Re: [igraph] troubles building igraph-0.6.5 ubuntu 64bit

[Giovanni Marco Dall'Olio]

Hello Kent,
On Ubuntu you can use the igraph ppa, to install the 0.6.5 version without having to compile it by yourself:

https://launchpad.net/~igraph/+archive/ppa

sudo add-apt-repository ppa:igraph/ppa
sudo apt-get update
sudo apt-get install igraph python-igraph

Gio

On Tue, Feb 11, 2014 at 9:14 AM, Kent Mein <address@hidden> wrote:

Hi I'm trying to install igraph-0.6.5 on an ubuntu 12.04 64bit box.

./configure works just fine, but durring the final link stage I'm
getting the following error.  Any tips on how to fix this?

Thanks,

Kent Mein

[3:06] address@hidden % make
make  all-recursive
make[1]: Entering directory `/home/staff01/mein/Downloads/igraph-0.6.5'
Making all in src
make[2]: Entering directory `/home/staff01/mein/Downloads/igraph-0.6.5/src'
make  all-am
make[3]: Entering directory `/home/staff01/mein/Downloads/igraph-0.6.5/src'
/bin/bash ../libtool --tag=CXX   --mode=link g++ -I../include -I../include -Wall -I../optional/glpk -g -O2 -no-undefined -lgmp -o libigraph.la -rpath /soft/python-2.7/ubuntuamd1/lib libigraph_la-basic_query.lo libigraph_la-games.lo libigraph_la-cocitation.lo libigraph_la-iterators.lo libigraph_la-structural_properties.lo libigraph_la-components.lo libigraph_la-layout.lo libigraph_la-structure_generators.lo libigraph_la-conversion.lo libigraph_la-type_indexededgelist.lo libigraph_la-spanning_trees.lo libigraph_la-igraph_error.lo libigraph_la-interrupt.lo libigraph_la-other.lo libigraph_la-foreign.lo libigraph_la-random.lo libigraph_la-attributes.lo libigraph_la-foreign-ncol-parser.lo libigraph_la-foreign-ncol-lexer.lo libigraph_la-foreign-lgl-parser.lo libigraph_la-foreign-lgl-lexer.lo libigraph_la-foreign-pajek-parser.lo libigraph_la-foreign-pajek-lexer.lo libigraph_la-foreign-gml-parser.lo libigraph_la-foreign-gml-lexer.lo libigraph_la-dqueue.lo libigraph_la-heap.lo libigraph_la-igraph_heap.lo libigraph_la-igraph_stack.lo libigraph_la-igraph_strvector.lo libigraph_la-igraph_trie.lo libigraph_la-matrix.lo libigraph_la-vector.lo libigraph_la-vector_ptr.lo libigraph_la-memory.lo libigraph_la-adjlist.lo libigraph_la-visitors.lo libigraph_la-igraph_grid.lo libigraph_la-atlas.lo libigraph_la-topology.lo libigraph_la-motifs.lo libigraph_la-progress.lo libigraph_la-operators.lo libigraph_la-igraph_psumtree.lo libigraph_la-array.lo libigraph_la-igraph_hashtable.lo libigraph_la-foreign-graphml.lo libigraph_la-flow.lo libigraph_la-igraph_buckets.lo libigraph_la-NetDataTypes.lo libigraph_la-NetRoutines.lo libigraph_la-clustertool.lo libigraph_la-pottsmodel_2.lo libigraph_la-spectral_properties.lo libigraph_la-cores.lo libigraph_la-igraph_set.lo libigraph_la-cliques.lo libigraph_la-revolver_cit.lo libigraph_la-revolver_grow.lo libigraph_la-walktrap.lo libigraph_la-walktrap_heap.lo libigraph_la-walktrap_graph.lo libigraph_la-walktrap_communities.lo libigraph_la-infomap.lo libigraph_la-infomap_Greedy.lo libigraph_la-infomap_Node.lo libigraph_la-infomap_FlowGraph.lo libigraph_la-spmatrix.lo libigraph_la-community.lo libigraph_la-fast_community.lo libigraph_la-evolver_cit.lo libigraph_la-gml_tree.lo libigraph_la-bliss_orbit.lo libigraph_la-bliss_eqrefhash.lo libigraph_la-bliss_partition.lo libigraph_la-bliss_graph.lo libigraph_la-bliss_timer.lo libigraph_la-bliss_heap.lo libigraph_la-bliss_utils.lo libigraph_la-bliss.lo libigraph_la-cattributes.lo libigraph_la-revolver_ml_cit.lo libigraph_la-zeroin.lo libigraph_la-bfgs.lo libigraph_la-math.lo libigraph_la-forestfire.lo libigraph_la-microscopic_update.lo libigraph_la-blas.lo libigraph_la-arpack.lo libigraph_la-centrality.lo libigraph_la-drl_layout.lo libigraph_la-drl_parse.lo libigraph_la-drl_graph.lo libigraph_la-DensityGrid.lo libigraph_la-gengraph_box_list.lo libigraph_la-gengraph_degree_sequence.lo libigraph_la-gengraph_graph_molloy_hash.lo libigraph_la-gengraph_graph_molloy_optimized.lo libigraph_la-gengraph_mr-connected.lo libigraph_la-gengraph_powerlaw.lo libigraph_la-gengraph_random.lo libigraph_la-decomposition.lo libigraph_la-bipartite.lo libigraph_la-drl_layout_3d.lo libigraph_la-drl_graph_3d.lo libigraph_la-DensityGrid_3d.lo libigraph_la-foreign-dl-parser.lo libigraph_la-foreign-dl-lexer.lo libigraph_la-cs_add.lo libigraph_la-cs_happly.lo libigraph_la-cs_pvec.lo libigraph_la-cs_amd.lo libigraph_la-cs_house.lo libigraph_la-cs_qr.lo libigraph_la-cs_chol.lo libigraph_la-cs_ipvec.lo libigraph_la-cs_qrsol.lo libigraph_la-cs_cholsol.lo libigraph_la-cs_leaf.lo libigraph_la-cs_randperm.lo libigraph_la-cs_compress.lo libigraph_la-cs_load.lo libigraph_la-cs_reach.lo libigraph_la-cs_counts.lo libigraph_la-cs_lsolve.lo libigraph_la-cs_scatter.lo libigraph_la-cs_cumsum.lo libigraph_la-cs_ltsolve.lo libigraph_la-cs_scc.lo libigraph_la-cs_dfs.lo libigraph_la-cs_lu.lo libigraph_la-cs_schol.lo libigraph_la-cs_dmperm.lo libigraph_la-cs_lusol.lo libigraph_la-cs_spsolve.lo libigraph_la-cs_droptol.lo libigraph_la-cs_malloc.lo libigraph_la-cs_sqr.lo libigraph_la-cs_dropzeros.lo libigraph_la-cs_maxtrans.lo libigraph_la-cs_symperm.lo libigraph_la-cs_dupl.lo libigraph_la-cs_multiply.lo libigraph_la-cs_tdfs.lo libigraph_la-cs_entry.lo libigraph_la-cs_norm.lo libigraph_la-cs_transpose.lo libigraph_la-cs_ereach.lo libigraph_la-cs_permute.lo libigraph_la-cs_updown.lo libigraph_la-cs_etree.lo libigraph_la-cs_pinv.lo libigraph_la-cs_usolve.lo libigraph_la-cs_fkeep.lo libigraph_la-cs_post.lo libigraph_la-cs_util.lo libigraph_la-cs_gaxpy.lo libigraph_la-cs_print.lo libigraph_la-cs_utsolve.lo libigraph_la-sparsemat.lo libigraph_la-mixing.lo libigraph_la-bigint.lo libigraph_la-bignum.lo libigraph_la-version.lo libigraph_la-optimal_modularity.lo libigraph_la-igraph_fixed_vectorlist.lo libigraph_la-separators.lo libigraph_la-igraph_marked_queue.lo libigraph_la-igraph_estack.lo libigraph_la-st-cuts.lo libigraph_la-cohesive_blocks.lo libigraph_la-statusbar.lo libigraph_la-lapack.lo libigraph_la-complex.lo libigraph_la-eigen.lo libigraph_la-feedback_arc_set.lo libigraph_la-sugiyama.lo libigraph_la-glpk_support.lo libigraph_la-igraph_hrg_types.lo libigraph_la-igraph_hrg.lo libigraph_la-distances.lo libigraph_la-fortran_intrinsics.lo libigraph_la-matching.lo libigraph_la-scg.lo libigraph_la-scg_approximate_methods.lo libigraph_la-scg_exact_scg.lo libigraph_la-scg_kmeans.lo libigraph_la-scg_utils.lo libigraph_la-scg_optimal_method.lo libigraph_la-qsort.lo libigraph_la-qsort_r.lo libigraph_la-types.lo libigraph_la-hacks.lo  -lm -L/soft/python-2.7/ubuntuamd1/lib -Wl,-rpath -WL,/soft/python-2.7/ubuntuamd1/lib -lxml2 -lz -lm libf2c.la libblas.la liblapack.la libdlamch.la libarpack.la libglpk.la libplfit.la
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.6/crtbeginS.o  .libs/libigraph_la-basic_query.o .libs/libigraph_la-games.o .libs/libigraph_la-cocitation.o .libs/libigraph_la-iterators.o .libs/libigraph_la-structural_properties.o .libs/libigraph_la-components.o .libs/libigraph_la-layout.o .libs/libigraph_la-structure_generators.o .libs/libigraph_la-conversion.o .libs/libigraph_la-type_indexededgelist.o .libs/libigraph_la-spanning_trees.o .libs/libigraph_la-igraph_error.o .libs/libigraph_la-interrupt.o .libs/libigraph_la-other.o .libs/libigraph_la-foreign.o .libs/libigraph_la-random.o .libs/libigraph_la-attributes.o .libs/libigraph_la-foreign-ncol-parser.o .libs/libigraph_la-foreign-ncol-lexer.o .libs/libigraph_la-foreign-lgl-parser.o .libs/libigraph_la-foreign-lgl-lexer.o .libs/libigraph_la-foreign-pajek-parser.o .libs/libigraph_la-foreign-pajek-lexer.o .libs/libigraph_la-foreign-gml-parser.o .libs/libigraph_la-foreign-gml-lexer.o .libs/libigraph_la-dqueue.o .libs/libigraph_la-heap.o .libs/libigraph_la-igraph_heap.o .libs/libigraph_la-igraph_stack.o .libs/libigraph_la-igraph_strvector.o .libs/libigraph_la-igraph_trie.o .libs/libigraph_la-matrix.o .libs/libigraph_la-vector.o .libs/libigraph_la-vector_ptr.o .libs/libigraph_la-memory.o .libs/libigraph_la-adjlist.o .libs/libigraph_la-visitors.o .libs/libigraph_la-igraph_grid.o .libs/libigraph_la-atlas.o .libs/libigraph_la-topology.o .libs/libigraph_la-motifs.o .libs/libigraph_la-progress.o .libs/libigraph_la-operators.o .libs/libigraph_la-igraph_psumtree.o .libs/libigraph_la-array.o .libs/libigraph_la-igraph_hashtable.o .libs/libigraph_la-foreign-graphml.o .libs/libigraph_la-flow.o .libs/libigraph_la-igraph_buckets.o .libs/libigraph_la-NetDataTypes.o .libs/libigraph_la-NetRoutines.o .libs/libigraph_la-clustertool.o .libs/libigraph_la-pottsmodel_2.o .libs/libigraph_la-spectral_properties.o .libs/libigraph_la-cores.o .libs/libigraph_la-igraph_set.o .libs/libigraph_la-cliques.o .libs/libigraph_la-revolver_cit.o .libs/libigraph_la-revolver_grow.o .libs/libigraph_la-walktrap.o .libs/libigraph_la-walktrap_heap.o .libs/libigraph_la-walktrap_graph.o .libs/libigraph_la-walktrap_communities.o .libs/libigraph_la-infomap.o .libs/libigraph_la-infomap_Greedy.o .libs/libigraph_la-infomap_Node.o .libs/libigraph_la-infomap_FlowGraph.o .libs/libigraph_la-spmatrix.o .libs/libigraph_la-community.o .libs/libigraph_la-fast_community.o .libs/libigraph_la-evolver_cit.o .libs/libigraph_la-gml_tree.o .libs/libigraph_la-bliss_orbit.o .libs/libigraph_la-bliss_eqrefhash.o .libs/libigraph_la-bliss_partition.o .libs/libigraph_la-bliss_graph.o .libs/libigraph_la-bliss_timer.o .libs/libigraph_la-bliss_heap.o .libs/libigraph_la-bliss_utils.o .libs/libigraph_la-bliss.o .libs/libigraph_la-cattributes.o .libs/libigraph_la-revolver_ml_cit.o .libs/libigraph_la-zeroin.o .libs/libigraph_la-bfgs.o .libs/libigraph_la-math.o .libs/libigraph_la-forestfire.o .libs/libigraph_la-microscopic_update.o .libs/libigraph_la-blas.o .libs/libigraph_la-arpack.o .libs/libigraph_la-centrality.o .libs/libigraph_la-drl_layout.o .libs/libigraph_la-drl_parse.o .libs/libigraph_la-drl_graph.o .libs/libigraph_la-DensityGrid.o .libs/libigraph_la-gengraph_box_list.o .libs/libigraph_la-gengraph_degree_sequence.o .libs/libigraph_la-gengraph_graph_molloy_hash.o .libs/libigraph_la-gengraph_graph_molloy_optimized.o .libs/libigraph_la-gengraph_mr-connected.o .libs/libigraph_la-gengraph_powerlaw.o .libs/libigraph_la-gengraph_random.o .libs/libigraph_la-decomposition.o .libs/libigraph_la-bipartite.o .libs/libigraph_la-drl_layout_3d.o .libs/libigraph_la-drl_graph_3d.o .libs/libigraph_la-DensityGrid_3d.o .libs/libigraph_la-foreign-dl-parser.o .libs/libigraph_la-foreign-dl-lexer.o .libs/libigraph_la-cs_add.o .libs/libigraph_la-cs_happly.o .libs/libigraph_la-cs_pvec.o .libs/libigraph_la-cs_amd.o .libs/libigraph_la-cs_house.o .libs/libigraph_la-cs_qr.o .libs/libigraph_la-cs_chol.o .libs/libigraph_la-cs_ipvec.o .libs/libigraph_la-cs_qrsol.o .libs/libigraph_la-cs_cholsol.o .libs/libigraph_la-cs_leaf.o .libs/libigraph_la-cs_randperm.o .libs/libigraph_la-cs_compress.o .libs/libigraph_la-cs_load.o .libs/libigraph_la-cs_reach.o .libs/libigraph_la-cs_counts.o .libs/libigraph_la-cs_lsolve.o .libs/libigraph_la-cs_scatter.o .libs/libigraph_la-cs_cumsum.o .libs/libigraph_la-cs_ltsolve.o .libs/libigraph_la-cs_scc.o .libs/libigraph_la-cs_dfs.o .libs/libigraph_la-cs_lu.o .libs/libigraph_la-cs_schol.o .libs/libigraph_la-cs_dmperm.o .libs/libigraph_la-cs_lusol.o .libs/libigraph_la-cs_spsolve.o .libs/libigraph_la-cs_droptol.o .libs/libigraph_la-cs_malloc.o .libs/libigraph_la-cs_sqr.o .libs/libigraph_la-cs_dropzeros.o .libs/libigraph_la-cs_maxtrans.o .libs/libigraph_la-cs_symperm.o .libs/libigraph_la-cs_dupl.o .libs/libigraph_la-cs_multiply.o .libs/libigraph_la-cs_tdfs.o .libs/libigraph_la-cs_entry.o .libs/libigraph_la-cs_norm.o .libs/libigraph_la-cs_transpose.o .libs/libigraph_la-cs_ereach.o .libs/libigraph_la-cs_permute.o .libs/libigraph_la-cs_updown.o .libs/libigraph_la-cs_etree.o .libs/libigraph_la-cs_pinv.o .libs/libigraph_la-cs_usolve.o .libs/libigraph_la-cs_fkeep.o .libs/libigraph_la-cs_post.o .libs/libigraph_la-cs_util.o .libs/libigraph_la-cs_gaxpy.o .libs/libigraph_la-cs_print.o .libs/libigraph_la-cs_utsolve.o .libs/libigraph_la-sparsemat.o .libs/libigraph_la-mixing.o .libs/libigraph_la-bigint.o .libs/libigraph_la-bignum.o .libs/libigraph_la-version.o .libs/libigraph_la-optimal_modularity.o .libs/libigraph_la-igraph_fixed_vectorlist.o .libs/libigraph_la-separators.o .libs/libigraph_la-igraph_marked_queue.o .libs/libigraph_la-igraph_estack.o .libs/libigraph_la-st-cuts.o .libs/libigraph_la-cohesive_blocks.o .libs/libigraph_la-statusbar.o .libs/libigraph_la-lapack.o .libs/libigraph_la-complex.o .libs/libigraph_la-eigen.o .libs/libigraph_la-feedback_arc_set.o .libs/libigraph_la-sugiyama.o .libs/libigraph_la-glpk_support.o .libs/libigraph_la-igraph_hrg_types.o .libs/libigraph_la-igraph_hrg.o .libs/libigraph_la-distances.o .libs/libigraph_la-fortran_intrinsics.o .libs/libigraph_la-matching.o .libs/libigraph_la-scg.o .libs/libigraph_la-scg_approximate_methods.o .libs/libigraph_la-scg_exact_scg.o .libs/libigraph_la-scg_kmeans.o .libs/libigraph_la-scg_utils.o .libs/libigraph_la-scg_optimal_method.o .libs/libigraph_la-qsort.o .libs/libigraph_la-qsort_r.o .libs/libigraph_la-types.o .libs/libigraph_la-hacks.o  -Wl,--whole-archive ./.libs/libf2c.a ./.libs/libblas.a ./.libs/liblapack.a ./.libs/libdlamch.a ./.libs/libarpack.a ./.libs/libglpk.a ./.libs/libplfit.a -Wl,--no-whole-archive  -Wl,-rpath -Wl,/soft/python-2.7/ubuntuamd1/lib -Wl,-rpath -Wl,/soft/python-2.7/ubuntuamd1/lib -L/soft/python-2.7/ubuntuamd1/lib /soft/python-2.7/ubuntuamd1/lib/libxml2.so -lz -lgmp -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/4.6/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crtn.o  -O2 -Wl,-rpath   -Wl,-soname -Wl,libigraph.so.0 -o .libs/libigraph.so.0.0.0
/usr/bin/ld: cannot find libigraph.so.0: No such file or directory
collect2: ld returned 1 exit status
make[3]: *** [libigraph.la] Error 1
make[3]: Leaving directory `/home/staff01/mein/Downloads/igraph-0.6.5/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/staff01/mein/Downloads/igraph-0.6.5/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/staff01/mein/Downloads/igraph-0.6.5'
make: *** [all] Error 2


--
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http://www.cs.umn.edu/~mein

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Giovanni Marco Dall'Olio, PhD
IBE, Institut de Biologia Evolutiva, CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it