[Debian-med-packaging] Other ways to help the Debian Med team: Ping about free licenses (Was: maude new version and standard outdated)
Andreas Tille
andreas at fam-tille.de
Fri Apr 17 08:37:15 BST 2020
Hi Ben,
On Fri, Apr 17, 2020 at 01:58:02AM +0200, Ben Tris wrote:
> Hello Andreas,
>
> Glad to hear.
> That reminds me. If it is helpfull I can notice about warnings like these
> (Or what would be helpfull to notice about looking at the tracker?):
>
> I noticed some packages that has this test warning: a new source-only
> upload is needed to allow migration
> like this: https://tracker.debian.org/pkg/q2templates
The need for a source only upload is actually a nice notice. However,
in our COVID-19 effort I'm mainly busy to enhance the Blends framework
by this kind of quality assurance features. So we will have (hopefully
not in the too far distant future) an overview about this which will
help spotting this soonish.
> These two together contain all high warnings for (shorten) debci
> appstream build binary
> https://tracker.debian.org/pkg/sofa-framework
> https://tracker.debian.org/pkg/pbgenomicconsensus
Hmmmm, well these are pretty hard packages. Sofa needs to be repackaged
from scratch. We had no manpower to cope with upstream changes.
Currently it can not be built - probably we will loose that package
completely. :-(
Similar with pbgenomicconsensus. Several packages from Pacific
Bioscience (pb*) are affected by the Python3 removal. This package
currently can not be build without fixing predependencies first.
> Very rare: high standards and (low) translations:
> https://tracker.debian.org/pkg/qcumber
This also needs to be repackaged. Its on my desk since a long time
but other stuff just had higher priority.
> Sorted out high warnings: debci appstream build binary and test with
> warnings.
> Also sorted out last news from 2020, 2019, 2018-older.
> Probably less interesting sorted out: new commits, version VCS newer,
> VCS not up to date, Failed analyze VCS
Please do not warn about this. Usually there is a reason why VCS
is newer but no upload had happened.
> This is what I use for https://www.gezapig.nl/covid.html (more for
> people comming from FSD)
> Last news 2020: gone, new, recent (source) update, new upstream, old
> upstream, autoremove
Thanks for the pointer. However, I'd like to repeat my doubt that
manually maintaining a page like this is exhaustive for you and likely
to be outdated pretty soon (for instance after next upload of a package
... and I personally have a statistics of uploading more than one
package per day since 2014 ( see
http://blends.debian.net/liststats/uploaders_debian-med.png ) )
Considering that you are from FSF I see potentially a more valuable
field where you can be extremely helpful for our project. You might
have read about our Software liberation Wiki:
https://wiki.debian.org/DebianMed/SoftwareLiberation
The discussion is sometimes hard and frustrating - mainly when being
ignored. The reason of beeing ignored is different - partly it can
perfectly be that people do not read their mail (for whatever reason -
overworked, mail ending up in SPAM, whetever). So it would really help
to have somebody who tries to ping people repeatedly and possibly on
different channels. For instance for my last ping to ffp
https://lists.debian.org/debian-med/2020/04/msg00213.html
I received the mail I appended here. The summary is that the author
"seems" to be happy with a free license but he failed to confirm this
properly and is not reachable.
Way more important than ffp is blat which I pinged here
https://lists.debian.org/debian-med/2020/04/msg00078.html
but it might be that the copyright owner Jim Kent is not reading his
e-mail. So pinging him on other channels and explain the importance
of a free blat would help.
I have also two packages in the R team I need to investigate
https://alioth-lists.debian.net/pipermail/r-pkg-team/2020-April/011420.html
https://alioth-lists.debian.net/pipermail/r-pkg-team/2020-April/011493.html
The latter goes deeper since in principle we would love to package
http://meme-suite.org/tools/meme
but my motivation to package non-free stuff is limited since it always
makes technical hassle inside Debian (no autobuilders, no autopkgtest,
etc). So if you would volunteer to dedicate your time to contact authors
about free licenses this would be a highly appreciated contribution which
in the end is more effective than hunting down issues that are inprinciple
exposed by automatic tools (and possibly overlooked here).
Kind regards and thanks again for your help
Andreas.
Andreas,
You'll have to wait for Gregory as the Lab nor UC Berkeley has any IP rights
here as far as we could tell. I also don't know him nor have ever met him.
Sebastian
-----Original Message-----
From: Andreas Tille <andreas at an3as.eu>
Sent: Thursday, April 16, 2020 7:09 AM
To: Sebastian Ainslie <sainslie at lbl.gov>; 'Suzanne Storar'
<ststorar at lbl.gov>; 'Gregory Sims' <gsims1997 at yahoo.com>; Debian Med Project
List <debian-med at lists.debian.org>
Subject: Re: free license for ffp-phylogeny Fwd: Debian project request
Hi again,
sorry for bothering you again, but the licensing issue for ffp is not solved
and despite I tried to contact Gregory Sims several times he never responded
via e-mail. The only statement he gave is just looking promising but its
not sufficient. His answer was:
From: Gregory Sims <gsims1997 at yahoo.com>
Date: July 13, 2018 at 2:22:40 PM PDT
To: Sebastian Ainslie <sainslie at lbl.gov>, "andreas at an3as.eu"
<andreas at an3as.eu>
Subject: Re: FW: FW: Debian project request
Andreas,
Then it is fine with me if you include the FFP code into a Debian
package.
Send me whatever release you need.
Gregory E. Sims, PhD
240-328-3327
In our COVID-19 effort we try to review all interesting software for
licensing issues and that's why I want to come back to you - possibly you
might have a better channel to Gregory than e-mail since my repeated mails
asking for clarification did not seem to reach him.
Why are the statements Gregory gave are not sufficient?
"Then it is fine with me if you include the FFP code into a Debian
package."
It does not specify the conditions, like the right to modify the source code
which is important to be considered free. It is simply in contrast to the
file COPYING inside the source tarball.
"Send me whatever release you need."
I can not even parse this sentence. We usually need the latest version
which is available from sourceforge. We can simply download it.
So what would be an optimal solution:
Please replace the file COPYING inside the file ffp-3.19.tar.gz which
can be downloaded from
https://sourceforge.net/projects/ffp-phylogeny/files/
by something containing one of the well established licenses like BSD,
MIT or GPL and release this with a new version for instance
ffp-3.19free.tar.gz
If this is to much effort (may be you lost sourceforge access after many
years of inactivity there?) it would be OK to send a mail to this public
list debian-med at lists.debian.org stating:
I'm the author and copyright holder of
https://sourceforge.net/projects/ffp-phylogeny/files/
I hereby release this software under ... (License of your choice)
which overrides the COPYRIGHT file that can be found inside the
source tarball.
Thanks a lot for supporting us in our attempt fo fight COVID-19 by providing
relevant software to researchers
Andreas.
On Mon, Sep 17, 2018 at 09:36:27AM -0700, Sebastian Ainslie wrote:
> Andreas. Please work with Gregory Simms on this. Our investigation
> through Berkeley Lab and UC Berkeley Tech Transfer offices had neither
> of us at UC owning the IP. It is all Gregory's and what he says goes.
> I believe he said it was ok but please look back through his
correspondence.
>
> Best
>
> Sebastian
>
> -----Original Message-----
> From: Andreas Tille [mailto:andreas at an3as.eu]
> Sent: Monday, September 17, 2018 4:51 AM
> To: Suzanne Storar <ststorar at lbl.gov>; Gregory Sims
> <gsims1997 at yahoo.com>
> Cc: Berkeley Lab Intellectual Property Office <ipo at lbl.gov>; Peter
> Bluford <pbluford at lbl.gov>; Sebastian Ainslie <sainslie at lbl.gov>;
> Debian Med Project List <debian-med at lists.debian.org>
> Subject: Re: free license for ffp-phylogeny Fwd: Debian project
> request
>
> Hi again,
>
> I hope I did not missed another mail of yours.
>
> May be my answer was not clear enough. According to the Debian Free
> Software Guidelines
>
> https://www.debian.org/social_contract#guidelines
>
> specifically item 8. "License Must Not Be Specific to Debian" it does
> not help if we send something to you and you give permission. It is
> you who needs to put the source code under a free license for everybody.
> For the Debian release the latest version (if not all versions) would
> be sufficient.
>
> Hope this clarifies my request
>
> Andreas.
>
> On Mon, Aug 27, 2018 at 09:28:12PM +0200, Andreas Tille wrote:
> > Hi Suzanne, hi Gregory,
> >
> > thanks for forwarding this mail. I actially missed it - and can not
> > find it in my mail folder archive.
> >
> > To answer Gregory's question: We usually package the latest version
> > - in this case as far as I can see on sourceforge[1] version 3.19.
> > It would help a lot if you could issue a "new version" (may be
> > 3.19.1 or
> > so) where you replace the COPYING file by the text of a free license.
> >
> > Thanks a lot
> >
> > Andreas.
> >
> > [1] http://sourceforge.net/projects/ffp-phylogeny/files/
> >
> > On Mon, Aug 27, 2018 at 10:22:03AM -0700, Suzanne Storar wrote:
> > > Hi Andreas,
> > >
> > > Regarding your inquiry, I had understood that Gregory Sims
> > > responded (see forwarded email below).
> > >
> > > Please let me know if anything else is required to meet your request.
> > >
> > > Best regards,
> > > Suzanne
> > >
> > > Suzanne T. Storar, P.E.
> > > 510-486-4306
> > > Communications and Outreach
> > > Intellectual Property Office (IPO) - Lawrence Berkeley National
> > > Laboratory
> > > - Berkeley, CA
> > > Available Technologies: http://ipo.lbl.gov/tech-index/ *Follow us
> > > on
> > > Twitter: @techLBNL*
> > >
> > > *From:* Gregory Sims <gsims1997 at yahoo.com>
> > > *Date:* July 13, 2018 at 2:22:40 PM PDT
> > > *To:* Sebastian Ainslie <sainslie at lbl.gov>, "andreas at an3as.eu" <
> > > andreas at an3as.eu>
> > > *Subject:* *Re: FW: FW: Debian project request*
> > >
> > > Andreas,
> > >
> > > Then it is fine with me if you include the FFP code into a Debian
> package.
> > > Send me whatever release you need.
> > >
> > > Gregory E. Sims, PhD
> > > 240-328-3327
> > >
> > >
> > > >>>> On Wed, Feb 7, 2018 at 10:28 PM, Andreas Tille
> > > >>>> <andreas at an3as.eu
> > > <mailto:andreas at an3as.eu> > wrote:
> > > >>>>
> > > >>>> Dear ladies and gentlemen,
> > > >>>>
> > > >>>> I was told by the copyright holder of ffp-phylogeny Gregory E.
> > > >>>> Sims that I should address my question to the Lawrence
> > > >>>> Berkeley National Lab which I'm hereby doing.
> > > >>>>
> > > >>>> I'm writing you on behalf of the Debian Med team that has the
> > > >>>> objective to package Free Software that is relevant in
> > > >>>> Biology and Medicine for main Debian. There is an overview
> > > >>>> what we have assembled
> > > up to now[1].
> > > >>>>
> > > >>>> One of my users asked me to package the programm
ffp-phylogeny[1].
> > > >>>> The creation of package files went smoothly thanks to your
> > > >>>> well designed build system. The needed files are injected
> > > >>>> into our packaging repository[3].
> > > >>>>
> > > >>>> Unfortunately the license of ffp-phylogeny does not permit
> > > >>>> distribution by Debian since it is in contrast with item 5. and
6.
> > > >>>> with the Debian Free Software Guidelines[4] since commercial
> > > >>>> users / usage are discriminated by your license statement. I
> > > >>>> wonder whether you might consider to change this license to
> > > >>>> one of the common free licenses for instance GPL or BSD.
> > > >>>>
> > > >>>> Thanks for considering
> > > >>>>
> > > >>>> Andreas.
> > > >>>>
> > > >>>>
> > > >>>> [1] http://blends.debian.org/med/tasks/bio
> > > >>>> [2] http://sourceforge.net/projects/ffp-phylogeny/
> > > >>>> [3] https://anonscm.debian.org/git/debian-med/ffp.git
> > > >>>> [4] https://www.debian.org/social_contract#guidelines
> > > >>>>
> > > >>>> --
> > > >>>> http://fam-tille.de
> > > >>>>
> > > >>>>
> > > >>
> > > >> --
> > > >> http://fam-tille.de
> > > >>
> > > >>
> > > >>
> > > >
> > > > --
> > > > http://fam-tille.de
> >
> > --
> > http://fam-tille.de
> >
> >
>
> --
> http://fam-tille.de
>
>
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