[Bioc-devel] BiocInstaller: next generation

Neumann, Steffen @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
> Bioconductor 
> version?

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

	BiocManager::install(X, version=0.8.15)
	BiocManager::install(X, release=3.8)
	BiocManager::install(X, release=devel) 

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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