[Bioc-devel] name for new BioC package

Wolfgang Huber wo||g@ng@huber @end|ng |rom emb|@org
Fri Feb 10 10:06:05 CET 2023

Hi Kevin & all

I guess there are two basic scenarios:

- PKG2 is a plug-in replacement for PKG. In this case the API should change as little as possible. PKG should be deprecated. One can even argue whether the name change is necessary. (It may be opportune for reasons of credit / assignment of responsibility.)

- PKG2 is a fundamentally better approach than PKG, and a new API is appropriate. In this case, it’s fair to still keep PKG around, for all the people who like and use it, and let them decide at their own pace if and when they migrate. We did this e.g. with DESeq/DESeq2, which co-existed for several years.

Thanks for the feedback on MOFA/MOFA2. I was a co-author of MOFA but not MOFA2, and it seems we did not follow the above advice. Sorry.

Thanks and best wishes

Wolfgang Huber

> Il giorno 04.02.2023, alle ore 14:26, Kevin Coombes <kevin.r.coombes using gmail.com> ha scritto:
> 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
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>> --
>> Hervé Pagès
>> Bioconductor Core Team
>> hpages.on.github using gmail.com
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