[Bioc-devel] Short URLs for packages?

Fischer, Bernd b.fischer at dkfz-heidelberg.de
Tue Mar 24 17:15:03 CET 2015

I just think there are a couple of subtleties here. I certainly don't
begrudge people wanting to type less and find packages easier. But if a
naive user with a default (read: release) Bioc installation goes to
http://bioconductor.org/CoolAwesomePkg and see's that it is "available in
bioconductor" but then can't install it because it is only in devel, are
they going to be less confused, or more? I don't know the answer to that,
but I think it's something to consider.

We have (and already had many times) exactly this problem.
A paper is published and refers to a new BioC-package. The naive user
is not able to find the package. We want to show the naive user that this package
is indeed part of bioconductor and point him/her to a way to install the package.

The devel-webpage makes a clear statement on top saying
“This is the development version of BiocGenerics; for the stable release version, see MyPackage.”
If this is not prominent enough, one can highlight this with yellow color.

Also, as I have said elsewhere, though I acknowledge that you seem to
disagree, I think such urls are substantially less appropriate for
credit/citation in publications. A link that brought users to the version
in question, but which - if not current - had a prominent link to the
current version would be better imho.

This discussion is off-topic. The versioning system of Bioconductor provides
a sufficient way to cite the right version of the packages to ensure reproducible
research. We (try to) do this in the papers as well. We do not request that short
URLs should replace the correct citation of package versions.

Here, we ask for a stable, short URL that links to the most current, stable version
of the package (which is in devel for the time between acceptance and first
release of the package). Most users reading about a bioconductor package
want to install the current version of the package, that is best tested,with the
lowest number of bugs, installable on a current machine, with a current version
of R, … .
We want to put a stable URL into a paper, that does not need to be
changed anymore, when the BioC-package moves from devel to release. There
is no way to change the paper after publication.


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