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

[Paul Tagliamonte]

On Fri, Aug 30, 2013 at 11:09:42AM -0700, Hervé Pagès wrote:
> Hi,
> 
> A little bit of background: .rda files are created in R with the save()
> function. This function has an 'ascii' argument that is set to FALSE by
> default. AFAIK almost nobody uses 'ascii=TRUE' because there is no
> benefit in doing that (the .rda file will be bigger and will then take
> longer to load with load()). But from a content point-of-view, binary
> and ascii representations are equivalent. Furthermore, you can always

Does this hold if the R data saved is code (you can do this, yes?)

> switch from one representation to the other with no loss of information:
> just load the dataset with load() and re-save it with whatever value of
> 'ascii' you which (TRUE or FALSE).
> 
> One last note: the "ascii" representation is maybe a little bit more
> user-friendly than the "binary" one but not much. Maybe you'll be able
> to open it in an editor but it will probably still be a little bit too
> cryptic for people not familiar with the RDA format to be able to read
> and understand.

Again, this isn't the issue. Even if we had a CSV full of data, so long
as that data was *GENERATED*, it's no longer the prefered form of
modification, and not considered source.

Cheers,
  Paul

> 
> HTH,
> H.
> 
> 
> FWIW you can always convert a "binary" .rda
> 
> On 08/29/2013 02:05 PM, Maintainer wrote:
> >[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
> >
> >
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

-- 
 .''`.  Paul Tagliamonte <paultag at debian.org>
: :'  : Proud Debian Developer
`. `'`  4096R / 8F04 9AD8 2C92 066C 7352  D28A 7B58 5B30 807C 2A87
 `-     http://people.debian.org/~paultag
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 836 bytes
Desc: Digital signature
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20130830/43d306e0/attachment.sig>