Re: [igraph] Bug report, building without libxml2

[Tamás Nepusz]

Hi Mark, 

Unfortunately I couldn't reproduce your problem on my machine -- would it be 
possible to send me config.log so I could compare it with the output on my 
machine? 

Best,-- 
T.


On Wednesday, 13 June 2012 at 17:56, Asbach, Mark wrote:

> Hi there,
> 
> I'm just installing the igraph package for a colleague and ran into a small 
> glitch: when building from source tarball igraph-0.5.4.tar.gz without libxml2 
> present, configure reports correctly, but automake still tries to link the 
> library. Building and installing are both fine with libxml2 present, though.
> 
> I'm not subscribing to the list, so please CC: me in case of questions.
> 
> Best,
> Mark
> 
> mybox:~/igraph-0.5.4$ ./configure 
> checking for a BSD-compatible install... /usr/bin/install -c
> [...]
> checking for xml2-config... none
> checking for xmlSAXUserParseFile in -lxml2... no
> checking for __gmpz_add in -lgmp... no
> configure: creating ./config.status
> config.status: creating tests/Makefile
> config.status: creating tests/atlocal
> config.status: creating Makefile
> config.status: creating src/Makefile
> config.status: creating igraph.pc
> config.status: creating igraph_Info.plist
> config.status: creating doc/Makefile
> config.status: creating doc/book/Makefile
> config.status: creating interfaces/R/configure.in (http://configure.in)
> config.status: creating interfaces/R/Makefile
> config.status: creating interfaces/R/src/Makevars.win
> config.status: creating interfaces/R/DESCRIPTION
> config.status: creating interfaces/Makefile
> config.status: creating interfaces/shell/Makefile
> config.status: creating config.h
> config.status: executing tests/atconfig commands
> config.status: executing depfiles commands
> config.status: executing libtool commands
> igraph successfully configured.
> GraphML format support -- no
> GMP library support -- no
> Use internal ARPACK -- yes
> Use internal LAPACK -- yes
> Use internal BLAS -- yes
> Debug build -- no
> Profiling -- no
> Shell interface -- no
> 
> mybox:~/igraph-0.5.4$ make
> [....]
> /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -no-undefined -o 
> libigraph.la (http://libigraph.la) -rpath /usr/local/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-measure_dynamics.lo libigraph_la-type_indexededgelist.lo 
> libigraph_la-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-igr
aph_strvecto
> r.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-spmatrix.lo libigraph_la-community.lo 
> libigraph_la-fast_community.lo libi
> graph_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-dgetv0.lo libigraph_la-dmout.lo 
> libigraph_la-dsaitr.lo libigraph_la-dsapps.lo libigraph_la-dsaup2.lo 
> libigraph_la-dsaupd.lo libigraph_la-dsconv.lo libigraph_la-dseigt.lo 
> libigraph_la-dsesrt.lo libigraph_la-dseupd.lo libigraph_la-dsgets.lo 
> libigraph_la-dsortr.lo libigraph_la-dstats.lo libigraph_la-dstqrb.lo 
> libigraph_la-dvout.lo libigraph_la-ivout.lo libigraph_la-dnaitr.lo 
> libigraph_la-dnapps.lo libigraph_la-dnaup2.lo libigraph_la-dnaupd.lo 
> libigraph_la-dnconv.lo libigraph_la-dsortc.lo libigraph_la-dneigh.lo 
> libigraph_la-dngets.lo libigraph_la-d
> statn.lo libigraph_la-dlaqrb.lo libigraph_la-dneupd.lo libigraph_la-second.lo 
> libigraph_la-daxpy.lo libigraph_la-ddot.lo libigraph_la-dger.lo 
> libigraph_la-dscal.lo libigraph_la-lsame.lo libigraph_la-dcopy.lo 
> libigraph_la-dgemv.lo libigraph_la-dnrm2.lo libigraph_la-dswap.lo 
> libigraph_la-drot.lo libigraph_la-idamax.lo libigraph_la-dtrmm.lo 
> libigraph_la-dasum.lo libigraph_la-dgeqr2.lo libigraph_la-dlarnv.lo 
> libigraph_la-dlassq.lo libigraph_la-dlacpy.lo libigraph_la-dlartg.lo 
> libigraph_la-dorm2r.lo libigraph_la-dlae2.lo libigraph_la-dlaruv.lo 
> libigraph_la-dsteqr.lo libigraph_la-dlaev2.lo libigraph_la-dlascl.lo 
> libigraph_la-dlanst.lo libigraph_la-dlaset.lo libigraph_la-xerbla.lo 
> libigraph_la-dlarf.lo libigraph_la-dlasr.lo libigraph_la-dlapy2.lo 
> libigraph_la-dlarfg.lo libigraph_la-dlasrt.lo libigraph_la-dlabad.lo 
> libigraph_la-dlanhs.lo libigraph_la-dtrevc.lo libigraph_la-dlanv2.lo 
> libigraph_la-dlaln2.lo libigraph_la-dladiv.lo libigraph_la-dtrsen.lo 
> libigraph_la-dlahqr.lo libigraph
> _la-dlacon.lo libigraph_la-dtrsyl.lo libigraph_la-dtrexc.lo 
> libigraph_la-dlange.lo libigraph_la-dlaexc.lo libigraph_la-dlasy2.lo 
> libigraph_la-dlarfx.lo libigraph_la-d_sign.lo libigraph_la-etime_.lo 
> libigraph_la-pow_dd.lo libigraph_la-pow_di.lo libigraph_la-s_cmp.lo 
> libigraph_la-s_copy.lo libigraph_la-d_lg10.lo libigraph_la-i_dnnt.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-bipartite.lo 
> libigraph_la-drl_layout_3d.lo libigraph_la-drl_graph_3d.lo 
> libigraph_la-DensityGrid_3d.lo -lm -lxml2 -lz -lm libdlamch.la 
> (http://libdlamch.la) 
> libtool: link: g++ -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-measure_dynamics.o 
> .libs/libigraph_la-type_indexededgelist.o .libs/libigraph_la-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 .l
> ibs/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 .li
> bs/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-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-dgetv0.o 
> .libs/libigraph_la-dmout.o .libs/libigraph_la-dsaitr.o 
> .libs/libigraph_la-dsapps.o .
> libs/libigraph_la-dsaup2.o .libs/libigraph_la-dsaupd.o 
> .libs/libigraph_la-dsconv.o .libs/libigraph_la-dseigt.o 
> .libs/libigraph_la-dsesrt.o .libs/libigraph_la-dseupd.o 
> .libs/libigraph_la-dsgets.o .libs/libigraph_la-dsortr.o 
> .libs/libigraph_la-dstats.o .libs/libigraph_la-dstqrb.o 
> .libs/libigraph_la-dvout.o .libs/libigraph_la-ivout.o 
> .libs/libigraph_la-dnaitr.o .libs/libigraph_la-dnapps.o 
> .libs/libigraph_la-dnaup2.o .libs/libigraph_la-dnaupd.o 
> .libs/libigraph_la-dnconv.o .libs/libigraph_la-dsortc.o 
> .libs/libigraph_la-dneigh.o .libs/libigraph_la-dngets.o 
> .libs/libigraph_la-dstatn.o .libs/libigraph_la-dlaqrb.o 
> .libs/libigraph_la-dneupd.o .libs/libigraph_la-second.o 
> .libs/libigraph_la-daxpy.o .libs/libigraph_la-ddot.o 
> .libs/libigraph_la-dger.o .libs/libigraph_la-dscal.o 
> .libs/libigraph_la-lsame.o .libs/libigraph_la-dcopy.o 
> .libs/libigraph_la-dgemv.o .libs/libigraph_la-dnrm2.o 
> .libs/libigraph_la-dswap.o .libs/libigraph_la-drot.o 
> .libs/libigraph_la-idamax.o .libs/libigraph_la-dtrmm.
> o .libs/libigraph_la-dasum.o .libs/libigraph_la-dgeqr2.o 
> .libs/libigraph_la-dlarnv.o .libs/libigraph_la-dlassq.o 
> .libs/libigraph_la-dlacpy.o .libs/libigraph_la-dlartg.o 
> .libs/libigraph_la-dorm2r.o .libs/libigraph_la-dlae2.o 
> .libs/libigraph_la-dlaruv.o .libs/libigraph_la-dsteqr.o 
> .libs/libigraph_la-dlaev2.o .libs/libigraph_la-dlascl.o 
> .libs/libigraph_la-dlanst.o .libs/libigraph_la-dlaset.o 
> .libs/libigraph_la-xerbla.o .libs/libigraph_la-dlarf.o 
> .libs/libigraph_la-dlasr.o .libs/libigraph_la-dlapy2.o 
> .libs/libigraph_la-dlarfg.o .libs/libigraph_la-dlasrt.o 
> .libs/libigraph_la-dlabad.o .libs/libigraph_la-dlanhs.o 
> .libs/libigraph_la-dtrevc.o .libs/libigraph_la-dlanv2.o 
> .libs/libigraph_la-dlaln2.o .libs/libigraph_la-dladiv.o 
> .libs/libigraph_la-dtrsen.o .libs/libigraph_la-dlahqr.o 
> .libs/libigraph_la-dlacon.o .libs/libigraph_la-dtrsyl.o 
> .libs/libigraph_la-dtrexc.o .libs/libigraph_la-dlange.o 
> .libs/libigraph_la-dlaexc.o .libs/libigraph_la-dlasy2.o 
> .libs/libigraph_la-dlarfx.o .libs/libig
> raph_la-d_sign.o .libs/libigraph_la-etime_.o .libs/libigraph_la-pow_dd.o 
> .libs/libigraph_la-pow_di.o .libs/libigraph_la-s_cmp.o 
> .libs/libigraph_la-s_copy.o .libs/libigraph_la-d_lg10.o 
> .libs/libigraph_la-i_dnnt.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-bipartite.o .libs/libigraph_la-drl_layout_3d.o 
> .libs/libigraph_la-drl_graph_3d.o .libs/libigraph_la-DensityGrid_3d.o 
> -Wl,--whole-archive ./.libs/libdlamch.a -Wl,--no-whole-archive -lxml2 -lz 
> -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 
> -Wl,-soname -Wl,libigraph.so.0 -o .libs/libigraph.so.0.0.0
> /usr/bin/ld: cannot find -lxml2
> collect2: ld returned 1 exit status
> make[3]: *** [libigraph.la (http://libigraph.la)] Fehler 1
> make[3]: Verlasse Verzeichnis '/localhome/masbach-local/igraph-0.5.4/src'
> make[2]: *** [all] Fehler 2
> make[2]: Verlasse Verzeichnis '/localhome/masbach-local/igraph-0.5.4/src'
> make[1]: *** [all-recursive] Fehler 1
> make[1]: Verlasse Verzeichnis '/localhome/masbach-local/igraph-0.5.4'
> make: *** [all] Fehler 2
> 
> 
> _______________________________________________
> igraph-help mailing list
> address@hidden (mailto:address@hidden)
> https://lists.nongnu.org/mailman/listinfo/igraph-help