#996006 ghemical: Segmentation fault when starting

Package:
ghemical
Source:
ghemical
Description:
GNOME molecular modelling environment
Submitter:
Michael Stockenhuber
Date:
2025-08-13 09:31:13 UTC
Severity:
important
#996006#5
Date:
2021-10-09 23:42:01 UTC
From:
To:
Dear Maintainer,

Starting ghemical in gnome results in a segfault. An xwindow is opened for less
than a second and then closes. I see the following in syslog
kernel: [ 4311.905429] ghemical[6179]: segfault at 0 ip 0000000000000000 sp
00007ffe739c2328 error 14 in ghemical[5650ebcd0000+2a000]
kernel: [ 4311.905439] Code: Unable to access opcode bytes at RIP
0xffffffffffffffd6.

I do not see any other error messages. Makes the program unusable.
Any help would be appreciated.
Best regards
Michael

#996006#10
Date:
2021-10-10 01:00:11 UTC
From:
To:
Am Sonntag, dem 10.10.2021 um 10:42 +1100 schrieb Michael Stockenhuber:

Can you try this:

export GDK_BACKEND=x11
ghemical

Does it help?


Regards, Daniel

#996006#13
Date:
2021-10-10 01:00:11 UTC
From:
To:
Am Sonntag, dem 10.10.2021 um 10:42 +1100 schrieb Michael Stockenhuber:

Can you try this:

export GDK_BACKEND=x11
ghemical

Does it help?


Regards, Daniel

#996006#18
Date:
2021-10-10 23:36:25 UTC
From:
To:
Sorry, does not help either. Same, segfault.
Cheers
Michael

President Catalysis Society Australia, www.catalysis.org (http://www.catalysis.org/) |Elected Council Member International Zeolite Association, www.iza-online.org (http://www.iza-online.org/) |Treasurer Asia Pacific Association of Catalysis Societies, www.apacs.dicp.ac.cn (http://www.apacs.dicp.ac.cn/)| Scientific co-chair IZC2019, www.izc19.com| Editor Catalysis, Structure and Reactivity| Editor Asia Pacific J. Chem. Eng.|Guest editor Applied Catalysis B | Guest Editor Catalysis Today

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#996006#23
Date:
2021-10-26 20:24:58 UTC
From:
To:
Dear Maintainer,
I could reproduce this inside a minimal qemu VM.
Below [1] is a backtrace one instruction before the crash.
It looks like this "font" object has the create_hb_font
function pointer never initialized.
It also crashes with LANG=C set.

Unfortunately to me it is not certain if this is
an issue with pango or the application.
Additionally it looks like there were some changes in
pango (e.g. [2]) between the versions of bullseye and buster.
In the latter no such crash is observable.

Kind regards,
Bernhard


[1]
     (rr) reverse-stepi
     0x00007fb5b32b8c33 in pango_font_get_hb_font (font=font@entry=0x558dd5dcdb30) at ../pango/fonts.c:1928
     1928      priv->hb_font = PANGO_FONT_GET_CLASS (font)->create_hb_font (font);
     1: x/i $pc
     => 0x7fb5b32b8c33 <pango_font_get_hb_font+83>:  call   *0xc0(%r12)
     (rr) bt
     #0  0x00007fb5b32b8c33 in pango_font_get_hb_font (font=font@entry=0x558dd5dcdb30) at ../pango/fonts.c:1928
     #1  0x00007fb5b32d4e13 in pango_font_get_hb_font_for_context (context=0x7ffc5f4f04c0, font=0x558dd5dcdb30) at ../pango/pangofc-shape.c:277
     #2  pango_hb_shape (font=0x558dd5dcdb30, item_text=item_text@entry=0x7fb5b32dff4e <lang_pool+1006> "Zwölf Boxkämpfer jagen Viktor quer über den großen Sylter Deich.", item_length=item_length@entry=68, analysis=analysis@entry=0x7ffc5f4f0850, glyphs=glyphs@entry=0x558dd5acc6c0, paragraph_text=paragraph_text@entry=0x7fb5b32dff4e <lang_pool+1006> "Zwölf Boxkämpfer jagen Viktor quer über den großen Sylter Deich.", paragraph_length=68) at ../pango/pangofc-shape.c:345
     #3  0x00007fb5b32d466f in pango_shape_with_flags (item_text=0x7fb5b32dff4e <lang_pool+1006> "Zwölf Boxkämpfer jagen Viktor quer über den großen Sylter Deich.", item_length=<optimized out>, paragraph_text=<optimized out>, paragraph_length=68, analysis=0x7ffc5f4f0850, glyphs=0x558dd5acc6c0, flags=PANGO_SHAPE_NONE) at ../pango/shape.c:205
     #4  0x00007fb5b32d4adb in pango_shape_full (item_text=<optimized out>, item_length=<optimized out>, paragraph_text=<optimized out>, paragraph_length=<optimized out>, analysis=analysis@entry=0x7ffc5f4f0850, glyphs=glyphs@entry=0x558dd5acc6c0) at ../pango/shape.c:96
     #5  0x00007fb5b32d4af0 in pango_shape (text=<optimized out>, length=<optimized out>, analysis=analysis@entry=0x7ffc5f4f0850, glyphs=glyphs@entry=0x558dd5acc6c0) at ../pango/shape.c:63
     #6  0x00007fb5b264b273 in itemize_string_foreach (font=font@entry=0x558dd5dcdb30, language=language@entry=0x0, str=<optimized out>, func=func@entry=0x7fb5b264b010 <get_subfonts_foreach>, data=data@entry=0x7ffc5f4f08f0) at pangox.c:777
     #7  0x00007fb5b264b9b4 in get_font_metrics_from_string (metrics=0xffffffffd60e1730, str=<optimized out>, language=0x0, font=0x558dd5dcdb30) at pangox.c:922
     #8  pango_x_font_get_metrics (font=0x558dd5dcdb30, language=0x0) at pangox.c:984
     #9  0x0000558dd55f4556 in pangofont_wcl::ogl_InitPangoFont(char const*) (this=0x558dd5c19bc0, fs=0x558dd5623360 "courier 12") at pangofont_wcl.cpp:79
     #10 0x0000558dd55f492a in oglview_wcl::InitGL() (this=0x558dd5c19bc0) at oglview_wcl.cpp:929
     #11 0x00007fb5b2c3eebe in base_wcl::LinkWnd(base_wnd*) (this=0x558dd5c19bc0, w=0x558dd5c18fa0) at base_wcl.cpp:111
     #12 0x0000558dd55eb93d in project::AddGraphicsClient(custom_camera*, bool) (this=this@entry=0x558dd5a83df0, cam=0x558dd5c8fae0, cam@entry=0x0, detached=detached@entry=false) at project.cpp:622
     #13 0x0000558dd561dc12 in gtk_project::DoSafeStart() (this=0x558dd5a83df0) at gtk_project.cpp:80
     #14 0x0000558dd561aed3 in gtk_app::gtk_app() (this=0x558dd59fde70) at gtk_app.cpp:450
     #15 0x0000558dd561b165 in gtk_app::GetAppX() () at gtk_app.cpp:465
     #16 0x0000558dd55d49d4 in main(int, char**) (argc=<optimized out>, argv=<optimized out>) at gtk_main.cpp:116
     (rr) x/1xg $r12+0xc0
     0x558dd60e1e70: 0x0000000000000000


[2]
https://gitlab.gnome.org/GNOME/pango/-/commit/b5634799586ed8e3496ffc237b8d08e6d4e64d67

#996006#28
Date:
2021-10-27 01:18:36 UTC
From:
To:
Am Dienstag, dem 26.10.2021 um 22:24 +0200 schrieb Bernhard Übelacker:

Thanks.

The program doesn't crash in Sid though.

Is it possible that we hit https://bugs.debian.org/958017 ?


Regards, Daniel

#996006#33
Date:
2021-10-27 01:24:28 UTC
From:
To:
Am Mittwoch, dem 27.10.2021 um 03:18 +0200 schrieb Daniel Leidert:

Sorry, this is fixed in Bullseye already. I was reading the versions too
quickly. My fault. Still, the problem is not present in Sid.

Regards, Daniel

#996006#38
Date:
2025-08-13 09:30:40 UTC
From:
To:
Dear submitter,

as the package ghemical has just been removed from the Debian archive
unstable we hereby close the associated bug reports.  We are sorry
that we couldn't deal with your issue properly.

For details on the removal, please see https://bugs.debian.org/1110863

The version of this package that was in Debian prior to this removal
can still be found using https://snapshot.debian.org/.

Please note that the changes have been done on the master archive and
will not propagate to any mirrors until the next dinstall run at the
earliest.

This message was generated automatically; if you believe that there is
a problem with it please contact the archive administrators by mailing
ftpmaster@ftp-master.debian.org.

Debian distribution maintenance software
pp.
Thorsten Alteholz (the ftpmaster behind the curtain)