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

David J. H. Shih dshih at jimmy.harvard.edu
Thu Jan 26 05:52:59 CET 2017

Thank you for the clarification.

I'll look into replacing BLAT with SHRiMP2, which is under a permissive 
FOSS license. SHRiMP2 has comparable or superior performance across 
different data types in multiple independent studies anyway. I just 
wished I had not wasted three weeks scrubbing and refactoring BLAT's C 


On 2017-01-25 21:20, Martin Morgan wrote:
> 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
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