[Debian-med-packaging] Bug#807580: Bug#807580: [devteam-bioc] Bug#807580: r-bioc-rtracklayer: src/ucsc/* is stolen from another project with non-DFSG free license
Michael Crusoe
michael.crusoe at gmail.com
Thu Dec 10 22:01:59 UTC 2015
Thank you, Martin for the clarification; and my apologies for the strong
wording.
For your own information, I don't think the Kent code license is at *all*
compatible with the Artistic 2.0 license. It doesn't give anyone the right
to redistribute the code, for example. Let along the other enumerated
rights in the Artistic 2.0 license text.
For everyone's convenience I hope this is resolved quickly!
On Thu, Dec 10, 2015, 23:33 Andreas Tille <andreas at an3as.eu> wrote:
> 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
> > >
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> > >
> >
> > --
> > http://fam-tille.de
> >
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