ghemical crash on startup - pango, courier font missing

I get the same error message when I attempt to run ghemical on Ubuntu Natty. I have also attached a bug report from Debian¸ which describes the same issue. It contained a workaround by installing another package, but it didn't work for me (don't know why).

I get this error whether I install the package or if I compile myself. I was able to compile ghemical 2.10. However, as an aside, I noticed very strange results for optimizing ethane as a test using mopac (distorted structures) and mpqc crashed before optimization.

i tried to install from software center and command line, it works fine up to installation but crashes similarly during execution.

There is a user on the Ubuntu absolute beginners forum with a similar problem trying to start ghemical, ubuntu 11.10. I also run 11.10 and installed it via synaptic package manager and tried to run it but get the same abort as the user:

ghemical: symbol lookup error: /usr/lib/libghemical.so.5: undefined symbol: _ZTIN2sc7RefBaseE

I double-checked all of the dependencies on the Ubuntu ghemical page and everything is up to date.

If more information is needed, please let me know.

David Eaton
anewguy on the Ubuntu forums

@anewguy:

This report is about a problem with a missing/not finding font"*** ERROR : Can't load font 'courier 12".

What you have looks different. You should openup a new report for this.

anewguy: Please see bug 885740 (which should be fixed now, but I don't know the details)

This bug also affects quantal.

Vadim: Could you elaborate a bit on why you marked this fixed? I still see this crash on Ubuntu Raring.

This probably isn't terribly useful, but this bit me today using the current 12.04 LTS Ubuntu. Installing xfonts-75dpi and/or msttcorefonts did nothing to fix the problem.

I installed Raring (64 bit) a few weeks ago and found this bug still present, however when I did a 32 bit install on the same system (EM64T) there was no problem and ghemical was fully functional. Maybe there is a difference in the fonts installed on the 32 bit 13.04.

Bill: I just wanted to follow up as I found the time today to sort of test what you did. While I was using virtualized 32 debian systems (I actually tried several different virtualization methods), I was unable to get anything to perform differently in any way. While the fonts might be different between the two systems you have installed, this bug certainly persists across different architectures. Debian was what I had handy and I have neither the time nor the inclination to actually install Raring 2 different ways to test (plus other versions) trying to track down any breakage.

I have basically given up on trying to use this project for the time being. They say that a fix has been released, though I see no info on it. I guess I will wait for that to eventually arrive, but I'm not holding my breath.

setting back to confirm as the bug still exist per latest comment and no evidence that it is "fix released"

I upgraded my old 64 bit Lucid installation where Ghemical worked
(except for the old bug in running Mopac, in fact I in order to run
Ghemical with Mopac I ran the Windows binary on Wine which basically
worked OK). I had seen the the 64 bit missing font bug before on an
Ubuntu 12.04 live disk when I tested it.

When I installed Raring 64 bit the bug was still present. When I
changed to the 32 bit release to check another problem, there was no
problem with the 32 bit ghemical binary, everything worked. I plan to
reinstall the 64 bit raring release when I get time and to see if I
can get the 32 Ghemical binary working with the 32 bit libraries.

According to the Debian bug report, this should be fixed via the xfonts recommended package. However, I still get the same error message when attempting to run ghemical (3.0.0-2 on Ubuntu Zesty). Tested with installing all the xfont packages listed on http://packages.ubuntu.com/zesty/ghemical, but same result.

Could anyone else test with Zesty to see if they see the same error, or (better yet) get the program to work?

I can confirm this issue on Ubuntu 18.04

$ cat /etc/issue
Ubuntu 18.04.1 LTS \n \l

$ ghemical

OpenGL extension version - 1.4
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/builder/amino.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/builder/nucleic.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/atomtypes.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/parameters1.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/parameters2.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/parameters3.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/parameters4.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/atomtypes.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters1.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters2.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters3.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters4.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters5.txt

(ghemical:27111): Gtk-WARNING **: 20:08:50.782: Unable to locate theme engine in module_path: "adwaita",

(ghemical:27111): Gtk-WARNING **: 20:08:50.785: Unable to locate theme engine in module_path: "adwaita",
Added local light.

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

(ghemical:27111): GdkGLExt-WARNING **: 20:08:50.855: cannot load PangoFont
*** ERROR : Can't load font 'courier 12'