[adegenet-forum] problems loading adegenet

Jombart, Thibaut t.jombart at imperial.ac.uk
Wed Jun 1 12:00:24 CEST 2011


No probs
Cheers
Thibaut

________________________________
From: Alastair Potts [potts.a at gmail.com]
Sent: 01 June 2011 10:57
To: Jombart, Thibaut
Cc: adegenet-forum at r-forge.wu-wien.ac.at
Subject: Re: [adegenet-forum] problems loading adegenet

It works!!! Thank you very much! Didn't think to look under the FAQ section - will do in future.
Cheers,
Alastair


On 2011/06/01 11:37 AM, Jombart, Thibaut wrote:
Dear Alastair,

are you sure this is not 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"<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<mailto:adegenet-forum-bounces at r-forge.wu-wien.ac.at> [adegenet-forum-bounces at r-forge.wu-wien.ac.at<mailto:adegenet-forum-bounces at r-forge.wu-wien.ac.at>] on behalf of Alastair Potts [potts.a at gmail.com<mailto:potts.a at gmail.com>]
Sent: 01 June 2011 10:34
To: adegenet-forum at r-forge.wu-wien.ac.at<mailto:adegenet-forum at r-forge.wu-wien.ac.at>
Subject: [adegenet-forum] problems loading adegenet

Hi All,
I have read the posts and followed the advice surrounding the problems with loading the adegenet package. But I am still getting the familiar error:
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

Now adegenet was working fine on my R 2.12.2. Then I (stupidly?) updated all my packages. All of a sudden - this error pops up. I tracked it down to the MASS package - this now requires a minimum R version of R 2.13 (wowsers, that sure was fast).
I downloaded R 2.13 (over my very slow internet) - and installed MASS_7.3-13.zip and adegenet_1.2-8.zip while running R 2.13 with administrator privileges (#$I*^# Vista) - and I still get the above error.

So, I think there may be problems for any new users trying to install adegenet. If you are using R 2.12, I suggest you don't update your MASS package anytime soon.

Any help would be greatly appreciated.

Cheers,
Alastair








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Alastair Potts
PhD candidate
Botany Department
University of Cape Town
Alastair.Potts at uct.ac.za<mailto:Alastair.Potts at uct.ac.za> or potts.a at gmail.com<mailto:potts.a at gmail.com>
University Private Bag, Rondebosch 7700, South Africa
or
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Cell: 082 491-7275
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