CRAN Package Check Results for Package StAMPP

Last updated on 2014-07-30 22:47:32.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 2.98 40.78 43.76 OK
r-devel-linux-x86_64-debian-gcc 1.2 2.69 40.90 43.59 OK
r-devel-linux-x86_64-fedora-clang 1.2 93.18 OK
r-devel-linux-x86_64-fedora-gcc 1.2 86.19 OK
r-devel-osx-x86_64-clang 1.2 81.96 OK
r-devel-windows-ix86+x86_64 1.2 11.00 71.00 82.00 OK
r-patched-linux-x86_64 1.2 2.74 40.86 43.59 OK
r-patched-solaris-sparc 1.2 499.00 ERROR
r-patched-solaris-x86 1.2 119.60 OK
r-release-linux-ix86 1.2 3.38 52.73 56.10 OK
r-release-linux-x86_64 1.2 2.80 41.65 44.45 OK
r-release-osx-x86_64-mavericks 1.2 OK
r-release-osx-x86_64-snowleopard 1.2 OK
r-release-windows-ix86+x86_64 1.2 13.00 76.00 89.00 OK
r-oldrel-windows-ix86+x86_64 1.2 14.00 104.00 118.00 OK

Check Details

Version: 1.2
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