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Thanks Vojtěch<i>,</i><br>
<div class="moz-cite-prefix"><br>
I normally install packages through the normal CRAN server. And
all other packages work fine.<br>
R is installed through the Ubuntu repo. But there is only a
limited collection of other R packages (not including adegenet).<br>
Also "<i>install.packages("adegenet", dependencies=TRUE)</i><i>"</i>
produces the same error.<i><br>
</i><br>
Under linux, the source is downloaded and compiled during
installation (see the lines starting with gcc). This seems to go
all fine.<br>
Also when downloading the "<a
href="http://cran.r-project.org/src/contrib/adegenet_1.4-2.tar.gz">adegenet_1.4-2.tar.gz"</a>
file and installing that, the same error occurs.<br>
<br>
I have no idea, what else I could try.<br>
<br>
Other ideas?<br>
<br>
<br>
On 12.07.2014 20:57,
<a class="moz-txt-link-abbreviated" href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">adegenet-forum-request@lists.r-forge.r-project.org</a> wrote:<br>
</div>
<blockquote
cite="mid:mailman.1271.1405191473.1134.adegenet-forum@lists.r-forge.r-project.org"
type="cite">
<pre wrap="">Date: Sat, 12 Jul 2014 20:57:32 +0200
From: Vojt?ch Zeisek <a class="moz-txt-link-rfc2396E" href="mailto:vojta@trapa.cz"><vojta@trapa.cz></a>
To: <a class="moz-txt-link-abbreviated" href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>
Subject: Re: [adegenet-forum] Problem installation on Ubuntu
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:1823086.272X4meaJe@veles.site"><1823086.272X4meaJe@veles.site></a>
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 <a class="moz-txt-link-freetext" href="https://help.ubuntu.com/community/CompilingSoftware">https://help.ubuntu.com/community/CompilingSoftware</a> Might
be You can try to install the package directly from Ubuntu binary package
repository, see <a class="moz-txt-link-freetext" href="http://cran.r-project.org/bin/linux/ubuntu/README">http://cran.r-project.org/bin/linux/ubuntu/README</a> 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):
</pre>
<blockquote type="cite">
<pre wrap="">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
'<a class="moz-txt-link-freetext" href="http://ftp.igh.cnrs.fr/pub/CRAN/src/contrib/adegenet_1.4-2.tar.gz">http://ftp.igh.cnrs.fr/pub/CRAN/src/contrib/adegenet_1.4-2.tar.gz</a>'
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
////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////
</pre>
</blockquote>
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