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

[Andreas Tille]

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this can be clarified by possibly some outdated licensing information.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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