[Bioc-devel] Bioconductor package license: dependency on work under non-commercial license

Martin Morgan martin.morgan at roswellpark.org
Thu Jan 26 03:20:01 CET 2017


On 01/25/2017 08:12 PM, Dan Tenenbaum wrote:
> I can't speak to the license question (I'd guess the answer is no) but I am pretty sure that any dependencies of a Bioconductor package have to be available on CRAN or in Bioconductor itself. So you can't depend on packages that are only in GitHub.
>

A very small number of Bioconductor packages have (or depend on packages 
with) restrictive licenses, almost all for legacy reasons; a few 
packages have gone to great lengths to ensure that their use of 
otherwise restrictive code can be licensed in an open way. I'd be 
extremely discouraging of a new package with a direct or implied 
academic-only license.

There is some additional discussion on technical aspects of specifying 
licenses in Writing R Extension section 1.1.2.

     RShowDoc("R-exts")

Martin Morgan
Bioconductor

> Dan
>
>
> ----- Original Message -----
>> From: "David J. H. Shih" <dshih at jimmy.harvard.edu>
>> To: "bioc-devel" <bioc-devel at r-project.org>
>> Sent: Wednesday, January 25, 2017 12:48:31 PM
>> Subject: [Bioc-devel] Bioconductor package license: dependency on work under	non-commercial license
>
>> Hello,
>>
>>
>> I'd like to ask whether Bioconductor will allow a dependency package
>> under a non-commercial license:
>>
>> https://github.com/djhshih/mlat/blob/master/LICENSE_blat.txt
>>
>> I read the package guidelines:
>> http://bioconductor.org/developers/package-guidelines/#license but it
>> does not address this question.
>>
>>
>> I am putting together a package for somatic variant filtering. One of
>> the filters involve re-aligning the supporting reads using a heavily
>> refactored version of BLAT: MLAT (https://github.com/djhshih/mlat). BLAT
>> remains under a license that restricts commercial users. Although the
>> original license mentions no restriction on derivative work, I contacted
>> the author, and he maintains that the non-commercial license applies to
>> derivative works. Eventually, I'll probably replace BLAT (with another
>> aligner like SHRiMP2, which appears to have superior sensitivity and has
>> a permissive license), but I was wondering how I might be able to
>> assemble my package in the short term.
>>
>> Here is my plan:
>>
>> 1. Create a BLAT/MLAT package under BLAT's non-commercial license.
>> 2. Create the main package under GPLv3 that optionally depends on BLAT.
>>
>> Will Bioconductor permit a optional dependency package under a
>> non-commercial license?
>>
>>
>> Best regards,
>>
>> Postdoctoral Research Fellow
>> Department of Biostatistics and Computational Biology, Dana-Farber
>> Cancer Institute
>> Department of Biostatistics, Harvard T.H. Chan School of Public Health
>> Cancer Program, Broad Institute
>> 3 Blackfan Circle, CLS-11082
>> Boston, MA 02115
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


This email message may contain legally privileged and/or...{{dropped:2}}



More information about the Bioc-devel mailing list