[Debian-med-packaging] Binary (rda) files in source tarball of BioC graph

[Andreas Tille]

[Put ftpmaster in CC]
Hi Martin,

thanks for your quick and helpful response.

On Thu, Aug 29, 2013 at 01:19:52PM -0700, Martin Morgan wrote:
> Hi Andreas --
> 
> On 08/29/2013 05:42 AM, Maintainer wrote:
> >Hello,
> >
> >I'm writing you on behalf of the Debian Med team that tries to package
> >software for biologists and medical care straight into Debian and thus
> >BioConductor is one of our targets.  While we just have some
> >BioConductor modules included we need several more and I'm now busy
> >packaging graph[1].  I noticed that inside the data/ dir some *.rda
> >files are stored.  Recently on the Debian list some
> >flamew^Wdiscussion[2] happened whether we should regard this as
> >acceptable as "human editable source" or just chunks of binary code
> >without source.
> 
> >You as R experts might have some opinion on it and I will not question
> >this.  However, it would make the process of integration into Debian way
> >more smooth if you could deliver some ASCII representation of these data
> >as well as some recipe to create the according *.rda files.  I admit I'm
> >not very educated in R - I just was told this is possible and easy but
> >my personal R knowledge is just about the fact that it is pretty easy to
> >create Debian packages and so I'm doing this - sorry for my ignorance.
> 
> The serialized R objects can be input and manipulated in R by
> humans, I guess in the same way that png files are read by image
> viewers.
> 
> In general, data objects in Bioconductor packages are complicated --
> not simple tables, but highly coordinated data structures. They have
> diverse origins, and the binary representation offers benefits to
> users and to our build and distribution channels; many are used to
> test or illustrate (in vignettes or man page examples) package
> functionality. It's not logistically feasible for us to provide
> ASCII representations of these objects.
> 
> It's not escaped our notice that binary files are not a good engineering solution!
> 
> I hope that provides some context,

Yes, it does.  Thanks for the hint.  I tried to document this issue on a
newly created Wiki page

   https://wiki.debian.org/GNU_R

which hopefully might be helpful for future R packagers.

Ftpmasters, if you need some further information / clarification I
should put on the Wiki page, please let me know.

Kind regards and thanks again for your insight

    Andreas.

> Martin
> 
> >So if you would be able to do us a favour and provide something our
> >ftpmaster could regard as "human editable source" this would really help
> >our effort to bring BioConductor straight into Debian.
> >
> >Kind regards and thanks for providing the free BioConductor suite
> >
> >       Andreas.
> >
> >[1] http://bioconductor.org/packages/2.12/bioc/html/graph.html
> >[2] https://lists.debian.org/debian-devel/2013/08/msg00069.html


-- 
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