[adegenet-forum] problems loading adegenet

[Alastair Potts]

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")
> 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 Alastair 
> Potts [potts.a at gmail.com]
> *Sent:* 01 June 2011 10:34
> *To:* 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
>
>
>
>
>
>
>
>
> -- 
> -----------------------------------------------------------------
> Alastair Potts
> PhD candidate
> Botany Department
> University of Cape Town
> Alastair.Potts at uct.ac.za or potts.a at gmail.com
> University Private Bag, Rondebosch 7700, South Africa
> or
> PO Box 115, Loxton 6985, South Africa
> Cell: 082 491-7275
> -----------------------------------------------------------------
>
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