[Debian-med-packaging] Bug#815176: staden: Gap4 contig editor does not show sequences

[Kerstin Hoef-Emden]

Hi to all,

On Tue, 23 Feb 2016, Andreas Tille wrote:

>
> Kerstin, you can either download the staden packages from unstable from
> here:
>
>   https://packages.debian.org/source/unstable/staden
>
> and install manually on your Jessie system

I had a look at the requirements in the README.build file. Manual 
install is not straightforward. Itcl, itk and iwidgets are not available 
for jessie. Also configure complains about a missing io_lib. I search 
the packages and found staden-io-lib-utils, but could not find a 
staden-io_lib.so or something to which I could point with a path. 
Libstaden is something different is it? All other dependencies seem to 
be sufficient.

> or you add unstable to your
> /etc/apt/sources.list.  ATTENTION: You need to adapt
> /etc/apt/preferences to make sure you will not bump your whole system
> to unstable!

The most "dangerous" and possibly destabilizing actions I did, were 
installations of backports. I usually don't dare to touch sid. Probably 
the install will also result in the missing itcl etc. being installed? 
Will it work, if I restrict it as such?

Package: staden
Pin: release n=sid
Pin-Priority: 900

Best wishes,

Kerstin

>
> On Mon, Feb 22, 2016 at 05:42:38PM +0000, James Bonfield wrote:
>> On Mon, Feb 22, 2016 at 04:34:13PM +0100, Andreas Tille wrote:
>>> if I understand you correctly you are suggesting a further change.  Could
>>> you please confirm that this patch
>>>
>>>     https://anonscm.debian.org/viewvc/debian-med/trunk/packages/staden/trunk/debian/patches/cope_with_modern_windowmanager.patch?view=markup
>>
>> Yes that's it.
>>
>> The other change was an improvement to resizing.
>>
>> This is long and tedious so feel free to ignore, but if you're curious
>> then here are the details.  Typically window managers treat windows as
>> one of two flavours:
>>
>> 1) The program set the size, so it's permitted to change it again
>> itself.
>>
>> 2) The user resized the window, so the application request to resize
>> it will be ignored.
>>
>> Tk wm geometry command allows you to programatically change the size
>> of window or with the blank size (wm geometry . {} {}) it'll reset the
>> window to case 1 - governed by the program rather than the user.
>>
>> This is all very ICKY and it gets worse.  Gap4's contig editor is
>> "courageously" setting the Y dimension itself based on how many rows
>> of sequences it wants to display.  The X dimension can be controlled
>> by the user, but as the user increases the size in X, more sequences
>> can become visible causing the Y dimension to be resized.  In the past
>> this caused massive fights between various parts of tcl/tk and window
>> managers, sometimes triggering event loops with oscillating window
>> dimensions.  The workaround for this was to have a 1 second delay
>> between resizing the window and asking the program to recompute the
>> size.
>>
>> That in turn though broke all modern window managers.  Basically if
>> you resized quickly and let go it'd just snap back - you had to
>> resize, hold and wait for 1 sec, and then release. Bizantine...  Try
>> hard as I may I couldn't recreate the strange oscillations so this
>> change basically pushes it back to how it used to be with instant
>> recomputation.  It seems to work much better in general, but still
>> isn't perfect.
>>
>> Perfection isn't possible when you start with the premise of X being
>> user controlled and Y being program controlled!  With Gap5 fortunately
>> we had an attack of sanity and chose a more traditional strategy.
>>
>> James
>>
>> PS. Kerstin if you're still reading this, if set -x doesn't work then
>> just editing the first #! line to be "#!/bin/sh -x" (without the
>> quotes) should do the same thing, or simpler still typing in
>>
>>   sh -x `which pregap4`
>>
>> --
>> James Bonfield (jkb at sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
>>                                   | Plurima gyrabant gymbolitare vabo;
>>   A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
>> https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi.
>>
>>
>> --
>>  The Wellcome Trust Sanger Institute is operated by Genome Research
>>  Limited, a charity registered in England with number 1021457 and a
>>  company registered in England with number 2742969, whose registered
>>  office is 215 Euston Road, London, NW1 2BE.
>>
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>>
>
>

-- 

PD Dr. Kerstin Hoef-Emden			Zülpicher Str. 47b
Universität zu Köln				50674 Köln
Biozentrum Köln (Cologne Biocenter)		Germany
Botanisches Institut

http://www.uni-koeln.de/~aeb25/