[Bioc-devel] How to integrate code from a package not available on bioconductor
Ana Carolina Leote
@n@c@ro||n@|eote @end|ng |rom gm@||@com
Wed Feb 10 18:57:01 CET 2021
This is the repository: https://github.com/Vivianstats/scImpute
*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 6:44 PM Vincent Carey <stvjc using channing.harvard.edu>
wrote:
> It is wise to be careful here. If we don't know the provenance of the
> code in github it might actually be someone else's.
> It reminds me of the Numerical Recipes events, in which folks
> redistributed proprietary code without permission.
> What repo are we talking about anyway?
>
> On Wed, Feb 10, 2021 at 12:38 PM Martin Morgan <mtmorgan.bioc using gmail.com>
> wrote:
>
>> 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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