Re: [R] R package building

From: Spencer Graves <spencer.graves_at_pdf.com>
Date: Sat, 17 May 2008 07:26:15 -0700

      My experience with building R packages has been extremely positive. I've been using computers since I started writing Fortran in 1963. Before I started building R packages, debugging require excessive amounts of time. Now, I write help file(s) first, including good test cases in the Examples section. Examples that are more than I want to show readers go in a "dontshow" subsection. After each change in a package, I rebuild the package. This way, if a change to function D breaks something in function A, I find out quickly -- unless I failed to test something important in Examples.

      Currently, I write code for both Matlab and R. I know of no such system for Matlab, and it is a problem for me. I've tried testing Matlab from within Examples in an R help file, but I have not yet made that work.

      Hope this helps. 
      Spencer Graves

Jay Emerson wrote:
> I agree with others that the packaging system is generally easy to
> use, and between the "Writing R Extensions" documentation and other
> scattered sources (including these lists) there shouldn't be many
> obstacles. Using "package.skeleton()" is a great way to get started:
> I'd recommend just having one data object and one new function in the
> session for starters. You can build up from there.
>
> I've only ran into time-consuming walls on more advanced, obscure
> issues. For example: the "Suggests:" field in DESCRIPTION generated
> quite some debate back in 2005, but until I found that thread in the
> email lists I didn't understand the issue. For completeness, I'll
> round out this discussion, hoping I'm correct. In essence, I think
> the choice of the word "Suggests:" was intended for the package user,
> not for the developer. The user isn't required to have a suggested
> package in order to load and use the desired package. But the
> developer is required (in the R CMD check) to have the suggested
> package in order to avoid warnings or fails. This does, actually,
> make sense, because we assume a developer would want/need to check
> features that involve the suggested package. In a few isolated cases
> (I think I had one of them), this caused a problem, where a desired
> suggested package isn't distributed by CRAN on all platforms, so I
> would risk getting into trouble with R CMD check on the platform
> without the suggested package. But this is pretty obscure, and the
> issue was obviously well-debated in the past. The addition of a line
> or two about this in "Writing R Extensions" would be friendly (the
> current content is correct and minimal sufficient I believe). Maybe I
> should draft this and submit it to the group.
>
> Secondly, I would advice a newbie to the packaging system to avoid S4
> at first. Ultimately, I think it's pretty cool. But, for example,
> documentation on proper documentation (to handle the man pages
> correctly) has puzzled me, and even though I can create a package with
> S4 that passes R CMD check cleanly, I'm not convinced I've got it
> quite right. If someone has recently created more documentation or a
> 'white pages' on this, please do spread the word.
>
> Thanks to all who have -- and continue -- to work on the system!
>
> Jay
>
>
>> Subject: [R] R package building
>>
>> In a few days I'll give a talk on R package development and my
>> personal experience, at the 3rd Free / Libre / Open Source Software
>> (FLOSS) Conference which will take place on May 27th & 28th 2008, in
>> the National Technical University of Athens, in Greece.
>>
>> I would appreciate if you could share
>> your thoughts with me; What are today's obstacles on R package
>> building, according to your
>> opinion and personal experience.
>>
>> Thanks,
>> --
>> Angelos I. Markos
>> Scientific Associate, Dpt of Exact Sciences, TEI of Thessaloniki, GR
>> "I'm not an outlier; I just haven't found my distribution yet"
>>
>
>
>
>



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