apblair
commented
7 years ago I am having the same issue on my Ubuntu 16.04 vm. Have you been able to fix this?
Open geboro opened 7 years ago
apblair
commented
7 years ago I am having the same issue on my Ubuntu 16.04 vm. Have you been able to fix this?
Working under Ubuntu 16.04 and following the installation instructions for Ubuntu. The build crashers with a "collect2: error: ld returned 1 exit status" and undefined references. I understand this could be typos in the code. I also ran a "make clean" + "make" with the same result. Below is the last part of the screen output (just before failing):
g++ -Wl,-O1 -Wl,-rpath,/home/gbonilla/Software/BioTools/Anaconda/lib -o Bandage main.o settings.o globals.o graphlayoutworker.o debruijnnode.o debruijnedge.o graphicsitemnode.o graphicsitemedge.o mainwindow.o graphicsviewzoom.o settingsdialog.o mygraphicsview.o mygraphicsscene.o aboutdialog.o enteroneblastquerydialog.o blasthit.o blastqueries.o blastsearchdialog.o infotextwidget.o assemblygraph.o verticalscrollarea.o myprogressdialog.o nodewidthvisualaid.o verticallabel.o load.o image.o commoncommandlinefunctions.o mytablewidget.o buildblastdatabaseworker.o colourbutton.o blastquery.o runblastsearchworker.o blastsearch.o path.o pathspecifydialog.o graphlocation.o tablewidgetitemint.o tablewidgetitemdouble.o tablewidgetitemshown.o memory.o querypathspushbutton.o querypathsdialog.o blastquerypath.o blasthitfiltersdialog.o scinot.o changenodenamedialog.o querypathsequencecopybutton.o querypaths.o info.o reduce.o Graph.o GraphAttributes.o FMMMLayout.o geometry.o ClusterGraphAttributes.o FruchtermanReingold.o NMM.o GmlParser.o simple_graph_alg.o basic.o XmlParser.o String.o Hashing.o PoolMemoryAllocator.o GraphCopy.o CombinatorialEmbedding.o OgmlParser.o ClusterGraph.o Math.o EdgeAttributes.o NodeAttributes.o MAARPacking.o Multilevel.o numexcept.o Set.o Ogml.o DinoXmlParser.o DinoXmlScanner.o DinoTools.o DinoLineBuffer.o System.o QuadTreeNM.o QuadTreeNodeNM.o Constraint.o MultilevelGraph.o graphinfodialog.o tablewidgetitemname.o changenodedepthdialog.o qrc_images.o moc_graphlayoutworker.o moc_mainwindow.o moc_graphicsviewzoom.o moc_settingsdialog.o moc_mygraphicsview.o moc_mygraphicsscene.o moc_aboutdialog.o moc_enteroneblastquerydialog.o moc_blastquery.o moc_blastsearchdialog.o moc_infotextwidget.o moc_assemblygraph.o moc_verticalscrollarea.o moc_myprogressdialog.o moc_nodewidthvisualaid.o moc_verticallabel.o moc_mytablewidget.o moc_buildblastdatabaseworker.o moc_colourbutton.o moc_runblastsearchworker.o moc_pathspecifydialog.o moc_querypathspushbutton.o moc_querypathsdialog.o moc_blasthitfiltersdialog.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.o moc_graphinfodialog.o moc_changenodedepthdialog.o -L/usr/lib -lQt5Svg -L/home/gbonilla/Software/BioTools/Anaconda/lib -lQt5Widgets -lQt5Gui -lQt5Core -lGL -lpthread ClusterGraphAttributes.o: In functionvoid std::cxx11::basic_string<char, std::char_traitsogdf::ClusterGraphAttributes::writeOGML(std::ostream&)': ClusterGraphAttributes.cpp:(.text+0x7404): undefined reference toVTT for std::cxx11::basic_ostringstream<char, std::char_traitsvtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >' ClusterGraphAttributes.cpp:(.text+0x74aa): undefined reference tovtable for std::cxx11::basic_stringbuf<char, std::char_traitsvtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >' ClusterGraphAttributes.cpp:(.text+0x75e5): undefined reference tovtable for std::cxx11::basic_stringbuf<char, std::char_traitsvtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >' ClusterGraphAttributes.cpp:(.text+0x8435): undefined reference tovtable for std::cxx11::basic_stringbuf<char, std::char_traitsvtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >' ClusterGraphAttributes.cpp:(.text+0x84d3): undefined reference tovtable for std::cxx11::basic_ostringstream<char, std::char_traitsstd::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::swap(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' ClusterGraphAttributes.cpp:(.text+0x89a6): undefined reference tostd::cxx11::basic_string<char, std::char_traitsstd::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()' ClusterGraphAttributes.cpp:(.text+0x89da): undefined reference tostd::cxx11::basic_ostringstream<char, std::char_traitsvtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >' ClusterGraphAttributes.o: In functionstd::cxx11::basic_stringbuf<char, std::char_traitsogdf::NMM::init_binko(int)': NMM.cpp:(.text+0x709d): undefined reference tocxa_throw_bad_array_new_length' NMM.o: In functionogdf::NMM::form_multipole_expansion_of_subtree(ogdf::NodeArray<ogdf::NodeAttributes>&, ogdf::QuadTreeNM&, ogdf::List<ogdf::QuadTreeNodeNM*>&)': NMM.cpp:(.text+0xb0e4): undefined reference to__cxa_throw_bad_array_new_length' NMM.cpp:(.text+0xb0fc): undefined reference to `cxa_throw_bad_array_new_length' simple_graph_alg.o: In functionogdf::topologicalNumbering(ogdf::Graph const&, ogdf::NodeArray<int>&)': simple_graph_alg.cpp:(.text+0x20da): undefined reference tocxa_throw_bad_array_new_length' simple_graph_alg.o: In functionogdf::strongComponents(ogdf::Graph const&, ogdf::NodeArray<int>&)': simple_graph_alg.cpp:(.text+0x3473): undefined reference to__cxa_throw_bad_array_new_length' simple_graph_alg.o:simple_graph_alg.cpp:(.text+0x3783): more undefined references to `cxa_throw_bad_array_new_length' follow collect2: error: ld returned 1 exit status Makefile:603: recipe for target 'Bandage' failed make: *** [Bandage] Error 1 `