[Debian-med-packaging] Bug#807580: [devteam-bioc] Bug#807580: r-bioc-rtracklayer: src/ucsc/* is stolen from another project with non-DFSG free license

[Morgan, Martin]

Hi Andreas --

I spoke with Michael Lawrence, who is listed as the package maintainer in the DESCRIPTION file, about this.

The package was written before R had formalized ways of documenting multiple licenses, and the DESCRIPTION file says

ExtraLicenses: The files in the 'src/ucsc' directory are licensed for all
  use by Jim Kent, in a manner compatible with the Artistic 2.0 license.

Michael has updated the package to follow R convention, with a License: tag that mentions Artistic-2.0 + file LICENSE, and the LICENSE file indicates the code and Kent's licensing text mentioned below. The commit is at

  https://github.com/Bioconductor-mirror/rtracklayer/commit/8d3505b31b7848af7cd9f9d930165c7beec93a8f

Since you know the licensing constraints under which packages are allowed in your project, please feel free to contact Jim Kent directly; Michael will be happy to make any subsequent changes to rtracklayer.

Also, please note that the src/ucsc/* is NOT 'stolen', and that the 'meat' of the rtracklayer package extends considerably beyond Kent's (very valuable) code.

Best,

Martin Morgan
Bioconductor 
________________________________________
From: devteam-bioc-bounces at lists.fhcrc.org [devteam-bioc-bounces at lists.fhcrc.org] on behalf of Maintainer [maintainer at bioconductor.org]
Sent: Thursday, December 10, 2015 12:56 PM
To: Bioconductor Package Maintainer; 807580 at bugs.debian.org
Subject: Re: [devteam-bioc] Bug#807580: r-bioc-rtracklayer: src/ucsc/* is stolen from another project with non-DFSG free license

Hi Michael,

I'm hereby forwarding this issue to the BioConductors list.  Hopefully
this can be clarified by possibly some outdated licensing information.
If not we should probably contact the authors whether they might be
consider a free license as we did with other projects in the past.
Otherwise we would loose quite a chain of depencencies of BioConductor
packages.

Thanks for spotting this

       Andreas.

On Thu, Dec 10, 2015 at 06:08:44AM -0800, Michael R. Crusoe wrote:
> Package: r-bioc-rtracklayer
> Version: 1.30.1-1
> Severity: important
>
> Dear friends,
>
> I am sorry to report that I have recently discovered that the meat of this
> package is not under the Artistic-2.0 license as one might guess, but it from
> another source with a non-DFSG license.
>
> src/ucsc/* is cobbled together from src/lib/*, src/inc/*, and src/utils/* from
> http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src;h=5c83e0e5dd23c4a1cbe330db3be7dc7fe72c8251;hb=HEAD
>
> The license for that project is: "All files are copyrighted, but license is
> hereby granted for personal, academic, and non-profit use.  A license is also
> granted for the contents of the src/lib, src/inc and src/utils and python
> directories for commercial users."
> http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=README;hb=HEAD
>
> This license mail fail the DFSG guidelines. It doesn't explicitly permit
> derived works and it does not automatically apply to redistributions.
>
> -- System Information:
> Debian Release: stretch/sid
>   APT prefers unstable
>   APT policy: (500, 'unstable')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 4.2.0-1-amd64 (SMP w/8 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
>
> Versions of packages r-bioc-rtracklayer depends on:
> ii  libc6                     2.21-3
> ii  r-base-core [r-api-3]     3.2.2.20151203-1
> ii  r-bioc-genomicalignments  1.6.1-1
> ii  r-cran-rcurl              1.95-4.7-1
> ii  r-cran-xml                3.98-1.3-1
> ii  zlib1g                    1:1.2.8.dfsg-2+b1
>
> r-bioc-rtracklayer recommends no packages.
>
> r-bioc-rtracklayer suggests no packages.
>
> -- no debconf information
>
> _______________________________________________
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> Debian-med-packaging at lists.alioth.debian.org
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>

--
http://fam-tille.de

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