[Debian-med-packaging] Comments regarding samblaster_0.1.24-1_amd64.changes

[Steffen Möller]

Hi Thorsten, hi Anthony,

Thank you both!

I'll timely follow your comments on salsa and the next version should 
then have it all. Need to read up about "Expat".

Cheers,

Steffen


On 21.01.19 16:27, Thorsten Alteholz wrote:
> Hi Steffen,
>
> I marked your package for accept and don't want to withhold the comment from our FTP trainee.
>
>    Thorsten
>
>
>
> ACCEPT
>
> samblaster was nicely Debianized with modern Debian practice.
> The C++ program is written entirely by Greg Faust the upstream author
> with very minor changes from other contributors for things like
> macOS support.
>
> Looks good to me!
>
> Some nitpickings:
>
> 1. MIT vs Expat
>
> I recall reading somewhere that it is preferable to use "Expat"
> rather than "MIT" as the name of the license if it indeeds matches
> the Expat variant of the MIT license in debian/copyright.
> That appears to be the case here, so, maybe call it "Expat" instead?
> :-)
>
>
> 2. License and authorship of of SAMBLASTER_Supplemental.pdf
>
> The PDF file seems to be a supplement of the main journal paper
> which Gregory G. Faust and Dr. Ira M. Hall co-wrote
> (see https://academic.oup.com/bioinformatics/article/30/17/2503/2748175)
> I suppose it is the case where G.G. Faust did the bulk of the work while
> I.M. Hall provided supervision and guidance.
>
> Indeed, in the supplemental material, the authors uses "we" for
> self-reference, and, in the footnote:
>
>    ©The Author(s) 2014.  This is the authors' un-refereed supplemental
>    material for the following publication: Faust, G.G. and Hall, I.M.,
>    SAMBLASTER: fast duplicate marking and structural variant read
>    extraction. _Bioinformatics_ Sept. 2014; 30(17): 2503-2505.
>
> No license was explicitly mentioned in the PDF file, but then,
> it was the upstream author Gregory Faust's decision to place
> SAMBLASTER_Supplemental.pdf alongside the LICENSE.txt file
> citing the MIT License, so I think it is safe to say that the PDF file
> is also placed under the MIT/Expat License.
>
> The PDF file was printed/generated from Microsoft Word file
> SAMBLASTER_SupplementalV5.docx whose author is "gf4ea", which is
> Greg Faust's handle at the University of Virginia (gf4ea at virginia.edu).
>
> So, while the PDF might have been written entirely by Greg Faust,
> it is recommended to list Ira M. Hall is its co-author too, so perhaps
> it would be better to add these lines to debian/copyright?
>
>      Files: SAMBLASTER_Supplemental.pdf
>      Copyright: 2014 Gregory G. Faust <gf4ea at virginia.edu>
>                 2014 Ira M. Hall <imh4y at virginia.edu>
>      License: Expat
>
> Of course, a clarification from Greg Faust would be helpful too.
>
> And, if the license for the PDF file is clear, then I personally would
> list it in debian/samblaster.docs too, even though it does take up 107kB
> of space.  ;-)
>
> Cheers,
>
> Anthony Fok (Debian FTP Trainee)
>
>