is \R{a}
| - the value of a + 3 is \R{a + 3}
`----
,----[ tmp2.org ]
| #+BEGIN_LaTeX
| \begin{Schunk}
| \begin{Sinput}
| > a <- 3
| > a
| \end{Sinput}
| \begin{Soutput}
| [1] 3
| \end{Soutput}
| \end{Schunk}
| #+END_LaTeX
|
| - the value of a is 3
| - the value of a + 3 is 6
|
| #+BEGIN_LaTeX
| \begin{Schunk}
| \begin{Sinput}
| > a <- 8
| > a
| \end{Sinput}
| \begin{Soutput}
| [1] 8
| \end{Soutput}
| \end{Schunk}
| #+END_LaTeX
|
| - the value of a is 8
| - the value of a + 3 is 11
`----
> With that questions answered it should be relatively straightforward
> to implement exporting as you described using only org-mode's block
> processing, and letting ESS do the actual calculations all without any
> dependence on Sweave.
There is a Sweave.sty that handles formatting of the Schunk, Sinput, and
Soutput environments. While you may not need to depend on Sweave for
the preprocessing step, it would be nice if the formatted document at
least had the option of having the same appearance as Sweave-processed
files. Still, I suppose I could just add a #+LATEX_HEADER line for
these files.
> if you have examples of graphic creation, I'd be interested to see how
> they work, and relatedly how difficult it would be to move that
> functionality into org-mode.
OK, here comes the first attempt. The additional feature demonstrated
in this example is the inclusion of options to the Sweave preprocessor
at the beginning of the block. In this case I've specified fig=TRUE to
tell the preprocessor to generate image files for the plot commands
contained in the block. By default, Sweave creates a .eps and a .pdf
file for each block that contains a plotting or printing command and has
the fig=TRUE argument, and then inserts an \includegraphics{} command in
the output file.
,----[ tmp3.Rorg ]
| * first figure
| #+BEGIN_R fig=TRUE
| x <- rnorm(100)
| y <- rnorm(100)
|
| plot(x,y)
| #+END_R
`----
,----[ tmp3.org ]
| * first figure
| #+BEGIN_LaTeX
| \begin{Schunk}
| \begin{Sinput}
| > x <- rnorm(100)
| > y <- rnorm(100)
| > plot(x, y)
| \end{Sinput}
| \end{Schunk}
| #+END_LaTeX
| #+LaTeX: \includegraphics{tmp3-001}
`----
,----[ tmp3.tex ]
| % Created 2008-11-12 Wed 23:46
| \documentclass[11pt,a4paper]{article}
| \usepackage[utf8]{inputenc}
| \usepackage[T1]{fontenc}
| \usepackage{graphicx}
| \usepackage{hyperref}
| \usepackage{Sweave}
|
| \title{tmp3}
| \author{Austin Frank}
| \date{12 November 2008}
|
| \begin{document}
|
| \maketitle
|
|
| \section*{first figure}
| \label{sec-1}
|
| \begin{Schunk}
| \begin{Sinput}
| > x <- rnorm(100)
| > y <- rnorm(100)
| > plot(x, y)
| \end{Sinput}
| \end{Schunk}
| \includegraphics{tmp3-001}
|
| \end{document}
`----
And the pdf is attached.
[-- Attachment #1.1.2: tmp3.pdf --]
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I haven't looked into it too closely, but I would guess that when
fig=TRUE is specified, first the R block is run, and then the additional
R commands
dev.copy2eps()
dev.copy2pdf()
are run. This results in the creation of eps and pdf files based on the
last thing plotted. The functions could each take a file="foo" argument
(the filename defaults to Rplots.[eps|pdf]). Sweave uses automatically
incremented names for its generated graphics files. If your block
system could have an after-block hook, you could evaluate the original
block, then the appropriate dev.copy function, and then add an
additional line to the exported file for inclusion of the graphics file.
> However I think the rest of the point you make immediately below would
> be easily addressed through using an org-mode only approach.
Exciting! If you're interested in what other options the Sweave
preprocessor contains, the manual can be found at
http://www.stat.auckland.ac.nz/~dscott/782/Sweave-manual-20060104.pdf.
Sweave also has a processing option called "tangle". This extracts all
of the R code from a document and puts into its own file. This would be
a useful feature in a generic block exporter as well, I would think.
Take all of the blocks of a certain type and dump the content into a
file with the appropriate extension for whatever the major mode was for
that block.
Finally , a couple of systems for caching Sweave output have sprung up.
I think these use the strategy of hashing the content of each block,
saving the output of each block, and only re-running the block if the
content has changed. A general-purpose option like this for the block
exporting system in org could be very nice to have. It's possible that
the attachment system with git integration already gets us very close to
a working version of this.
The more I think about this last possibility, the more potential I think
it has. With the caching turned on, at export time you create files
containing the contents of each block to be cached, one file per block.
You create a second set of files that has the results of block export,
again one file per block. You add the directory of block files and
results using org-attach. On the next export, block files are generated
again. You use git to ask which ones have changed. For those that have
changed, you go on to do the normal block export, saving the results
again. Finally, you pull the results files back into the original
document in the right places. It would be neat if something like this
could work.
> If you happen to use yasnippets, I find it makes the creation of
> blocks in org files a very quick/easy experience. See
> http://legito.net/worg/org-configs/index.php#sec-2.1 for details.
I'll check it out, thanks. Sorry to ramble, hope this was useful!
Looking forward to seeing what you come up with!
/au
--
Austin Frank
http://aufrank.net
GPG Public Key (D7398C2F): http://aufrank.net/personal.asc
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Emacs-orgmode mailing list
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^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Org-mode and ESS
2008-11-13 5:40 ` Austin Frank
@ 2008-11-14 1:22 ` Eric Schulte
2008-11-16 1:50 ` Eric Schulte
0 siblings, 1 reply; 10+ messages in thread
From: Eric Schulte @ 2008-11-14 1:22 UTC (permalink / raw)
To: Austin Frank; +Cc: emacs-orgmode
Austin Frank <austin.frank@gmail.com> writes:
> On Wed, Nov 12 2008, Eric Schulte wrote:
>
>
> I'll check it out, thanks. Sorry to ramble, hope this was useful!
>
Not at all, this is all very interesting. I've never used Sweave, but I
have been using org-mode for "reproducible research" type functionality
on some of my projects at work, and this is right up my alley.
>
> Looking forward to seeing what you come up with!
Me too :) Hopefully I will continue to be able to put time into this. I
hope you don't mind, I've populated my TODO files with much of the text
from your last email. I'm keeping my development mirrored on github at
http://github.com/eschulte/org-contrib/tree/master
and as usual, I will be sure to post to the list if anything really good
emerges.
Thanks -- Eric
>
> /au
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: Org-mode and ESS
2008-11-14 1:22 ` Eric Schulte
@ 2008-11-16 1:50 ` Eric Schulte
0 siblings, 0 replies; 10+ messages in thread
From: Eric Schulte @ 2008-11-16 1:50 UTC (permalink / raw)
To: Austin Frank; +Cc: emacs-orgmode
"Eric Schulte" <schulte.eric@gmail.com> writes:
> Austin Frank <austin.frank@gmail.com> writes:
>
>> Looking forward to seeing what you come up with!
>
> Me too :) Hopefully I will continue to be able to put time into this. I
> hope you don't mind, I've populated my TODO files with much of the text
> from your last email. I'm keeping my development mirrored on github at
>
> http://github.com/eschulte/org-contrib/tree/master
>
> and as usual, I will be sure to post to the list if anything really good
> emerges.
>
Just to update. The basic Sweave type processing of R blocks and \R{}
chunks is now working for both html and latex exporting. Please take a
look and let me know if there are parts which aren't working as
expected.
I haven't started looking at the image creation yet.
Cheers -- Eric
^ permalink raw reply [flat|nested] 10+ messages in thread
end of thread, other threads:[~2008-11-16 1:50 UTC | newest]
Thread overview: 10+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2008-11-11 18:00 Org-mode and ESS Graham Smith
2008-11-11 18:30 ` Detlef Steuer
2008-11-11 19:13 ` Graham Smith
2008-11-12 19:42 ` Austin Frank
2008-11-12 19:51 ` Graham Smith
2008-11-12 20:45 ` Detlef Steuer
2008-11-13 3:22 ` Eric Schulte
2008-11-13 5:40 ` Austin Frank
2008-11-14 1:22 ` Eric Schulte
2008-11-16 1:50 ` Eric Schulte
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