[Debichem-devel] ghemical 3.0.0-2 in sid does not display color or allow building

[Carlo Segre]

Hello:

Apologies in advance for the long post but I wanted to be thorough.

I am not yet filing a bug on this becuase I am not sure that ghemical is 
the correct package to file against.  This is a problem I am having in my 
sid installation and it prevents me from upgrading a bunch of packages.

When I install ghemical 3.0.0-2 and all of its dependencies, the display 
only appears in greyscale.  This happens both when I load a *.gpr file or 
import a *.xyz file.

I can rotate the models and select atoms over which to measure distances 
and bond lengths.  I can delete atoms or bonds too.  However, when I try 
to add atoms or construct bonds, nothing appears on the display.

The ghemical packages installed are:

ghemical  3.0.0-2  amd64  GNOME molecular modelling environment
libghemical-data  3.0.0-4.1  all  Molecular Modelling Library (data files)
libghemical5v5  3.0.0-4.1+b3 amd64  Molecular Modelling Library

In the terminal window where I start ghemical, I have the following 
text

---
OpenGL visual configurations :

gdk_gl_config_is_rgba (glconfig) = TRUE
gdk_gl_config_is_double_buffered (glconfig) = TRUE
gdk_gl_config_is_stereo (glconfig) = FALSE
gdk_gl_config_has_alpha (glconfig) = FALSE
gdk_gl_config_has_depth_buffer (glconfig) = TRUE
gdk_gl_config_has_stencil_buffer (glconfig) = FALSE
gdk_gl_config_has_accum_buffer (glconfig) = FALSE

PrintToLog : A new project created.
DEBUG : draw state is 1
DEBUG : orbit_xy skipped ; counter = 1
---

I can continue to have the color and building behavior work in sid if I 
keep the following versions:

ghemical  3.0.0-1  amd64  GNOME molecular modelling environment
libghemical-data  3.0.0-2  all  Molecular Modelling Library (data files)
libghemical5  3.0.0-2  amd64  Molecular Modelling Library

If I want to upgrade ghemical, three packages would be removed:

  libghemical5
  libopenbabel4
  libsc7

and the following packages are upgraded or installed:

  ghemical
  libghemical-data
  libsc-data
  mpqc
  libghemical5v5
  libopenbabel4v5
  libsc7v5

In my still working configuration, I see the following in the text 
terminal when I start ghemical and try to create atoms.

---
OpenGL visual configurations :

gdk_gl_config_is_rgba (glconfig) = TRUE
gdk_gl_config_is_double_buffered (glconfig) = TRUE
gdk_gl_config_is_stereo (glconfig) = FALSE
gdk_gl_config_has_alpha (glconfig) = FALSE
gdk_gl_config_has_depth_buffer (glconfig) = TRUE
gdk_gl_config_has_stencil_buffer (glconfig) = TRUE
gdk_gl_config_has_accum_buffer (glconfig) = FALSE

PrintToLog : A new project created.
DEBUG : draw state is 1
DEBUG : orbit_xy skipped ; counter = 1
---

The significant difference is the TRUE value for 
gdk_gl_config_has_stencil_buffer (glconfig) compared to the grescale 
version.

This is why I suspect the problem is not in ghemical but somewhere else. 
Another clue is that avogadro also fails to display atoms completely when 
upgraded to the same state.

I wonder if anyone else has seen this behavior and if anyone on the list 
has an idea of which package the bug should be filed against.  Maybe I am 
just not installing things correctly but I have verified this behavior on 
a fresh sid install with both amd64 and i386 and it is not available in 
jessie at all although avogadro seems to have no problems in jessie.

In contrast the same problems are evident in stretch for both ghemical and 
avogadro.


Thanks

Carlo

-- 
Carlo U. Segre -- Duchossois Leadership Professor of Physics
Interim Chair, Department of Chemistry
Director, Center for Synchrotron Radiation Research and Instrumentation
Illinois Institute of Technology
Voice: 312.567.3498            Fax: 312.567.3494
segre at iit.edu   http://phys.iit.edu/~segre   segre at debian.org