[adegenet-forum] error

Sébastien Puechmaille s.puechmaille at gmail.com
Wed Mar 30 17:59:55 CEST 2011


Hi Mariana,

I guess this is because you did not install the dependencies (see FAQ N. 2,
section 'contacts/FAQ' of the Adegenet website):
Typing this should solve the problem:

install.packages("adegenet", dep=TRUE)

Sebastien.

On 29 March 2011 09:04, Mariana Varela <mv307 at cam.ac.uk> wrote:

> Hi, I am trying to implement the seqTrack function and I get this error
> when I require adegenet:
> Failed with error:  ‘no item called "newtable" on the search list’
> In addition: Warning messages:
> 1: In objects(newtable, all.names = TRUE) :
>  ‘newtable’ converted to character string
> 2: In objects(newtable, all.names = TRUE) :
>  ‘newtable’ converted to character string
>
> then I get this when I try to execute seqTract:
>
> Error: could not find function "seqTrack"
>
> this is my code:
>
> seq <- read.dna("106.fasta", format = "fasta", as.matrix = FALSE)
>
> seq.dist <- dist.dna(seq, model = "N")
>
> print(seq.dist)
>
> seq.names <- names(seq)
> numseq <- length(seq.names)
> seq.times <- rep(0, numseq)
> seq.times[grep("W2", seq.names)] <- 2 * 7
> seq.times[grep("W12", seq.names)] <- 12 * 7
> seq.dates <- rep(as.POSIXct("2011-01-01"), numseq)
> seq.dates <- seq.dates + 60 * 60 * 24 * seq.times
>
> seq.st <- seqTrack(as.matrix(seq.dist), seq.names, seq.dates)
> seq.st
>
> I have this R version:
> R 2.12.1 GUI 1.35 Leopard build 32-bit (5665)
>
> Any suggestions?
>
> Many thanks
>
> Mariana Varela, DVM, PhD.
> University of Cambridge
> Department of Veterinary Medicine
> Madingley Road
> Cambridge
> CB3 0ES
> email: mv307 at cam.ac.uk
> tel: +44 (1223) 339042
>
>
>
> _______________________________________________
> 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
>
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