[R-sig-Debian] igraph build problems

[Michael Dewey]

At 19:58 24/07/2012, Jim Kusznir wrote:
>Hello:
>
>I've been trying for days now to get igraph working on a debian sarge
>install.  There does not appear to be any pre-built packages, and when
>I try and install within R, it blows up on the final linking, claiming
>its unable to find libgfortran (which IS installed, and IS working for
>all other users of the compiler).

You do seem to have rather an old version of Debian. I suspect you 
are going to have increasing difficulty installing packages in it. 
You may have to bite the bullet and persuade your IT support to update.


>I started up R and ran: install.packages("igraph").  It compiled for a
>good long while (including many gfortran compile calls), and
>eventually ended with:
>
>++ -shared -o igraph.so DensityGrid.o DensityGrid_3d.o NetDataTypes.o
>NetRoutines.o adjlist.o amd_1.o amd_2.o amd_aat.o amd_control.o
>amd_defaults.o amd_dump.o amd_info.o amd_order.o amd_post_tree.o
>amd_postorder.o amd_preprocess.o amd_valid.o arpack.o array.o atlas.o
>attributes.o basic_query.o bfgs.o bigint.o bignum.o bipartite.o blas.o
>bliss.o bliss_eqrefhash.o bliss_graph.o bliss_heap.o bliss_orbit.o
>bliss_partition.o bliss_timer.o bliss_utils.o cattributes.o
>centrality.o cliques.o clustertool.o cocitation.o cohesive_blocks.o
>colamd.o community.o complex.o components.o conversion.o cores.o
>cs_add.o cs_amd.o cs_chol.o cs_cholsol.o cs_compress.o cs_counts.o
>cs_cumsum.o cs_dfs.o cs_dmperm.o cs_droptol.o cs_dropzeros.o cs_dupl.o
>cs_entry.o cs_ereach.o cs_etree.o cs_fkeep.o cs_gaxpy.o cs_happly.o
>cs_house.o cs_ipvec.o cs_leaf.o cs_load.o cs_lsolve.o cs_ltsolve.o
>cs_lu.o cs_lusol.o cs_malloc.o cs_maxtrans.o cs_multiply.o cs_norm.o
>cs_permute.o cs_pinv.o cs_post.o cs_print.o cs_pvec.o cs_qr.o
>cs_qrsol.o cs_randperm.o cs_reach.o cs_scatter.o cs_scc.o cs_schol.o
>cs_spsolve.o cs_sqr.o cs_symperm.o cs_tdfs.o cs_transpose.o
>cs_updown.o cs_usolve.o cs_util.o cs_utsolve.o decomposition.o
>dgetv0.o distances.o dlaqrb.o dmout.o dnaitr.o dnapps.o dnaup2.o
>dnaupd.o dnconv.o dneigh.o dneupd.o dngets.o dqueue.o drl_graph.o
>drl_graph_3d.o drl_layout.o drl_layout_3d.o drl_parse.o dsaitr.o
>dsapps.o dsaup2.o dsaupd.o dsconv.o dseigt.o dsesrt.o dseupd.o
>dsgets.o dsortc.o dsortr.o dstatn.o dstats.o dstqrb.o dvout.o eigen.o
>error.o evolver_cit.o f2c_dummy.o fast_community.o feedback_arc_set.o
>flow.o foreign-dl-lexer.o foreign-dl-parser.o foreign-gml-lexer.o
>foreign-gml-parser.o foreign-graphml.o foreign-lgl-lexer.o
>foreign-lgl-parser.o foreign-ncol-lexer.o foreign-ncol-parser.o
>foreign-pajek-lexer.o foreign-pajek-parser.o foreign.o forestfire.o
>fortran_intrinsics.o games.o gengraph_box_list.o
>gengraph_degree_sequence.o gengraph_graph_molloy_hash.o
>gengraph_graph_molloy_optimized.o gengraph_mr-connected.o
>gengraph_powerlaw.o gengraph_random.o glpapi01.o glpapi02.o glpapi03.o
>glpapi04.o glpapi05.o glpapi06.o glpapi07.o glpapi08.o glpapi09.o
>glpapi10.o glpapi11.o glpapi12.o glpapi13.o glpapi14.o glpapi15.o
>glpapi16.o glpapi17.o glpapi18.o glpapi19.o glpavl.o glpbfd.o glpbfx.o
>glpcpx.o glpdmp.o glpdmx.o glpenv01.o glpenv02.o glpenv03.o glpenv04.o
>glpenv05.o glpenv06.o glpenv07.o glpenv08.o glpfhv.o glpgmp.o glphbm.o
>glpini01.o glpini02.o glpios01.o glpios02.o glpios03.o glpios04.o
>glpios05.o glpios06.o glpios07.o glpios08.o glpios09.o glpios10.o
>glpios11.o glpios12.o glpipm.o glpk_support.o glplib01.o glplib02.o
>glplib03.o glplpf.o glplpx01.o glplpx02.o glplpx03.o glpluf.o glplux.o
>glpmat.o glpmpl01.o glpmpl02.o glpmpl03.o glpmpl04.o glpmpl05.o
>glpmpl06.o glpmps.o glpnet01.o glpnet02.o glpnet03.o glpnet04.o
>glpnet05.o glpnet06.o glpnet07.o glpnet08.o glpnet09.o glpnpp01.o
>glpnpp02.o glpnpp03.o glpnpp04.o glpnpp05.o glpqmd.o glprgr.o
>glprng01.o glprng02.o glpscf.o glpscl.o glpsdf.o glpspm.o glpspx01.o
>glpspx02.o glpsql.o glpssx01.o glpssx02.o glptsp.o gml_tree.o heap.o
>igraph_buckets.o igraph_estack.o igraph_fixed_vectorlist.o
>igraph_grid.o igraph_hashtable.o igraph_heap.o igraph_hrg.o
>igraph_hrg_types.o igraph_marked_queue.o igraph_psumtree.o
>igraph_set.o igraph_stack.o igraph_strvector.o igraph_trie.o infomap.o
>infomap_FlowGraph.o infomap_Greedy.o infomap_Node.o interrupt.o
>iterators.o ivout.o lapack.o layout.o matching.o math.o matrix.o
>memory.o microscopic_update.o mixing.o motifs.o operators.o
>optimal_modularity.o other.o pottsmodel_2.o progress.o qsort.o
>qsort_r.o random.o revolver_cit.o revolver_grow.o revolver_ml_cit.o
>rinterface.o scg.o scg_approximate_methods.o scg_exact_scg.o
>scg_kmeans.o scg_optimal_method.o scg_utils.o second.o separators.o
>spanning_trees.o sparsemat.o spectral_properties.o spmatrix.o
>st-cuts.o statusbar.o structural_properties.o structure_generators.o
>sugiyama.o topology.o type_indexededgelist.o types.o vector.o
>vector_ptr.o version.o visitors.o walktrap.o walktrap_communities.o
>walktrap_graph.o walktrap_heap.o zeroin.o -lxml2 -lgmp -lgfortran -lm
>-llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR
>/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.4.5/libstdc++.a(functexcept.o):
>relocation R_X86_64_32 against `std::bad_typeid::~bad_typeid()' can
>not be used when making a shared object; recompile with -fPIC
>/usr/lib/gcc/x86_64-linux-gnu/4.4.5/libstdc++.a: could not read
>symbols: Bad value
>collect2: ld returned 1 exit status
>make: *** [igraph.so] Error 1
>
>
>Previously, I kept getting errors about -lgfortran not found.  In the
>process of writing this e-mail and trying things, I attempted to build
>a deb from source I found on the ppa for igraph. After doing that, the
>error changed to the above, which I don't know if its better or worse
>than my original error...
>
>--Jim
>
>_______________________________________________
>R-SIG-Debian mailing list
>R-SIG-Debian at r-project.org
>https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Michael Dewey
info at aghmed.fsnet.co.uk
http://www.aghmed.fsnet.co.uk/home.html