Contig List stops gap5 exiting (OS X only)

John Nash
2011-11-03
2013-04-18
  • John Nash
    John Nash
    2011-11-03

    When I close the Contig List window on my Mac version of gap5, I am not able to exit gap5 cleanly afterwards.

    This only happens on my Mac, not on my Ubuntu box.  To make sure everything was recent, both systems have a fresh build of the Staden package via svn from today.

    The chain of events:

    1. Select View -> Contig List

    2. When I try to close the window by "Cancel" or "Save Contig Order" or by pressing the close window button, the following occurs:

    A pop-up box appears with:
    Application Error -> Error: bad variable name "NGList(contigs": upvar …

    Details >> bad variable name "NGList(contigs)": upvar won't create a scalar variable that looks like an array element
    bad variable name "NGList(contigs)": upvar won't create a scalar variable that looks like an array element
        while executing
    "global NGList(contigs)"
        (procedure "ListContigsExit" line 2)
        invoked from within
    "ListContigsExit io=0x10159f900 .list_contigs {ListContigsUpdate io=0x10159f900 .list_contigs.list}"
        (command bound to event)
       
    3. Clicking "OK" presents several more windows with similar messages.

    4. Clicking "Skip messages" stop this behaviour.

    5. The following appears in the terminal window:

    "registration_callback: bad window path name ".list_contigs.list"registration_callback: bad window path name ".list_contigs.list"registration_callback: bad window path name ".list_contigs.list"registration_callback: bad window path name ".list_contigs.list""

    6. In either case, closing gap5 (either immediately or after lots of work) by "File -> Exit" or by pressing the close window button results in a pop-up with:

    "Please shut down any editing displays before quitting"

    The only way to close gap5 is to Ctrl-C from a terminal.

    cheers,
    John

    PS I use gap5 almost every day so that's why I'm here often