bugGnome Chemistry Utils - Bugs: bug #24853, gchempaint segmentation fault when...

 
 

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bug #24853: gchempaint segmentation fault when trying to link 2 molecules

Submitted by:  Marios A. <marios>
Submitted on:  Sun 16 Nov 2008 08:17:00 PM UTC  
 
Category: NoneSeverity: 3 - Normal
Item Group: NoneStatus: Fixed
Privacy: PublicAssigned to: Jean Bréfort <jean_brefort>
Open/Closed: Closed

Sat 29 Nov 2008 01:31:38 PM UTC, comment #4:

Closed after 0.10.2 release.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 18 Nov 2008 07:07:19 AM UTC, comment #3:

Fixed (patch commited).

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Mon 17 Nov 2008 08:44:48 PM UTC, comment #2:

I have not been able to reproduce the error after applying the patch. It seems to have worked.

Marios A. <marios>
Sun 16 Nov 2008 08:36:33 PM UTC, comment #1:

Hard to say what happens since I'm unable to reproduce after about 10 attempts. You might compile with debug information on so that lines numbers would be there.
You might also test the attached patch, it might fix the issue, but this condition should never happen.

(file #16856)

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 16 Nov 2008 08:17:00 PM UTC, original submission:

As shown in the attached screenshots, I have two molecules of α-D-glucopyranose (taken from the included templates).

When I try to link them with a bond (green line in second screenshot), I sometimes get a segmentation fault.
When backtraced, it gives this (full output in attachment).

(gdb) bt
#0 0xa7b9dbea in gnome_canvas_path_def_duplicate () from /usr/lib/libgnomecanvas-2.so.0
#1 0xa6c01fdb in gnome_canvas_shape_ext_set_path_def () from /usr/lib/libgcpcanvas-0.10.so.0
#2 0xa6c057f2 in gnome_canvas_bpath_ext_set_property () from /usr/lib/libgcpcanvas-0.10.so.0
#3 0xa6fe4d75 in g_object_set_valist () from /usr/lib/libgobject-2.0.so.0
#4 0xa6fe51c6 in g_object_set () from /usr/lib/libgobject-2.0.so.0
#5 0xa7ec15dc in gcp::Bond::Update () from /usr/lib/libgchempaint-0.10.so.0
#6 0xa6c71e3a in gcu::Object::Update () from /usr/lib/libgcu-0.10.so.0
#7 0xa6c71e3a in gcu::Object::Update () from /usr/lib/libgcu-0.10.so.0
#8 0xa7efc1ed in gcp::View::Update () from /usr/lib/libgchempaint-0.10.so.0
#9 0xa7efd56d in gcp::View::UpdateSize () from /usr/lib/libgchempaint-0.10.so.0
#10 0xa7efdce9 in gnome_canvas_gcp_update_bounds () from /usr/lib/libgchempaint-0.10.so.0
#11 0xa6fed254 in g_cclosure_marshal_VOID__VOID () from /usr/lib/libgobject-2.0.so.0
#12 0xa6fde349 in g_type_class_meta_marshal () from /usr/lib/libgobject-2.0.so.0
#13 0xa6fdfbd3 in g_closure_invoke () from /usr/lib/libgobject-2.0.so.0
#14 0xa6ff3ad5 in signal_emit_unlocked_R () from /usr/lib/libgobject-2.0.so.0
#15 0xa6ff5364 in g_signal_emit_valist () from /usr/lib/libgobject-2.0.so.0
#16 0xa6ff566d in g_signal_emit_by_name () from /usr/lib/libgobject-2.0.so.0
#17 0xa7ef9868 in gcp::Tool::OnRelease () from /usr/lib/libgchempaint-0.10.so.0
#18 0xa7efe31d in gcp::View::OnEvent () from /usr/lib/libgchempaint-0.10.so.0
#19 0xa7efe7b6 in gcp::on_event () from /usr/lib/libgchempaint-0.10.so.0
#20 0xa7bb4856 in gnome_canvas_marshal_BOOLEAN__BOXED () from /usr/lib/libgnomecanvas-2.so.0
#21 0xa6fdfbd3 in g_closure_invoke () from /usr/lib/libgobject-2.0.so.0
#22 0xa6ff3e4d in signal_emit_unlocked_R () from /usr/lib/libgobject-2.0.so.0
#23 0xa6ff51db in g_signal_emit_valist () from /usr/lib/libgobject-2.0.so.0
---Type <return> to continue, or q <return> to quit---
#24 0xa6ff57c6 in g_signal_emit () from /usr/lib/libgobject-2.0.so.0
#25 0xa7baf8a8 in emit_event () from /usr/lib/libgnomecanvas-2.so.0
#26 0xa7bb2825 in gnome_canvas_button () from /usr/lib/libgnomecanvas-2.so.0
#27 0xa77cce86 in _gtk_marshal_BOOLEAN__BOXED () from /usr/lib/libgtk-x11-2.0.so.0
#28 0xa6fde349 in g_type_class_meta_marshal () from /usr/lib/libgobject-2.0.so.0
#29 0xa6fdfbd3 in g_closure_invoke () from /usr/lib/libgobject-2.0.so.0
#30 0xa6ff3ad5 in signal_emit_unlocked_R () from /usr/lib/libgobject-2.0.so.0
#31 0xa6ff51db in g_signal_emit_valist () from /usr/lib/libgobject-2.0.so.0
#32 0xa6ff57c6 in g_signal_emit () from /usr/lib/libgobject-2.0.so.0
#33 0xa78e191e in gtk_widget_event_internal () from /usr/lib/libgtk-x11-2.0.so.0
#34 0xa77c596a in gtk_propagate_event () from /usr/lib/libgtk-x11-2.0.so.0
#35 0xa77c6d27 in gtk_main_do_event () from /usr/lib/libgtk-x11-2.0.so.0
#36 0xa7526f0a in gdk_event_dispatch () from /usr/lib/libgdk-x11-2.0.so.0
#37 0xa6f5a2c1 in g_main_context_dispatch () from /usr/lib/libglib-2.0.so.0
#38 0xa6f5d953 in g_main_context_iterate () from /usr/lib/libglib-2.0.so.0
#39 0xa6f5de72 in g_main_loop_run () from /usr/lib/libglib-2.0.so.0
#40 0xa77c7209 in gtk_main () from /usr/lib/libgtk-x11-2.0.so.0
#41 0x08049f86 in main ()

Marios A. <marios>

 

Attached Files
file #16856:  24853.patch added by jean_brefort (725B - text/x-patch)
file #16853:  Step_1.jpg added by marios (66KiB - image/jpeg)
file #16855:  Step_2.jpg added by marios (69KiB - image/jpeg)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by jean_brefort (Updated the item)
  • -unavailable- added by marios (Submitted the item)
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    Follow 7 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Sat 29 Nov 2008 01:31:38 PM UTCjean_brefortOpen/ClosedOpen=>Closed
    Tue 18 Nov 2008 07:07:19 AM UTCjean_brefortStatusNone=>Fixed
      Assigned toNone=>jean_brefort
    Sun 16 Nov 2008 08:36:33 PM UTCjean_brefortAttached File-=>Added 24853.patch, #16856
    Sun 16 Nov 2008 08:17:00 PM UTCmariosAttached File-=>Added Step_1.jpg, #16853
      Attached File-=>Added gchempaint_error_output.txt, #16854
      Attached File-=>Added Step_2.jpg, #16855

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