Bug 642248

Summary: avogadro SIGABRT from __cxa_rethrow of boost::python::error_already_set - The _C_API object in the sip python module is invalid
Product: [Fedora] Fedora Reporter: Vytas <vytautas1987>
Component: avogadroAssignee: Kevin Kofler <kevin>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: medium Docs Contact:
Priority: low    
Version: 14CC: acrribeiro, david.ploye, ejsheldrake, gregor, kevin, lionel.nauton, marbolangos, mark.wilson, pamodeo
Target Milestone: ---Keywords: Patch
Target Release: ---   
Hardware: x86_64   
OS: Linux   
Whiteboard: abrt_hash:5d412730fcf4c3f88a4e83889376390bf3250c32
Fixed In Version: avogadro-1.0.1-10.fc14 Doc Type: Bug Fix
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2010-11-24 22:39:40 UTC Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Embargoed:
Attachments:
Description Flags
File: backtrace
none
possible fix none

Description Vytas 2010-10-12 13:00:42 UTC 
abrt version: 1.1.13
architecture: x86_64
Attached file: backtrace
cmdline: /usr/bin/avogadro
component: avogadro
crash_function: __gnu_cxx::__verbose_terminate_handler()
executable: /usr/bin/avogadro
kernel: 2.6.34.7-56.fc13.x86_64
package: avogadro-1.0.1-6.fc14
rating: 3
reason: Process /usr/bin/avogadro was killed by signal 6 (SIGABRT)
release: Fedora release 14 (Laughlin)
time: 1286888373
uid: 500

How to reproduce
-----
1. Just run it.
Comment 1 Vytas 2010-10-12 13:00:45 UTC 
Created attachment 452958 [details]
File: backtrace
Comment 2 Kevin Kofler 2010-11-15 17:14:18 UTC 
*** Bug 646375 has been marked as a duplicate of this bug. ***
Comment 3 Kevin Kofler 2010-11-15 17:14:32 UTC 
*** Bug 649236 has been marked as a duplicate of this bug. ***
Comment 4 Kevin Kofler 2010-11-15 17:18:06 UTC 
Bug 649236 has more information about what exactly is being rethrown:

comment
-----
Eventually this is not an avogadro bug. here is the console output

The _C_API object in the sip python module is invalid.
Could not initialize SIP API !
terminate called after throwing an instance of
'boost::python::error_already_set'
Aborted (core dumped)
Comment 5 Kevin Kofler 2010-11-15 17:19:31 UTC 
*** Bug 650943 has been marked as a duplicate of this bug. ***
Comment 6 Kevin Kofler 2010-11-15 17:19:51 UTC 
*** Bug 653547 has been marked as a duplicate of this bug. ***
Comment 7 Pietro Amodeo 2010-11-18 17:00:44 UTC 
Package: avogadro-1.0.1-6.fc14
Architecture: x86_64
OS Release: Fedora release 14 (Laughlin)


How to reproduce
-----
1.Just started the program
2.
3.
Comment 8 Kevin Kofler 2010-11-19 15:37:08 UTC 
*** Bug 655079 has been marked as a duplicate of this bug. ***
Comment 9 Kevin Kofler 2010-11-22 14:32:40 UTC 
*** Bug 655848 has been marked as a duplicate of this bug. ***
Comment 10 Edward Sheldrake 2010-11-23 20:04:50 UTC 
Created attachment 462431 [details]
possible fix

The problem appears to be avogadro being incompatible with sip + python 2.7, because sip started using PyCapsule (sip 4.10.4 NEWS).

I don't know python, the patch is entirely based on http://docs.python.org/whatsnew/2.7.html#capsules
Comment 11 Kevin Kofler 2010-11-23 20:15:02 UTC 
Hmmm, I wonder if bug 646375 is actually a different issue, because that one is on F13, which doesn't have Python 2.7. All the others are on F14, which makes sense.
Comment 12 Kevin Kofler 2010-11-23 20:19:23 UTC 
Have you tested this patch?
Comment 13 Edward Sheldrake 2010-11-23 20:27:30 UTC 
Yes, it appears to work - open a sample file, then in the python console:

import Avogadro
Avogadro.molecule.clear()

And, avogadro also starts up.
Comment 14 Fedora Update System 2010-11-23 21:13:32 UTC 
avogadro-1.0.1-10.fc14 has been submitted as an update for Fedora 14.
https://admin.fedoraproject.org/updates/avogadro-1.0.1-10.fc14
Comment 15 Fedora Update System 2010-11-24 22:39:35 UTC 
avogadro-1.0.1-10.fc14 has been pushed to the Fedora 14 stable repository.  If problems still persist, please make note of it in this bug report.