[adegenet-forum] Problem installation on Ubuntu

Sat Jul 12 20:57:32 CEST 2014

Hello,
generally, R packages have to be compiled on Linux. Do You have basic tools 
for compilation? See https://help.ubuntu.com/community/CompilingSoftware Might 
be You can try to install the package directly from Ubuntu binary package 
repository, see http://cran.r-project.org/bin/linux/ubuntu/README I don't use 
Ubuntu, so that I'm not sure about usability of that repository... And then 
try install.packages("adegenet", dependencies=TRUE)
Good luck,
Vojtěch

Dne So 12. července 2014 20:50:23, Samuel Knapp napsal(a):
> Dear all,
> 
> I'm running R on Ubuntu and can't install the adegenet package.
> 
> Versions:
> - Ubuntu: 14.04 (Trusty)
> - R.Version()
> $platform
> [1] "x86_64-pc-linux-gnu"
> $version.string
> [1] "R version 3.1.1 (2014-07-10)"
> 
> In order to exclude other problems, I have reinstalled a clear R version
> and tried to install adegenet as the first package. I get the output below.
> 
> Have tried to search for "Error in namespaceExport(ns, exports)" and
> "ERROR: lazy loading failed for package ‘adegenet’", but can't find
> anything.
> Also I tried to install older versions of adegenet and got the same
> error report. The error occurs both, if I run R as sudo or as normal user.
> 
> If anybody has an idea what the problem could be, please let me know.
> 
> Thanks,
> Samuel
> 
> ////////////////////////////////////////////////////////////////////////////
> ////////////////////////////////////////////////////////////////////////////
> //////////////////////////////////////////////////////////////
>  > install.packages("adegenet")
> 
> Installing package into ‘/home/samuel/R/x86_64-pc-linux-gnu-library/3.1’
> (as ‘lib’ is unspecified)
> trying URL
> 'http://ftp.igh.cnrs.fr/pub/CRAN/src/contrib/adegenet_1.4-2.tar.gz'
> Content type 'application/octet-stream' length 1588751 bytes (1.5 Mb)
> opened URL
> ==================================================
> downloaded 1.5 Mb
> 
> * installing *source* package ‘adegenet’ ...
> ** package ‘adegenet’ successfully unpacked and MD5 sums checked
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c GLfunctions.c -o
> GLfunctions.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c adesub.c -o adesub.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c monmonier-utils.c -o
> monmonier-utils.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sharedAll.c -o sharedAll.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c snpbin.c -o snpbin.o
> gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o
> adegenet.so GLfunctions.o adesub.o monmonier-utils.o sharedAll.o
> snpbin.o -L/usr/lib/R/lib -lR
> installing to /home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet/libs
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Warning: S3 methods ‘[.igraph’, ‘[[.igraph’, ‘[<-.igraph’, ‘+.igraph’,
> ‘-.igraph’, ‘$.igraph’, ‘$<-.igraph’, ‘$.igraph.vs’, ‘[.igraph.vs’,
> ‘[[.igraph.vs’, ‘[<-.igraph.vs’, ‘[[<-.igraph.vs’, ‘$<-.igraph.vs’,
> ‘$.igraph.es’, ‘[.igraph.es’, ‘[[.igraph.es’, ‘[<-.igraph.es’,
> ‘[[<-.igraph.es’, ‘$<-.igraph.es’, ‘print.igraph.vs’, ‘print.igraph.es’,
> ‘str.igraph’, ‘print.communities’, ‘modularity.communities’,
> ‘length.communities’, ‘as.dendrogram.communities’,
> ‘as.hclust.communities’, ‘asPhylo.communities’, ‘modularity.igraph’,
> ‘dendPlot.communities’, ‘compare.communities’, ‘compare.numeric’,
> ‘compare.default’, ‘rglplot.igraph’, ‘layout.svd.igraph’,
> ‘print.cohesiveBlocks’, ‘summary.cohesiveBlocks’, ‘plot.cohesiveBlocks’,
> ‘length.cohesiveBlocks’, ‘print.igraphHRG’, ‘print.igraphHRGConsensus’,
> ‘as.dendrogram.igraphHRG’, ‘as.hclust.igraphHR [... truncated]
> Error in namespaceExport(ns, exports) :
> undefined exports: add.vertices, delete.edges, delete.vertices, ecount,
> neighbors, incident, get.edges, get.edge.ids, [.igraph, [[.igraph,
> [<-.igraph, edge, edges, vertex, vertices, path, +.igraph, -.igraph,
> get.graph.attribute, set.graph.attribute, graph.attributes,
> get.vertex.attribute, set.vertex.attribute, vertex.attributes,
> get.edge.attribute, set.edge.attribute, edge.attributes,
> list.graph.attributes, list.vertex.attributes, list.edge.attributes,
> remove.graph.attribute, remove.vertex.attribute, remove.edge.attribute,
> graph.attributes<-, vertex.attributes<-, edge.attributes<-, V, E,
> $.igraph.vs, $.igraph.es, [.igraph.vs, [[.igraph.vs, [.igraph.es,
> [[.igraph.es, [<-.igraph.vs, [<-.igraph.es, [[<-.igraph.vs,
> [[<-.igraph.es, $<-.igraph.vs, $<-.igraph.es, V<-, E<-, print.igraph.vs,
> print.igraph.es, %--%, %->%, %<-%, is.igraph, is.named, is.weighted,
> is.bipartite, are.connected, print.igraph, str.igraph, summary.igraph,
> is.directed, get.edge, graph, graph.adjacency, graph.star, graph.tree,
> graph.lattice, graph.ring, graph.full, graph.atlas, graph.data.frame,
> graph.edgelist, graph.extended.chordal.ring, line.graph,
> graph.de.bruijn, graph.kautz, graph.formula, graph.famous,
> erdos.renyi.game, random.graph.game, degree.sequence.game,
> aging.prefatt.game, aging.barabasi.game, aging.ba.game,
> growing.random.game, barabasi.game, ba.game, callaway.traits.game,
> establishment.game, grg.game, preference.game,
> asymmetric.preference.game, connect.neighborhood, rewire.edges,
> watts.strogatz.game, lastcit.game, cited.type.game,
> citing.cited.type.game, bipartite.random.game,
> edge.betweenness.community, spinglass.community, walktrap.community,
> edge.betweenness.community.merges, fastgreedy.community,
> community.to.membership, membership, modularity, sizes, algorithm,
> is.hierarchical, merges, cutat, communities, crossing, plot.communities,
> compare, compare.communities, showtrace, code.length, asPhylo, dendPlot,
> create.communities, get.adjacency, get.edgelist, as.directed,
> as.undirected, get.adjlist, get.adjedgelist, igraph.from.graphNEL,
> igraph.to.graphNEL, get.data.frame, power.law.fit, running.mean,
> igraph.sample, srand, read.graph, write.graph, graph.graphdb,
> layout.auto, layout.random, layout.circle, layout.spring,
> layout.kamada.kawai, layout.lgl, layout.fruchterman.reingold.grid,
> layout.sphere, layout.merge, layout.reingold.tilford, layout.norm,
> piecewise.layout, igraph.drl.default, igraph.drl.coarsen,
> igraph.drl.coarsest, igraph.drl.refine, igraph.drl.final, subgraph,
> degree, degree.distribution, diameter, subcomponent, betweenness,
> bibcoupling, cocitation, shortest.paths, minimum.spanning.tree,
> get.shortest.paths, average.path.length, transitivity,
> get.all.shortest.paths, get.diameter, farthest.nodes, constraint,
> page.rank, reciprocity, rewire, graph.density, neighborhood.size,
> neighborhood, graph.neighborhood, graph.coreness, topological.sort,
> girth, is.loop, is.multiple, count.multiple, plot.igraph, tkplot,
> tkplot.close, tkplot.off, tkplot.fit.to.screen, tkplot.reshape,
> tkplot.export.postscript, tkplot.getcoords, tkplot.center,
> tkplot.rotate, tkplot.canvas, tkplot.setcoords, rglplot.igraph, rglplot,
> autocurve.edges, vertex.shapes, add.vertex.shape, igraph.shape.noclip,
> igraph.shape.noplot, cluster.distribution, is.connected,
> decompose.graph, no.clusters, evcent, bonpow, alpha.centrality,
> subgraph.centrality, igraph.arpack.default, igraph.eigen.default,
> revolver.d, revolver.error.d, revolver.ad, revolver.error.ad,
> revolver.ade, revolver.error.ade, revolver.e, revolver.error.e,
> revolver.de, revolver.error.de, revolver.l, revolver.error.l,
> revolver.dl, revolver.error.dl, revolver.el, revolver.error.el,
> revolver.r, revolver.error.r, revolver.ar, revolver.error.ar,
> revolver.di, revolver.error.di, revolver.adi, revolver.error.adi,
> revolver.il, revolver.error.il, revolver.ir, revolver.error.ir,
> revolver.air, revolver.error.air, revolver.d.d, revolver.p.p, evolver.d,
> graph.isoclass, graph.isomorphic, graph.motifs, graph.motifs.est,
> graph.isocreate, graph.motifs.no, graph.isomorphic.vf2,
> graph.subisomorphic.vf2, graph.count.isomorphisms.vf2,
> graph.count.subisomorphisms.vf2, graph.get.isomorphisms.vf2,
> graph.get.subisomorphisms.vf2, graph.disjoint.union, %du%,
> graph.intersection, %s%, graph.union, %u%, graph.difference, %m%,
> graph.complementer, graph.compose, %c%, igraph.par, igraph.options,
> getIgraphOpt, igraphtest, igraph.version, igraph.console,
> .igraph.progress, .igraph.status, graph.mincut, vertex.connectivity,
> edge.connectivity, edge.disjoint.paths, vertex.disjoint.paths,
> graph.adhesion, graph.cohesion, cliques, largest.cliques,
> maximal.cliques, clique.number, independent.vertex.sets,
> largest.independent.vertex.sets, maximal.independent.vertex.sets,
> independence.number, layout.svd, blocks, blockGraphs, cohesion,
> hierarchy, parent, plotHierarchy, exportPajek, maxcohesion, arpack,
> tkigraph, igraphdemo, scg, nexus.get, nexus.list, nexus.info,
> nexus.search, as.igraph, graphlets, graphlets.project, plot.sir,
> time_bins, graph.empty, add.edges, vcount, graph.full.citation,
> graph.lcf, graph.adjlist, graph.full.bipartite, forest.fire.game,
> interconnected.islands.game, static.fitness.game, static.power.law.game,
> k.regular.game, sbm.game, closeness, closeness.estimate,
> betweenness.estimate, edge.betweenness, edge.betweenness.estimate,
> page.rank.old, induced.subgraph, subgraph.edges, path.length.hist,
> simplify, is.dag, is.simple, has.multiple, hub.score, authority.score,
> arpack.unpack.complex, unfold.tree, is.mutual,
> maximum.cardinality.search, is.chordal, graph.knn, graph.strength,
> centralize.scores, centralization.degree, centralization.degree.tmax,
> centralization.betweenness, centralization.betweenness.tmax,
> centralization.closeness, centralization.closeness.tmax,
> centralization.evcent, centralization.evcent.tmax,
> assortativity.nominal, assortativity, assortativity.degree,
> contract.vertices, eccentricity, radius, graph.diversity,
> is.degree.sequence, is.graphical.degree.sequence, graph.bfs, graph.dfs,
> bipartite.projection.size, bipartite.projection, graph.bipartite,
> graph.incidence, get.incidence, bipartite.mapping, graph.laplacian,
> clusters, articulation.points, biconnected.components,
> maximal.cliques.count, layout.star, layout.grid, layout.grid.3d,
> layout.fruchterman.reingold, layout.graphopt, layout.drl,
> layout.sugiyama, layout.mds, layout.bipartite, similarity.jaccard,
> similarity.dice, similarity.invlogweighted, community.le.to.membership,
> mod.matrix, leading.eigenvector.community, label.propagation.community,
> multilevel.community, optimal.community, hrg.fit, hrg.game,
> hrg.dendrogram, hrg.consensus, hrg.predict, hrg.create,
> infomap.community, graphlets.candidate.basis, get.stochastic,
> dyad.census, triad.census, adjacent.triangles, graph.maxflow,
> dominator.tree, stCuts, stMincuts, is.separator, is.minimal.separator,
> minimal.st.separators, minimum.size.separators, cohesive.blocks,
> graph.isoclass.subgraph, graph.isomorphic.34, canonical.permutation,
> permute.vertices, graph.isomorphic.bliss, graph.automorphisms,
> graph.subisomorphic.lad, scgGrouping, scgSemiProjectors, scgNormEps,
> is.matching, is.maximal.matching, maximum.bipartite.matching,
> graph.eigen, sir, convex.hull, revolver.ml.d, revolver.probs.d,
> revolver.ml.de, revolver.probs.de, revolver.ml.ade, revolver.probs.ade,
> revolver.ml.f, revolver.ml.df, revolver.ml.l, revolver.ml.ad,
> revolver.probs.ad, revolver.ml.D.alpha, revolver.ml.D.alpha.a,
> revolver.ml.DE.alpha.a, revolver.ml.AD.alpha.a.beta,
> revolver.ml.AD.dpareto, revolver.ml.AD.dpareto.eval,
> revolver.ml.ADE.alpha.a.beta, revolver.ml.ADE.dpareto,
> revolver.ml.ADE.dpareto.eval, revolver.ml.ADE.dpareto.evalf,
> revolver.probs.ADE.dpareto
> ERROR: lazy loading failed for package ‘adegenet’
> * removing ‘/home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet’
> 
> The downloaded source packages are in
> ‘/tmp/RtmpRguHDL/downloaded_packages’
> Warning message:
> In install.packages("adegenet") :
> installation of package ‘adegenet’ had non-zero exit status
> ////////////////////////////////////////////////////////////////////////////
> ////////////////////////////////////////////////////////////////////////////
> //////////////////////////////////////////////////////////////
-- 
Vojtěch Zeisek
http://trapa.cz/en/

Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/

Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ
http://www.ibot.cas.cz/en/

Czech Republic
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