[Bioc-devel] name for new BioC package

[Kevin Coombes]

For the record, as a user, I  *hated* the move from MOFA to MOFA2. Not the
new package name, but the fact that they also Schanged all the function
names and argument names. Mostly, they switched from using periods to
underscores. But this meant having to tediously hand-edit every script that
used MOFA in order to continue using that script in newer versions of R
(since they also discontinued supporting the MOFA package in newer
versions). Also, some of the changes produced less useful graphical
summaries, to the extent that I took the time to write my own code to
reproduce the original versions.

So, I would suggest that you at least think about how much work you are
creating for your established users before making the change. And make
choices that minimize the burden you are imposing on them.

Best,
  Kevin

On Sat, Feb 4, 2023, 1:03 AM Hervé Pagès <hpages.on.github using gmail.com> wrote:

> Hi Matteo.
>
> We had DESeq2 after DESeq, Rbowtie2 after Rbowtie, MOFA2 after MOFA,
> etc.. so I don't see any problem, but thanks for asking!
>
> Best,
>
> H.
>
> On 03/02/2023 00:08, Matteo Tiberti wrote:
> > dear maintainers,
> >
> > I am currently listed as maintainer of Bioconductor package MoonlightR,
> designed for the prediction of cancer driver genes, which implements the
> Moonlight workflow.
> >
> > We are currently working on a second version of our workflow, called
> Moonlight2, and would like to have it released on Bioconductor as well, in
> form of the Moonlight2R package. The new package uses similar principles as
> the current one, but will have significant changes and updates, both in
> terms of new functionality and revision of old functionalities. The
> Moonlight2R project/paper will also have in part a different corresponding
> authorship respect to the current one. MoonlightR and Moonlight2R currently
> reside in two separate GitHub repositories.
> >
> > Ideally we would like to have both packages on BioConductor for the
> moment, the old one (called MoonlightR) and the new one that we intend to
> submit before the April cut-off for 3.17 (called Moonlight2R), where the
> number signifies the version of the protocol rather than the software.
> However on the package submission list, I see that having package names
> that "imply a temporal relationship" respect to an existing package is
> discouraged. Given the circumstances, do you think it would be possible to
> use the Moonlight2R name for the package (i.e. would it be a reason for
> rejection or object of revision during submission) or is it fair to keep it
> as is?
> >
> > Many thanks
> >
> > Matteo Tiberti
> >
> > Danish Cancer Society Research Center
> > Strandboulevarden 49
> > DK-2100 Copenhagen
> > Telephone: +45 35 25 73 07
> >
> >
> > [https://i.xink.io/Images/Get/K116/d1.png]<
> https://www.cancer.dk/?utm_source=email&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_content=cancerdk
> >
> >
> > www.cancer.dk<https://www.cancer.dk/international/> | Vores
> privatlivspolitik<https://www.cancer.dk/om-os/privatlivspolitik/>
> >
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
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>

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