[R-sig-Debian] igraph build problems

[Jim Kusznir]

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).

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