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

[Paul Tagliamonte]

On Thu, Aug 29, 2013 at 11:05:47PM +0200, Andreas Tille wrote:
> > 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.

Erm, wat?

X is created by humans like Y is consumed by humans?

Also, this doesn't exactly hold, since Y may be created by Z (and often
is, in the case of SVG files), and renders Y a binary result of the
prefered form of modification.

This is Binaries 101, guys :)

The issue I brought up was *ensuring* that we *can* reproduce *all*
binaries. *I* would very much like to see such binaries rebuilt a
build-time, unless it's samped data from some sort instrument, or
actually created by hand lovingly.

> > In general, data objects in Bioconductor packages are complicated --
> > not simple tables, but highly coordinated data structures. They have

As are ELF files ;)

> > 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.

I don't understand this. Not feasible? Is this to say we don't have the
ability to rebuild this binary using the package data in main?

This is like saying "This PNG is from overlaying this 9 SVGs. Providing
the SVGs is too much work so we didn't do it"

> > It's not escaped our notice that binary files are not a good engineering solution!

I don't mind this (personally), I do mind the fact that we can't rebuild
these generated binaries.

> > 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

I would strongly encourage you to tell folks to treat them as we treat
any binary - rebuild it at build time from source, if it's come from
*any* sort of generated means.

> 
>     Andreas.

Cheers,
  Paul


-- 
 .''`.  Paul Tagliamonte <paultag at debian.org>
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