[adegenet-forum] Problem installation on Ubuntu

[Samuel Knapp]

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
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////