Opened 7 years ago

Last modified 5 years ago

#252 new defect

Create species from consensus fails under certain conditions

Reported by: guest Owned by: devel
Priority: normal Milestone:
Component: no idea Version: SVN
Keywords: Cc:

Description (last modified by westram)

Reproduce:

  1. start edit4 on demo.arb
  2. set cursor into 'LacViri2'
  3. select 'Create/Create? new species from consensus'
  4. enter name + press go

⇒ works

Moving 'LacViri2' to top level (i.e. out of group outer) and then performing 2. - 4. crashes the editor.

Note: doing the above in a bigger database performs "a lot of work" before it crashes


Original ticket description:

Using the release 108 of silva database, I was trying to "create new species from consensus" in ARB sequence editor, but it crashes (actually quit) and I get the following error message in the console :

[Action: 'arb_edit4 -c 'default_configuration' &']
Using properties from '.arb_prop/edit4.arb'
Note: SINA (SILVA Aligner) disabled (Reason: sina not found)
      Visit http://www.ribocon.com/sina/ for more information.
[Action: '($ARBHOME/bin/arb_name_server -d/opt/arb/lib/nas/names.dat -T:3020) &']
Starting ARB_name_server..
* Loading /opt/arb/lib/nas/names.dat
* Parsing data
* Loaded NAMEDB v5 (contains 4 names)
ARB_name_server is up.
No changes to ARB_name_server data.

-------------------- ARB-backtrace for 'received signal 11':
/opt/arb/lib/libARBDB.so(GBK_dump_backtrace+0x2e)[0x7ff329f4ea0e]
/opt/arb/lib/libARBDB.so(sigsegv_handler_dump+0x32)[0x7ff329f51312]
/lib/libc.so.6(+0x32230)[0x7ff328116230]
arb_edit4(_ZNK8ED4_base10get_parentE9ED4_level+0x0)[0x44d6a0]
arb_edit4(_Z27ED4_get_and_jump_to_speciesPKc+0x125)[0x444ab5]
arb_edit4[0x464b08]
/opt/arb/lib/libAW.so(_Z18AW_server_callbackP10_WidgetRecPvS1_+0xb3)[0x7ff329d15393]
/usr/lib/libXt.so.6(XtCallCallbackList+0x12f)[0x7ff329125a1f]
/usr/lib/libXm.so.3(+0xe4915)[0x7ff329667915]
/usr/lib/libXt.so.6(+0x49abe)[0x7ff32915aabe]
/usr/lib/libXt.so.6(_XtTranslateEvent+0x337)[0x7ff32915b237]
/usr/lib/libXt.so.6(XtDispatchEventToWidget+0x40a)[0x7ff32913332a]
/usr/lib/libXt.so.6(+0x229f6)[0x7ff3291339f6]
/usr/lib/libXt.so.6(XtDispatchEvent+0xdb)[0x7ff329132b3b]
/usr/lib/libXt.so.6(XtAppMainLoop+0x33)[0x7ff329132ca3]
arb_edit4(main+0x3e8)[0x4470a8]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7ff328102c8d]
arb_edit4[0x42d039]
-------------------- End of backtrace
[Terminating with signal 11]
ARB_DB_SERVER: a client died abnormally

Does someone have any idea what's going wrong ? Thanks. Laure

Change History (2)

comment:1 Changed 5 years ago by westram

  • Description modified (diff)
  • Summary changed from Trouble using arb_edit4 to Create species from consensus fails under certain conditions
  • Version set to SVN

unable to reproduce original problem (worksforme)

comment:2 Changed 5 years ago by westram

stack:

(gdb) whe
#0  0x000000000050f2fe in provoke_core_dump () at /home/ralf/ARB-bilbo/ARB.trunk.default/INCLUDE/arb_assert.h:100
#1  0x0000000000512fc2 in ED4_base::is_group_manager (this=0x0) at ed4_class.hxx:1247
#2  0x0000000000513498 in ED4_base::to_group_manager (this=0x0) at ed4_class.hxx:2271
#3  0x0000000000513508 in ED4_base::to_group_manager (this=0x0) at ed4_class.hxx:2271
#4  0x00000000004e50a1 in create_new_species (cl_creation_mode=1) at ED4_no_class.cxx:1825
#5  0x00007ffff6ecd1fc in StrictlyTypedCallback<void, AW_window*, long, long>::operator() (this=0xc36b18, p1=0xc2f660, p2=1, p3=0) at /home/ralf/ARB-bilbo/ARB.trunk.default/INCLUDE/cbtypes.h:117
#6  0x00007ffff6ecd178 in Callback_FVV<void, AW_window*>::operator() (this=0xc36b18, fixed=0xc2f660) at /home/ralf/ARB-bilbo/ARB.trunk.default/INCLUDE/cbtypes.h:172
#7  0x00007ffff6eccf87 in AW_cb::run_callbacks (this=0xc36b10) at AW_cb_struct.cxx:148
#8  0x00007ffff6efafd5 in AW_server_callback (aw_cb_struct=0xc36b10) at AW_window.cxx:1217
#9  0x00007ffff6550c7f in XtCallCallbackList () from /usr/lib/libXt.so.6
#10 0x00007ffff6a96b05 in ?? () from /usr/lib/libXm.so.3
#11 0x00007ffff6587b2d in ?? () from /usr/lib/libXt.so.6
#12 0x00007ffff6588395 in _XtTranslateEvent () from /usr/lib/libXt.so.6
#13 0x00007ffff655ef5b in XtDispatchEventToWidget () from /usr/lib/libXt.so.6
#14 0x00007ffff655f7a3 in ?? () from /usr/lib/libXt.so.6
#15 0x00007ffff655e714 in XtDispatchEvent () from /usr/lib/libXt.so.6
#16 0x00007ffff655e8bb in XtAppMainLoop () from /usr/lib/libXt.so.6
#17 0x00007ffff6eedc7e in AW_root::main_loop (this=0x906310) at AW_root.cxx:547
#18 0x00000000004ced93 in ARB_main (argc=1, argv=0x7fffffffe318) at ED4_main.cxx:579
#19 0x00000000004ab26f in main (argc=3, argv=0x7fffffffe308) at arb_main.cxx:10
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