[adegenet-forum] Problem installation on Ubuntu

[Jombart, Thibaut]

Hi there, 

I suspect a problem specific to your settings, as CRAN says adegenet is relatively well-behaved these days:
http://cran.r-project.org/web/checks/check_results_adegenet.html

The error message you report looks like a possible broken dependency with igraph. Can you install this package and load it? 

It may also be worth checking that you're not loading any related library in your .Rprofile.

Cheers
Thibaut


==============================
Dr Thibaut Jombart
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
Norfolk Place, London W2 1PG, UK
Tel. : 0044 (0)20 7594 3658
http://sites.google.com/site/thibautjombart/
http://sites.google.com/site/therepiproject/
http://adegenet.r-forge.r-project.org/
Twitter: @thibautjombart
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Samuel Knapp [samuel.k at gmx.de]
Sent: 12 July 2014 21:21
To: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] Problem installation on Ubuntu

Thanks Vojtěch,

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<mailto: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><mailto:vojta at trapa.cz>
To: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: Re: [adegenet-forum] Problem installation on Ubuntu
Message-ID: <1823086.272X4meaJe at veles.site><mailto: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
////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////