[Bioc-devel] BiocInstaller: next generation
@neum@nn @ending from ipb-h@lle@de
Fri May 18 09:28:48 CEST 2018
On Wed, 2018-05-09 at 18:11 -0400, Martin Morgan wrote:
> - version() version of Bioconductor in use
> - valid() are all Bioconductor packages from the same
I'd like to challenge the concept of the release
and the pretty strong term valid(). I think BioC
is the only R package repository that has the release concept,
and this is good to have a consistent well tested environment
of packages for a given R version. It is also great to pick
the most recent package version within a release for installation,
but that also prevents installing a package newer than
the one tied to the R version at hand.
But R already has the concept of versioned dependencies,
so in theory we wouldn't /need/ the release concept.
I'd like to suggest to make it easier to shoot yourself
into the foot by installing less tested combinations
of R and BioC packages, and to support installing
i.e. a package from a given BioC release, or a specific version
of a package, regardless from which release it comes.
The valid() is a bit unspecific name, what is probably meant here
is BiocManager::tainted(), which indicates that packages come
from different BioC versions, and all hell might break loose
and it'll eat your kittens.
This also means that Package developers would ask for the tainted()
status in bug reports, and (c|sh)ould refuse help for unsupported
combination. It also means that packagers would have to be more careful
with the versioned dependencies, and supply minimal versions.
If they give a versioned dependency on the Biobase,
they essentially forbid installing on old BioC releases,
which would be fine.
Just my 2c,
IPB Halle AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann http://www.IPB-Halle.DE
Weinberg 3 http://msbi.bic-gh.de
06120 Halle Tel. +49 (0) 345 5582 - 1470
+49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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