[BioC] GeneticsPed Pedigree object creation error: recursive indexing failed at level 2

[Dan Tenenbaum]

CC'ing GeneticsPed maintainer.

On Sun, Jul 21, 2013 at 12:56 PM, Liz Hare <doggene at earthlink.net> wrote:
> Hello,
>
> I'm trying to make a Pedigree object in GeneticsPed.
>
> Data in test2.csv:
>
> id,sire,dam
> 1,,
> 2,,
> 3,,
> 4,,
> 5,1,2
> 6,3,4
> 7,5,6
> 8,5,6
>
> R session:
>
>> tp <- read.csv("test2.csv", header=TRUE)
>> ped.1 <- Pedigree(ped, subject = tp$id, ascendant = c("sire", "dam"))
> Error in .subset2(x, i, exact = exact) :
>   recursive indexing failed at level 2
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GeneticsPed_1.18.0 genetics_1.3.8     mvtnorm_0.9-9995   MASS_7.3-23
> [5] gtools_3.0.0       combinat_0.0-8     gdata_2.13.2
>
> loaded via a namespace (and not attached):
> [1] compiler_2.15.1 tools_2.15.1
>
> ==============================================
>
> I also had this problem with R 3.0.1 and GeneticsPed 1.22.0 in 64-bit
> Windows. I've tried it with other pedigrees and it doesn't work there,
> either.
>
> I have read the package documentation and searched the Bioconductor site,
> and not found anything that appears to apply to this situation.
>
> Thanks for any ideas!
>
> Liz
>
> --
> Liz Hare PhD
> Dog Genetics LLC
> doggene at earthlink.net
> http://www.doggenetics.com
>
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