[adegenet-forum] Problem installation on Ubuntu

[Samuel Knapp]

Thanks Vojte(ch/,/

I normally install packages through the normal CRAN server. And all 
other packages work fine.
R is installed through the Ubuntu repo. But there is only a limited 
collection of other R packages (not including adegenet).
Also "/install.packages("adegenet", dependencies=TRUE)//"/ produces the 
same error./
/
Under linux, the source is downloaded and compiled during installation 
(see the lines starting with gcc). This seems to go all fine.
Also when downloading the "adegenet_1.4-2.tar.gz" 
<http://cran.r-project.org/src/contrib/adegenet_1.4-2.tar.gz> file and 
installing that, the same error occurs.

I have no idea, what else I could try.

Other ideas?


On 12.07.2014 20:57, adegenet-forum-request at lists.r-forge.r-project.org 
wrote:
> Date: Sat, 12 Jul 2014 20:57:32 +0200
> From: Vojt?ch Zeisek <vojta at trapa.cz>
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] Problem installation on Ubuntu
> Message-ID: <1823086.272X4meaJe at veles.site>
> Content-Type: text/plain; charset="utf-8"
>
> 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,
> Vojt?ch
>
> Dne So 12. ?ervence 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
>> ////////////////////////////////////////////////////////////////////////////
>> ////////////////////////////////////////////////////////////////////////////
>> //////////////////////////////////////////////////////////////

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