[adegenet-forum] Loading problem adegenet_1.2-8, Mac (R64)

[Jombart, Thibaut]

Hi there,

this is FAQ 4:
# 4: Loading adegenet fails with this error (R >= 2.13.0):
Error in as.environment(pos) : no item called "newtable" on the search list
This is because the package 'graph', on which adegenet depends, has been removed from CRAN. You need to install graph from bioconductor first, and then install adegenet:

source("http://bioconductor.org/biocLite.R")
biocLite("graph")
install.packages("adegenet", dep=TRUE)


Cheers

Thibaut
________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Martin van der Meer [martinhvandermeer at gmail.com]
Sent: 26 May 2011 05:17
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] Loading problem adegenet_1.2-8, Mac (R64)

Hi

I can seem to load up adegenet v1.2-8 on R64. It comes up with the following errors:

[History restored from /Users/jc216923/.Rapp.history]

Warning: dependencies ‘hierfstat’, ‘graph’ are not available
trying URL 'http://cran.ms.unimelb.edu.au/bin/macosx/leopard/contrib/2.13/adegenet_1.2-8.tgz'
Content type 'application/x-tar' length 3046842 bytes (2.9 Mb)
opened URL
==================================================
downloaded 2.9 Mb


The downloaded packages are in
    /var/folders/RU/RUdQ1Y1lEcamHshypf82kLM8L+s/-Tmp-//RtmpYi0SS0/downloaded_packages
Loading required package: MASS
   ==========================
    adegenet 1.2-8 is loaded
   ==========================

 - to start, type '?adegenet'
 - to browse adegenet website, type 'adegenetWeb()'
 - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>


Error in as.environment(pos) :
  no item called "newtable" on the search list
In addition: Warning message:
In objects(newtable, all.names = TRUE) :
  ‘newtable’ converted to character string
Error in as.environment(pos) :
  no item called "newtable" on the search list
In addition: Warning message:
In objects(newtable, all.names = TRUE) :
  ‘newtable’ converted to character string
starting httpd help server ... done


I then tried:

> install.packages("adegenet", dep=TRUE)
Installing package(s) into ‘/Users/jc216923/Library/R/2.13/library’
(as ‘lib’ is unspecified)
Warning: dependencies ‘hierfstat’, ‘graph’ are not available
trying URL 'http://cran.ms.unimelb.edu.au/bin/macosx/leopard/contrib/2.13/adegenet_1.2-8.tgz'
Content type 'application/x-tar' length 3046842 bytes (2.9 Mb)
opened URL
==================================================
downloaded 2.9 Mb


The downloaded packages are in
    /var/folders/RU/RUdQ1Y1lEcamHshypf82kLM8L+s/-Tmp-//RtmpYi0SS0/downloaded_packages


But its still not being able to load.

Please can someone suggest a solution for a Mac OS system.

cheers
Martin

--
Martin van der Meer
PhD candidate
Molecular Ecology and Evolutionary Laboratory
Australian Tropical Sciences and Innovation Precinct
School of Marine and Tropical Biology
James Cook University
Townsville
Australia

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