[R-sig-Debian] igraph build problems

Tue Jul 24 23:12:45 CEST 2012

Sorry, I mis-typed.  I have squeeze, not sarge.  Debian 6.0, which as
far as I know, is latest stable.

--Jim

On Tue, Jul 24, 2012 at 12:18 PM, Michael Dewey <info at aghmed.fsnet.co.uk> wrote:
> 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
>>
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>> R-SIG-Debian at r-project.org
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>
>
> Michael Dewey
> info at aghmed.fsnet.co.uk
> http://www.aghmed.fsnet.co.uk/home.html
>