From: Vlastimil Zíma (zima_at_karlov.mff.cuni.cz)
Date: Wed Aug 13 2014 - 12:21:12 CDT

Yet another build on debian wheezy, but on different machine. Not to build
a package.

=== Build dependencies ===
latex2html 2008-debian1-7
libfltk1.3-dev 1.3.0-8
libglu1-mesa-dev 8.0.5-4+deb7u2
libnetcdf-dev 1:4.1.3-6+b1
libxi-dev 2:1.6.1-1+deb7u1
make 3.81-8.2
python-dev 2.7.3-4+deb7u1
python-numpy 1:1.6.2-1.2
tcl-dev 8.5.0-2.1
texlive-latex-base 2012.20120611-5
tk-dev 8.5.0-2.1

=== Build process ===
tar -xzf vmd_1.9.1.orig.tar.gz
cd vmd-1.9.1
mv ../plugins plugins_src
export PLUGINDIR=$PWD/plugins
export TCL_INCLUDE_DIR=/usr/include/tcl
export TK_INCLUDE_DIR=/usr/include/tk
export PYTHON_INCLUDE_DIR=/usr/include/python2.7
export NUMPY_INCLUDE_DIR=/usr/include/python2.7/numpy
export VMDINSTALLBINDIR=$PWD/root/bin
export VMDINSTALLLIBRARYDIR=$PWD/root/lib
# Compile plugins
make -C plugins_src LINUXAMD64 TCLINC=-I${TCL_INCLUDE_DIR} TCLLIB=
-I/usr/share/tcltk/tcl8.5
make -C plugins_src distrib
sed -i 's|python2.5|python2.7|' configure
./configure LINUXAMD64 OPENGL FLTK TK IMD XINPUT NETCDF CONTRIB TCL PYTHON
PTHREADS NUMPY NOSTATICPLUGINS
make -C src
make -C src install

And it's broken again.

Vlastimil

2014-08-13 18:34 GMT+02:00 Vlastimil Zíma <zima_at_karlov.mff.cuni.cz>:

> 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/
>>>>
>>>
>>>
>>
>>
>