Issue installing igraph python in Macosx Lion

Have you got a file named igraph_arpack.h in /opt/local/include/igraph?

Hello,
no, in fact I don't have the /igraph folder.
Maybe is in another place?

Thanks for your time.

Ok, following the other thread I erased that folder... so I restored it and now it give me this error at the install:

Include path: /opt/local/include/igraph
Library path: /opt/local/lib
running install
running bdist_egg
running egg_info
writing python_igraph.egg-info/PKG-INFO
writing top-level names to python_igraph.egg-info/top_level.txt
writing dependency_links to python_igraph.egg-info/dependency_links.txt
writing python_igraph.egg-info/PKG-INFO
writing top-level names to python_igraph.egg-info/top_level.txt
writing dependency_links to python_igraph.egg-info/dependency_links.txt
reading manifest file 'python_igraph.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'python_igraph.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.7-x86_64/egg
running install_lib
running build_py
running build_ext
building 'igraph._igraph' extension
/Developer/usr/bin/llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -pipe -O2 -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/local/include/igraph -I../../build/include -I../../include -I/usr/local/include -I/usr/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/arpackobject.c -o build/temp.macosx-10.7-x86_64-2.7/src/arpackobject.o
In file included from src/arpackobject.c:24:
src/arpackobject.h:28:27: error: igraph_arpack.h: No such file or directory
In file included from src/arpackobject.c:26:
src/error.h:28:26: error: igraph_error.h: No such file or directory
error: command '/Developer/usr/bin/llvm-gcc-4.2' failed with exit status 1

Thanks a lot.

Okay, so after you have restored the folder, do you have a file called igraph_arpack.h in that folder? There should be one -- the folder itself is created when you invoke "make install" on the C core.

Note that you have to use the C core from the 0.6 version; please ensure that you are using the 0.6 version for the core because the naming of the header files was different in 0.5 so there is no file called "igraph_arpack.h" if you happen to use a 0.5 core.

Thanks a lot for the quick reply.

There is no file called igraph_arpack.h, but I thing I got the correct version of the core.

I tried to do another time the process with the configure, that seems everything went ok.
Then I do the make, make install and sudo make installcheck. This last testing phase gave me two errors:

Making installcheck in src
make[1]: Nothing to be done for `installcheck'.
Making installcheck in tests
/bin/sh testsuite AUTOTEST_PATH=/usr/local/bin
## ------------------------------ ##
## igraph 0.6 test suite: igraph. ##
## ------------------------------ ##

igraph version number.

  1: Simple version query (igraph_version): ok

Utility types (vector_t, etc.)

  2: Vector (vector_t): ok
  3: Vector (more) (vector_t): ok
  4: Vector (even more) (vector_t): ok
  5: Matrix (matrix_t): ok
  6: Matrix (more) (matrix_t): ok
  7: Matrix (even more) (matrix_t): ok
  8: Double ended queue (dqueue_t): ok
  9: Vector of pointers (vector_ptr_t): ok
 10: Stack (stack_t): ok
 11: Heap (heap_t): ok
 12: Indexed heap (indheap_t): ok
 13: Doubly indexed heap (d_indheap_t): ok
 14: String vector (igraph_strvector_t): ok
 15: Trie (igraph_trie_t): ok
 16: Partial Sum-Tree (igraph_psumtree_t): ok
 17: Three dimensional array (igraph_array3_t): ok
 18: Hash table (string->string) (igraph_hashtable_t): ok
 19: Special heap for minimum cuts (igraph_i_cutheap_t): ok
 20: Set (igraph_set_t): ok
 21: 2-way heap (igraph_2wheap_t): ok
 22: Sparse matrix (igraph_sparsemat_t): ok
 23: Sparse matrix, multiplications (igraph_sparsemat_t): ok
 24: Sparse matrix, indexing (igraph_sparsemat_t): ok
 25: Sparse matrix, solvers (igraph_sparsemat_t): ok
 26: Sparse matrix, ARPACK eigensolver (igraph_sparsemat_t): ok
 27: Sparse matrix, conversion to dense (igraph_sparsemat_t): ok
 28: Sparse matrix, min & max (igraph_sparsemat_t): ok
 29: Sparse matrix, other operations (igraph_sparsemat_t): ok
 30: Sparse matrix, multiplications with dense (igraph_sparsemat_t): ok
 31: Sparse matrix, is symmetric? (igraph_sparsemat_t): ok
 32: Another sparse matrix (igraph_spmatrix_t): ok
 33: Arbitrarily big integers (igraph_biguint_t): ok
 34: Marked double ended queue (igraph_marked_queue_t): ok
 35: Complex numbers (igraph_complex_t): ok

Basic (interface) functions.

 36: Creating an empty graph (igraph_empty): ok
 37: Copying a graph (igraph_copy): ok
 38: Adding edges to a graph (igraph_add_edges): ok
 39: Adding vertices (igraph_add_vertices): ok
 40: Deleting edges (igraph_delete_edges): ok
 41: Deleting vertices (igraph_delete_vertices): ok
 42: Neighbors (igraph_neighbors): ok
 43: Is the graph directed? (igraph_is_directed): ok
 44: Degree of the vertices (igraph_degree): ok
 45: Query edge ids (igraph_get_eid): ok
 46: Query many edge ids (igraph_get_eids): ok

Iterators aka vertex and edge sequences

 47: Vertices in a vector (igraph_vs_vector): ok
 48: Non-adjacent vertices (igraph_vs_nonadj): ok
 49: Sequence (igraph_vs_seq): ok
 50: Edges given by end points (igraph_es_pairs): ok
 51: Edges in a path (igraph_es_path): ok

Structure generators

 52: Simple graph creation (igraph_create): ok
 53: Barabasi-Albert model (igraph_barabasi_game): ok
 54: More Barabasi-Albert model (igraph_barabasi_game): ok
 55: Erdos-Renyi model (igraph_erdos_renyi_game): ok
 56: Degree sequence(igraph_degree_sequence_game): ok
 57: Growing random (igraph_growing_random_game): ok
 58: Preference model (igraph_preference_game): ok
 59: From adjacency matrix (igraph_adjacency): ok
 60: From weighted adjacency matrix (igraph_weighted_adjacency): ok
 61: Star graph (igraph_star): ok
 62: Lattice graph (igraph_lattice): ok
 63: Ring graph (igraph_ring): ok
 64: Tree graph (igraph_tree): ok
 65: Full graph (igraph_full): ok
 66: Graph atlas (igraph_atlas): ok
 67: Small graph (igraph_small): ok
 68: Geomeric random graphs (igraph_grg_game): ok
 69: Graphs in LCF notation (igraph_lcf{,_vector}): ok
 70: Watts-Strogatz graphs (igraph_watts_strogatz_game): ok

Structural properties

 71: Two vertices connected by an edge: ok
 72: Diameter of a graph (igraph_diameter): ok
 73: Average geodesic length (igraph_average_path_length): ok
 74: Google PageRank (igraph_pagerank): ok
 75: Random rewiring (igraph_rewire): ok
 76: Get the shortest paths (igraph_get_shortest_paths): ok
 77: Weighted shortest paths (Dijkstra): ok
 78: Weighted shortest paths (Bellman-Ford): ok
 79: Get the weighted shortest paths (Dijkstra): ok
 80: Get all weighted shortest paths (Dijkstra): ok
 81: Shortest path wrappers for single target node: ok
 82: Betweenness (igraph_betweenness): ok
 83: Betweenness, big integers (igraph_betweenness): ok
 84: Edge betweenness (igraph_edge_betweenness): ok
 85: Transitivity (igraph_transitivity): ok
 86: Local transitivity (igraph_local_transitivity): ok
 87: Reciprocity (igraph_reciprocity): ok
 88: Minimum spanning tree (igraph_minimum_spanning_tree_*): ok
 89: Cocitation and bibcoupling (igraph_cocitation,igraph_bibcoupling): ok
 90: Similarity coefficients (igraph_similarity_*): ok
 91: Simplification of non-simple graphs (igraph_simplify): ok
 92: Topological sorting (igraph_topological_sorting, igraph_is_dag): ok
 93: Feedback arc sets, Eades heuristics (igraph_feedback_arc_set): ok
 94: Feedback arc sets, integer programming (igraph_feedback_arc_set): ok
 95: Loop edges test (igraph_is_loop): ok
 96: Multiple edges test (igraph_is_multiple): ok
 97: Multiple edges test (igraph_has_multiple): ok
 98: Girth (igraph_girth): ok
 99: Convergence degree (igraph_convergence_degree): ok
100: Assortativity coefficient (igraph_assortativity): ok
101: Average nearest neighbor degree (igraph_avg_nearest_neighbor_degree): ok
102: Transitive closure of a DAG (igraph_transitive_closure_dag): ok
103: Eccentricity (igraph_eccentricity): ok
104: Radius (igraph_radius): ok

Components

105: Decompose a graph (igraph_decompose): ok
106: Biconnected components (igraph_biconnected_components): ok

Layouts

107: Grid layout (igraph_layout_grid, igraph_layout_grid_3d): ok
108: Large Graph Layout (igraph_layout_lgl): ok
109: Reingold-Tilford tree layout (igraph_layout_reingold_tilford): ok
110: Sugiyama layout (igraph_layout_sugiyama): ok
111: Multidimensional scaling (igraph_layout_mds): ok
112: Covering circle and sphere (igraph_i_layout_sphere_{2,3}d): ok
113: Merging layouts (igraph_i_layout_merge): ok

Visitors

114: Internal breadth-first search (igraph_i_bfs): ok
115: Breadth-first search (igraph_bfs): ok

Graph topology

116: The isomorphism class of a subgraph (igraph_isolass_subgraph) ok
117: The VF2 isomorphism algorithm ok

Motifs

118: RAND-ESU algorithm (igraph_motifs_randesu) ok

Foreign formats

119: Reading Pajek (igraph_read_graph_pajek): ok
120: GraphML (igraph_{read,write}_graph_graphml): ok
121: Writing Pajek (igraph_write_graph_pajek): ok
122: Pajek with number of edges present (igraph_read_graph_pajek): ok
123: Reading an LGL file (igraph_read_graph_lgl): ok
124: Writing LGL (igraph_write_graph_lgl): ok
125: Reading a graph from the graph database (igraph_read_graph_graphdb): ok
126: Reading a GML file (igraph_read_graph_gml): ok
127: Writing a DOT file (igraph_write_graph_dot): ok
128: Different line endings: ok
129: UNICET DL format: ok
130: LEDA format: ok

Miscellaneous functions

131: Convex hull calculation (igraph_convex_hull): ok

Graphs operators

132: Disjoint union (igraph_disjoint_union, igraph_dosjoint_union_many): ok
133: Union (igraph_union, igraph_union_many): ok
134: Intersection (igraph_intersection, igraph_intersection_many): ok
135: Difference (igraph_difference): ok
136: Complementer (igraph_complementer): ok
137: Composition (igraph_compose): ok

Conversion functions

138: Directed to undirected (igraph_to_undirected): ok
139: Graphs from adjacency list (igraph_adjlist): ok
140: Graph to Laplacian matrix (igraph_laplacian): ok

Maximum flows and such

141: Maximum flow value (igraph_maxflow_value): ok
142: Maximum flow (igraph_maxflow): ok
143: Minimum cut (igraph_mincut): ok
144: Even-Tarjan reduction (igraph_even_tarjan_reduction): ok
145: Dominator tree of a flow graph (igraph_dominator_tree): ok
146: All s-t cuts of a graph (igraph_all_st_cuts): ok
147: All minimal s-t cuts of a graph (igraph_all_st_mincuts): ok

Community structure

148: Spinglass clustering (igraph_spinglass_community): ok
149: Walktrap community structure (igraph_walktrap_community): ok
150: Edge betweenness community structure (igraph_community_edge_betweenness): ok
151: Modularity optimization (igraph_community_fastgreedy): ok
152: Leading eigenvector community structure (igraph_community_leading_eigenvector) : ok
153: Label propagation algorithm (igraph_community_label_propagation) : ok
154: Multilevel community detection (igraph_community_multilevel) : ok
155: Modularity optimization, integer programming (igraph_community_optimal_modularity) : ok
156: Infomap community structure (igraph_community_infomap) : ok

Cliques and independent vertex sets.

157: Calculating cliques (igraph_cliques): ok
158: Additional test for maximal cliques (igraph_maximal_cliques): ok
159: Calculating independent vertex sets (igraph_independent_vertex_sets): ok

Eigenvalues, eigenvectors

160: Symmetric matrix, LAPACK (igraph_eigen_matrix_symmetric): ok
161: General matrix, LAPACK, LM, SM (igraph_eigen_matrix): ok
162: General matrix, LAPACK, LR, SR (igraph_eigen_matrix): ok
163: General matrix, LAPACK, LI, SI (igraph_eigen_matrix): ok
164: General matrix, LAPACK, SELECT (igraph_eigen_matrix): ok

Attributes from C

165: Reading a Pajek file with attributes: ok
166: Writing an attributed graph in GML and GraphML: ok
167: Combining numeric attributes: ok
168: Combining string attributes: ok

BLAS, LAPACK and ARPACK based functions

169: Basic BLAS functions (igraph_blas_*): ok
170: Dense symmetric eigenvalues and eigenvectors (igraph_lapack_dsyevr): ok
171: Dense non-symmetric eigenvalues and eigenvectors (igraph_lapack_dgeev): ok
172: Dense non-symmetric eigenvalues and eigenvectors (igraph_lapack_dgeevx): ok
173: Solving linear systems with LU factorization (igraph_lapack_dgesv): ok
174: Upper Hessenberg transformation (igraph_lapack_dgehrd): ok
175: Eigenvector centrality (igraph_eigenvector_centrality): ok

Bipartite graphs

176: Create bipartite graphs (igraph_create_bipartite): ok
177: Projection of bipartite graphs (igraph_bipartite_projection): ok

Centralization

178: Centralization (igraph_centralization_*): ok

Minimal separators

179: Decision problem (igraph_is_separator): ok
180: Decision problem, minimal separator (igraph_is_minimal separator): ok
181: Minimal separators (igraph_all_minimal_ab_separators): ok
182: Minimum size separators (igraph_minimum_size_separators): ok
183: Cohesive blocking (igraph_cohesive_blocks): ok

Hierarchical random graphs

184: Fitting a hierarchical model (igraph_hrg_fit) : ok
185: Consensus tree (igraph_hrg_consensus) : ok
186: Missing edge prediction (igraph_hrg_predict) : ok

Microscopic updates

187: Deterministic optimal imitation: ok
188: Stochastic imitation via uniform selection: ok
189: Stochastic imitation via roulette selection: ok
190: Moran process: ok

Thread-safety tests

191: Simple error handling test : skipped (mt.at:26)
192: Thread-safe ARPACK: skipped (mt.at:31)

Spectral coarse graining

193: Solving the SCG problem (igraph_scg_grouping) : ok
194: Solving the SCG problem, adjacency matrix (igraph_scg_grouping) : ok
195: Solving the SCG problem, stochastic matrix (igraph_scg_grouping) : FAILED (scg.at:38)
196: Solving the SCG problem, laplacian matrix (igraph_scg_grouping) : ok
197: SCG semi-projectors, symmetric (igraph_scg_semiprojectors) : ok
198: SCG semi-projectors, stochastic (igraph_scg_semiprojectors) : FAILED (scg.at:56)
199: SCG semi-projectors, laplacian (igraph_scg_semiprojectors) : ok
200: SCG of a graph, adjacency matrix (igraph_scg) : ok
201: SCG of a graph, stochastic matrix (igraph_scg) : ok
202: SCG of a graph, laplacian matrix (igraph_scg) : ok

Random number generators

203: Random seed: ok
204: MT19937 RNG on 64 bit machines: ok
205: Exponentially distributed random numbers: ok
206: Random sampling from consecutive sequence: ok
207: Fisher-Yates shuffle: ok

Quick sort

208: Regular qsort (igraph_qsort): ok
209: qsort with extra argument (igraph_qsort_r): ok

## ------------- ##
## Test results. ##
## ------------- ##

ERROR: 207 tests were run,
2 failed unexpectedly.
2 tests were skipped.
## -------------------------- ##
## testsuite.log was created. ##
## -------------------------- ##

Please send `tests/testsuite.log' and all information you think might help:

   To: <email address hidden>
   Subject: [igraph 0.6] testsuite: 195 198 failed

You may investigate any problem if you feel able to do so, in which
case the test suite provides a good starting point. Its output may
be found below `tests/testsuite.dir'.

make[1]: *** [installcheck-local] Error 1
make: *** [installcheck-recursive] Error 1

Thanks for your help.

Yes, we are aware of these two test case failures and they do not affect the core part of the library unless you use the spectral coarse graining algorithm (for which we don't have a definite interface yet). Can you please post the output of "make install"?

Yes, it is:

Making install in src
make install-am
test -z "/usr/local/lib" || .././install-sh -c -d "/usr/local/lib"
 /bin/sh ../libtool --mode=install /usr/bin/install -c libigraph.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libigraph.0.dylib /usr/local/lib/libigraph.0.dylib
libtool: install: (cd /usr/local/lib && { ln -s -f libigraph.0.dylib libigraph.dylib || { rm -f libigraph.dylib && ln -s libigraph.0.dylib libigraph.dylib; }; })
libtool: install: /usr/bin/install -c .libs/libigraph.lai /usr/local/lib/libigraph.la
libtool: install: /usr/bin/install -c .libs/libigraph.a /usr/local/lib/libigraph.a
libtool: install: chmod 644 /usr/local/lib/libigraph.a
libtool: install: ranlib /usr/local/lib/libigraph.a
ranlib: file: /usr/local/lib/libigraph.a(libf2c_la-ctype.o) has no symbols
ranlib: file: /usr/local/lib/libigraph.a(libglpk_la-amd_dump.o) has no symbols
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/usr/local/include/igraph" || .././install-sh -c -d "/usr/local/include/igraph"
 /usr/bin/install -c -m 644 ../include/igraph.h ../include/igraph_memory.h ../include/igraph_random.h ../include/igraph_types.h ../include/igraph_vector.h ../include/igraph_matrix.h ../include/igraph_array.h ../include/igraph_dqueue.h ../include/igraph_stack.h ../include/igraph_heap.h ../include/igraph_arpack.h ../include/igraph_attributes.h ../include/igraph_error.h ../include/igraph_pmt.h ../include/igraph_pmt_off.h ../include/igraph_adjlist.h ../include/igraph_iterators.h ../include/igraph_bipartite.h ../include/igraph_layout.h ../include/igraph_centrality.h ../include/igraph_motifs.h ../include/igraph_cliques.h ../include/igraph_neighborhood.h ../include/igraph_cocitation.h ../include/igraph_nongraph.h ../include/igraph_community.h ../include/igraph_operators.h ../include/igraph_components.h ../include/igraph_paths.h ../include/igraph_constructors.h ../include/igraph_progress.h ../include/igraph_conversion.h ../include/igraph_revolver.h ../include/igraph_datatype.h ../include/igraph_structural.h ../include/igraph_flow.h ../include/igraph_topology.h ../include/igraph_foreign.h ../include/igraph_transitivity.h ../include/igraph_games.h '/usr/local/include/igraph'
 /usr/bin/install -c -m 644 ../include/igraph_visitor.h ../include/igraph_interface.h ../include/igraph_constants.h ../include/igraph_vector_pmt.h ../include/igraph_matrix_pmt.h ../include/igraph_array_pmt.h ../include/igraph_dqueue_pmt.h ../include/igraph_stack_pmt.h ../include/igraph_heap_pmt.h ../include/igraph_vector_ptr.h ../include/igraph_spmatrix.h ../include/igraph_strvector.h ../include/igraph_psumtree.h ../include/igraph_sparsemat.h ../include/igraph_mixing.h ../include/igraph_version.h ../include/igraph_blas.h ../include/igraph_separators.h ../include/igraph_cohesive_blocks.h ../include/igraph_lapack.h ../include/igraph_complex.h ../include/igraph_eigen.h ../include/igraph_statusbar.h ../include/igraph_hrg.h ../include/igraph_microscopic_update.h ../include/igraph_interrupt.h ../include/igraph_threading.h ../include/igraph_scg.h ../include/igraph_qsort.h '/usr/local/include/igraph'
Making install in tests
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
Making install in interfaces
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make install-exec-hook
if test -f ./src/.libs/cygigraph-0.dll ; \
  then cp ./src/.libs/cygigraph-0.dll \
  /usr/local/lib ; fi
test -z "/usr/local/lib/pkgconfig" || ./install-sh -c -d "/usr/local/lib/pkgconfig"
 /usr/bin/install -c -m 644 igraph.pc '/usr/local/lib/pkgconfig'

As the message says above, "make install" installed the libraries in /usr/local/lib and the include files in /usr/local/include/igraph. So either you copy /usr/local/include/igraph to /opt/local/include/igraph (you can delete the old /opt/local/include/igraph folder) and /usr/local/lib/libigraph.* to /opt/local/lib, or you adjust setup.cfg in the folder of the Python interface to use /usr/local/include/igraph and /usr/local/lib.

Thanks a lot.
It works perfect just moving the folders.

And I want to say i'm very happy for the quick responses and the service.

Best regards,
Pau.