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

[Martin Morgan]

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,

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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