[Debian-med-packaging] Other ways to help the Debian Med team: Ping about free licenses (Was: maude new version and standard outdated)
Ben Tris
benattris at gezapig.nl
Fri Apr 17 23:22:03 BST 2020
Hello Andreas,
Added the link to SoftwareLiberation to my page, with ask extra help for
ffp, blat, meme.
Earlier I had already tried to draw attention, and I investigated a
little how I could help.
(Sometimes I do bug reports and mail about license issues.)
That page I'm not keeping up forever, today was the last update.
Hopefully it draws some extra help for Debian Med (There is a link to it
indirect from the homepage of the FSD).
I didn't really understand if you would liked to be noticed, but these
are probably all those test messages at this moment:
(Was the last time I'm going to check.)
arch amd64 binaries uploaded / arch all binaries uploaded, source-only
upload is needed:
https://tracker.debian.org/pkg/fasta3
arch all binaries uploaded, source-only upload is needed:
https://tracker.debian.org/pkg/dnapi
https://tracker.debian.org/pkg/hdmf
https://tracker.debian.org/pkg/python-bel-resources
https://tracker.debian.org/pkg/python-bids-validator (new version
available)
https://tracker.debian.org/pkg/pyxid
https://tracker.debian.org/pkg/resfinder-db (new version available)
https://tracker.debian.org/pkg/smart-open
arch amd64 binaries uploaded:
https://tracker.debian.org/pkg/idba
https://tracker.debian.org/pkg/orthanc-python
https://tracker.debian.org/pkg/skewer
More issues:
arch all binaries uploaded, source-only upload is needed
https://tracker.debian.org/pkg/pbsuite
https://tracker.debian.org/pkg/jalview (new version available)(bio
(Debian Java Maintainers))
I wish you all the best with this project.
Nice Day,
On 17-04-20 09:37, Andreas Tille wrote:
> 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
>>
>>
> --
> http://fam-tille.de
>
>
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 819 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20200418/8a86460e/attachment.sig>
More information about the Debian-med-packaging
mailing list