[adegenet-forum] Problem installation on Ubuntu

Jombart, Thibaut t.jombart at imperial.ac.uk
Mon Jul 14 12:52:36 CEST 2014

Makes sense. In general, an 'update.packages(ask=FALSE)' is good policy before installing new stuff. Bear in mind, though, that attached packages won't generally be updated.
From: Samuel Knapp [samuel.k at gmx.de]
Sent: 14 July 2014 11:27
To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] Problem installation on Ubuntu

Hi Thibaut,

I tried to reproduce the problem. Complete removal of the igraph package
and R. Then after installing R, installing adegenet. igraph is then also
installed as dependency and adegenet goes fine as well.

So, I'm guessing that I had either an old or somehow corrupted version
of igraph. When installing adegenet, this old/corrupted version of
igraph could not be loaded properly and thus adegenet could not be

Let's hope that nobody else is experiencing this problem or than at
least finds this threat.


On 14.07.2014 11:51, Jombart, Thibaut wrote:
> Argh, just seeing this one. Well done on nailing it.
> Yep, probably best reporting this to the igraph maintainer. You may not be the only one going through this issue.
> Cheers
> Thibaut
> ________________________________________
> 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 22:06
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] Problem installation on Ubuntu
> I could now narrow down the problem:
> After commenting out the importFrom(igraph,.. [see below] in the
> NAMESPACE file, I could install adegenet without any problem.
> #importFrom(igraph, "graph.data.frame", "V", "V<-", "E", "E<-",
> #         "layout.fruchterman.reingold",
> #         "as.igraph", "plot.igraph", "print.igraph", "graph.adjacency",
> "clusters")
> So, this error must be due to the igraph package. When loading igraph
> with library("igraph") the long error message was also produced. After
> install.packages("igraph"), I can also load it normally and install
> adegenet without commenting out the above.
> Probably this should rather be reported to igraph...
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