Ping: Upgrading glam2 (Was: Installation of binary tools inside MEME)
Ping,
I really need the help of testers for the new glam packages I uploaded
for review here
http://blends.debian.net/tmp/packages/glam2/
Any opinion would be very welcome.
Kind regards
Andreas.
On Tue, Nov 12, 2013 at 04:45:55PM +0100, Andreas Tille wrote:
> [original discussion on developer list on alioth - since it is down
> I "misuse" this list]
>
> Hi,
>
> in the past we had some positive feedback from meme authors (not only
> the one below also others - searchable once alioth might be back) to use
> the glam2 copy inside Debian under the old PD license. Since I'm doing
> a "month of upgrading of packages not touched >3 years" currently I
> stumbled upon glam2 and was giving it a try. You can see my preliminary
> work here:
>
> http://blends.debian.net/tmp/packages/glam2/
>
> The reason why I'm publishing this here is, that alioth is down but also
> that I want to hear opinions first.
>
> 1. I have choosen the same version number as meme (using epoch in
> changelog)
> 2. I have used enhanced uscan[1] to strip everything that is not
> needed.
> 3. I droped some makefile and missing files I kept from old glam2
> packages into debian/ dir
> 4. glam2-purge is lost.
>
> The thing is that unfortunately some files from main meme, namely
>
> alphabet.[ch]
> array.[ch]
> array-list.[ch]
> binary-search.[ch]
> ceqlogo.[ch]
> eps2png.[ch]
> hash_alph.h
> io.[ch]
> macros.h
> matrix.[ch]
> motif.[ch]
> motif-in-flags.h
> motif-in.h
> motif-spec.h
> red-black-tree.[ch]
> regex-utils.[ch]
> string-builder.[ch]
> string-list.h
> user.h
> utils.[ch]
>
> (see debian/README.source).
>
> So before we could distribute the given orig.tar.xz tarball we need to
> ask upstream whether they might extend the permission to use a free
> license also to these files which are actually some general utilities
> and surely not the main part of MEME itself.
>
> Even if I see good chances that upstream will agree here I would like
> you to run some tests (perhaps even write some test case) whether the
> new code really behaves like the old one. Otherwise I do not think that
> it is worth the trouble to start a licensing discussion and we might
> rather stick to the old code.
>
> I also wonder whether there is any need for glam2-purge which was not
> taken over by the MEME project. If it is needed the issue is quite
> simple and we could create a separate package since the code remains
> freely available anyway.
>
> The next step would be to pick up the meme packaging for non-free and
> just leave out the glam2 binaries for the installation.
>
> Kind regards
>
> Andreas.
>
> [1] http://wiki.debian.org/UscanEnhancements
>
> On Thu, Feb 28, 2013 at 11:58:46AM +1000, Timothy Bailey wrote:
> > James,
> >
> > On 28/02/13 11:09 AM, James Johnson wrote:
> > >Hi Tim,
> > >
> > >On 28/02/13 11:05, Timothy Bailey wrote:
> > >>David,
> > >>
> > >>I assume the most important thing is that the copyright and "for
> > >>non-profit use only"
> > >>warning is included in the Debian repackaging. If those are
> > >>preserved, I'm happy.
> > >If you refer to the original email, that's exactly what they were
> > >hoping to avoid. GLAM2 has a more permissive license than the MEME
> > >Suite. The reason they want to keep the 2 packages is so that
> > >people can use GLAM2 under the more permissive license... They
> > >were hoping to back-port any improvements to GLAM2 while keeping
> > >its original license.
> >
> > Sorry about the confusion I may have called. I am completely happy
> > to have them
> > back-port changes from MEME Suite Glam2 to stand-alone Glam2. The Glam2
> > license can remain as before.
> >
> > My earlier comment referred to the Debian port of MEME Suite, not
> > stand-alone Glam2.
> >
> > Cheers,
> >
> > Tim
> > >
> > >~James
> > >>
> > >>Cheers,
> > >>
> > >>Tim
> > >>On 28/02/13 2:07 AM, Gibbons, David wrote:
> > >>>
> > >>>Hi Tim,
> > >>>
> > >>>My only concern would be that we not create any conflict with
> > >>>the arrangement we have between the University of Washington,
> > >>>UC San Diego and the University of Queensland regarding The
> > >>>Meme Suite. The technical compatibilities of the various
> > >>>versions are outside of my scope, but as long as we are not
> > >>>deviating from the agreement between our institutions, I have
> > >>>no issues with the request.
> > >>>
> > >>>
> > >>>Thanks for copying me.
> > >>>
> > >>>Dave
> > >>>
> > >>>David G. Gibbons, PE, MBA
> > >>>
> > >>>Assistant Director
> > >>>
> > >>>Physical Sciences Licensing
> > >>>
> > >>>Technology Transfer Office, UC San Diego
> > >>>
> > >>>9500 Gilman Drive, MC 0910
> > >>>
> > >>>La Jolla, CA 92093-0910
> > >>>
> > >>>(858)534-0175
> > >>>
> > >>>dgibbons@ucsd.edu
> > >>>
> > >>>http://invent.ucsd.edu
> > >>>
> > >>>*From:*Timothy Bailey [mailto:t.bailey@imb.uq.edu.au]
> > >>>*Sent:* Wednesday, February 27, 2013 12:13 AM
> > >>>*To:* James Johnson
> > >>>*Cc:* Gibbons, David; Martin Frith; MEME Support; Debian Med
> > >>>Packaging Team
> > >>>*Subject:* Re: Fwd: Re: [j.johnson@imb.uq.edu.au: Re:
> > >>>Installation of binary tools inside MEME]
> > >>>
> > >>>James,
> > >>>
> > >>>On 18/02/13 11:51 AM, James Johnson wrote:
> > >>>
> > >>> Hi Tim, Dave,
> > >>>
> > >>> The Debian Med Packaging Team want to know if they can backport
> > >>> GLAM2 improvements (presuming there are any?) in the MEME Suite
> > >>> to the more permissively licensed GLAM2 repository?
> > >>>
> > >>>I have no problems with this as long as they do the work.
> > >>>
> > >>>However, that will mean that the Debian version of Glam2
> > >>>differs from the "standalone" version
> > >>>Martin created. It will match the "MEME Suite" version, though.
> > >>>
> > >>>Cheers,
> > >>>
> > >>>Tim
> > >>>
> > >>>
> > >>>~James
> > >>>
> > >>>
> > >>>-------- Original Message --------
> > >>>
> > >>>*Subject: *
> > >>>
> > >>>
> > >>>
> > >>>Re: [j.johnson@imb.uq.edu.au <mailto:j.johnson@imb.uq.edu.au>:
> > >>>Re: Installation of binary tools inside MEME]
> > >>>
> > >>>*Date: *
> > >>>
> > >>>
> > >>>
> > >>>Fri, 15 Feb 2013 11:04:58 +0000
> > >>>
> > >>>*From: *
> > >>>
> > >>>
> > >>>
> > >>>Tim Booth <avarus@fastmail.fm> <mailto:avarus@fastmail.fm>
> > >>>
> > >>>*To: *
> > >>>
> > >>>
> > >>>
> > >>>Andreas Tille <andreas@fam-tille.de> <mailto:andreas@fam-tille.de>
> > >>>
> > >>>*CC: *
> > >>>
> > >>>
> > >>>
> > >>>Debian Med Packaging Team
> > >>><debian-med-packaging@lists.alioth.debian.org>
> > >>><mailto:debian-med-packaging@lists.alioth.debian.org>, James
> > >>>Johnson <j.johnson@imb.uq.edu.au>
> > >>><mailto:j.johnson@imb.uq.edu.au>
> > >>>
> > >>>Hi,
> > >>>> On Thu, Feb 14, 2013 at 06:08:08PM +0000, Tim Booth wrote:
> > >>>> > Yes, I did start looking at Meme but quickly realised it was a lot more
> > >>>> > work than I thought to do a proper job on it. I think all I wanted to
> > >>>> > do in the first instance was to get an updated glam2 binary package
> > >>>> > based upon the improved glam2 source within the meme code. I guess this
> > >>>> > is now the definitive glam2 as the original standalone source hasn't
> > >>>> > been updated since 2008.
> > >>>>
> > >>>> We might try to do some comparison. Charles previously mentioned that
> > >>>> we should keep the glam2 package from Debian which is free (PD) and meme
> > >>>> currently has a non-free license (according to DFSG). So if glam2 inside
> > >>>> meme is basically unchanged it might be reasonable to ignore the code
> > >>>> inside meme (or asking upstream for permission to backport the changes.)
> > >>>A quick "diff" across the original glam2 vs. the meme glam2 suggests
> > >>>that several new options have been added for meme - see
> > >>>src/glam2_args.c.
> > >>>I would imagine that scripts within meme rely on these options. In
> > >>>fact, a quick grepping shows that scripts/glam2_webservice.pl.in calls
> > >>>"glam2 -M" which is an option added for meme. I've not looked for other
> > >>>examples.
> > >>>I hope that upstream can at least be persuaded to put their changes to
> > >>>glam2 under a free license like the original glam2. They may not be
> > >>>legally bound to do so but it would be highly disingenuous of them to
> > >>>refuse.
> > >>>Cheers,
> > >>>TIM
> > >>>--
> > >>>If you can't find an apposite quote for your sig, just make one up.
> > >>> - Anon
> > >>>
> > >>>--
> > >>>
> > >>>Timothy L. Bailey
> > >>>
> > >>>
> > >>>
> > >>>t.bailey@imb.uq.edu.au <mailto:t.bailey@imb.uq.edu.au>
> > >>>
> > >>>Institute for Molecular Bioscience
> > >>>
> > >>>
> > >>>
> > >>>VOICE: (61)-(7)-3346-2614
> > >>>
> > >>>The University of Queensland
> > >>>
> > >>>
> > >>>
> > >>>FAX: (61)-(7)-3346-2101
> > >>>
> > >>>Brisbane, Qld. 4072 Australia
> > >>>
> > >>>
> > >>>
> > >>>http://research.imb.uq.edu.au/~tbailey
> > >>><http://research.imb.uq.edu.au/%7Etbailey>
> > >>>
> > >>
> > >>--
> > >>Timothy L. Bailey
> > >> t.bailey@imb.uq.edu.au <mailto:t.bailey@imb.uq.edu.au>
> > >>Institute for Molecular Bioscience
> > >> VOICE: (61)-(7)-3346-2614
> > >>The University of Queensland
> > >> FAX: (61)-(7)-3346-2101
> > >>Brisbane, Qld. 4072 Australia
> > >> http://research.imb.uq.edu.au/~tbailey
> > >>
> > >
> >
> > --
> > Timothy L. Bailey
> > t.bailey@imb.uq.edu.au <mailto:t.bailey@imb.uq.edu.au>
> > Institute for Molecular Bioscience
> > VOICE: (61)-(7)-3346-2614
> > The University of Queensland
> > FAX: (61)-(7)-3346-2101
> > Brisbane, Qld. 4072 Australia
> > http://research.imb.uq.edu.au/~tbailey
> >
>
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging@lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
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