From: Vlastimil Zíma (zima_at_karlov.mff.cuni.cz)
Date: Wed Aug 13 2014 - 11:34:42 CDT

Hi Josh,

thanks for the reply. I've tried to build VMD as is quite some time ago,
but as far as I can remember I had the same issue. The paths doesn't seem
to be an issue, as I've defined all Tcl related variables, otherwise the
compilation would break. In my experience debian builds complain quite
effectively. Anyway I checked (grep -i 'error\|fail') the output and
haven't found any errors in there.

I'll try to build VMD without packaging and provide further info.

Vlastimil

2014-08-13 16:48 GMT+02:00 Josh Vermaas <vermaas2_at_illinois.edu>:

> Hi Vlastimil,
>
> I've compiled VMD for Ubuntu and packaged it for myself as you've done,
> and that isn't something I've seen before. Others have noticed that
> depending on your linux installation, some characters are missing from the
> system defaults (Angstrom seems to be the most common one). Have you tried
> to build VMD in a non-packaged way first? Looking at the rules file, the
> set directories look plausible depending on your system setup, but I
> vaguely remember for instance needing to specify a version number to pick
> up the appropriate header files and shared libraries (so
> /usr/include/tcl8.5 instead of /usr/include/tcl, and actually specifying a
> TCL_LIBRARY_DIR since the shared object wasn't in /usr/lib). The debian
> package building process in my limited experience hides errors very
> effectively, so if something went wrong, it won't stop dpkg from building
> and making something that looks plausible as a package that is totally
> broken.
>
> I'm just spitballing here. There is nothing obviously wrong (to my eyes at
> least) with your configuration, and I've never seen the error that you
> report, so I'm sorry I can't be more helpful. :(
> -Josh Vermaas
>
>
> On 8/13/14, 5:12 AM, Vlastimil Zíma wrote:
>
> Hi everyone,
>
> continuing on this issue as there is indication I'm not the only one
> suffering by this problem, see
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21361.html.
>
> Sum up the configuration:
> * Debian wheezy (stable), using system libraries, so they're not likely
> to be broken.
> * I run VMD from console on my machine.
> * Doesn't look like problem with font installation. "font families"
> returns the same result for tcl shell and vmd tcl shell.
> * I don't have SCIM installed which may cause troubles.
> * All my machines run under English locales "en_US.UTF-8".
>
> Since first error is
>
> X_QueryColors: BadValue (integer parameter out of range for operation)
> 0xff000000
>
> I begin to suspect it may not be a problem related to fonts but rather to
> the graphics in more general manner, e.g. wrong order of layers.
>
> I tried to debug Tcl a bit and find out the errors appears after function
> `::timeline::startTimeline` is finished. But this may be of course caused
> by delay between window setup and its rendering.
>
> I've published debian packaging metadata at github
> https://github.com/ziima/vmd-debian. I'd be glad if anyone cares to
> investigate or build the package using my metadata.
> Alternatively I'm looking for somebody who compiled VMD successfully on
> Debian or Ubuntu.
>
> Regards,
> Vlastimil
>
>
> 2013-12-04 10:11 GMT+01:00 Vlastimil Zíma <zima_at_karlov.mff.cuni.cz>:
>
>> Hi John,
>>
>> I haven't compiled Tk myself, I use system library. But all code which
>> is based on Tk works to my knowledge.
>>
>> As noted in my first email, I created a simple script based on code I
>> considered to cause problems in Timeline plugin:
>>
>> $ cat tk_test.tcl
>> package require Tk
>>
>> font create tkFixedTimeline -family Courier -size -12
>> ttk::label .l -text "Attention!" -font tkFixedTimeline
>> grid .l -row 0
>>
>> This script works as expected. I also use a program Seaview, which uses
>> libfltk1.3 as well, without any problems. For these reasons I expect that
>> the system Tcl/Tk libraries work as they should.
>>
>> I was not able to find any other problematic code in Timeline plugin
>> and I'm not able to run the Timeline plugin outside of VMD, so I don't have
>> any other Tk GUI script to test. If you can recommend any tests I'd like to
>> try them out.
>>
>> Vlastimil
>>
>> 2013/11/27 John Stone <johns_at_ks.uiuc.edu>
>>
>>> Vlastimil,
>>> If your compilation of Tk is misbehaving, but our pre-compiled VMD
>>> binaries work okay, I would check what options were used when you
>>> compiled your Tk, and consider disabling antialiased fonts and see if
>>> that makes any difference. Are you able to run an Tk scripts with
>>> just the Tcl/Tk builds you did on your machine? In other words, is
>>> the problem isolated to Tcl/Tk on your machine, or do you have a
>>> Tk GUI script that works in 'wishx' but fails within VMD? It would be
>>> useful to narrow down the problem and see if it is purely an issue
>>> with your Tcl/Tk, or if it is something unique to running within VMD.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Wed, Nov 27, 2013 at 05:11:34PM +0100, Vlastimil Zíma wrote:
>>> > Hi everybody,
>>> >
>>> > wheezy became stable, but I still experience this problem.
>>> >
>>> > Anyway, I now suggests this may not be a problem of fonts, but
>>> rather
>>> > colors. I tried to check the error output, see my previous post
>>> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19942.html
>>> and I
>>> > have an impression that fonts might be properly rendered but they
>>> are over
>>> > painted by some other invalid entity (images or colored blocks).
>>> >
>>> > Is there any other Tk-related build/runtime dependency that is not
>>> mention
>>> > in documentation?
>>> >
>>> > Regards,
>>> > Vlastimil
>>> >
>>> > 2012/10/5 Vlastimil ZAma <zima_at_karlov.mff.cuni.cz>
>>> >
>>> > Hi,
>>> >
>>> > when I compared my compiled VMD with precompiled binary some time
>>> ago,
>>> > the fonts were present in the precompiled one. That is why I
>>> expect
>>> > problems in compilation. I also did not noticed any lack of fonts
>>> in
>>> > system paths, but I do not know which fonts to look for.
>>> >
>>> > > tclsh
>>> > % package require Tk
>>> > 8.5.11
>>> > % puts "$tcl_version"
>>> > 8.5
>>> > % puts "$tk_version"
>>> > 8.5
>>> >
>>> > All tcl and tk packages I have are for amd64 bit architecture (all
>>> > libraries are in /usr/lib). Specifically
>>> >
>>> > http://packages.debian.org/wheezy/tcl8.5 version 8.5.11-2
>>> > http://packages.debian.org/wheezy/tk8.5 version 8.5.11-2
>>> >
>>> > Regards,
>>> > Vlastimil
>>> >
>>> > On 10/05/2012 04:08 PM, John Stone wrote:
>>> >
>>> > Hi,
>>> > A A Problems with Tk fonts are generally caused not by the
>>> > compilation of
>>> > VMD (or FLTK) but are usually the result of a lack of fonts
>>> installed
>>> > with the X11 Windowing system. A Tk obtains its fonts by
>>> querying the
>>> > host windowing system for fonts that match the characteristics
>>> of a
>>> > request.
>>> > If the host windowing system has no match, then Tk tries to
>>> fallback
>>> > to
>>> > some font that is available.
>>> >
>>> > A From the description below, it sounds to me like there might
>>> be
>>> > something
>>> > amiss the X11 window system fonts or one of the X11 libraries
>>> on the
>>> > machine
>>> > you're using, and that this is preventing the Tk library
>>> embedded in
>>> > VMD from getting anything other than the default font.
>>> >
>>> > Since you're able to get a simple test to work in a standalone
>>> > interpreter,
>>> > one thing that may be worth checking is whether there might be
>>> some
>>> > problem with the 64-bit libs on your machine. A Is the "tclsh"
>>> that
>>> > you
>>> > run in your example below a 32-bit or 64-bit library? A What do
>>> you
>>> > get
>>> > from this command, when you run it in your tclsh:
>>> > A A puts "$tcl_version"
>>> > A A puts "$tk_version"
>>> >
>>> > Cheers,
>>> > A A John Stone
>>> > A A vmd_at_ks.uiuc.edu
>>> >
>>> > On Thu, Oct 04, 2012 at 11:07:03AM +0200, Vlastimil ZAma wrote:
>>> >
>>> > A A Hi,
>>> >
>>> > A A after several attempts I still can not resolve troubles
>>> with
>>> > tk fonts when
>>> > A A I compile VMD.
>>> >
>>> > A A I am using 64bit Debian with following vmd
>>> configuration:
>>> >
>>> > A A ./configure LINUXAMD64 OPENGL FLTK TK IMD XINPUT NETCDF
>>> > CONTRIB TCL PYTHON
>>> > A A PTHREADS NUMPY NOSTATICPLUGINS
>>> >
>>> > A A and tk packages:
>>> > A A libfltk1.3-dev 1.3.0-8 (I also tried fltk1.1)
>>> > A A tcl-dev 8.5.0-2
>>> > A A tk-dev 8.5.0-2
>>> >
>>> > A A Still timeline, sequence viewer and other plugins which
>>> uses
>>> > customized
>>> > A A fonts has invisible texts. I tried anything I found on
>>> this
>>> > mailing list,
>>> > A A including LC_ALL=C in environment and $HOME/.tkconrc
>>> file. I
>>> > also tried a
>>> > A A simple script with uses custom font based on code of
>>> timeline
>>> > which works:
>>> >
>>> > A A > A tclsh
>>> > A A package require Tk
>>> > A A font create tkFixedTimeline -family Courier -size -12
>>> > A A ttk::label .l -text "Attention!" -font tkFixedTimeline
>>> > A A grid .l -row 0
>>> >
>>> > A A This shows nice small box with monofont "Attention!" in
>>> it.
>>> >
>>> > A A I will be glad for any help which would help to resolve
>>> this
>>> > problem.
>>> > A A Vlastimil
>>>
>>> --
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/
>>>
>>
>>
>
>