[Bioc-devel] How to integrate code from a package not available on bioconductor

[Ana Carolina Leote]

Dear all,
Thank you so much for the great input and to Wolfgang for raising these
points.
I am afraid I gain more than I lose by including this particular package,
as it is somewhat commonly used in the scRNA-seq community. It seems not to
be maintained in over a year, however, judging by the dates of the latest
response to issues and commits on GitHub. For this reason I think the
probability of it being updated is low, so I was planning to take the code
"as is" and assume maintainership - this after contacting the authors as
suggested.

Thanks and best wishes,
Carolina

*Ana Carolina Leote*
*MSc. Biological Engineering*
*PhD student at the Cologne Graduate School for Ageing Research*
*Cellular networks and systems biology (Beyer group), **CECAD Research
Center*
https://www.linkedin.com/in/anacarolinaleote/


On Wed, Feb 10, 2021 at 2:51 PM Wolfgang Huber <wolfgang.huber using embl.org>
wrote:

>
>
> > Il giorno 10feb2021, alle ore 14:31, Kern, Lori
> <Lori.Shepherd using RoswellPark.org> ha scritto:
> >
> > Have you reached out to the maintainer of the github package to see if
> they would plan on submitting to CRAN or Bioconductor?
> > If they do not,  you could see if they are okay with you including the
> code in your package and then clearly indicate their authorship in the man
> pages and by giving contributor credit in the DESCRIPTION. They might also
> include CITATION information in their package to include?
> >
> > Others might have additional thoughts?
>
> Ana,
>
> if you are in a position to take that other code “as is” and then assume
> maintainership over it, this may be a way forward. However, consider these
> issues in advance:
> - What happens if these other authors change their code on GitHub? Will
> you also synchronize the copy in your own package, or leave it as is? This
> requires a process and potentially continuous resources.
> - Who is responsible for fixing bugs in that copied code?
> - There are many reasons why people might not put their code on CRAN and
> Bioconductor, but in case it is a sign of low confidence in the quality of
> the code or low commitment to maintain it, depending on it incurs
> additional technical debt for you.
>
> Are there maybe other packages (on CRAN/Bioconductor) that provide what
> you need?
>
>         Kind regards
>                 Wolfgang
>
>
> >
> > Cheers,
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > ________________________________
> > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Ana
> Carolina Leote <anacarolinaleote using gmail.com>
> > Sent: Wednesday, February 10, 2021 5:14 AM
> > To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> > Subject: [Bioc-devel] How to integrate code from a package not available
> on bioconductor
> >
> > Dear all,
> >
> > I am a package maintainer and would like to add a functionality that
> > depends on another package which is not available in bioconductor, only
> via
> > GitHub. I would like to make the necessary changes in order to be able to
> > use their code in my package. Can anyone point me towards the best way to
> > proceed without undermining the authorship of the original developers? Is
> > copying their code to my package and editing it to bioconductor standards
> > appropriate?
> >
> > Thank you and best wishes,
> > Carolina
> >
> > *Ana Carolina Leote*
> > *MSc. Biological Engineering*
> > *PhD student at the Cologne Graduate School for Ageing Research*
> > *Cellular networks and systems biology (Beyer group), **CECAD Research
> > Center*
> >
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