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" <san...@scripps.edu> > > An: "Steffen Möller" <steffen_moel...@gmx.de>, "Andreas Tille" > > <andr...@an3as.eu> > > Cc: "Stefano Forli" <fo...@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: fo...@scripps.edu > > >>>> http://www.scripps.edu/~forli/ > > >>>> ________________________________________ > > >>>> From: Steffen Möller [steffen_moel...@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 <sgolo...@nes.ru> ----- > > >>>>> > > >>>>> Date: Thu, 24 Dec 2015 10:52:27 +0300 > > >>>>> From: Sergei Golovan <sgolo...@nes.ru> > > >>>>> To: Andreas Tille <andr...@an3as.eu> > > >>>>> Cc: Senthil Kumaran <style...@gmail.com>, 767...@bugs.debian.org, > > >>>>> Tcl/Tk Debian Packagers <pkg-tcltk-de...@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 <andr...@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 san...@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 san...@scripps.edu http://www.scripps.edu/~sanner > > ----------------------------------------------------------------------- > > > > > -- http://fam-tille.de
