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20 hours ago •
charto
charto
binding VG on linux
Hi,
I have trouble binding the vg lib on linux. Somehow the linking does not work and I don't know why. If I add a wrong library path, then the linker throughs an error, so all the libs are recognized, but not linked against.....
ERROR:
npm run -- node-gyp configure build
> [email protected] node-gyp /home1/simon/git/genome-graph-visualization
> node-gyp "configure" "build"
make: Entering directory '/home1/simon/git/genome-graph-visualization/build'
CXX(target) Release/obj.target/nbind/private/cpp/JS_AG.o
../private/cpp/JS_AG.cpp:83:9: warning: "/*" within comment [-Wcomment]
/*
^
../private/cpp/JS_AG.cpp:273:1: warning: "/*" within comment [-Wcomment]
/*
^
In file included from ../private/cpp/../../../genome-graph-visualization/src/vg.hpp:31:0,
from ../private/cpp/JS_AG.cpp:7:
../../genome-graph-visualization/include/lru_cache.h:52:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Impl> impl_;
^
In file included from /usr/include/c++/5/memory:81:0,
from ../private/cpp/JS_AG.cpp:3:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from ../private/cpp/../../../genome-graph-visualization/src/xag.hpp:12:0,
from ../private/cpp/JS_AG.cpp:10:
../../genome-graph-visualization/include/xg.hpp: In constructor ‘xg::XG::XG()’:
../../genome-graph-visualization/include/xg.hpp:265:10: warning: ‘xg::XG::end_marker’ will be initialized after [-Wreorder]
char end_marker;
^
../../genome-graph-visualization/include/xg.hpp:90:12: warning: ‘size_t xg::XG::seq_length’ [-Wreorder]
size_t seq_length;
^
../../genome-graph-visualization/include/xg.hpp:54:5: warning: when initialized here [-Wreorder]
XG(void) : start_marker('#'),
^
../private/cpp/JS_AG.cpp: In function ‘std::shared_ptr<vg::AG> getSubgraphFromXagByRange(vg::AG&, vg::XAG&, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, bool, bool, bool)’:
../private/cpp/JS_AG.cpp:213:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < ptr_ag->graph.node_size(); ++i) {
^
../private/cpp/JS_AG.cpp: In function ‘void graphToJsonOut(vg::AG*, std::__cxx11::string)’:
../private/cpp/JS_AG.cpp:360:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t idx = 0; idx < ag->graph.path_size(); ++idx) {
^
CXX(target) Release/obj.target/nbind/node_modules/nbind/src/common.o
CXX(target) Release/obj.target/nbind/node_modules/nbind/src/reflect.o
CXX(target) Release/obj.target/nbind/node_modules/nbind/src/v8/Buffer.o
CXX(target) Release/obj.target/nbind/node_modules/nbind/src/v8/Binding.o
SOLINK_MODULE(target) Release/obj.target/nbind.node
COPY Release/nbind.node
make: Leaving directory '/home1/simon/git/genome-graph-visualization/build'
simon@osa0:~/git/genome-graph-visualization$ node app.js
module.js:598
return process.dlopen(module, path._makeLong(filename));
^
Error: /home1/simon/git/genome-graph-visualization/build/Release/nbind.node: undefined symbol: _ZN4sdsl4bits6lt_selE
at Object.Module._extensions..node (module.js:598:18)
at Module.load (module.js:488:32)
at tryModuleLoad (module.js:447:12)
at Function.Module._load (module.js:439:3)
at Module.require (module.js:498:17)
at require (internal/module.js:20:19)
at initNode (/home1/simon/git/genome-graph-visualization/node_modules/nbind/dist/nbind.js:140:15)
at /home1/simon/git/genome-graph-visualization/node_modules/nbind/dist/nbind.js:114:13
at findCompiledModule (/home1/simon/git/genome-graph-visualization/node_modules/nbind/dist/nbind.js:78:13)
at find (/home1/simon/git/genome-graph-visualization/node_modules/nbind/dist/nbind.js:92:13)
at Object.init (/home1/simon/git/genome-graph-visualization/node_modules/nbind/dist/nbind.js:103:5)
at Object.<anonymous> (/home1/simon/git/genome-graph-visualization/private/javascripts/ag.js:2:17)
at Module._compile (module.js:571:32)
at Object.Module._extensions..js (module.js:580:10)
at Module.load (module.js:488:32)
at tryModuleLoad (module.js:447:12)
at Function.Module._load (module.js:439:3)
at Module.require (module.js:498:17)
at require (internal/module.js:20:19)
at Object.<anonymous> (/home1/simon/git/genome-graph-visualization/private/javascripts/data_set_supervisor.js:8:13)
at Module._compile (module.js:571:32)
at Object.Module._extensions..js (module.js:580:10)
The binding.gyp:
{
"make_global_settings": [
["CXX", "../node_modules/nbind/bin/g++"],
["LINK", "../node_modules/nbind/bin/g++"]
],
"targets": [
{
"includes": [
"auto.gypi"
],
"sources": [
"private/cpp/JS_AG.cpp"
# ,"cpp/JS_VG.cpp"
],
"conditions": [
["OS=='mac'", {
"xcode_settings": {
"OTHER_CPLUSPLUSFLAGS": [
"-c",
"-msse4.1",
"-fopenmp",
"-frtti",
"-ggdb",
# "-o cpp/JS_AG",
# "-Wall",
# "-pedantic",
"-g",
"-I../../genome-graph/",
"-I../../genome-graph/include"
],
"OTHER_LDFLAGS": [
"-msse4.1",
"-fopenmp",
"-ggdb",
# "-Wall",
# "-pedantic",
"-g",
"-I../../genome-graph/",
"-I../../genome-graph/include",
"-lvg",
"-lsdsl",
"-lxg",
"-lvcflib",
"-lgssw",
"-lrocksdb",
"-lhts",
"-lgcsa2",
"-lprotobuf",
"-lraptor2",
"-lgfakluge",
"-lsupbub",
"-lpinchesandcacti",
"-l3edgeconnected",
"-lsonlib",
"-lm",
"-lpthread",
"-ly",
"-lbz2",
"-lsnappy",
"-ldivsufsort",
"-ldivsufsort64",
"-ljansson",
"-lgff",
"-L../../genome-graph/src",
"-L../../genome-graph/lib"
]
}
}],
["OS=='linux'", {
"cflags_cc+": [
"-c",
"-msse4.1",
"-fopenmp",
"-frtti",
"-ggdb",
"-g",
"-I../../genome-graph/",
"-I../../genome-graph/include"
],
"link_settings": {
"ldflags": [
"-msse4.1",
"-fopenmp",
"-ggdb",
"-g",
"-I../../genome-graph/",
"-I../../genome-graph/include",
"-lvg",
"-lsdsl",
"-lxg",
"-lvcflib",
"-lgssw",
"-lrocksdb",
"-lhts",
"-lgcsa2",
"-lprotobuf",
"-lraptor2",
"-lgfakluge",
"-lsupbub",
"-lpinchesandcacti",
"-l3edgeconnected",
"-lsonlib",
"-lm",
"-lpthread",
"-ly",
"-lbz2",
"-lsnappy",
"-ldivsufsort",
"-ldivsufsort64",
"-ljansson",
"-lgff",
"-L../../genome-graph/src",
"-L../../genome-graph/lib"
]
}
}]
]
}
],
"includes": [
"auto-top.gypi"
]
}
Any help would be highly appreciated.
Somehow solved this problem with shared libraries, but for another library. using this tutorial Did it like this. Additionally added "libraries": [ "/home/jasurn/CLionProjects/SecondC/libSome.so" ], into nbind.gyp file(location './node_modules/nbind/srt').
I'm having this same issue, things look okay when using Debian Jessie, but break on Stretch 😢
I fixed my issue by adding 'cflags': [ '-D_GLIBCXX_USE_CXX11_ABI=0' ], to my build target.
Seemed the library was adding [abi:cxx11] to my symbols. I don't know enough to understand why! Hopefully this will help someone else.
@ISNIT0 Would it make sense to integrate your solution as an optional fix into the tutorial? So I would enhance it ;)