diff --git a/BioArchLinux/r-igraph/PKGBUILD b/BioArchLinux/r-igraph/PKGBUILD index 7bfa3681a4..4952ded971 100644 --- a/BioArchLinux/r-igraph/PKGBUILD +++ b/BioArchLinux/r-igraph/PKGBUILD @@ -5,10 +5,10 @@ # Contributor: Oleg Smirnov _pkgname=igraph -_pkgver=2.0.2 +_pkgver=2.0.3 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} -pkgrel=1 +pkgrel=0 pkgdesc="Network Analysis and Visualization" arch=(x86_64) url="https://cran.r-project.org/package=$_pkgname" @@ -34,6 +34,7 @@ makedepends=( ) checkdepends=( r-graph + r-rgl r-testthat r-vdiffr ) @@ -54,10 +55,10 @@ optdepends=( ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz" "igraph-system-libs.patch") -md5sums=('5ec60d660bedd8242751ed0b8720280f' - '6c7d29860961ff06147a1ca2819dcad5') -b2sums=('5ac558f237ce339c2e27a349eae6651c0b38333e2fb902b9378bde72773989520f48fb83b5ddccbb7c9aa1f93e0b211fee6489537d45a4a1ec8ab2ad5e8c5cfe' - 'b7547dbd5d8bd30bb59fc15937fb99df18f17025d8f4fc8ba5164b5257a7dbcf46271eb7d262aa0e6d17868007e15f2fa1aebc43cb7f85c377a109b87b963f3b') +md5sums=('36b28af2a8910060551629b306165f75' + '5a958a08aa13c94de5820924a5e964ad') +b2sums=('3cc8510e01db17a4f5dffd43b9dbbe2e01d9e631289efcadcacecd8a577555cca2848eebb68299147e22618bd0e96691b2fc0a5eb0a59c549af66dc5c0d7ef25' + 'd2bd23dc816abfc33908b5583ee1129981fdccb8cd8b067cfb46e41f89d346135353ed6525467f14333064b601ae8544d0fa14931c34594bfdbcbcf45edf7c4b') prepare() { # Build using system libraries diff --git a/BioArchLinux/r-igraph/igraph-system-libs.patch b/BioArchLinux/r-igraph/igraph-system-libs.patch index 139f4596f0..1363c51701 100644 --- a/BioArchLinux/r-igraph/igraph-system-libs.patch +++ b/BioArchLinux/r-igraph/igraph-system-libs.patch @@ -1,34 +1,47 @@ +diff --git a/igraph/configure b/igraph/configure +index 22fd44f..5ed8a79 100755 +--- a/igraph/configure ++++ b/igraph/configure +@@ -32,7 +32,7 @@ if [ "$libxml_unavilable" = true ]; then + echo "GraphML import will not be available." + fi + +-OBJECTS='${SOURCES} ${MINIGMPSOURCES}' ++OBJECTS='${SOURCES}' + + if echo '#include ' | `"${R_HOME}/bin/R" CMD config CC` -E $CPPFLAGS - > /dev/null 2>&1; then + echo "Using installed GLPK" diff --git a/igraph/src/Makevars.in b/igraph/src/Makevars.in -index 0e5529b..1cb3fcf 100644 +index 456a7fe..4fe973f 100644 --- a/igraph/src/Makevars.in +++ b/igraph/src/Makevars.in -@@ -4,12 +4,12 @@ PKG_CFLAGS=$(C_VISIBILITY) +@@ -6,12 +6,12 @@ PKG_CFLAGS=$(C_VISIBILITY) PKG_CXXFLAGS=$(CXX_VISIBILITY) PKG_FFLAGS=$(F_VISIBILITY) --PKG_CPPFLAGS=-DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp @cflags@ \ -+PKG_CPPFLAGS=-DUSING_R -I/usr/include/uuid -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor @cflags@ \ +-PKG_CPPFLAGS=-DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/io/parsers @cflags@ \ ++PKG_CPPFLAGS=-DUSING_R -I/usr/include/uuid -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/io/parsers @cflags@ \ -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= \ -DPRPACK_IGRAPH_SUPPORT \ -DHAVE_GFORTRAN=1 \ -D_GNU_SOURCE=1 --PKG_LIBS = -lglpk @libs@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -+PKG_LIBS = -lglpk -lgmp @libs@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -larpack -lplfit -luuid +-PKG_LIBS = @libs@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) ++PKG_LIBS = @libs@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -lgmp -larpack -lplfit -luuid - OBJECTS=${SOURCES} + OBJECTS=@objects@ diff --git a/igraph/src/sources.mk b/igraph/src/sources.mk -index 499f874..dbdde72 100644 +index 463ae21..71e35b1 100644 --- a/igraph/src/sources.mk +++ b/igraph/src/sources.mk @@ -1 +1 @@ --SOURCES=simpleraytracer.o rinterface_extra.o rrandom.o rinterface.o cpp11.o cpprinterface.o lazyeval.o init.o vendor/arpack/dnaupd.o vendor/arpack/dstatn.o vendor/arpack/dsaupd.o vendor/arpack/dvout.o vendor/arpack/dstqrb.o vendor/arpack/dlaqrb.o vendor/arpack/dsaup2.o vendor/arpack/dmout.o vendor/arpack/dngets.o vendor/arpack/dneupd.o vendor/arpack/dsortc.o vendor/arpack/dnaup2.o vendor/arpack/dseigt.o vendor/arpack/dneigh.o vendor/arpack/dseupd.o vendor/arpack/dsgets.o vendor/arpack/dnapps.o vendor/arpack/dsaitr.o vendor/arpack/dstats.o vendor/arpack/dnconv.o vendor/arpack/second.o vendor/arpack/dsesrt.o vendor/arpack/dsapps.o vendor/arpack/dgetv0.o vendor/arpack/dnaitr.o vendor/arpack/dsortr.o vendor/arpack/dsconv.o vendor/arpack/wrap.o vendor/arpack/ivout.o vendor/cigraph/src/version.o vendor/cigraph/src/centrality/eigenvector.o vendor/cigraph/src/centrality/truss.o vendor/cigraph/src/centrality/prpack.o vendor/cigraph/src/centrality/pagerank.o vendor/cigraph/src/centrality/closeness.o vendor/cigraph/src/centrality/hub_authority.o vendor/cigraph/src/centrality/coreness.o vendor/cigraph/src/centrality/centralization.o vendor/cigraph/src/centrality/betweenness.o vendor/cigraph/src/centrality/centrality_other.o vendor/cigraph/src/centrality/prpack/prpack_utils.o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.o vendor/cigraph/src/centrality/prpack/prpack_base_graph.o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.o vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.o vendor/cigraph/src/centrality/prpack/prpack_result.o vendor/cigraph/src/centrality/prpack/prpack_solver.o vendor/cigraph/src/cliques/glet.o vendor/cigraph/src/cliques/maximal_cliques.o vendor/cigraph/src/cliques/cliquer_wrapper.o vendor/cigraph/src/cliques/cliques.o vendor/cigraph/src/cliques/cliquer/cliquer.o vendor/cigraph/src/cliques/cliquer/reorder.o vendor/cigraph/src/cliques/cliquer/cliquer_graph.o vendor/cigraph/src/community/voronoi.o vendor/cigraph/src/community/optimal_modularity.o vendor/cigraph/src/community/modularity.o vendor/cigraph/src/community/leiden.o vendor/cigraph/src/community/fluid.o vendor/cigraph/src/community/fast_modularity.o vendor/cigraph/src/community/louvain.o vendor/cigraph/src/community/label_propagation.o vendor/cigraph/src/community/community_misc.o vendor/cigraph/src/community/leading_eigenvector.o vendor/cigraph/src/community/edge_betweenness.o vendor/cigraph/src/community/infomap/infomap_Greedy.o vendor/cigraph/src/community/infomap/infomap.o vendor/cigraph/src/community/infomap/infomap_FlowGraph.o vendor/cigraph/src/community/spinglass/NetRoutines.o vendor/cigraph/src/community/spinglass/clustertool.o vendor/cigraph/src/community/spinglass/pottsmodel_2.o vendor/cigraph/src/community/spinglass/NetDataTypes.o vendor/cigraph/src/community/walktrap/walktrap.o vendor/cigraph/src/community/walktrap/walktrap_graph.o vendor/cigraph/src/community/walktrap/walktrap_heap.o vendor/cigraph/src/community/walktrap/walktrap_communities.o vendor/cigraph/src/connectivity/components.o vendor/cigraph/src/connectivity/cohesive_blocks.o vendor/cigraph/src/connectivity/separators.o vendor/cigraph/src/constructors/circulant.o vendor/cigraph/src/constructors/adjacency.o vendor/cigraph/src/constructors/famous.o vendor/cigraph/src/constructors/lcf.o vendor/cigraph/src/constructors/full.o vendor/cigraph/src/constructors/kautz.o vendor/cigraph/src/constructors/prufer.o vendor/cigraph/src/constructors/lattices.o vendor/cigraph/src/constructors/basic_constructors.o vendor/cigraph/src/constructors/regular.o vendor/cigraph/src/constructors/de_bruijn.o vendor/cigraph/src/constructors/atlas.o vendor/cigraph/src/constructors/generalized_petersen.o vendor/cigraph/src/constructors/trees.o vendor/cigraph/src/constructors/linegraph.o vendor/cigraph/src/core/memory.o vendor/cigraph/src/core/heap.o vendor/cigraph/src/core/interruption.o vendor/cigraph/src/core/array.o vendor/cigraph/src/core/strvector.o vendor/cigraph/src/core/cutheap.o vendor/cigraph/src/core/stack.o vendor/cigraph/src/core/fixed_vectorlist.o vendor/cigraph/src/core/vector.o vendor/cigraph/src/core/dqueue.o vendor/cigraph/src/core/indheap.o vendor/cigraph/src/core/printing.o vendor/cigraph/src/core/set.o vendor/cigraph/src/core/psumtree.o vendor/cigraph/src/core/trie.o vendor/cigraph/src/core/vector_list.o vendor/cigraph/src/core/matrix_list.o vendor/cigraph/src/core/estack.o vendor/cigraph/src/core/error.o vendor/cigraph/src/core/progress.o vendor/cigraph/src/core/genheap.o vendor/cigraph/src/core/vector_ptr.o vendor/cigraph/src/core/marked_queue.o vendor/cigraph/src/core/statusbar.o vendor/cigraph/src/core/grid.o vendor/cigraph/src/core/sparsemat.o vendor/cigraph/src/core/matrix.o vendor/cigraph/src/core/buckets.o vendor/cigraph/src/flow/flow.o vendor/cigraph/src/flow/st-cuts.o vendor/cigraph/src/flow/flow_conversion.o vendor/cigraph/src/games/forestfire.o vendor/cigraph/src/games/static_fitness.o vendor/cigraph/src/games/correlated.o vendor/cigraph/src/games/erdos_renyi.o vendor/cigraph/src/games/growing_random.o vendor/cigraph/src/games/recent_degree.o vendor/cigraph/src/games/islands.o vendor/cigraph/src/games/preference.o vendor/cigraph/src/games/dotproduct.o vendor/cigraph/src/games/sbm.o vendor/cigraph/src/games/barabasi.o vendor/cigraph/src/games/citations.o vendor/cigraph/src/games/watts_strogatz.o vendor/cigraph/src/games/degree_sequence.o vendor/cigraph/src/games/k_regular.o vendor/cigraph/src/games/callaway_traits.o vendor/cigraph/src/games/grg.o vendor/cigraph/src/games/establishment.o vendor/cigraph/src/games/tree.o vendor/cigraph/src/games/degree_sequence_vl/gengraph_random.o vendor/cigraph/src/games/degree_sequence_vl/gengraph_graph_molloy_hash.o vendor/cigraph/src/games/degree_sequence_vl/gengraph_degree_sequence.o vendor/cigraph/src/games/degree_sequence_vl/gengraph_mr-connected.o vendor/cigraph/src/games/degree_sequence_vl/gengraph_graph_molloy_optimized.o vendor/cigraph/src/graph/graph_list.o vendor/cigraph/src/graph/basic_query.o vendor/cigraph/src/graph/visitors.o vendor/cigraph/src/graph/iterators.o vendor/cigraph/src/graph/type_indexededgelist.o vendor/cigraph/src/graph/cattributes.o vendor/cigraph/src/graph/caching.o vendor/cigraph/src/graph/type_common.o vendor/cigraph/src/graph/attributes.o vendor/cigraph/src/graph/adjlist.o vendor/cigraph/src/hrg/hrg_types.o vendor/cigraph/src/hrg/hrg.o vendor/cigraph/src/internal/glpk_support.o vendor/cigraph/src/internal/qsort_r.o vendor/cigraph/src/internal/qsort.o vendor/cigraph/src/internal/utils.o vendor/cigraph/src/internal/hacks.o vendor/cigraph/src/internal/lsap.o vendor/cigraph/src/internal/zeroin.o vendor/cigraph/src/io/graphdb.o vendor/cigraph/src/io/dot.o vendor/cigraph/src/io/gml-tree.o vendor/cigraph/src/io/ncol.o vendor/cigraph/src/io/edgelist.o vendor/cigraph/src/io/lgl.o vendor/cigraph/src/io/dimacs.o vendor/cigraph/src/io/pajek.o vendor/cigraph/src/io/parse_utils.o vendor/cigraph/src/io/graphml.o vendor/cigraph/src/io/dl.o vendor/cigraph/src/io/gml.o vendor/cigraph/src/io/leda.o vendor/cigraph/src/isomorphism/isomorphism_misc.o vendor/cigraph/src/isomorphism/lad.o vendor/cigraph/src/isomorphism/queries.o vendor/cigraph/src/isomorphism/isoclasses.o vendor/cigraph/src/isomorphism/bliss.o vendor/cigraph/src/isomorphism/vf2.o vendor/cigraph/src/isomorphism/bliss/utils.o vendor/cigraph/src/isomorphism/bliss/graph.o vendor/cigraph/src/isomorphism/bliss/uintseqhash.o vendor/cigraph/src/isomorphism/bliss/defs.o vendor/cigraph/src/isomorphism/bliss/orbit.o vendor/cigraph/src/isomorphism/bliss/heap.o vendor/cigraph/src/isomorphism/bliss/partition.o vendor/cigraph/src/layout/reingold_tilford.o vendor/cigraph/src/layout/layout_bipartite.o vendor/cigraph/src/layout/graphopt.o vendor/cigraph/src/layout/davidson_harel.o vendor/cigraph/src/layout/umap.o vendor/cigraph/src/layout/merge_dla.o vendor/cigraph/src/layout/merge_grid.o vendor/cigraph/src/layout/kamada_kawai.o vendor/cigraph/src/layout/gem.o vendor/cigraph/src/layout/sugiyama.o vendor/cigraph/src/layout/large_graph.o vendor/cigraph/src/layout/fruchterman_reingold.o vendor/cigraph/src/layout/layout_grid.o vendor/cigraph/src/layout/circular.o vendor/cigraph/src/layout/mds.o vendor/cigraph/src/layout/layout_random.o vendor/cigraph/src/layout/drl/drl_layout_3d.o vendor/cigraph/src/layout/drl/drl_parse.o vendor/cigraph/src/layout/drl/drl_graph_3d.o vendor/cigraph/src/layout/drl/drl_graph.o vendor/cigraph/src/layout/drl/drl_layout.o vendor/cigraph/src/layout/drl/DensityGrid.o vendor/cigraph/src/layout/drl/DensityGrid_3d.o vendor/cigraph/src/linalg/eigen.o vendor/cigraph/src/linalg/arpack.o vendor/cigraph/src/linalg/lapack.o vendor/cigraph/src/linalg/blas.o vendor/cigraph/src/math/complex.o vendor/cigraph/src/math/safe_intop.o vendor/cigraph/src/math/utils.o vendor/cigraph/src/misc/order_cycle.o vendor/cigraph/src/misc/feedback_arc_set.o vendor/cigraph/src/misc/bipartite.o vendor/cigraph/src/misc/spanning_trees.o vendor/cigraph/src/misc/degree_sequence.o vendor/cigraph/src/misc/embedding.o vendor/cigraph/src/misc/cycle_bases.o vendor/cigraph/src/misc/motifs.o vendor/cigraph/src/misc/mixing.o vendor/cigraph/src/misc/chordality.o vendor/cigraph/src/misc/scan.o vendor/cigraph/src/misc/microscopic_update.o vendor/cigraph/src/misc/sir.o vendor/cigraph/src/misc/cocitation.o vendor/cigraph/src/misc/graphicality.o vendor/cigraph/src/misc/other.o vendor/cigraph/src/misc/matching.o vendor/cigraph/src/misc/power_law_fit.o vendor/cigraph/src/misc/conversion.o vendor/cigraph/src/misc/coloring.o vendor/cigraph/src/operators/connect_neighborhood.o vendor/cigraph/src/operators/rewire.o vendor/cigraph/src/operators/simplify.o vendor/cigraph/src/operators/contract.o vendor/cigraph/src/operators/complementer.o vendor/cigraph/src/operators/difference.o vendor/cigraph/src/operators/union.o vendor/cigraph/src/operators/disjoint_union.o vendor/cigraph/src/operators/subgraph.o vendor/cigraph/src/operators/permute.o vendor/cigraph/src/operators/reverse.o vendor/cigraph/src/operators/intersection.o vendor/cigraph/src/operators/rewire_edges.o vendor/cigraph/src/operators/misc_internal.o vendor/cigraph/src/operators/add_edge.o vendor/cigraph/src/operators/compose.o vendor/cigraph/src/paths/voronoi.o vendor/cigraph/src/paths/histogram.o vendor/cigraph/src/paths/all_shortest_paths.o vendor/cigraph/src/paths/dijkstra.o vendor/cigraph/src/paths/sparsifier.o vendor/cigraph/src/paths/bellman_ford.o vendor/cigraph/src/paths/widest_paths.o vendor/cigraph/src/paths/floyd_warshall.o vendor/cigraph/src/paths/distances.o vendor/cigraph/src/paths/shortest_paths.o vendor/cigraph/src/paths/unweighted.o vendor/cigraph/src/paths/eulerian.o vendor/cigraph/src/paths/random_walk.o vendor/cigraph/src/paths/johnson.o vendor/cigraph/src/paths/astar.o vendor/cigraph/src/paths/simple_paths.o vendor/cigraph/src/properties/constraint.o vendor/cigraph/src/properties/girth.o vendor/cigraph/src/properties/basic_properties.o vendor/cigraph/src/properties/neighborhood.o vendor/cigraph/src/properties/spectral.o vendor/cigraph/src/properties/convergence_degree.o vendor/cigraph/src/properties/ecc.o vendor/cigraph/src/properties/triangles.o vendor/cigraph/src/properties/loops.o vendor/cigraph/src/properties/dag.o vendor/cigraph/src/properties/degrees.o vendor/cigraph/src/properties/multiplicity.o vendor/cigraph/src/properties/trees.o vendor/cigraph/src/properties/perfect.o vendor/cigraph/src/random/rng_pcg32.o vendor/cigraph/src/random/random.o vendor/cigraph/src/random/rng_mt19937.o vendor/cigraph/src/random/rng_pcg64.o vendor/cigraph/src/random/rng_glibc2.o vendor/cigraph/vendor/cs/cs_load.o vendor/cigraph/vendor/cs/cs_ipvec.o vendor/cigraph/vendor/cs/cs_reach.o vendor/cigraph/vendor/cs/cs_chol.o vendor/cigraph/vendor/cs/cs_pvec.o vendor/cigraph/vendor/cs/cs_dmperm.o vendor/cigraph/vendor/cs/cs_lsolve.o vendor/cigraph/vendor/cs/cs_qrsol.o vendor/cigraph/vendor/cs/cs_symperm.o vendor/cigraph/vendor/cs/cs_schol.o vendor/cigraph/vendor/cs/cs_droptol.o vendor/cigraph/vendor/cs/cs_entry.o vendor/cigraph/vendor/cs/cs_randperm.o vendor/cigraph/vendor/cs/cs_scatter.o vendor/cigraph/vendor/cs/cs_leaf.o vendor/cigraph/vendor/cs/cs_post.o vendor/cigraph/vendor/cs/cs_dupl.o vendor/cigraph/vendor/cs/cs_malloc.o vendor/cigraph/vendor/cs/cs_dfs.o vendor/cigraph/vendor/cs/cs_lusol.o vendor/cigraph/vendor/cs/cs_add.o vendor/cigraph/vendor/cs/cs_updown.o vendor/cigraph/vendor/cs/cs_utsolve.o vendor/cigraph/vendor/cs/cs_cholsol.o vendor/cigraph/vendor/cs/cs_compress.o vendor/cigraph/vendor/cs/cs_transpose.o vendor/cigraph/vendor/cs/cs_maxtrans.o vendor/cigraph/vendor/cs/cs_print.o vendor/cigraph/vendor/cs/cs_lu.o vendor/cigraph/vendor/cs/cs_multiply.o vendor/cigraph/vendor/cs/cs_gaxpy.o vendor/cigraph/vendor/cs/cs_ltsolve.o vendor/cigraph/vendor/cs/cs_usolve.o vendor/cigraph/vendor/cs/cs_fkeep.o vendor/cigraph/vendor/cs/cs_spsolve.o vendor/cigraph/vendor/cs/cs_happly.o vendor/cigraph/vendor/cs/cs_ereach.o vendor/cigraph/vendor/cs/cs_sqr.o vendor/cigraph/vendor/cs/cs_amd.o vendor/cigraph/vendor/cs/cs_cumsum.o vendor/cigraph/vendor/cs/cs_dropzeros.o vendor/cigraph/vendor/cs/cs_permute.o vendor/cigraph/vendor/cs/cs_house.o vendor/cigraph/vendor/cs/cs_etree.o vendor/cigraph/vendor/cs/cs_pinv.o vendor/cigraph/vendor/cs/cs_scc.o vendor/cigraph/vendor/cs/cs_qr.o vendor/cigraph/vendor/cs/cs_norm.o vendor/cigraph/vendor/cs/cs_tdfs.o vendor/cigraph/vendor/cs/cs_counts.o vendor/cigraph/vendor/cs/cs_util.o vendor/cigraph/vendor/pcg/pcg-advance-64.o vendor/cigraph/vendor/pcg/pcg-rngs-128.o vendor/cigraph/vendor/pcg/pcg-output-64.o vendor/cigraph/vendor/pcg/pcg-output-128.o vendor/cigraph/vendor/pcg/pcg-output-32.o vendor/cigraph/vendor/pcg/pcg-rngs-64.o vendor/cigraph/vendor/pcg/pcg-advance-128.o vendor/cigraph/vendor/plfit/kolmogorov.o vendor/cigraph/vendor/plfit/plfit.o vendor/cigraph/vendor/plfit/mt.o vendor/cigraph/vendor/plfit/sampling.o vendor/cigraph/vendor/plfit/platform.o vendor/cigraph/vendor/plfit/gss.o vendor/cigraph/vendor/plfit/rbinom.o vendor/cigraph/vendor/plfit/hzeta.o vendor/cigraph/vendor/plfit/lbfgs.o vendor/cigraph/vendor/plfit/options.o vendor/cigraph/vendor/plfit/plfit_error.o vendor/io/pajek-lexer.o vendor/io/pajek-parser.o vendor/io/lgl-parser.o vendor/io/dl-lexer.o vendor/io/ncol-parser.o vendor/io/gml-parser.o vendor/io/dl-parser.o vendor/io/gml-lexer.o vendor/io/lgl-lexer.o vendor/io/ncol-lexer.o vendor/mini-gmp/mini-gmp.o vendor/simpleraytracer/RayTracer.o vendor/simpleraytracer/Light.o vendor/simpleraytracer/Ray.o vendor/simpleraytracer/RayVector.o vendor/simpleraytracer/unit_limiter.o vendor/simpleraytracer/Color.o vendor/simpleraytracer/Point.o vendor/simpleraytracer/Shape.o vendor/simpleraytracer/Triangle.o vendor/simpleraytracer/Sphere.o vendor/uuid/compare.o vendor/uuid/unpack.o 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vendor/cigraph/src/paths/shortest_paths.o vendor/cigraph/src/paths/simple_paths.o vendor/cigraph/src/paths/sparsifier.o vendor/cigraph/src/paths/unweighted.o vendor/cigraph/src/paths/voronoi.o vendor/cigraph/src/paths/widest_paths.o vendor/cigraph/src/properties/basic_properties.o vendor/cigraph/src/properties/complete.o vendor/cigraph/src/properties/constraint.o vendor/cigraph/src/properties/convergence_degree.o vendor/cigraph/src/properties/dag.o vendor/cigraph/src/properties/degrees.o vendor/cigraph/src/properties/ecc.o vendor/cigraph/src/properties/girth.o vendor/cigraph/src/properties/loops.o vendor/cigraph/src/properties/multiplicity.o vendor/cigraph/src/properties/neighborhood.o vendor/cigraph/src/properties/perfect.o vendor/cigraph/src/properties/spectral.o vendor/cigraph/src/properties/trees.o vendor/cigraph/src/properties/triangles.o vendor/cigraph/src/random/random.o vendor/cigraph/src/random/rng_glibc2.o vendor/cigraph/src/random/rng_mt19937.o vendor/cigraph/src/random/rng_pcg32.o vendor/cigraph/src/random/rng_pcg64.o vendor/cigraph/src/version.o vendor/cigraph/vendor/cs/cs_add.o vendor/cigraph/vendor/cs/cs_amd.o vendor/cigraph/vendor/cs/cs_chol.o vendor/cigraph/vendor/cs/cs_cholsol.o vendor/cigraph/vendor/cs/cs_compress.o vendor/cigraph/vendor/cs/cs_counts.o vendor/cigraph/vendor/cs/cs_cumsum.o vendor/cigraph/vendor/cs/cs_dfs.o vendor/cigraph/vendor/cs/cs_dmperm.o vendor/cigraph/vendor/cs/cs_droptol.o vendor/cigraph/vendor/cs/cs_dropzeros.o vendor/cigraph/vendor/cs/cs_dupl.o vendor/cigraph/vendor/cs/cs_entry.o vendor/cigraph/vendor/cs/cs_ereach.o vendor/cigraph/vendor/cs/cs_etree.o vendor/cigraph/vendor/cs/cs_fkeep.o vendor/cigraph/vendor/cs/cs_gaxpy.o vendor/cigraph/vendor/cs/cs_happly.o vendor/cigraph/vendor/cs/cs_house.o vendor/cigraph/vendor/cs/cs_ipvec.o vendor/cigraph/vendor/cs/cs_leaf.o vendor/cigraph/vendor/cs/cs_load.o vendor/cigraph/vendor/cs/cs_lsolve.o vendor/cigraph/vendor/cs/cs_ltsolve.o vendor/cigraph/vendor/cs/cs_lu.o vendor/cigraph/vendor/cs/cs_lusol.o vendor/cigraph/vendor/cs/cs_malloc.o vendor/cigraph/vendor/cs/cs_maxtrans.o vendor/cigraph/vendor/cs/cs_multiply.o vendor/cigraph/vendor/cs/cs_norm.o vendor/cigraph/vendor/cs/cs_permute.o vendor/cigraph/vendor/cs/cs_pinv.o vendor/cigraph/vendor/cs/cs_post.o vendor/cigraph/vendor/cs/cs_print.o vendor/cigraph/vendor/cs/cs_pvec.o vendor/cigraph/vendor/cs/cs_qr.o vendor/cigraph/vendor/cs/cs_qrsol.o vendor/cigraph/vendor/cs/cs_randperm.o vendor/cigraph/vendor/cs/cs_reach.o vendor/cigraph/vendor/cs/cs_scatter.o vendor/cigraph/vendor/cs/cs_scc.o vendor/cigraph/vendor/cs/cs_schol.o vendor/cigraph/vendor/cs/cs_spsolve.o vendor/cigraph/vendor/cs/cs_sqr.o vendor/cigraph/vendor/cs/cs_symperm.o vendor/cigraph/vendor/cs/cs_tdfs.o vendor/cigraph/vendor/cs/cs_transpose.o vendor/cigraph/vendor/cs/cs_updown.o vendor/cigraph/vendor/cs/cs_usolve.o vendor/cigraph/vendor/cs/cs_util.o vendor/cigraph/vendor/cs/cs_utsolve.o vendor/cigraph/vendor/pcg/pcg-advance-128.o vendor/cigraph/vendor/pcg/pcg-advance-64.o vendor/cigraph/vendor/pcg/pcg-output-128.o vendor/cigraph/vendor/pcg/pcg-output-32.o vendor/cigraph/vendor/pcg/pcg-output-64.o vendor/cigraph/vendor/pcg/pcg-rngs-128.o vendor/cigraph/vendor/pcg/pcg-rngs-64.o vendor/io/dl-lexer.o vendor/io/dl-parser.o vendor/io/gml-lexer.o vendor/io/gml-parser.o vendor/io/lgl-lexer.o vendor/io/lgl-parser.o vendor/io/ncol-lexer.o vendor/io/ncol-parser.o vendor/io/pajek-lexer.o vendor/io/pajek-parser.o vendor/simpleraytracer/Color.o vendor/simpleraytracer/Light.o vendor/simpleraytracer/Point.o vendor/simpleraytracer/Ray.o vendor/simpleraytracer/RayTracer.o vendor/simpleraytracer/RayVector.o vendor/simpleraytracer/Shape.o vendor/simpleraytracer/Sphere.o vendor/simpleraytracer/Triangle.o vendor/simpleraytracer/unit_limiter.o vendor/uuid/R.o diff --git a/igraph/src/vendor/config.h b/igraph/src/vendor/config.h -index 2f49059..68695a2 100644 +index 0664bf7..89f8df0 100644 --- a/igraph/src/vendor/config.h +++ b/igraph/src/vendor/config.h -@@ -27,9 +27,6 @@ +@@ -26,9 +26,6 @@ /* #undef INTERNAL_BLAS */ /* #undef INTERNAL_LAPACK */ diff --git a/BioArchLinux/r-igraph/lilac.py b/BioArchLinux/r-igraph/lilac.py index eeade6e426..d74d45fbac 100644 --- a/BioArchLinux/r-igraph/lilac.py +++ b/BioArchLinux/r-igraph/lilac.py @@ -9,7 +9,7 @@ from lilac_r_utils import r_pre_build def pre_build(): r_pre_build( _G, - expect_systemrequirements = "libxml2, glpk (>= 4.57)", + expect_systemrequirements = "libxml2 (optional), glpk (>= 4.57, optional)", ignore_fortran_files = True, ) diff --git a/BioArchLinux/r-igraph/lilac.yaml b/BioArchLinux/r-igraph/lilac.yaml index 3d76ce2f6a..a294ba013e 100644 --- a/BioArchLinux/r-igraph/lilac.yaml +++ b/BioArchLinux/r-igraph/lilac.yaml @@ -12,6 +12,7 @@ repo_depends: repo_makedepends: - r-cpp11 - r-graph +- r-rgl - r-testthat - r-vdiffr update_on: