[adegenet-forum] Importing data

[Jombart, Thibaut]

Hello,

please see my post on the forum from yesterday; this is now FAQ #4 on the website:

# 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)

It should be fixed in the next release.

Cheers

Thibaut


--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Cheng-Hua Huang [arhua at ufl.edu]
Sent: 16 May 2011 19:23
To: adegenet-forum at r-forge.wu-wien.ac.at
Cc: arhuahuang at gmail.com
Subject: [adegenet-forum] Importing data

Dear adegenet users,

I am a beginner of Adegenet and have been playing around how to import my Struture and Genepop files. However, I am stuck here because I cannot import my files for DAPC. I appreciate if anyone could helps this out. Thank you in advance. My questions are listed as follow:

1. After loading MASS, Ade4, I loaded the Adegenet package (either 1.3.0 or 1.2.8). R. 2.13.0 shows the following message. How do I need to do to fix this problem?

   ==========================
    adegenet 1.3-0 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


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

2. I used “Change dir” to direct R to read files in a folder and then used following commands to import files.
obj <- import2genind ("structure.str") or
obj <- read.structure ("structure.str", package="adegenet", onerowperind=TRUE,n.ind=85, n.loci=10, col.lab=1, col.pop=3,ask=true)

But R shows “Error: could not find function "import2genind"” and Error: could not find function "read.structure""

Thank you for your time and help.

Regards,

Arhua

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20110517/9315b884/attachment.htm>