Re: [Seqan-dev] RazerS 3 compilation issue

["Weese, David" <weese@campus.fu-berlin.de>]

Hi,

the "internal compiler error" in correlation with the heavy templating in RazerS3 is usually an indicator for insufficient memory of your build machine. If you compile using the gcc make sure you have at least 4GB of free memory available.

Cheers,
David

--
David Weese, Ph.D.              david.weese@fu-berlin.de
Freie Universität Berlin        http://www.inf.fu-berlin.de/
Institut für Informatik         Phone: +49 30 838 75137
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Am 27.02.2014 um 06:23 schrieb Tran Ngoc Hieu (Dr) <NHTran@ntu.edu.sg>:

> Dear All,
>  
> I encountered the following errors when trying to compile RazerS 3 (everything was fine when I tried other tools such as Mason, Masai). Could anyone please help with some advice? Thank you very much!
>  
> $ make razers3
> [  0%] Built target seqan_extras
> [  0%] Built target seqan_core
>  
> [100%] Building CXX object extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o
> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/basic/test_system.h:73: warning: âclass seqan::Testâ has virtual functions but non-virtual destructor
> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:197: warning: âclass seqan::ToolDocPrinter_â has virtual functions but non-virtual destructor
> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:210: warning: âclass seqan::ManToolDocPrinter_â has virtual functions but non-virtual destructor
> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:223: warning: âclass seqan::HtmlToolDocPrinter_â has virtual functions but non-virtual destructor
> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:318: warning: âclass seqan::TextToolDocPrinter_â has virtual functions but non-virtual destructor
>  
> /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_parallel.h: In function âvoid seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String<seqan::ThreadLocalStorage<seqan::MapPairedReads<seqan::String<seqan::MatchRecord<long unsigned int>, seqan::Alloc<void> >, seqan::FragmentStore<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig> >, seqan::Finder<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > > >, seqan::Finder<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > > >, seqan::Pattern<seqan::Index<seqan::StringSet<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, seqan::Tag<seqan::OpenAddressing_> > >, seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > > >, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, seqan::RazerSOptions<seqan::RazerSSpec<false, false> >, seqan::String<seqan::String<short unsigned int, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSMode<seqan::RazerSGlobal, seqan::RazerSGapped, seqan::RazerSErrors, seqan::NMatchesNone_> > >, seqan::Alloc<void> >, TFragmentStore = seqan::FragmentStore<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig> >, TSplitters = seqan::String<unsigned int, seqan::Alloc<void> >, TShape = const seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, TOptions = seqan::RazerSOptions<seqan::RazerSSpec<false, false> >]â:
>  
> /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_parallel.h:338: internal compiler error: in single_succ_edge, at basic-block.h:620
> Please submit a full bug report,
> with preprocessed source if appropriate.
> See <URL:http://bugzilla.redhat.com/bugzilla> for instructions.
> Preprocessed source stored into /tmp/ccHRTako.out file, please attach this to your bugreport.
> make[3]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o] Error 1
> make[2]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/all] Error 2
> make[1]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/rule] Error 2
> make: *** [razers3] Error 2
> 
> 
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