[Bioc-devel] Moving minfi classes definition to a lighter package

Kasper Daniel Hansen k@@perd@n|e|h@n@en @end|ng |rom gm@||@com
Wed Mar 3 13:28:34 CET 2021

I am happy to engage in a discussion about this, although I'm not sure that
I am ultimately interested in having two packages.

But first I would like to look at some dependency graphs. I am wondering
what makes the dependency tree this big (and my tree is smaller than yours,
but still big: library(minfi) gives me 16 attached packages and 89 loaded
packages for the current release). This includes some part of the tidyverse
which we don't really use much though (and which could probably get removed
from the package with almost no work).

What's the current best tool for dependency graphs in Bioconductor?


On Mon, Mar 1, 2021 at 6:24 PM Carlos Ruiz <carlos.ruiz using isglobal.org> wrote:

> Dear Bioc developers,
> I have been developing different packages to analyze DNA methylation. In
> all of them, I have used minfi's class GenomicRatioSet to manage DNA
> methylation data, in order to take profit of the features of
> RangedSummarizedExperiment.
> Although I am very happy with the potential of the class, importing its
> definition from minfi, makes me add the package to imports. As minfi has a
> high number of dependencies (129 in the current release), my packages end
> up having hundreds of dependencies too. This is particularly problematic as
> I do not use any of the other functions of minfi.
> I am wondering whether it could be possible to move minfi's class (or at
> least GenomicRatioSet) to a lighter package, so people developing packages
> on DNA methylation could rely on this class without having to import the
> whole minfi package and its dependencies.
> Thank you very much,
> --
> Carlos Ruiz
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