Bug#721801: [devteam-bioc] Precomputed results in GenomicRanges [Was: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED]
Hi Martin,
On Wed, Oct 16, 2013 at 06:02:03AM -0700, Martin Morgan wrote:
>
> For precomputed_results above, it looks like these could be
> generated by a script, but the specific results depend on a web
> service query and the web service changes from time to time. So the
> script will become out-of-date, creating data that are no longer
> consistent with the illustrative puruposes of the vignette. Also,
> the time cost of generating data is not consistent with our
> (nightly) build process; we will not generate this data on the fly,
> and it would be a mistake for your release process to generate data
> different from the data used in our release.
Defintely. The only thing our ftpmaster needs is this kind of
explanation (hopefully).
> These (expense of
> computation, consistency of external data sources) are typical
> reasons.
>
> When the 'affy' maintainer recieves one of these emails, and the
> email mentions three data sets, and the three data sets are
> documented in the man page as data sets from an experiment (e.g.,
> ?SpikeIn), what is one supposed to do?
Sorry, I just missed this part of the documentation, my fault.
> Or rather, why is he being
> contacted in the first place?
That's simple: He is listed on the affy homepage
http://bioconductor.org/packages/release/bioc/html/affy.html
as maintainer and this is what I take over into the according Debian
package metainformation field (in debian/copyright). I have to admit
that I'm personally totally unconnected to BioConductor and have only a
very rough understanding of R. The problem is that in the Debian Med
team some people started to package some BioConductor modules and these
people now vanished from the team or are overworked. My goal is to
keep on their work for our users and namely cummerbund needs some
update with several new preconditions. So I tried to dive into
BioConductor internals and I'm very sorry if I did not yet found all
details how this project is organised
In short: Should I generally override the contact e-mail for
any BioConductor part by
Upstream-Contact: BioConductor Maintainer <maintainer@bioconductor.org>
independently what might be written on the according homepage?
> From a non-technical perspective: (1) It's presumptuous to suggest
> that the data files are not important for user documentation; if
> they where not important why would the author have gone to the
> trouble to include them in the first place?
It seems BioConductor is quite good organised but trust me in my 15
years experience of Debian package building that I found lots of files
in upstream sources which are not (any more) needed or not important
enough to keep them inside while an online download would be perfectly
sufficient. Just guessing from this experience I was just suggesting a
possible solution. I hoped to get some helping point for the decision
which was obviously not the case.
> (2) If you are going to
> contact our maintainers, then please let me know about the extent of
> the contact and the intention; I would rather have a discussion on
> our developer mailing list than have each maintainer wondering how
> to react.
I'll respect this in the future. The intention is simply letting the
package pass ftpmasters criterion - the extent of the contact is hardly
to estimate in advance.
Thanks again for your patience
Andreas.
--
http://fam-tille.de
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