Nan - nbind - NonCopyablePersistentTraits - Error - VG

[subwaystation]

Hi,

@jjrv maybe you could help me out here?
Of a given graph I want to create an index to find a sequence in it efficiently.

Thanks in advance :)

[subwaystation]

Hi,

@jjrv maybe you could help me out here?
Of a given graph I want to create an index to find a sequence in it efficiently.
Only trying to build the first part of the index, GCSA I run into the following problem.
Code:

std::shared_ptr<gcsa::GCSA> buildGcsa(VG& vg) {
    vg::id_t head_id = 0, tail_id = 0;
    int kmer_size = 13;
    int doubling_steps = 2;
    bool path_only = false;
    bool forward_only = true;
    // TODO change this to 200 or more
    size_t size_limit = 2; // in Gigabytes
    std::string base_file_name = ".vg-kmers-tmp-";
    string tmpfile = vg.write_gcsa_kmers_to_tmpfile(kmer_size, path_only,
    			forward_only, head_id, tail_id, doubling_steps, size_limit,
    			base_file_name);
    // set up the input graph using the kmers
    gcsa::InputGraph input_graph( { tmpfile }, true);
    gcsa::ConstructionParameters params;
    params.setSteps(doubling_steps);
    params.setLimit(size_limit);
    // run the GCSA construction
    //gcsa = new gcsa::GCSA(input_graph, params);
    //auto ag = std::make_shared<AG>(in_vg, in_ff);
    auto gcsa = std::make_shared<gcsa::GCSA>(input_graph, params);
    // and the LCP array construction
    // lcp = new gcsa::LCPArray(input_graph, params);
    // delete the temporary debruijn graph file
    remove(tmpfile.c_str());
    return gcsa;
}

Traceback:

Thread 1 received signal SIGSEGV, Segmentation fault.
0x000000010614307e in v8::Local<v8::Function> Nan::New<v8::Function, v8::NonCopyablePersistentTraits<v8::Function> >(Nan::Persistent<v8::Function, v8::NonCopyablePersistentTraits<v8::Function> > const&) ()
   from /Users/heumos/git/genome-graph/build/Release/nbind.node
(gdb) bt
#0  0x000000010614307e in v8::Local<v8::Function> Nan::New<v8::Function, v8::NonCopyablePersistentTraits<v8::Function> >(Nan::Persistent<v8::Function, v8::NonCopyablePersistentTraits<v8::Function> > const&) ()
   from /Users/heumos/git/genome-graph/build/Release/nbind.node
#1  0x000000010613cc22 in nbind::BindingType<std::shared_ptr<gcsa::GCSA> >::toWireType(std::shared_ptr<gcsa::GCSA>&&) ()
   from /Users/heumos/git/genome-graph/build/Release/nbind.node
#2  0x000000010613eb51 in void nbind::TemplatedBaseSignature<nbind::FunctionSignature<std::shared_ptr<gcsa::GCSA> (*)(vg::AG&), decltype(nullptr), nbind::PolicyListType<>, std::shared_ptr<gcsa::GCSA><vg::AG&> >, std::shared_ptr<gcsa::GCSA><vg::AG&>, std::shared_ptr<gcsa::GCSA><vg::AG&> >::callInnerSafely<void, Nan::FunctionCallbackInfo<v8::Value> const, Nan::FunctionCallbackInfo<v8::Value> >(Nan::FunctionCallbackInfo<v8::Value> const&, Nan::FunctionCallbackInfo<v8::Value>&, unsigned int) ()
   from /Users/heumos/git/genome-graph/build/Release/nbind.node
#3  0x00000001061311d7 in Nan::imp::FunctionCallbackWrapper(v8::FunctionCallbackInfo<v8::Value> const&) ()
   from /Users/heumos/git/genome-graph/build/Release/nbind.node
#4  0x000000010017c59a in v8::internal::FunctionCallbackArguments::Call(void (*)(v8::FunctionCallbackInfo<v8::Value> const&)) ()
#5  0x00000001001e029c in v8::internal::MaybeHandle<v8::internal::Object> v8::internal::(anonymous namespace)::HandleApiCallHelper<false>(v8::internal::Isolate*, v8::internal::Handle<v8::internal::HeapObject>, v8::internal::Handle<v8::internal::HeapObject>, v8::internal::Handle<v8::internal::FunctionTemplateInfo>, v8::internal::Handle<v8::internal::Object>, v8::internal::BuiltinArguments) ()
#6  0x00000001001df6d9 in v8::internal::Builtin_Impl_HandleApiCall(v8::internal::BuiltinArguments, v8::internal::Isolate*) ()
#7  0x0000365ae28063a7 in ?? ()
#8  0x0000365ae28062e1 in ?? ()
#9  0x00007fff5fbfe3e0 in ?? ()
#10 0x0000000300000000 in ?? ()
#11 0x00007fff5fbfe448 in ?? ()
#12 0x0000365ae2c0c61a in ?? ()
#13 0x00003ab3e9904311 in ?? ()
#14 0x0000168da24a70d9 in ?? ()
#15 0x0000000500000000 in ?? ()
#16 0x00001dea6d052399 in ?? ()
#17 0x00001dea6d005399 in ?? ()
#18 0x0000168da24a70d9 in ?? ()
#19 0x00001dea6d014319 in ?? ()
#20 0x00002197b4ce9779 in ?? ()
#21 0x00007fff5fbfe4b8 in ?? ()
#22 0x0000365ae2c09169 in ?? ()
#23 0x00001dea6d052399 in ?? ()
#24 0x00002197b4ce5499 in ?? ()
#25 0x00001dea6d014319 in ?? ()

It seems to me that v8 is trying to copy something that is not copyable?

[subwaystation]

It occured to me that it is the same problem as in here: https://github.com/charto/nbind/issues/39#issuecomment-261890364