From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rainer M Krug Subject: Re: [babel] Writing R-packages the org way? Date: Thu, 7 Oct 2010 18:18:26 +0200 Message-ID: References: <4CADD83B.4000602@ccbr.umn.edu> <8762xeniy6.fsf@stats.ox.ac.uk> <4CADE357.1090803@ccbr.umn.edu> <87y6aam1sq.fsf@stats.ox.ac.uk> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="===============2060406746==" Return-path: Received: from [140.186.70.92] (port=41676 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1P3tAs-0004qi-KB for emacs-orgmode@gnu.org; Thu, 07 Oct 2010 12:18:32 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1P3tAq-0007lL-TA for emacs-orgmode@gnu.org; Thu, 07 Oct 2010 12:18:30 -0400 Received: from mail-qy0-f169.google.com ([209.85.216.169]:40076) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1P3tAq-0007lC-Q0 for emacs-orgmode@gnu.org; Thu, 07 Oct 2010 12:18:28 -0400 Received: by qyk31 with SMTP id 31so30797qyk.0 for ; Thu, 07 Oct 2010 09:18:28 -0700 (PDT) In-Reply-To: <87y6aam1sq.fsf@stats.ox.ac.uk> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Dan Davison Cc: emacs-orgmode --===============2060406746== Content-Type: multipart/alternative; boundary=00163630f1d1738e800492093e99 --00163630f1d1738e800492093e99 Content-Type: text/plain; charset=ISO-8859-1 On Thu, Oct 7, 2010 at 5:59 PM, Dan Davison wrote: > Erik Iverson writes: > > > Dan Davison wrote: > >> Erik Iverson writes: > >> > >>> Rainer M Krug wrote: > >>>> Hi > >>>> > >>>> I am about to write an R package, and as I am an org-mode and > >>>> org-babel user, I would (obviously) like to use org-mode for that. > >>>> > >>>> Is there a recommended way of writing an R package in org-babel, or > >>>> do I have effectively wrap the R code for the documentation > >>>> etc. into source blocks in babel? > >>> That's what I do. I've looked into converting an org-file to > >>> Roxygen or Rd markup, but never got very far. My idea at the time > >>> was to do something like: > >>> > >>> * function1 > >>> ** Help > >>> *** Title > >>> this is function 1 title > >>> *** Description > >>> function1 does this... > >>> *** Usage > >>> function1(arg1, arg2, ...) > >>> *** Arguments > >>> arg1: the first argument > >>> *** Examples > >>> function1(arg1 = x, arg2 = y) > >>> **Definition > >>> begin_src R :tangle R/package.R > >>> function1 <- function(arg1, arg2) { > >>> > >>> } > >>> > >>> > >>>> 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. > >> > >> 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, > > Yes perfectly, thanks. I had only thought of the solution you mention > involving writing Rd explicitly; I hadn't thought of Rd as an export > target. > I would not say that an Rd export target would be the solution, as only parts of the document have to exported to .Rd format, and others (the code) has to be tangled --- well, I guess one could do it in a two step process: first exporting to .Rd based on the headers, and then tangling the code blocks (which were not exported) into the same structure. > > Well, anyone who wants to put Bastien's new export machinery to the > test, I'll have a texinfo and an Rd backend please. > Agreed. > > :) > > Dan > > > Erik > Dan > > _______________________________________________ > > Emacs-orgmode mailing list > > Please use `Reply All' to send replies to the list. > > Emacs-orgmode@gnu.org > > http://lists.gnu.org/mailman/listinfo/emacs-orgmode > -- NEW GERMAN FAX NUMBER!!! Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax: +27 - (0)86 516 2782 Fax: +49 - (0)321 2125 2244 email: Rainer@krugs.de Skype: RMkrug Google: R.M.Krug@gmail.com --00163630f1d1738e800492093e99 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

On Thu, Oct 7, 2010 at 5:59 PM, Dan Davi= son <davison= @stats.ox.ac.uk> wrote:
Erik Iverson <eriki@ccbr.umn.edu> writes:

> Dan Davison wrote:
>> Erik Iverson <eriki@ccbr.= umn.edu> writes:
>>
>>> Rainer M Krug wrote:
>>>> Hi
>>>>
>>>> I am about to write an R package, and as I am an org-mode = and
>>>> org-babel user, I would (obviously) like to use org-mode f= or that.
>>>>
>>>> Is there a recommended way of writing an R package in org-= babel, or
>>>> do I have effectively wrap the R code for the documentatio= n
>>>> etc. into source blocks in babel?
>>> That's what I do. =A0I've looked into converting an or= g-file to
>>> Roxygen or Rd markup, but never got very far. =A0My idea at th= e time
>>> was to do something like:
>>>
>>> * function1
>>> ** Help
>>> *** Title
>>> =A0 =A0 this is function 1 title
>>> *** Description
>>> =A0 =A0 function1 does this...
>>> *** Usage
>>> =A0 =A0 function1(arg1, arg2, ...)
>>> *** Arguments
>>> =A0 =A0 arg1: the first argument
>>> *** Examples
>>> =A0 =A0 function1(arg1 =3D x, arg2 =3D y)
>>> **Definition
>>> =A0 =A0 begin_src R :tangle R/package.R
>>> =A0 =A0 function1 <- function(arg1, arg2) {
>>>
>>> =A0 =A0 }
>>>
>>>
>>>> Any suggestions how to best proceed?
>>>>
>>>> Dream: I would like to have one org file which contains ev= erything
>>>> (documentation, code, other relevant files) and if I expor= t or
>>>> tangle the file, I have the package ready.
>>> Well, that functionality is essentially present with code bloc= ks
>>> and tangling, except the documentation part.
>>
>> 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 generat= ing
> .Rd files (the LaTeX-like syntax) automatically from some org-syntax > that does *not* depend on code blocks. =A0I.e., it would be cool to > specify syntax like I have above for documentation. =A0Using org-mode<= br> > 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. =A0No big= deal,
> just a convenience feature. =A0I 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. =A0That's what I currently = do.
>
> Hope that explains it,

Yes perfectly, thanks. I had only thought of the solution you m= ention
involving writing Rd explicitly; I hadn't thought of Rd as an export target.

I would not say that an Rd expo= rt target would be the solution, as only parts of the document have to expo= rted to .Rd format, and others (the code) has to be tangled --- well, I gue= ss one could do it in a two step process: first exporting to .Rd based on t= he headers, and then tangling the code blocks (which were not exported) int= o the same structure.
=A0

Well, anyone who wants to put Bastien's new export machinery to the
test, I'll have a texinfo and an Rd backend please.

Agreed.
=A0

:)

Dan

> Erik > Dan
> ____________________________________= ___________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode



--
NEW GERMAN = FAX NUMBER!!!

Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (= Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellen= ce for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch UniversityMain Campus, Merriman Avenue
Stellenbosch
South Africa

Cell:= =A0 =A0 =A0 =A0 =A0=A0 +27 - (0)83 9479 042
Fax:=A0 =A0 =A0 =A0 =A0 =A0 = +27 - (0)86 516 2782
Fax:=A0 =A0 =A0 =A0 =A0 =A0 +49 - (0)321 2125 2244
email:=A0 =A0 =A0 =A0= =A0 Rainer@krugs.de

Skype:= =A0 =A0 =A0 =A0 =A0 RMkrug
Google:=A0 =A0 =A0 =A0=A0 R.M.Krug@gmail.com

--00163630f1d1738e800492093e99-- --===============2060406746== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode --===============2060406746==--