[Networkit] problem installing networkit on mac

Kayhan Batmanghelich batmanghelich at gmail.com
Thu Dec 3 20:30:53 CET 2015


Dear all,

I am trying to install networkit on macox 10.10 using pip but I get the
following error message (see below). Here are system specs:

MacOX 10.10.5
gcc veriosn

$ gcc --version
Configured with:
--prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn)
Target: x86_64-apple-darwin14.5.0
Thread model: posix

Python version :

$ python --version
Python 3.3.5 :: Anaconda 2.3.0 (x86_64)

It seems it failed during linking. Is it the compiler issue? Any idea how
to solve it?

Thanks,
Kayhan

(py3k)kayhan·kayhans-mbp·12/03,14:25:14·~

pip install networkit
[...]
  .buildOpt/AdamicAdarIndex.o .buildOpt/AdjustedRandIndex.o
.buildOpt/AlgebraicDistanceIndex.o .buildOpt/CommonNeighborsIndex.o
.buildOpt/EvaluationMetric.o .buildOpt/JaccardIndex.o
.buildOpt/KatzIndex.o .buildOpt/LinkPredictor.o
.buildOpt/LinkThresholder.o .buildOpt/MissingLinksFinder.o
.buildOpt/NeighborhoodDistanceIndex.o .buildOpt/NeighborhoodUtility.o
.buildOpt/NeighborsMeasureIndex.o .buildOpt/PrecisionRecallMetric.o
.buildOpt/PredictionsSorter.o .buildOpt/PreferentialAttachmentIndex.o
.buildOpt/RandomLinkSampler.o .buildOpt/ResourceAllocationIndex.o
.buildOpt/ROCMetric.o .buildOpt/SameCommunityIndex.o
.buildOpt/TotalNeighborsIndex.o .buildOpt/UDegreeIndex.o
.buildOpt/VDegreeIndex.o .buildOpt/LocalMaxMatcher.o
.buildOpt/Matcher.o .buildOpt/Matching.o
.buildOpt/PathGrowingMatcher.o .buildOpt/HashingOverlapper.o
.buildOpt/Overlapper.o .buildOpt/RegionGrowingOverlapper.o
.buildOpt/ApproximatePageRank.o .buildOpt/GCE.o
.buildOpt/PageRankNibble.o .buildOpt/SelectiveCommunityDetector.o
.buildOpt/ChanceCorrectedTriangleScore.o .buildOpt/ForestFireScore.o
.buildOpt/GlobalThresholdFilter.o .buildOpt/LocalDegreeScore.o
.buildOpt/LocalSimilarityScore.o .buildOpt/MultiscaleScore.o
.buildOpt/RandomEdgeScore.o .buildOpt/RandomNodeEdgeScore.o
.buildOpt/SCANStructuralSimilarityScore.o
.buildOpt/SimmelianOverlapScore.o .buildOpt/SimmelianScore.o
.buildOpt/Sparsifiers.o .buildOpt/Cover.o .buildOpt/Partition.o
.buildOpt/UnionFind.o .buildOpt/FruchtermanReingold.o
.buildOpt/Layouter.o .buildOpt/MaxentStress.o
.buildOpt/MultilevelLayouter.o .buildOpt/PostscriptWriter.o
     ranlib libNetworKit-Core-Opt.a
     building '_NetworKit' extension
     g++-4.9 -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -I/Users/kayhan/anaconda/envs/py3k/include -arch
x86_64 -I/Users/kayhan/anaconda/envs/py3k/include/python3.3m -c
networkit/_NetworKit.cpp -o
build/temp.macosx-10.5-x86_64-3.3/networkit/_NetworKit.o -fopenmp
-std=c++14 -O3 -DNOGTEST
     cc1plus: warning: command line option '-Wstrict-prototypes' is
valid for C/ObjC but not for C++
     networkit/_NetworKit.cpp: In function 'void
__pyx_pf_10_NetworKit_17EdgeScoreAsWeight_2__dealloc__(__pyx_obj_10_NetworKit_EdgeScoreAsWeight*)':
     networkit/_NetworKit.cpp:66453:24: warning: deleting object of
polymorphic class type 'NetworKit::EdgeScoreAsWeight' which has
non-virtual destructor might cause undefined behaviour
[-Wdelete-non-virtual-dtor]
        delete __pyx_v_self->_this;
                             ^
     networkit/_NetworKit.cpp: In function 'std::vector<long long
unsigned int> __pyx_convert_vector_from_py___pyx_t_10_NetworKit_count(PyObject*)':
     networkit/_NetworKit.cpp:71640:79: warning: comparison between
signed and unsigned integer expressions [-Wsign-compare]
          __pyx_t_5 = __Pyx_PyInt_As_uint64_t(__pyx_v_item); if
(unlikely(__pyx_t_5 == -1LL && PyErr_Occurred())) {__pyx_filename =
__pyx_f[1]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto
__pyx_L1_error;}

             ^
     networkit/_NetworKit.cpp:624:43: note: in definition of macro 'unlikely'
        #define unlikely(x) __builtin_expect(!!(x), 0)
                                                ^
     networkit/_NetworKit.cpp: In function 'std::vector<long long
unsigned int> __pyx_convert_vector_from_py___pyx_t_10_NetworKit_node(PyObject*)':
     networkit/_NetworKit.cpp:71816:79: warning: comparison between
signed and unsigned integer expressions [-Wsign-compare]
          __pyx_t_5 = __Pyx_PyInt_As_uint64_t(__pyx_v_item); if
(unlikely(__pyx_t_5 == -1LL && PyErr_Occurred())) {__pyx_filename =
__pyx_f[1]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto
__pyx_L1_error;}

             ^
     networkit/_NetworKit.cpp:624:43: note: in definition of macro 'unlikely'
        #define unlikely(x) __builtin_expect(!!(x), 0)
                                                ^
     networkit/_NetworKit.cpp: In function 'std::set<unsigned int>
__pyx_convert_set_from_py_unsigned_int(PyObject*)':
     networkit/_NetworKit.cpp:71937:83: warning: comparison between
signed and unsigned integer expressions [-Wsign-compare]
          __pyx_t_5 = __Pyx_PyInt_As_unsigned_int(__pyx_v_item); if
(unlikely(__pyx_t_5 == -1 && PyErr_Occurred())) {__pyx_filename =
__pyx_f[1]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto
__pyx_L1_error;}

                 ^
     networkit/_NetworKit.cpp:624:43: note: in definition of macro 'unlikely'
        #define unlikely(x) __builtin_expect(!!(x), 0)
                                                ^
     networkit/_NetworKit.cpp: In function 'std::pair<long long
unsigned int, long long unsigned int>
__pyx_convert_pair_from_py___pyx_t_10_NetworKit_node__and___pyx_t_10_NetworKit_node(PyObject*)':
     networkit/_NetworKit.cpp:72070:74: warning: comparison between
signed and unsigned integer expressions [-Wsign-compare]
        __pyx_t_5 = __Pyx_PyInt_As_uint64_t(__pyx_v_x); if
(unlikely(__pyx_t_5 == -1LL && PyErr_Occurred())) {__pyx_filename =
__pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto
__pyx_L1_error;}
                                                                               ^
     networkit/_NetworKit.cpp:624:43: note: in definition of macro 'unlikely'
        #define unlikely(x) __builtin_expect(!!(x), 0)
                                                ^
     networkit/_NetworKit.cpp:72071:74: warning: comparison between
signed and unsigned integer expressions [-Wsign-compare]
        __pyx_t_6 = __Pyx_PyInt_As_uint64_t(__pyx_v_y); if
(unlikely(__pyx_t_6 == -1LL && PyErr_Occurred())) {__pyx_filename =
__pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto
__pyx_L1_error;}
                                                                               ^
     networkit/_NetworKit.cpp:624:43: note: in definition of macro 'unlikely'
        #define unlikely(x) __builtin_expect(!!(x), 0)
                                                ^
     networkit/_NetworKit.cpp: At global scope:
     networkit/_NetworKit.cpp:30388:18: warning: 'PyObject*
__pyx_pw_10_NetworKit_9Partition_5__getitem__(PyObject*, PyObject*)'
defined but not used [-Wunused-function]
      static PyObject
*__pyx_pw_10_NetworKit_9Partition_5__getitem__(PyObject *__pyx_v_self,
PyObject *__pyx_arg_e) {
                       ^
     g++-4.9 -bundle -undefined dynamic_lookup
-L/Users/kayhan/anaconda/envs/py3k/lib -arch x86_64
build/temp.macosx-10.5-x86_64-3.3/networkit/_NetworKit.o -L./
-L/Users/kayhan/anaconda/envs/py3k/lib -lNetworKit-Core-Opt -o
build/lib.macosx-10.5-x86_64-3.3/_NetworKit.so -fopenmp -std=c++14
     ld: library not found for -lgcc_s.10.5
     collect2: error: ld returned 1 exit status
     error: command 'g++-4.9' failed with exit status 1



    ----------------------------------------
 Command "/Users/kayhan/anaconda/envs/py3k/bin/python3 -c "import
setuptools, tokenize;__file__='/private/var/folders/kh/s846jbks2539yqq9g1fs3fqr0000gn/T/pip-build-ghpb0i/networkit/setup.py';exec(compile(getattr(tokenize,
'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
'exec'))" install --record
/var/folders/kh/s846jbks2539yqq9g1fs3fqr0000gn/T/pip-wxhsjn-record/install-record.txt
--single-version-externally-managed --compile" failed with error code
1 in /private/var/folders/kh/s846jbks2539yqq9g1fs3fqr0000gn/T/pip-build-ghpb0i/networkit

​
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