VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Aug 13 2014 - 09:48:33 CDT

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
> <mailto: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 <mailto: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 <mailto: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
> <mailto: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 <mailto: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/
> <http://www.ks.uiuc.edu/%7Ejohns/> Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
>
>