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Guix and Bioconductor.

From: Giovanni Biscuolo
Subject: Guix and Bioconductor.
Date: Fri, 20 Dec 2019 12:55:20 +0100

To all Guix interested in Bioconductor,

forgive me if I raise this question here and not to "upstream", but IMHO
this issue should escalate to Bioconductor and Guix community could do
better than single package maintainers, zimoun in this case

I'm not a user of Bioconductor packages so I have no "weight" on this
matter, but I guess in Guix community there are **many** (potential?)
users of Bioconductor packages: could you please organize a "pressure
group" to convince Bioconductor be strict in their package acceptance

I fear flowPeacks will not be the last package with this kind licensing

Tobias Geerinckx-Rice <address@hidden> writes:

> Zimoun,


>> The issue is that upstream has disappeared, as usual in scientific
>> software. Someone writes a piece of code then publishes a paper and
>> sometimes the requirement for publication is to be pushed in
>> mainstream collection of packages (Bioconductor in this case). But
>> the copyright holder does not maintain the code and instead write
>> another piece of code, try to publish a paper, etc.. Well the
>> Reproducibility of Science crisis.
> That is a shame.  And that while other scientists (like you) are 
> working hard to make research more ‘open’ and reproducible.

Since «Bioconductor is committed to open source, collaborative,
distributed software development and literate, reproducible research.» [1]

The main point here is that legal aspects are an **integral part** of
reproducible research and the freedom of the developer to choose the
"open source" license he prefer should be _guided_ so he does not
involuntary harm the Bioconductor commitment to reproducible research
(redistribution is part of reproducibility).

In short: since "Clarifies Artistic License" aka "Artistic License
(Perl) 1.0" [2] (FSF approved) exists since long ago *and* since
"Artistic License v1" is not FSF approved, Biocounductor team should not
accept provide a list of accepted licenses that allows all free software
distributions to redistribute the packages (we have one if they wish :-)

...and yes, this means that Bioconductor does not accept an OSI approved
"Open Source" license [3], one of the **very few** cases (the only one)
in wich OSI and FSF disagrees on licenses.

To be clear, I'm pretty **sure** that an author generally does not
understand the difference between "Artistic License v1" and "Artistic
License (Perl) 1.0" and all he wants is his package will be freely
redistributable. He should be guided, in this case by Bioconductor.


Thanks. Gio'




    to be clear, the "diff" from Artistic License v1 is this clause
    «8.Aggregation of this Package with a commercial distribution is
    always permitted provided that the use of this Package is embedded;
    that is, when no overt attempt is made to make this Package's
    interfaces visible to the end user of the commercial
    distribution. Such use shall not be construed as a distribution of
    this Package.»

[3] Artistic License v.1 is OSI approved

Giovanni Biscuolo

Xelera IT Infrastructures

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