#51 Gap4 crashes when joining contigs

open
Gap4 (50)
5
2005-09-29
2005-09-28
Anonymous
No

Gap4 crashes sometimes when I use the join editor to
join contigs.
It happened in my old database, then I created a new
one (with pregap) to see if there was a problem with my
database, but I just got the same crash in the new
database also.

OS: Mac OSX 10.4.2 (PowerBook 1.5 GHz PowerPC G4)
Staden version: 1-5-3 for Mac OS X
Database: around 4000 characters, in 2 contigs

First I get a lot of:
> window name "trace_1" already exists in parent
> window name "trace_1" already exists in parent
> window name "trace_1" already exists in parent
> window name "trace_4" already exists in parent
> window name "trace_5" already exists in parent

in my xterm window while moving around in the join
editor, Then when I press the "ok" button after
selecting "join/quit" the program sometimes crashes
with the following messge:

> Wed 28 Sep 14:52:13 2005 signal_handler: Program
terminated unexpectedly with signal 11.
> Wed 28 Sep 14:52:13 2005 signal_handler: This is
probably a bug.
> Wed 28 Sep 14:52:13 2005 signal_handler: Please
report all bug reports at
https://sourceforge.net/projects/staden/

/Anja Rautenberg, Systematic Botany, EBC, Uppsala
University
anja.rautenberg@ebc.uu.se

Discussion

  • James Bonfield
    James Bonfield
    2005-09-29

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    user_id=154581

    I am about to build a new MacOS X version so would you mind
    testing it when this is ready?

    I believe this is the same join bug that I've already fixed,
    but I cannot be sure until it is tested.

    Alternative if you could please make the data available to
    me I will see if I can reproduce the bug here (with the old
    version and then with the latest source).

    James

     
  • James Bonfield
    James Bonfield
    2005-09-29

    • assigned_to: nobody --> jkbonfield
     
  • Anja R
    Anja R
    2005-12-21

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    user_id=1409208

    Sorry for late response. I didn't use Staden a lot since
    september, and when I did it worked. Until now. I also tried
    1.6.0 version, but it also crashes, but this time with
    another error code.

    > syst31:~/Sekvenser/XY1/01770 anjar$ Level 1: editor_quit
    .cedit0 .cedit0.0 .cedit0.0.seqs .cedit0.0.buttons.quit
    > Wed 21 Dec 13:08:14 2005 signal_handler: Program
    terminated unexpectedly with signal 11.
    > Wed 21 Dec 13:08:14 2005 signal_handler: This is probably
    a bug.
    > Wed 21 Dec 13:08:14 2005 signal_handler: Please report all
    bug reports at https://sourceforge.net/projects/staden/
    > syst31:~/Sekvenser/XY1/01770 anjar$

    I can also supply stash crash log file and dataset.

    /Anja

     
  • Carlos A.
    Carlos A.
    2007-05-16

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    user_id=1794406
    Originator: NO

    Hi, I use staden 1.6.0 with my Mac OSX 10.4.9 and Gap4 crashes when joining contigs.
    I just can join the first time, at second joining Gap4 crashes.
    The messege I get is "Program terminated unexpectedly with signal 10".

    I don't know what to do.

    Any idea?

     
  • Carlos A.
    Carlos A.
    2007-05-16

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    Originator: NO

    Hi, I use staden 1.6.0 with my Mac OSX 10.4.9 and Gap4 crashes when joining contigs.
    I just can join the first time, at second joining Gap4 crashes.
    The messege I get is "Program terminated unexpectedly with signal 10".

    I don't know what to do.

    Any idea?

     
  • Carlos A.
    Carlos A.
    2007-05-16

    Logged In: YES
    user_id=1794406
    Originator: NO

    Hi, I use staden 1.6.0 with my Mac OSX 10.4.9 and Gap4 crashes when joining contigs.
    I just can join the first time, at second joining Gap4 crashes.
    The messege I get is "Program terminated unexpectedly with signal 10".

    I don't know what to do.

    Any idea?

     
  • Carlos A.
    Carlos A.
    2007-05-16

    Logged In: YES
    user_id=1794406
    Originator: NO

    Hi, I use staden 1.6.0 with my Mac OSX 10.4.9 and Gap4 crashes when joining contigs.
    I just can join the first time, at second joining Gap4 crashes.
    The messege I get is "Program terminated unexpectedly with signal 10".

    I don't know what to do.

    Any idea?

     
  • Anja R
    Anja R
    2007-06-05

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    Since I turned off "embed trace", I haven't had any problems with crashes during join contig.

     
  • Carlos A.
    Carlos A.
    2007-06-26

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    Thanks a lot sbanjar. I've turned off "embed trace" and now it works properly.