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 <andr...@an3as.eu> > Sent: Thursday, April 16, 2020 7:09 AM > To: Sebastian Ainslie <sains...@lbl.gov>; 'Suzanne Storar' > <ststo...@lbl.gov>; 'Gregory Sims' <gsims1...@yahoo.com>; Debian Med Project > List <debian-med@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 <gsims1...@yahoo.com> > Date: July 13, 2018 at 2:22:40 PM PDT > To: Sebastian Ainslie <sains...@lbl.gov>, "andr...@an3as.eu" > <andr...@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@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:andr...@an3as.eu] >> Sent: Monday, September 17, 2018 4:51 AM >> To: Suzanne Storar <ststo...@lbl.gov>; Gregory Sims >> <gsims1...@yahoo.com> >> Cc: Berkeley Lab Intellectual Property Office <i...@lbl.gov>; Peter >> Bluford <pbluf...@lbl.gov>; Sebastian Ainslie <sains...@lbl.gov>; >> Debian Med Project List <debian-med@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 <gsims1...@yahoo.com> >>>> *Date:* July 13, 2018 at 2:22:40 PM PDT >>>> *To:* Sebastian Ainslie <sains...@lbl.gov>, "andr...@an3as.eu" < >>>> andr...@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 >>>>>>>> <andr...@an3as.eu >>>> <mailto:andr...@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 > > >
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