Last updated on 2014-11-24 23:47:16.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3 | 2.56 | 40.45 | 43.01 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3 | 2.52 | 38.32 | 40.84 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.3 | 90.78 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3 | 85.12 | OK | |||
| r-devel-osx-x86_64-clang | 1.3 | 82.13 | OK | |||
| r-devel-windows-ix86+x86_64 | 1.3 | 12.00 | 69.00 | 81.00 | OK | |
| r-patched-linux-x86_64 | 1.3 | 2.72 | 39.29 | 42.01 | OK | |
| r-patched-solaris-sparc | 1.3 | 445.90 | ERROR | |||
| r-patched-solaris-x86 | 1.3 | 120.60 | OK | |||
| r-release-linux-ix86 | 1.3 | 3.21 | 49.80 | 53.02 | OK | |
| r-release-linux-x86_64 | 1.3 | 2.74 | 40.90 | 43.65 | OK | |
| r-release-osx-x86_64-mavericks | 1.3 | OK | ||||
| r-release-osx-x86_64-snowleopard | 1.3 | OK | ||||
| r-release-windows-ix86+x86_64 | 1.3 | 15.00 | 74.00 | 89.00 | OK | |
| r-oldrel-windows-ix86+x86_64 | 1.3 | 13.00 | 73.00 | 86.00 | OK |
Version: 1.3
Check: examples
Result: ERROR
Running examples in ‘StAMPP-Ex.R’ failed
The error most likely occurred in:
> ### Name: StAMPP-package
> ### Title: Statistical Analysis of Mixed Ploidy Populations
> ### Aliases: StAMPP-package StAMPP
> ### Keywords: package
>
> ### ** Examples
>
> # import genotype data and convert to allele frequecies
> data(potato.mini, package="StAMPP")
> potato.freq <- stamppConvert(potato.mini, "r")
>
> # Calculate genetic distance between populations
> potato.D.pop <- stamppNeisD(potato.freq, TRUE)
>
> # Calculate genetic distance between individuals
> potato.D.ind <- stamppNeisD(potato.freq, FALSE)
>
> # Calculate AMOVA
> stamppAmova(potato.D.ind, potato.freq, 100)
Analysis of Molecular Variance
Call: amova(formula = dist ~ pop.names, nperm = perm)
SSD MSD df
pop.names 0.10701827 0.053509133 2
Error 0.01204481 0.004014937 3
Total 0.11906308 0.023812616 5
Variance components:
sigma2 P.value
pop.names 0.0247471 0.0495
Error 0.0040149
Variance coefficients:
a
2
>
> # Export the genetic distance matrix in Phylip format
> stamppPhylip(potato.D.pop, file="potato_distance.txt")
>
> # Calculate pairwise Fst values between each population
> potato.fst <- stamppFst(potato.freq, 100, 95, 1)
>
> # Calculate genomic relationship values between each individual
> potato.gmat <- stamppGmatrix(potato.freq)
>
> # Convert allele frequency genotype data frame to a genlight object for use in other packages
> potato.genlight <- stampp2genlight(potato.freq, TRUE)
*** caught segfault ***
address 3000000, cause 'memory not mapped'
Flavor: r-patched-solaris-sparc