Thank you! This was indeed the case. I have no idea why tcl/tk 8.4 was
installed with 8.5 at the same time. Removing 8.4 and using 8.5 seems to
have fixed the problem.
Ian
On Thu, Sep 24, 2009 at 2:38 PM, Warren DeLano <war...@delsci.com> wrote:
> Ian,
>
> Based on that traceback, it looks like you have two conflicting versions of
> Tcl (8.4 as well as 8.5) linked against and running in the same
> process...that could be the source of the crash.
>
> Cheers,
> Warren
>
> ------------------------------
> *From:* Ian Berke [mailto:ian.be...@yale.edu]
> *Sent:* Thursday, September 24, 2009 11:26 AM
> *To:* pymol-users@lists.sourceforge.net
> *Subject:* [PyMOL] Pymol segmentation fault
>
> Hi,
>
> I'm having an issue trying to run various plugins in pymol (apbs and
> autodock). Whenever I select a button that should bring up a file browser
> to choose a file (e.g. "Choose Externally generated pqr" in apbs) Pymol
> exits with: Segmentation fault (core dumped). Same thing happens when I go
> to Help>About. I can open and save files normally, and just about
> everything else works.
>
> I've tried this in pymol 1.1r2pre, where I can at least get the apbs plugin
> window to open, as well as the 1.2 trunk from svn (downloaded and compiled
> last week) which just crashes when I try to open the apbs window (I can
> install autodock.py and the window opens, but it crashes when I try to
> choose the location of files). I'm guessing this is something to do with
> the gui and tcl/tk, but don't have any idea how to troubleshoot (see the
> catchsegv output below). I'm running Ubuntu 9.10 on x86_64 and have a
> GeForce 8400M GS/PCI/SSE2 with the proprietory nvidia driver 185.18.36.
>
> Does anyone have any thoughts?
>
> Here is the backtrace portion from catchsegv:
> Backtrace:
> /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
> /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
> /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
> /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
> /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
> /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
> /usr/lib/libtcl8.5.so.0[0x7f639777dee6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtcl8.5.so.0[0x7f63977926d1]
> /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
> /usr/lib/libtcl8.5.so.0[0x7f6397793192]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x49c06f]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
> /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0[0x7f63977527b9]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
> /usr/lib/libtk8.5.so.0[0x7f6397a556f6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
> /usr/lib/libtcl8.5.so.0[0x7f639779668f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
> /usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
> /usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
> /usr/lib/libtk8.5.so.0[0x7f6397a37b48]
> /usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
> /usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52beed]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x4d0c4d]
> /lib/libpthread.so.0[0x7f639cf69a04]
> /lib/libc.so.6(clone+0x6d)[0x7f639c4317bd]
>
> Thanks,
> Ian
>
>
------------------------------------------------------------------------------
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9-12, 2009. Register now!
http://p.sf.net/sfu/devconf
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
