CRAN Package Check Results for Package StAMPP

Last updated on 2017-03-28 15:48:38.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4 4.46 64.79 69.25 OK
r-devel-linux-x86_64-debian-gcc 1.4 4.70 61.26 65.95 OK
r-devel-linux-x86_64-fedora-clang 1.4 134.80 OK --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.4 135.29 OK --no-stop-on-test-error
r-devel-macos-x86_64-clang 1.4 104.79 OK --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.4 17.00 112.00 129.00 OK
r-patched-linux-x86_64 1.4 4.62 61.77 66.39 OK
r-patched-solaris-sparc 1.4 797.40 ERROR
r-patched-solaris-x86 1.4 206.20 OK
r-release-linux-x86_64 1.4 4.50 58.01 62.51 OK
r-release-osx-x86_64-mavericks 1.4 OK
r-release-windows-ix86+x86_64 1.4 19.00 98.00 117.00 OK
r-oldrel-windows-ix86+x86_64 1.4 15.00 117.00 132.00 OK

Check Details

Version: 1.4
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 7800000, cause 'memory not mapped'
    
    Traceback:
     1: .C("binIntToBytes", vecSnp, length(vecSnp), vecRaw, nbBytes, PACKAGE = "adegenet")
     2: .bin2raw(temp)
     3: initialize(value, ...)
     4: initialize(value, ...)
     5: new("SNPbin", as.integer(input$gen[i, ]))
     6: FUN(X[[i]], ...)
     7: lapply(1:nrow(input$gen), function(i) new("SNPbin", as.integer(input$gen[i, ])))
     8: .local(.Object, ...)
     9: initialize(value, ...)
    10: initialize(value, ...)
    11: new("genlight", data, parallel = FALSE)
    12: stampp2genlight(potato.freq, TRUE)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-sparc