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
