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

[Vincent Carey]

i advocated pkgnet and included a png but email seems to have been rejected


On Wed, Mar 3, 2021 at 7:29 AM Kasper Daniel Hansen <
kasperdanielhansen using gmail.com> wrote:

> 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?
> pkgDepTools?
>
> Best,
> Kasper
>
> 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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> --
> Best,
> Kasper
>
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