[Bioc-devel] Question reg devtools in MacOS High Sierra

[Krithika Bhuvaneshwar]

Hello,

We are the package maintainers of the CINdex package. Our package is giving
build errors and we are investigating why. I'm currently working on setting
up the environment so I can replicate the error.

I have a MacOS High Sierra. Here is what I did:
* downloaded R 4.1 from  https://mac.r-project.org/ and
* Got the latest  BioC 3.13 using BiocManager::install(version = "devel")

* When I tried *install.packages("devtools")*, it said
*"Package which is only available in source form, and may need compilation
of **C/C++/Fortran: ‘gert’*

So Then I did *install.packages("devtools")*

It gave me an error saying
*"Configuration failed to find libgit2 library." Try installing: brew:
libgit2 (MacOS)*
I have tried installing libgit2 using both brew and within R. Neither
worked. So at this point, I'm unable to install devtools . And without
devtools, Check And Build are not working

Has anyone else encountered this issue, please advise on how to fix this.

Thanks,
Krithika

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[Bioc-devel] Adding maintainer to AMARETTO package

[Shaimaa Hesham Bakr]

Hello,
I am one of the authors of the AMARETTO package and would like to add myself as 
a maintainer along with 
olivier.geva...@gmail.com. I currently don’t 
have an account on Bioconductor. Please create an account and I will activate 
it.
Thank you,
Shaimaa


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

[Ana Carolina Leote]

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 
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 
> 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 
>> Date: Wednesday, February 10, 2021 at 10:24 AM
>> To: "Kern, Lori" 
>> Cc: Martin Morgan , Wolfgang Huber <
>> wolfgang.hu...@embl.org>, "bioc-devel@r-project.org" <
>> bioc-devel@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 > > 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-boun...@r-project.org>> on behalf of Martin Morgan <
>> mtmorgan.b...@gmail.com>
>> Sent: Wednesday, February 10, 2021 9:36 AM
>> To: Ana Carolina Leote > anacarolinale...@gmail.com>>; Wolfgang Huber > >
>> Cc: bioc-devel@r-project.org <
>> bioc-devel@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 

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

[Vincent Carey]

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 
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 
> Date: Wednesday, February 10, 2021 at 10:24 AM
> To: "Kern, Lori" 
> Cc: Martin Morgan , Wolfgang Huber <
> wolfgang.hu...@embl.org>, "bioc-devel@r-project.org" <
> bioc-devel@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  > 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-boun...@r-project.org>> on behalf of Martin Morgan <
> mtmorgan.b...@gmail.com>
> Sent: Wednesday, February 10, 2021 9:36 AM
> To: Ana Carolina Leote  anacarolinale...@gmail.com>>; Wolfgang Huber  >
> Cc: bioc-devel@r-project.org <
> bioc-devel@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 

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

[Martin Morgan]

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 
Date: Wednesday, February 10, 2021 at 10:24 AM
To: "Kern, Lori" 
Cc: Martin Morgan , Wolfgang Huber 
, "bioc-devel@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 
mailto:lori.sheph...@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 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Martin Morgan 
mailto:mtmorgan.b...@gmail.com>>
Sent: Wednesday, February 10, 2021 9:36 AM
To: Ana Carolina Leote 
mailto:anacarolinale...@gmail.com>>; Wolfgang Huber 
mailto:wolfgang.hu...@embl.org>>
Cc: bioc-devel@r-project.org 
mailto:bioc-devel@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" 
mailto:bioc-devel-boun...@r-project.org> on 
behalf of anacarolinale...@gmail.com> wrote:

Dear all,
Thank you so much for the great input and to Wolfgang for raising these
points.
I am 

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

[Ana Carolina Leote]

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 
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  on behalf of Martin
> Morgan 
> *Sent:* Wednesday, February 10, 2021 9:36 AM
> *To:* Ana Carolina Leote ; Wolfgang Huber <
> wolfgang.hu...@embl.org>
> *Cc:* bioc-devel@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-boun...@r-project.org on behalf of anacarolinale...@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*
>
> 

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

[Kern, Lori]

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  on behalf of Martin Morgan 

Sent: Wednesday, February 10, 2021 9:36 AM
To: Ana Carolina Leote ; Wolfgang Huber 

Cc: bioc-devel@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" 
 
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 
wrote:

>
>
> > Il giorno 10feb2021, alle ore 14:31, Kern, Lori
>  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 

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

[Martin Morgan]

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" 
 
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://www.linkedin.com/in/anacarolinaleote/


On Wed, Feb 10, 2021 at 2:51 PM Wolfgang Huber 
wrote:

>
>
> > Il giorno 10feb2021, alle ore 14:31, Kern, Lori
>  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  on behalf of Ana
> Carolina Leote 
> > Sent: Wednesday, February 10, 2021 5:14 AM
> > To: bioc-devel@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?
> >
  

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

[Wolfgang Huber]

> Il giorno 10feb2021, alle ore 14:31, Kern, Lori 
>  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  on behalf of Ana Carolina 
> Leote 
> Sent: Wednesday, February 10, 2021 5:14 AM
> To: bioc-devel@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*
> https://secure-web.cisco.com/1sN_yjFZ4rXsNHMf8Fp8CJTySgKw-1exyK2uoJVgve2HB-ffaKVZpjVqnqKkiHfvj-8XfBD5L-E-u5CSB1GVD7eouovHeu4HCMh60N2H2o2WA8SOPodHnGfUgo8J3fWYeoSrQCiNJ5M4yE2VTnUi-WGlGdJeBDFxKTQwTFVThCjoTyAwk1tTdVAznZxVTGkCNBmBuV1Na-a0-81QaIYra4grO9-57FesPlxZIA0WUU9icoS3LgqlPTUhsmLZUM0NmejCSrTNSDA9AzDs7tB66TW4lBTvaNpOHMrk5wPCYIPckLqpDkVL3HnRSiWmXdWJE/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fanacarolinaleote%2F
> 
>[[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://secure-web.cisco.com/1vxzYOt1Hk0jYyShxe8B714l2GGAvh6Qvfo2Ey_49Ro47iSw83aMqNIB5Qv3keiqGApswE2x6TuWzoZjp-NJuEJcrt-skDYLR1Lsd0m1gCdOno-5vOXu1DHnuKsRkZQEyXRX00TjWpnBjbIwuJq5ll1xYmpurSpXNAagbyUQpcfZ136DgLhfGEM63BY-2KzMOwYsXqzpFhqcGhYhR1BkRDJBlIK7NjrhbsQ_8f4Hn2n7yvll4i20POhhaeiLBMZwwu0HXiWtT8v6VNA8pbxf7YxHpISCef2JJErtEjx21uA1ZQxeTNYg3X_37zZDJYGcZ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> 
> 
> 
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [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 
wrote:

>
>
> > Il giorno 10feb2021, alle ore 14:31, Kern, Lori
>  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  on behalf of Ana
> Carolina Leote 
> > Sent: Wednesday, February 10, 2021 5:14 AM
> > To: bioc-devel@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*
> >
> https://secure-web.cisco.com/1sN_yjFZ4rXsNHMf8Fp8CJTySgKw-1exyK2uoJVgve2HB-ffaKVZpjVqnqKkiHfvj-8XfBD5L-E-u5CSB1GVD7eouovHeu4HCMh60N2H2o2WA8SOPodHnGfUgo8J3fWYeoSrQCiNJ5M4yE2VTnUi-WGlGdJeBDFxKTQwTFVThCjoTyAwk1tTdVAznZxVTGkCNBmBuV1Na-a0-81QaIYra4grO9-57FesPlxZIA0WUU9icoS3LgqlPTUhsmLZUM0NmejCSrTNSDA9AzDs7tB66TW4lBTvaNpOHMrk5wPCYIPckLqpDkVL3HnRSiWmXdWJE/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fanacarolinaleote%2F
> >
> >[[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://secure-web.cisco.com/1vxzYOt1Hk0jYyShxe8B714l2GGAvh6Qvfo2Ey_49Ro47iSw83aMqNIB5Qv3keiqGApswE2x6TuWzoZjp-NJuEJcrt-skDYLR1Lsd0m1gCdOno-5vOXu1DHnuKsRkZQEyXRX00TjWpnBjbIwuJq5ll1xYmpurSpXNAagbyUQpcfZ136DgLhfGEM63BY-2KzMOwYsXqzpFhqcGhYhR1BkRDJBlIK7NjrhbsQ_8f4Hn2n7yvll4i20POhhaeiLBMZwwu0HXiWtT8v6VNA8pbxf7YxHpISCef2JJErtEjx21uA1ZQxeTNYg3X_37zZDJYGcZ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
> >
> >
> > This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> 

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

[Vincent Carey]

On Wed, Feb 10, 2021 at 8:32 AM Kern, Lori 
wrote:

> 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?
>
>
This is what I would have suggested.  Also, if the github author needs
encouragement about submission to a regulated
ecosystem, have them get in touch with us.


> 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  on behalf of Ana
> Carolina Leote 
> Sent: Wednesday, February 10, 2021 5:14 AM
> To: bioc-devel@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*
>
> https://secure-web.cisco.com/1sN_yjFZ4rXsNHMf8Fp8CJTySgKw-1exyK2uoJVgve2HB-ffaKVZpjVqnqKkiHfvj-8XfBD5L-E-u5CSB1GVD7eouovHeu4HCMh60N2H2o2WA8SOPodHnGfUgo8J3fWYeoSrQCiNJ5M4yE2VTnUi-WGlGdJeBDFxKTQwTFVThCjoTyAwk1tTdVAznZxVTGkCNBmBuV1Na-a0-81QaIYra4grO9-57FesPlxZIA0WUU9icoS3LgqlPTUhsmLZUM0NmejCSrTNSDA9AzDs7tB66TW4lBTvaNpOHMrk5wPCYIPckLqpDkVL3HnRSiWmXdWJE/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fanacarolinaleote%2F
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
> https://secure-web.cisco.com/1vxzYOt1Hk0jYyShxe8B714l2GGAvh6Qvfo2Ey_49Ro47iSw83aMqNIB5Qv3keiqGApswE2x6TuWzoZjp-NJuEJcrt-skDYLR1Lsd0m1gCdOno-5vOXu1DHnuKsRkZQEyXRX00TjWpnBjbIwuJq5ll1xYmpurSpXNAagbyUQpcfZ136DgLhfGEM63BY-2KzMOwYsXqzpFhqcGhYhR1BkRDJBlIK7NjrhbsQ_8f4Hn2n7yvll4i20POhhaeiLBMZwwu0HXiWtT8v6VNA8pbxf7YxHpISCef2JJErtEjx21uA1ZQxeTNYg3X_37zZDJYGcZ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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The information in this e-mail is intended only for the ...{{dropped:18}}

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

[Kern, Lori]

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?

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  on behalf of Ana Carolina 
Leote 
Sent: Wednesday, February 10, 2021 5:14 AM
To: bioc-devel@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*
https://secure-web.cisco.com/1sN_yjFZ4rXsNHMf8Fp8CJTySgKw-1exyK2uoJVgve2HB-ffaKVZpjVqnqKkiHfvj-8XfBD5L-E-u5CSB1GVD7eouovHeu4HCMh60N2H2o2WA8SOPodHnGfUgo8J3fWYeoSrQCiNJ5M4yE2VTnUi-WGlGdJeBDFxKTQwTFVThCjoTyAwk1tTdVAznZxVTGkCNBmBuV1Na-a0-81QaIYra4grO9-57FesPlxZIA0WUU9icoS3LgqlPTUhsmLZUM0NmejCSrTNSDA9AzDs7tB66TW4lBTvaNpOHMrk5wPCYIPckLqpDkVL3HnRSiWmXdWJE/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fanacarolinaleote%2F

[[alternative HTML version deleted]]

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recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] How to integrate code from a package not available on bioconductor

[Ana Carolina Leote]

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*
https://www.linkedin.com/in/anacarolinaleote/

[[alternative HTML version deleted]]

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