I have the problem with clang 5.0.0 on Mac OS X 10.9.1 Mavericks. There is no problem with clang 4.2.0 on Mac OS X 10.7.5 Lion.
Matt On 13 Jan 2014, at 20:26, Noel O'Boyle <baoille...@gmail.com> wrote: > Is this a problem only a problem with clang? > > - Noel > > On 13 January 2014 12:43, Matt Swain <mattswain...@gmail.com> wrote: >> This problem with plugins loaded from the plugindefines.txt has been causing >> issues for me too, mainly when pybel sporadically complains that the list of >> descriptors is garbage. >> >> I've tried tracking it down, without much success. It seems to be a problem >> with all plugins that are loaded from a file using OBDefine in loader.cpp, >> not just the SMARTS descriptors. (Also, the SMARTS descriptors loaded >> manually at the end of smartsdescriptors.cpp look fine to me.) >> >> I think the problem is to do with plugins using const char* pointers for the >> ID, description etc. These pointers are created from std::strings using >> .c_str() in MakeInstance, and I think maybe the original string is being >> destroyed or going out of scope, hence the char* pointer becomes garbage. >> The only problem is, as far as I can tell, loader.cpp looks after the >> strings just fine so they shouldn't be destroyed. >> >> In loader.cpp, OBDefine reads the relevant strings from plugindefines.txt, >> then copies them into a private member vector _text, to ensure they stay >> around for the lifetime of the OBDefine instance. The strings in _text are >> then used to call MakeInstance on SmartsDescriptor, PatternFP, >> CompoundFilter, etc. which uses c_str() to create a pointer to the string in >> memory. Right after the descriptors are created, accessing GetID() returns >> it fine. But at some later point this becomes garbage, even when the >> OBDefine instance is still around and the strings in OBDefine's _text are >> still completely fine. >> >> If the original string hasn't been destroyed, one other thing that could >> invalidate the c_str() result is if a non-const member function of the >> string is called. I can't see this happening anywhere either though. >> >> Matt >> >> On 2 Jan 2014, at 21:32, Geoffrey Hutchison <geoff.hutchi...@gmail.com> >> wrote: >> >>>> Can you figure out a minimal plugindefines.txt that still causes the >>>> problem? >>> >>> Good point. I'm now seeing that the main issue is with SMARTS descriptors. >>> I'll see if I can find the problems later tonight. >>> >>> Thanks, >>> -Geoff >>> ------------------------------------------------------------------------------ >>> Rapidly troubleshoot problems before they affect your business. Most IT >>> organizations don't have a clear picture of how application performance >>> affects their revenue. With AppDynamics, you get 100% visibility into your >>> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics >>> Pro! >>> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
