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ghutchis / avogadro

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.
http://avogadro.cc/
GNU General Public License v2.0
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Crash when copying atoms on Ubuntu 12.04 #659

Closed ghutchis closed 8 years ago

ghutchis commented 11 years ago

To reproduce, draw a molecule (just click with the draw tool to draw methane).

Change to the select tool, select an atom, then go to the menu: Edit->Copy

Crash, with backtrace below.

This with a fresh build on Ubuntu with avogadro-squared, and the distribution Qt:

Application version: 1.1.0 Git revision d9e5d4f OpenBabel: 2.3.90 Qt: 4.8.1

Settings are missing for the next engines: () QStackedLayout::setCurrentWidget: Widget 0x945d50 not contained in stack dev warning: Extension "GAMESS" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. dev warning: Extension "Orbitals" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. dev warning: Extension "Vibration" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. PreCalculate Finished queue. GLWidget initialisation... GLWidget initialised... createObjects() libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area [Thread 0x7fffdedbf700 (LWP 26382) exited]

Program received signal SIGSEGV, Segmentation fault. 0x00007ffff62291e4 in OpenBabel::OBUnitCell::OBUnitCell (this=0x10d3b20, src=...) at /home/jmht/Documents/Avogadro/avogadro-squared/openbabel/src/generic.cpp:264 264 _lattice(src._lattice) (gdb) bt

0 0x00007ffff62291e4 in OpenBabel::OBUnitCell::OBUnitCell (this=0x10d3b20, src=...) at /home/jmht/Documents/Avogadro/avogadro-squared/openbabel/src/generic.cpp:264

1 0x000000000043b197 in Avogadro::MainWindow::prepareClipboardData (this=0x8a8ba0, selectedItems=...)

at /home/jmht/Documents/Avogadro/avogadro-squared/avogadro/avogadro/src/mainwindow.cpp:2423

2 0x000000000043bac3 in Avogadro::MainWindow::copy (this=0x8a8ba0) at /home/jmht/Documents/Avogadro/avogadro-squared/avogadro/avogadro/src/mainwindow.cpp:2495

3 0x000000000043f3d5 in Avogadro::MainWindow::qt_static_metacall (_o=, _c=, _id=, _a=)

at /home/jmht/Documents/Avogadro/avogadro-squared/avogadro-build/avogadro/avogadro/src/mainwindow.moc:180

4 0x00007ffff670c281 in QMetaObject::activate(QObject, QMetaObject const, int, void**) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4

5 0x00007ffff6c14132 in QAction::triggered(bool) () from /usr/lib/x86_64-linux-gnu/libQtGui.so.4

6 0x00007ffff6c1431f in QAction::activate(QAction::ActionEvent) () from /usr/lib/x86_64-linux-gnu/libQtGui.so.4

7 0x00007ffff6711446 in QObject::event(QEvent*) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4

8 0x00007ffff6c143f0 in QAction::event(QEvent*) () from /usr/lib/x86_64-linux-gnu/libQtGui.so.4

9 0x00007ffff6c1a894 in QApplicationPrivate::notifyhelper(QObject, QEvent_) () from /usr/lib/x86_64-linux-gnu/libQtGui.so.4

10 0x00007ffff6c1f713 in QApplication::notify(QObject, QEvent) () from /usr/lib/x86_64-linux-gnu/libQtGui.so.4

11 0x00007ffff66f7e9c in QCoreApplication::notifyInternal(QObject, QEvent) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4

12 0x00007ffff66fbc6a in QCoreApplicationPrivate::sendPostedEvents(QObject, int, QThreadData) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4

13 0x00007ffff6726f93 in ?? () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4

14 0x00007ffff4053d53 in g_main_context_dispatch () from /lib/x86_64-linux-gnu/libglib-2.0.so.0

15 0x00007ffff40540a0 in ?? () from /lib/x86_64-linux-gnu/libglib-2.0.so.0

16 0x00007ffff4054164 in g_main_context_iteration () from /lib/x86_64-linux-gnu/libglib-2.0.so.0

17 0x00007ffff67273bf in QEventDispatcherGlib::processEvents(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4

18 0x00007ffff6cc2d5e in ?? () from /usr/lib/x86_64-linux-gnu/libQtGui.so.4

19 0x00007ffff66f6c82 in QEventLoop::processEvents(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4

20 0x00007ffff66f6ed7 in QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4

21 0x00007ffff66fbf67 in QCoreApplication::exec() () from /usr/lib/x86_64-linux-gnu/libQtCore.so.4

22 0x000000000041f20c in main (argc=1, argv=) at /home/jmht

/Documents/Avogadro/avogadro-squared/avogadro/avogadro/src/main.cpp:251

Reported by: jensthomas

ghutchis commented 11 years ago

This problem isn't Ubuntu-specific. I got the same behaviour with Windows 7.

Original comment by: *anonymous