[adegenet-forum] installation problem

[Federico Calboli]

R 2.13.1 is out of date (current version is 2.15.1).  The first thing you should do is to upgrade the whole R installation.

BW

F


On 5 Aug 2012, at 22:19, Rute Fonseca <rute.r.da.fonseca at gmail.com> wrote:

> Hi, I'm trying to install adegenet on Ubuntu, R version 2.13.1 (2011-07-08) and I get the following error message:
> 
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> > install.packages("adegenet_1.3-4.tar.gz", dep = TRUE) 
> Installing package(s) into ‘/usr/local/lib/R/site-library’
> (as ‘lib’ is unspecified)
> inferring 'repos = NULL' from the file name
> * installing *source* package ‘adegenet’ ...
> ** libs
> gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c GLfunctions.c -o GLfunctions.o
> gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c adesub.c -o adesub.o
> gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c monmonier-utils.c -o monmonier-utils.o
> gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c sharedAll.c -o sharedAll.o
> gcc -I/usr/share/R/include      -fpic  -std=gnu99 -O3 -pipe  -g -c snpbin.c -o snpbin.o
> gcc -shared -o adegenet.so GLfunctions.o adesub.o monmonier-utils.o sharedAll.o snpbin.o -L/usr/lib/R/lib -lR
> installing to /usr/local/lib/R/site-library/adegenet/libs
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> 
> Attaching package: 'ade4'
> 
> The following object(s) are masked from 'package:base':
> 
>     within
> 
> Error in setGeneric(f, where = where) : 
>   must supply a function skeleton, explicitly or via an existing function
> Error : unable to load R code in package 'adegenet'
> ERROR: lazy loading failed for package ‘adegenet’
> * removing ‘/usr/local/lib/R/site-library/adegenet’
> Warning message:
> In install.packages("adegenet_1.3-4.tar.gz", dep = TRUE) :
>   installation of package 'adegenet_1.3-4.tar.gz' had non-zero exit status
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> 
> Can you help me with this? Thanks :)
> 
> Cheers
> Rute
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum

--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com