CRAN Package Check Results for Package StAMPP

Last updated on 2014-12-21 23:47:12.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3 2.64 39.54 42.18 OK
r-devel-linux-x86_64-debian-gcc 1.3 2.53 38.79 41.32 OK
r-devel-linux-x86_64-fedora-clang 1.3 91.15 OK
r-devel-linux-x86_64-fedora-gcc 1.3 85.62 OK
r-devel-osx-x86_64-clang 1.3 80.83 OK
r-devel-windows-ix86+x86_64 1.3 12.00 70.00 82.00 OK
r-patched-linux-x86_64 1.3 2.64 40.38 43.03 OK
r-patched-solaris-sparc 1.3 445.90 ERROR
r-patched-solaris-x86 1.3 121.70 OK
r-release-linux-ix86 1.3 3.10 49.84 52.94 OK
r-release-linux-x86_64 1.3 2.72 39.69 42.42 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 13.00 70.00 83.00 OK
r-oldrel-windows-ix86+x86_64 1.3 15.00 78.00 93.00 OK

Check Details

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