[Debian-med-packaging] Bug#783547: That long-standing nasty Tcl/Tk-bug with autodocktools (Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI))
Andreas Tille
andreas at an3as.eu
Wed Feb 10 14:00:49 UTC 2016
Hi Steffen,
On Wed, Feb 10, 2016 at 02:08:48PM +0100, "Steffen Möller" wrote:
> Hello Michel,
>
> > Gesendet: Mittwoch, 10. Februar 2016 um 01:14 Uhr
> > Von: "Michel Sanner" <sanner at scripps.edu>
> > An: "Steffen Möller" <steffen_moeller at gmx.de>, "Andreas Tille" <andreas at an3as.eu>
> > Cc: "Stefano Forli" <forli at scripps.edu>
> > Betreff: Re: That long-standing nasty Tcl/Tk-bug with autodocktools Re: Bitte weiterleiten (Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI))
> >
> > Hello Steffen
> >
> > Sorry for dropping the ball on this. I am a bit confused why this
> > happens as we ship MGLTools with the Tcl/Tk
> > libraries provided and 1.5.7 rc1 ships with Tcl Tk 8.5
>
> I admit to be tempted to just tar all you provide up and then redistribute
> just that. Would save us from quite some hassles.
... IMHO this will just replace the known hassles by new ones.
> But we would not have
> identified that bug for you, either :o) From what I had identified about
> half a year ago (two nights or so went into it) I had no idea why 8.5
> tolerated it. I could well imagine that this fix also helps the overall
> stability of your suite.
>
> The deep theory is that by note having independent (Windows-/Mac-like)
> software installation, i.e. by sharing as much as we all can, any improvemnt
> to any package would have as much of an effect as soon as possible on
> as many as possible other packages. And it should be fun, too. Debian has
> the stable distribution for what works (with Tk 8.5), testing and unstable
> are to get stuff synced up. And, you shall also benefit from 8.6.
>
> https://www.tcl.tk/software/tcltk/8.6.html overview
> http://wiki.tcl.tk/21276 changes
> http://www.tcl.tk/cgi-bin/tct/tip/311 release calendar - 8.6 started 2008 :)
>
> Admittedly, 8.5 is still mainained, also in Debian as it seems
> https://packages.debian.org/search?keywords=tk8.5
> but the default is 8.6 and all other modules and libraries depending on any
> libtk are rebuilt against the newer version, i.e. any Python module with it,
> https://packages.debian.org/de/sid/python-tk
I do not think that trying to safe the issue by forcing tk8.5 will be a
sustainable solution.
> > I suppose you guys rebuild from scratch and do not create an isolated
> > environment for running the Python
> > interpreter that runs AutoDockTools like we do when people install using
> > our installer ?
>
> That is correct.
>
> > I will look if I can find a quick fix as this happens in a gui that is
> > no often made visible
>
> It affects about everything that you can start with AutoDockTools. I will
> not let you alone with it all. I just saw your second email and will address
> that over the weekend the latest.
As I expressed in my other mail we now have an additional issue with numpy.
Kind regards
Andreas.
> > On 12/29/2015 05:00 PM, Steffen Möller wrote:
> > > Hello Michel, hello Stefano,
> > >
> > > nice to hear from you, indeed. I happen to be a recent El Capitan user
> > > myself and thus
> > > can help testing on that front, too.
> > >
> > > I was not aware of a release of 1.5.7, which I had seen only as a RC1,
> > > using the
> > > information shown on
> > > http://mgltools.scripps.edu/downloads
> > > The problem should manifest itself on any platform with TclTk 8.6 onwards.
> > > Until a few seconds ago I had truly thought that you were working on
> > > something
> > > completely different already that would be released once it is ready and as
> > > such you did not notice/care about that "works with 8.5" problem.
> > >
> > > How shall we proceed? I propose that we get the code base and tools in sync
> > > and I prepare an update of the Debian packages. Is the CVS repository of
> > > yours
> > > still the place where to look? What version of TclTk do you work with?
> > > Just instruct me.
> > >
> > > Concerning the time line I am swamped till mid January. We have our next
> > > Debian meeting in Copenhagen on the first February weekend. Would be nice to
> > > have the bug fixed till then.
> > >
> > > Best,
> > >
> > > Steffen
> > >
> > >
> > > On 29/12/15 21:29, Andreas Tille wrote:
> > >> Hi Michel,
> > >>
> > >> As far as I know installing Tcl/Tk 8.6 you should be able to reproduce
> > >> the problem. The best resource of information is probably
> > >>
> > >> https://lists.alioth.debian.org/pipermail/pkg-tcltk-devel/2015-December/002938.html
> > >>
> > >> Hope this helps
> > >>
> > >> Andreas.
> > >>
> > >> On Tue, Dec 29, 2015 at 11:20:20AM -0800, Michel Sanner wrote:
> > >>> Happy Holidays all
> > >>>
> > >>> I am not aware of this bug. Could you please let me know how to reproduce it
> > >>> ? and of course
> > >>> if you have a patch I'll be happy to incorporate it. We are working on a bug
> > >>> fix release of MGLTools 1.5.7
> > >>>
> > >>> This release has been postponed a little as we are trying to address some
> > >>> issues with the newest Mac OS
> > >>> El Capitan. This delay will hopefully gives us time to incorporate a bug fix
> > >>> for this problem as well
> > >>>
> > >>> -Michel
> > >>>
> > >>> On 12/29/15 10:22 AM, Stefano Forli wrote:
> > >>>> Hi Steffen (and Andreas),
> > >>>> I hope you're having happy Holidays yourselves. I'm currently in Italy enjoying some time with family.
> > >>>> No worries about bothering, you're all doing us a huge favor, so we're always in debt.
> > >>>>
> > >>>> I'm CC'ing Michel in the conversation, since he's in charge of the source code.
> > >>>> I got bit by these issues with Tcl with the old Raccoon version you packaged, but I wasn't aware of the problems with the main package AutoDockTools.
> > >>>> If you think it is something that can be solved with a reasonable amount of patches, I believe there's no problem in adding them to our CVS (but I'll let Michel chip in about this).
> > >>>>
> > >>>> I'll be happy to test the patched code, if you have any.
> > >>>>
> > >>>> Thanks!
> > >>>>
> > >>>> S
> > >>>>
> > >>>>
> > >>>> --
> > >>>>
> > >>>> Stefano Forli, PhD
> > >>>>
> > >>>> Assistant Professor of Integrative
> > >>>> Structural and Computational Biology,
> > >>>> Molecular Graphics Laboratory
> > >>>>
> > >>>> Dept. of Integrative Structural
> > >>>> and Computational Biology, MB-112F
> > >>>> The Scripps Research Institute
> > >>>> 10550 North Torrey Pines Road
> > >>>> La Jolla, CA 92037-1000, USA.
> > >>>>
> > >>>> tel: +1 (858)784-2055
> > >>>> fax: +1 (858)784-2860
> > >>>> email: forli at scripps.edu
> > >>>> http://www.scripps.edu/~forli/
> > >>>> ________________________________________
> > >>>> From: Steffen Möller [steffen_moeller at gmx.de]
> > >>>> Sent: Tuesday, December 29, 2015 12:55 AM
> > >>>> To: Andreas Tille; Stefano Forli
> > >>>> Subject: That long-standing nasty Tcl/Tk-bug with autodocktools Re: Bitte weiterleiten (Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI))
> > >>>>
> > >>>> Hi Stefano,
> > >>>>
> > >>>> some merry Christmas I hope you had and all the best for the New Year,
> > >>>> of course. The inter-annual time (as we say over here) is most likely
> > >>>> the most productive in the Open Source world :) Please forgive me
> > >>>> contacting you during all these festivities.
> > >>>>
> > >>>> I admit to know about this Tcl bug for some time, and I had even kind of
> > >>>> traced it down: the autodocktools do not pack their widgets right, i.e.
> > >>>> they are missing absolute and relative positions. Later versions than
> > >>>> 8.5 are apparently no longer tolerating it, and 8.6 is no longer any
> > >>>> recent version, I am afraid. Andreas is about to remove the package from
> > >>>> the distro as it is unusable as it is.
> > >>>>
> > >>>> How are your feelings about it all? Would you accept patches? Is there
> > >>>> something in your CVS that we should address, instead?
> > >>>>
> > >>>> All the best possible wishes
> > >>>>
> > >>>> Steffen
> > >>>>
> > >>>> On 29/12/15 08:40, Andreas Tille wrote:
> > >>>>> Hi Steffen,
> > >>>>>
> > >>>>> kannst Du das bitte mal an die Autoren weiterleiten (und den Bug in CC
> > >>>>> setzen). Ansonsten lasse ich das Paket entfernen, weil es ja
> > >>>>> offensichtlich zu nichts nütze ist, wenn es nicht mal startet.
> > >>>>>
> > >>>>> Viele Grüße
> > >>>>>
> > >>>>> Andreas.
> > >>>>>
> > >>>>> ----- Forwarded message from Sergei Golovan <sgolovan at nes.ru> -----
> > >>>>>
> > >>>>> Date: Thu, 24 Dec 2015 10:52:27 +0300
> > >>>>> From: Sergei Golovan <sgolovan at nes.ru>
> > >>>>> To: Andreas Tille <andreas at an3as.eu>
> > >>>>> Cc: Senthil Kumaran <stylesen at gmail.com>, 767145 at bugs.debian.org, Tcl/Tk Debian Packagers <pkg-tcltk-devel at lists.alioth.debian.org>
> > >>>>> Subject: Re: [Pkg-tcltk-devel] Tcl/Tk help needed (Was: Bug#767145: autodocktools: fails to start the GUI)
> > >>>>>
> > >>>>> Hi Andreas,
> > >>>>>
> > >>>>> On Wed, Dec 23, 2015 at 11:42 PM, Andreas Tille <andreas at an3as.eu> wrote:
> > >>>>>> Hi Tcl/Tk packaging team,
> > >>>>>>
> > >>>>>> unfortunately I got no help on debian-mentors and since we somehow need
> > >>>>>> to tackle bug #767144 I wonder if you Tcl/Tk experts might be able to
> > >>>>>> provide some help.
> > >>>>> As far as I can see, you've stumbled on the change between Tcl/Tk 8.5
> > >>>>> and 8.6. In Tcl/Tk 8.5 one could mix grid and pack geometry managers
> > >>>>> in one master window. It often works but sometimes leads to
> > >>>>> unpredictable results, sometimes an application which does that just
> > >>>>> hangs. In Tcl/Tk 8.6 this mixing of grid and pack was explicitly
> > >>>>> forbidden, hence this error message.
> > >>>>>
> > >>>>> I don't think that there is an easy way to fix this. You can't just
> > >>>>> revert to using Tcl/Tk 8.5 because Tkinter in Debian is already
> > >>>>> switched to Tk 8.6 (and I guess using custom Tkinter is not an
> > >>>>> option). So, one has to carefully find all mixed up packs and grids
> > >>>>> and make sure that only one of them is used in every particular master
> > >>>>> window. In plain Tcl/Tk I'd override the [pack] and [grid] routines to
> > >>>>> print some debug information (something like
> > >>>>>
> > >>>>> rename pack pack:orig
> > >>>>> proc pack {args} {
> > >>>>> puts stderr "pack: [info level -1] $args"
> > >>>>> pack:orig {*}$args
> > >>>>> }
> > >>>>>
> > >>>>> and similar for grid). This would help to trace where exactly the
> > >>>>> mixed geometry master windows appear. I don't know how you can do
> > >>>>> something similar in Python, but I'm pretty sure it's possible.
> > >>>>>
> > >>>>> Cheers!
> > >>> --
> > >>>
> > >>> -----------------------------------------------------------------------
> > >>> o
> > >>> / Michel F. Sanner Ph.D. The Scripps Research Institute
> > >>> o Associate Professor Department of Molecular Biology
> > >>> \ 10550 North Torrey Pines Road
> > >>> o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26
> > >>> / Fax. (858) 784-2341
> > >>> o sanner at scripps.edu http://www.scripps.edu/~sanner
> > >>> -----------------------------------------------------------------------
> > >>>
> > >>>
> >
> > --
> >
> > -----------------------------------------------------------------------
> > o
> > / Michel F. Sanner Ph.D. The Scripps Research Institute
> > o Associate Professor Department of Molecular Biology
> > \ 10550 North Torrey Pines Road
> > o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26
> > / Fax. (858) 784-2341
> > o sanner at scripps.edu http://www.scripps.edu/~sanner
> > -----------------------------------------------------------------------
> >
> >
>
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