[Bioc-devel] How to integrate code from a package not available on bioconductor
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Wed Feb 10 18:37:53 CET 2021
I don�t know what the legal requirement is.
As a human if I hadn�t given explicit consent I�d like to be asked. And if I had used someone else�s code I�d like it to be transparent that my use was legitimate, and a private exchange of email between me and the other individual consenting to use their code wouldn�t be transparent enough. Hopefully I�m not being hypocritical here.
Martin
From: Ana Carolina Leote <anacarolinaleote using gmail.com>
Date: Wednesday, February 10, 2021 at 10:24 AM
To: "Kern, Lori" <Lori.Shepherd using roswellpark.org>
Cc: Martin Morgan <mtmorgan.bioc using gmail.com>, Wolfgang Huber <wolfgang.huber using embl.org>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] How to integrate code from a package not available on bioconductor
My motivation to include this package is that my own package includes, but is not limited to, an ensemble of different packages that attempt to solve the same problem, besides my own solution, since I did some work showing they all have their pros and cons. At the moment my package does not include this one, because of all the problems here raised, but since it is arguably more popular than all other "alternative" packages, I felt I should include it. This is why using an alternative package unfortunately does not solve my problem. I also looked in the page Lori shared but this package is not there. However you do raise very valid points. I think I need to weigh the cost of changing the code against the additional usefulness my package can gain more carefully than I did so far.
I do have one additional question, though. Martin mentioned the license compatibility. There is no license at all in the GitHub repository of this package. I did some searching but I'm not sure what the default GitHub copyright means for bioconductor distribution. Does it mean I am not allowed to include this code in case I do wish to go forward with taking the code "as is"?
Thanks again for all your helpful responses. It's great as a new developer to have such support.
Best,
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 3:50 PM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
Have you looked at some of the scRNA packages that are already on Bioconductor to see if there is similar functionality in an existing package already accepted?
You can search for packages that have scRNA in the package name or title on this page:
http://bioconductor.org/packages/release/BiocViews.html#___Software
depending there is also a single cell workflow that might point to similar functionality
http://bioconductor.org/packages/release/workflows/html/simpleSingleCell.html
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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Martin Morgan <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>>
Sent: Wednesday, February 10, 2021 9:36 AM
To: Ana Carolina Leote <anacarolinaleote using gmail.com<mailto:anacarolinaleote using gmail.com>>; Wolfgang Huber <wolfgang.huber using embl.org<mailto:wolfgang.huber using embl.org>>
Cc: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] How to integrate code from a package not available on bioconductor
If the package is already widely used, then I guess it provides useful functionality, and so your package doesn't have to provide that functionality, so perhaps a better solution is to refer users to the unsupported package in your vignette??
What you say about not being maintained in over a year is probably the main concern with using code that is not in CRAN or Bioconductor. Already the code could be buggy, not well tested, and poorly documented (even if widely used! and of course the code / documentation could be excellent...) because it has not been subject to regular R CMD check etc or to initial review. And now the original author of the code is not maintaining it, so *you* have to fully understand it so that you can address bugs etc. As a 'developer' this could be my worst nightmare -- having to spend my time cursing at code somebody else wrote, instead of cursing at my own code!
The license of the package needs to permit use of the code, or may restrict how your own code is used (e.g., if the package is licensed for 'academic use only' then likely your package would need to be licensed similarly, and then would not be appropriate for Bioconductor).
All of these would discourage me from adopting this code.
Martin
On 2/10/21, 9:11 AM, "Bioc-devel on behalf of Ana Carolina Leote" <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org> on behalf of anacarolinaleote using gmail.com<mailto:anacarolinaleote using gmail.com>> wrote:
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://secure-web.cisco.com/1JCGueviBWl7DVrqkMofRc1S6sTjcVSsAg_KFX33Rpki72itBTsrUNlyADxYZ8tuocj7u69YtSf-7bFFmVOQMd1LvSaQzIL3jICkqmRGElXvH6G1o3ApsV6GOaWTR_XtENn8RxRS3QttiyUulE0H01k-_iWcOhrzOp-LHAeNI07GwXycEjob0NEObtaQ7SpF5MCbuDjEVhJyY2_-nmtHPv-WC5Z8PNo0Ua3teNqOKv2ki1VriQI-M9WQVuOr2S28BGuI69w0aQMQmbHz1wuNxeuWxqdYybR1_49yIN2ZLjcikEyXy-RetsPZByGvHX1_i/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fanacarolinaleote%2F
On Wed, Feb 10, 2021 at 2:51 PM Wolfgang Huber <wolfgang.huber using embl.org<mailto: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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Ana
> Carolina Leote <anacarolinaleote using gmail.com<mailto:anacarolinaleote using gmail.com>>
> > Sent: Wednesday, February 10, 2021 5:14 AM
> > To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto: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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