[Orgmode] Re: [babel] Writing R-packages the org way?

On Fri, Oct 8, 2010 at 2:10 PM, Dan Davison <address@hidden> wrote:

Hi Chuck,

I agree about making use of existing ESS tools and that a more
traditional Org approach might be appropriate.

OK. But I think I have a solution for the "One package in a single org file" approach - see below

> If you do decide to go all in for a 'one org file makes one package'
> approach, you might try to get Rd language support added, so you can
> edit Rd directly in an Org Src buffer in Rd-mode.

No extra code is needed to get editing support for languages.

#+begin_src XXX

provides an edit buffer in XXX-mode automatically, with no special
customization. Also fontification in the org buffer works automatically
if `org-src-fontify-natively' is set.

Agreed - and that is the key to it.

If one is using the post-tangle-hook to compile / check the package, the fuinctiona;ity is together:

Example, the name of the org file will be used as the packagename:

------------BEGIN-----------------------

* Internal configurations :noexport:

** Post tangle script

#+begin_src sh :tangle postTangleScript.sh :var PACKAGENAME=(or (buffer-file-name) org-current-export-file)

R CMD CHECK $PACKAGENAME

#+end_src

** Evaluate to run post tangle script

#+begin_src emacs-lisp :results silent :tangle no :exports none

(add-hook 'org-babel-post-tangle-hook

(

lambda ()

(call-process-shell-command "./postTangleScript.sh" nil 0 nil)

)

#+end_src

* Package description

#+begin_src :tangle ./PACKAGENAME/DESCRIPTION

#+end_src

* Content of the package

** Function1

*** man

#+begin_src Rd :tangle ./PACKAGENAME/man/Function1.Rd

#+end_src

*** Code

#+begin_src R :tangle ./PACKAGENAME/R/Function1.R

#+end_src

*** Tests

#+begin_src R :tangle ./PACKAGENAME/tests/Function1Tests.R

#+end_src

The output from the test needs to be saved in ./PACKAGENAME/tests/Function1Tests.R - I still have to think about that.

** Function2

*** man

#+begin_src Rd :tangle ./PACKAGENAME/man/Function2.Rd

#+end_src

*** Code

#+begin_src R :tangle ./PACKAGENAME/R/Function2.R

#+end_src

*** Tests

#+begin_src R :tangle ./PACKAGENAME/tests/Function2Tests.R

#+end_src

The output from the test needs to be saved in ./PACKAGENAME/tests/Function2Tests.R - I still have to think about that.

** data

#+begin_src ...

#+end_src

This depends on the type of the data.

------------END-----------------------

This is untested so far, but I will try it out. The only thing which would be nice, would be to automate a few things.

Cheers,

Rainer

Dan

> And get
> org-babel-Rd-evaluate to run Rd-preview-help or call Rd2HTML or
> whatnot.
>
> HTH,
>
> Chuck
>
>> Then, to insert a template, you can use
>>
>> #+call: R-pkg-template(function_name="do.something") :results output org raw
>>
>> which should give something like this:
>>
>> --8<---------------cut here---------------start------------->8---
>> #+results: R-pkg-template(function_name="do.something")
>> * do.something
>> ** Help
>> *** Title
>> this is do.something title
>> *** Description
>> do.something does this...
>> *** Usage
>> do.something(arg1, arg2, ...)
>> *** Arguments
>> arg1: the first argument
>> *** Examples
>> do.something(arg1 = x, arg2 = y)
>> ** Definition
>> begin_src R :tangle R/package.R
>> do.something <- function(arg1, arg2) {
>>
>> }
>> --8<---------------cut here---------------end--------------->8---
>>
>> While playing about you may want to get rid of the "raw" directive so
>> that the results will automatically be replaced on repeated evaluations.
>>
>> Dan
>>
>>>
>>>
>>>
>>>>
>>>>>> Any suggestions how to best proceed?
>>>>>>>
>>>>>>> Dream: I would like to have one org file which contains everything
>>>>>>> (documentation, code, other relevant files) and if I export or
>>>>>>> tangle the file, I have the package ready.
>>>>>>>
>>>>>> Well, that functionality is essentially present with code blocks
>>>>>> and tangling, except the documentation part.
>>>>>>
>>>>>
>>> Exactly - and that is the part I would like to have.
>>>
>>>
>>>>
>>>>> Hi Erik,
>>>>>
>>>>> Would you mind expanding on that -- what are we missing for the
>>>>> documentation part?
>>>>>
>>>>>
>>>> Dan, by "except for the documentation part", I meant generating
>>>> .Rd files (the LaTeX-like syntax) automatically from some org-syntax
>>>> that does *not* depend on code blocks. I.e., it would be cool to
>>>> specify syntax like I have above for documentation. Using org-mode
>>>> headlines for each section like Description, Usage, Arguments, etc.
>>>>
>>>> Just like exporting to LaTeX generates sections, some process would
>>>> use these headlines to generate the .Rd sections.
>>>>
>>>> That way, you don't have to use the .Rd syntax yourself. No big deal,
>>>> just a convenience feature. I don't know how you'd specify to org-mode
>>>> that a particular subtree was to generate .Rd syntax, and I don't know
>>>> if it would be on export or tangling.
>>>>
>>>> An alternative is simply just to use code blocks of type Rd within
>>>> org-mode and then tangle to .Rd files. That's what I currently do.
>>>>
>>>> Hope that explains it,
>>>> Erik
>>>>
>>>>
>>>> Dan
>>>>>
>>>>
>>
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>
> Charles C. Berry (858) 534-2098
> Dept of Family/Preventive Medicine
> E mailto:address@hidden UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
>
>
>
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From:	Rainer M Krug
Subject:	[Orgmode] Re: [babel] Writing R-packages the org way?
Date:	Fri, 8 Oct 2010 17:35:20 +0200