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

Thu Dec 10 21:14:55 UTC 2015

Hi Martin,

thanks for your quick reply.  I'll contact Jim and will keep you in CC.
(Please also excuse the term "stolen" which might have been a bit sloppy
in this context.)

Kind regards

       Andreas.

On Thu, Dec 10, 2015 at 08:50:53PM +0000, Morgan, Martin wrote:
> 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 this can be clarified by possibly some outdated licensing information.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
> >
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> >
> 
> --
> http://fam-tille.de
> 
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