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igraph build problems

8 messages · Michael Dewey, Jim Kusznir, Dirk Eddelbuettel +2 more

#
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
#
At 19:58 24/07/2012, Jim Kusznir wrote:
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.
Michael Dewey
info at aghmed.fsnet.co.uk
http://www.aghmed.fsnet.co.uk/home.html
#
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:
#
On 24 July 2012 at 14:12, Jim Kusznir wrote:
| Sorry, I mis-typed.  I have squeeze, not sarge.  Debian 6.0, which as
| far as I know, is latest stable.

Do you have the 'r-base-dev' metapackage installed? It should bring in the
compilers (incl Fortran) as well as the matching -dev packages for the
libraries you may need.

Dirk
#
Yep, r-base-dev is installed
On Tue, Jul 24, 2012 at 3:12 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
#
On 25 July 2012 at 14:30, Jim Kusznir wrote:
| Yep, r-base-dev is installed

Then I can't help.

To check, I installed igraph on my box without a hitch.  Takes a moment to
build, many sublibraries, but builds fine.  

So you may be missing something else.

Dirk
#
On Wednesday 25 July 2012 23:30:58 Jim Kusznir wrote:
Jim, for what it's worth, I just ran install.packages("igraph") on my squeeze 
laptop and it compiled, linked and installed just fine. Do you have the R 
2.15.1 packages for squeeze from CRAN installed? If not, have a look at the 
Debian README on CRAN:

http://cran.r-project.org/bin/linux/debian/

Regards,

Johannes
#
Dear Jim:

I hope this does not seem like we are piling on. It worked for me too.
 I uploaded the build output for your comparison.  This is from my
Debian Squeeze laptop:

http://pj.freefaculty.org/misc/igraph-build-20120706.Rt

If igraph is still causing trouble for you, I suggest you compare my
output with yours and figure where the trouble is.

pj
On Thu, Jul 26, 2012 at 2:47 AM, Johannes Ranke <jranke at uni-bremen.de> wrote: