Upgrading glam2 (Was: Installation of binary tools inside MEME)

[Andreas Tille <andreas@an3as.eu>]

[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
> 

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