Opened 9 years ago

Last modified 8 years ago

#159 new defect

Sec edit crashes when saving secondary structure

Reported by: fog Owned by: westram
Priority: major Milestone:
Component: ARB_SECEDIT Version: SVN
Keywords: Cc:

Description (last modified by westram)

-------------------- ARB-backtrace for 'received signal 11':
/arb/software/arbsvn_5766M_tum64/lib/libARBDB.so(GBK_dump_backtrace+0x2e)[0x2b286e5e2f5e]
/arb/software/arbsvn_5766M_tum64/lib/libARBDB.so(sigsegv_handler_dump+0x33)[0x2b286e5e5f73]
/megx/chroot/amd64_hardy/lib/libc.so.6[0x2b28705fb100]
/megx/chroot/amd64_hardy/lib/libc.so.6(strlen+0x30)[0x2b2870644080]
/arb/software/arbsvn_5766M_tum64/lib/libARBDB.so(GBS_strcat+0x21)[0x2b286e5e2781]
arb_edit4[0x4628ad]
arb_edit4[0x47801a]
/arb/software/arbsvn_5766M_tum64/lib/libAW.so(_Z18AW_server_callbackP10_WidgetRecPvS1_+0xb6)[0x2b286e8d6b76]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtCallCallbackList+0x12f)[0x2b286f6c9a8f]
/megx/chroot/amd64_hardy/usr/lib/libXm.so.3[0x2b286eec9dc5]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6[0x2b286f6ff1ae]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(_XtTranslateEvent+0x337)[0x2b286f6ff927]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtDispatchEventToWidget+0x43e)[0x2b286f6d756e]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6[0x2b286f6d7c70]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtDispatchEvent+0xdb)[0x2b286f6d6d1b]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtAppMainLoop+0x45)[0x2b286f6d6e95]
arb_edit4[0x4342d8]
/megx/chroot/amd64_hardy/lib/libc.so.6(__libc_start_main+0xf4)[0x2b28705e71c4]
arb_edit4[0x414ec9]
-------------------- End of backtrace
[Terminating with signal 11]
ARB_DB_SERVER: a client died abnormally

Attachments (1)

bt_secstr_save (1.7 KB) - added by meierh 9 years ago.

Download all attachments as: .zip

Change History (13)

comment:1 Changed 9 years ago by fog

  • Summary changed from Sec edit crashes when exporting secondary structure to Sec edit crashes when saving secondary structure

comment:2 Changed 9 years ago by westram

  • Description modified (diff)
  • Resolution set to worksforme
  • Status changed from new to closed
  • works perfectly for me. Please test again and in case reopen ticket and provide more info here.

comment:3 Changed 9 years ago by fog

  • Resolution worksforme deleted
  • Status changed from closed to reopened

I selected some sequences in e.g. the Living tree dataset, or in Silva 94/98, opened ARB Edit 4, clicked on one of the sequences and opened Sec Edit. Go to file→save structure, left name to noname.ass and clicked on EXPORT: Result: Sec Edit and the Editor crashed: ARB Version 5766, but its the same for 071207 (original Munich). Maybe something happens in combination with our machines??

-------------------- ARB-backtrace for 'received signal 11':
/arb/software/arbsvn_5766M_tum64_sina/lib/libARBDB.so(GBK_dump_backtrace+0x2e)[0x2b28cd9d7f5e]
/arb/software/arbsvn_5766M_tum64_sina/lib/libARBDB.so(sigsegv_handler_dump+0x33)[0x2b28cd9daf73]
/megx/chroot/amd64_hardy/lib/libc.so.6[0x2b28cf9f1100]
/megx/chroot/amd64_hardy/lib/libc.so.6(strlen+0x30)[0x2b28cfa3a080]
/arb/software/arbsvn_5766M_tum64_sina/lib/libARBDB.so(GBS_strcat+0x21)[0x2b28cd9d7781]
arb_edit4[0x4628ad]
arb_edit4[0x47801a]
/arb/software/arbsvn_5766M_tum64_sina/lib/libAW.so(_Z18AW_server_callbackP10_WidgetRecPvS1_+0xb6)[0x2b28cdccbb76]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtCallCallbackList+0x12f)[0x2b28ceabfa8f]
/megx/chroot/amd64_hardy/usr/lib/libXm.so.3[0x2b28ce2bfdc5]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6[0x2b28ceaf51ae]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(_XtTranslateEvent+0x337)[0x2b28ceaf5927]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtDispatchEventToWidget+0x43e)[0x2b28ceacd56e]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6[0x2b28ceacdc70]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtDispatchEvent+0xdb)[0x2b28ceaccd1b]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtAppMainLoop+0x45)[0x2b28ceacce95]
arb_edit4[0x4342d8]
/megx/chroot/amd64_hardy/lib/libc.so.6(__libc_start_main+0xf4)[0x2b28cf9dd1c4]
arb_edit4[0x414ec9]
-------------------- End of backtrace
[Terminating with signal 11]
ARB_DB_SERVER: a client died abnormally

comment:4 Changed 9 years ago by meierh

Confirmed for SVN 5990 on OpenSuse? 10.3 (64_bit !) tested with SSURef_98.

Structure is saved correctly, but arb_edit4 crashes (attached "bt_secstr_save").

Changed 9 years ago by meierh

comment:5 Changed 9 years ago by westram

  • Owner changed from devel to westram
  • Status changed from reopened to new

comment:6 Changed 9 years ago by westram

  • Status changed from new to assigned

comment:7 Changed 9 years ago by westram

  • related to #100
  • x-string and HELIX get out of sync (by inserting columns)

comment:8 Changed 9 years ago by westram

  • assertion fails with 32bit version as well
  • xstring (aka _REF) is broken in SILVA_98 (most likely by inserting columns). 'x' at position 420 should be at position 370 (behind end of left helix 6)

comment:9 Changed 9 years ago by westram

  • dont fix for upcoming release

comment:10 Changed 9 years ago by westram

  • Status changed from assigned to new

comment:11 Changed 8 years ago by westram

  • x-string design sucks, will easily break when inserting/deleting columns
    • needs some kind of re-design:
      • 'x' at helix start is at same position as '/'
      • 'x' at helix end is one position behind '/' - this one gets out of sync!

comment:12 Changed 8 years ago by westram

what i really meant was:

  • 'x' at helix start is at same position as '[' / ']'
  • 'x' at helix end is one position behind '[' / ']' - this one gets out of sync!
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