clicking Panel (with command avogadro2 %f) almost always crashes. starting from command line 'avogadro2' gives two outcomes with equal probability: ----------------- (2) successfully started ----------------- Extension plugins dynamically found... 24 OBProcess::executeObabel: Running "obabel" "-L formats read" OBProcess::executeObabel: Running "obabel" "-L formats write" OBProcess::executeObabel: Running "obabel" "-V" "obabel not found! Disabling Open Babel plugin actions." Checking for generator scripts in "/usr/bin/../lib64/avogadro2/scripts/inputGenerators" Checking for generator scripts in "/home/USERNAME/.local/share/OpenChemistry/Avogadro/dev/inputGenerators" Checking for generator scripts in "/usr/local/share/OpenChemistry/Avogadro/dev/inputGenerators" Checking for generator scripts in "/usr/share/OpenChemistry/Avogadro/dev/inputGenerators" Checking for file format scripts in "/usr/bin/../lib64/avogadro2/scripts/formatScripts" Error retrieving metadata for file format script: "/usr/lib64/avogadro2/scripts/formatScripts/cclibScript.py" ("Error running script '/usr/bin/python /usr/lib64/avogadro2/scripts/formatScripts/cclibScript.py --metadata': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n File \"/usr/lib64/avogadro2/scripts/formatScripts/cclibScript.py\", line 22, in <module>\n from cclib.io.ccio import ccopen\nModuleNotFoundError: No module named 'cclib'\n") Checking for generator scripts in "/home/USERNAME/.local/share/OpenChemistry/Avogadro/scripts/workflows" Checking for generator scripts in "/usr/local/share/OpenChemistry/Avogadro/scripts/workflows" Checking for generator scripts in "/usr/share/OpenChemistry/Avogadro/scripts/workflows" Checking for generator scripts in "/usr/bin/../lib64/avogadro2/scripts/workflows" "Navigator" added "Editor" added "Selection" added "Manipulator" added "BondCentric" added "MeasureTool" added "PlayerTool" added Process encountered an error, and did not execute correctly. Exit code: 0 Exit status: QProcess::NormalExit Exit output: "" Process encountered an error, and did not execute correctly. Exit code: 0 Exit status: QProcess::NormalExit Exit output: "" Process encountered an error, and did not execute correctly. Exit code: 255 Exit status: QProcess::NormalExit Exit output: "" ------------------------------------------------------------ ---------------- (1) crashed ------------------------------- Extension plugins dynamically found... 24 OBProcess::executeObabel: Running "obabel" "-L formats read" OBProcess::executeObabel: Running "obabel" "-L formats write" OBProcess::executeObabel: Running "obabel" "-L forcefields" OBProcess::executeObabel: Running "obabel" "-V" "obabel not found! Disabling Open Babel plugin actions." Checking for generator scripts in "/usr/bin/../lib64/avogadro2/scripts/inputGenerators" Checking for generator scripts in "/home/USERNAME/.local/share/OpenChemistry/Avogadro/dev/inputGenerators" Checking for generator scripts in "/usr/local/share/OpenChemistry/Avogadro/dev/inputGenerators" Checking for generator scripts in "/usr/share/OpenChemistry/Avogadro/dev/inputGenerators" Checking for file format scripts in "/usr/bin/../lib64/avogadro2/scripts/formatScripts" Error retrieving metadata for file format script: "/usr/lib64/avogadro2/scripts/formatScripts/cclibScript.py" ("Error running script '/usr/bin/python /usr/lib64/avogadro2/scripts/formatScripts/cclibScript.py --metadata': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n File \"/usr/lib64/avogadro2/scripts/formatScripts/cclibScript.py\", line 22, in <module>\n from cclib.io.ccio import ccopen\nModuleNotFoundError: No module named 'cclib'\n") Checking for generator scripts in "/home/USERNAME/.local/share/OpenChemistry/Avogadro/scripts/workflows" Checking for generator scripts in "/usr/local/share/OpenChemistry/Avogadro/scripts/workflows" Checking for generator scripts in "/usr/share/OpenChemistry/Avogadro/scripts/workflows" Checking for generator scripts in "/usr/bin/../lib64/avogadro2/scripts/workflows" KCrash: Application 'avogadro2' crashing... KCrash: Attempting to start /usr/lib64/libexec/drkonqi from kdeinit sock_file=/var/run/user/1000/kdeinit5__0 ------------------------------------------------------------ the line about cclib (filed another bug #698642) happens always and does not correlate with crashing. no suspicious dmesg messages. no lines in .xsession-errors the world is fresh (updated yesterday) and the crash problem is not new (happens all several months after install) Reproducible: Always Steps to Reproduce: 1. install sci-chemistry/avogadro2 2. start avogadro2 from Panel (click icon) or terminal (run 'avogadro2') Actual Results: 1. with approx. 50% probability the application does not start and we get a crash notification 2. in text console, the crash happens after line 'Checking for generator scripts in "/usr/bin/../lib64/avogadro2/scripts/workflows"' Expected Results: to always start without crashing to have email to send the debug information the application has no email to send the debug info, so citing here: -------------------------- Application: avogadro2 (avogadro2), signal: Segmentation fault Using host libthread_db library "/lib64/libthread_db.so.1". [Current thread is 1 (Thread 0x7f214de63bc0 (LWP 28767))] Thread 3 (Thread 0x7f2143fff700 (LWP 28769)): #0 0x00007f2151ec3773 in poll () from /lib64/libc.so.6 #1 0x00007f2150bbb546 in ?? () from /usr/lib64/libglib-2.0.so.0 #2 0x00007f2150bbb66c in g_main_context_iteration () from /usr/lib64/libglib-2.0.so.0 #3 0x00007f215247cfbb in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib64/libQt5Core.so.5 #4 0x00007f215242b1d3 in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib64/libQt5Core.so.5 #5 0x00007f215229dca6 in QThread::exec() () from /usr/lib64/libQt5Core.so.5 #6 0x00007f214d4a2565 in ?? () from /usr/lib64/libQt5DBus.so.5 #7 0x00007f215229eed1 in ?? () from /usr/lib64/libQt5Core.so.5 #8 0x00007f2151c0f408 in start_thread () from /lib64/libpthread.so.0 #9 0x00007f2151ecf7ff in clone () from /lib64/libc.so.6 Thread 2 (Thread 0x7f214c311700 (LWP 28768)): #0 0x00007f2151ec3773 in poll () from /lib64/libc.so.6 #1 0x00007f214e0a3cf7 in ?? () from /usr/lib64/libxcb.so.1 #2 0x00007f214e0a591a in xcb_wait_for_event () from /usr/lib64/libxcb.so.1 #3 0x00007f214d7d4c60 in ?? () from /usr/lib64/libQt5XcbQpa.so.5 #4 0x00007f215229eed1 in ?? () from /usr/lib64/libQt5Core.so.5 #5 0x00007f2151c0f408 in start_thread () from /lib64/libpthread.so.0 #6 0x00007f2151ecf7ff in clone () from /lib64/libc.so.6 Thread 1 (Thread 0x7f214de63bc0 (LWP 28767)): [KCrash Handler] #6 0x00007f2151d7c307 in Avogadro::Rendering::Camera::Camera() () from /usr/lib64/libAvogadroRendering.so.1 #7 0x00007f2151d82b37 in Avogadro::Rendering::GLRenderer::GLRenderer() () from /usr/lib64/libAvogadroRendering.so.1 #8 0x00007f21533e6045 in Avogadro::QtOpenGL::GLWidget::GLWidget(QWidget*) () from /usr/lib64/libAvogadroQtOpenGL.so.1 #9 0x000055a6c9763840 in ?? () #10 0x000055a6c9764772 in ?? () #11 0x000055a6c9756bfd in ?? () #12 0x00007f2151dedecb in __libc_start_main () from /lib64/libc.so.6 #13 0x000055a6c9756dfa in _start () [Inferior 1 (process 28767) detached] --------------------------------
(In reply to Petr F. Kartsev from comment #0) > clicking Panel (with command avogadro2 %f) almost always crashes. > starting from command line 'avogadro2' gives two outcomes with equal > probability: > > ----------------- (2) successfully started ----------------- > Extension plugins dynamically found... 24 > OBProcess::executeObabel: Running "obabel" "-L formats read" > OBProcess::executeObabel: Running "obabel" "-L formats write" > OBProcess::executeObabel: Running "obabel" "-V" > "obabel not found! Disabling Open Babel plugin actions." > Checking for generator scripts in > "/usr/bin/../lib64/avogadro2/scripts/inputGenerators" > Checking for generator scripts in > "/home/USERNAME/.local/share/OpenChemistry/Avogadro/dev/inputGenerators" > Checking for generator scripts in > "/usr/local/share/OpenChemistry/Avogadro/dev/inputGenerators" > Checking for generator scripts in > "/usr/share/OpenChemistry/Avogadro/dev/inputGenerators" > Checking for file format scripts in > "/usr/bin/../lib64/avogadro2/scripts/formatScripts" > Error retrieving metadata for file format script: > "/usr/lib64/avogadro2/scripts/formatScripts/cclibScript.py" > ("Error running script '/usr/bin/python > /usr/lib64/avogadro2/scripts/formatScripts/cclibScript.py --metadata': > Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback > (most recent call last):\n File > \"/usr/lib64/avogadro2/scripts/formatScripts/cclibScript.py\", line 22, in > <module>\n from cclib.io.ccio import ccopen\nModuleNotFoundError: No > module named 'cclib'\n") This is what you reported in bug #698642 so let's focus on the other problem here.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4f9bfa15743bd562d43831e436f4419790fd7560 commit 4f9bfa15743bd562d43831e436f4419790fd7560 Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2020-03-14 17:31:36 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2020-03-14 17:32:07 +0000 sci-chemistry/avogadro2: Bump to 1.93.0 Closes: https://bugs.gentoo.org/695180 Closes: https://bugs.gentoo.org/698644 Package-Manager: Portage-2.3.93, Repoman-2.3.20 Signed-off-by: Pacho Ramos <pacho@gentoo.org> sci-chemistry/avogadro2/Manifest | 1 + sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild | 56 +++++++++++++++++++++++++ 2 files changed, 57 insertions(+)
