CRAN Package Check Results for Package polysat

Last updated on 2015-08-01 03:49:05.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4-0 1.87 58.62 60.49 ERROR
r-devel-linux-x86_64-debian-gcc 1.4-0 1.79 55.78 57.57 ERROR
r-devel-linux-x86_64-fedora-clang 1.4-0 118.85 ERROR
r-devel-linux-x86_64-fedora-gcc 1.4-0 112.04 ERROR
r-devel-osx-x86_64-clang 1.4-0 99.71 ERROR
r-devel-windows-ix86+x86_64 1.4-0 10.00 99.00 109.00 ERROR
r-patched-linux-x86_64 1.4-0 1.76 56.03 57.79 ERROR
r-patched-solaris-sparc 1.4-0 721.60 ERROR
r-patched-solaris-x86 1.4-0 138.40 ERROR
r-release-linux-x86_64 1.4-0 1.75 56.30 58.05 ERROR
r-release-osx-x86_64-mavericks 1.4-0 OK
r-release-windows-ix86+x86_64 1.4-0 9.00 103.00 112.00 ERROR
r-oldrel-windows-ix86+x86_64 1.4-0 6.00 52.00 58.00 ERROR

Check Details

Version: 1.4-0
Check: R code for possible problems
Result: NOTE
    .unal1loc: no visible global function definition for ‘stack’
    Bruvo.distance: no visible global function definition for ‘combn’
    alleleCorrelations: no visible global function definition for
     ‘fisher.test’
    alleleCorrelations: no visible global function definition for ‘kmeans’
    alleleCorrelations: no visible global function definition for ‘cutree’
    alleleCorrelations: no visible global function definition for ‘hclust’
    alleleCorrelations: no visible global function definition for ‘as.dist’
    mergeAlleleAssignments: no visible global function definition for
     ‘kmeans’
    read.GeneMapper: no visible global function definition for ‘read.table’
    read.SPAGeDi: no visible global function definition for ‘read.table’
    read.STRand: no visible global function definition for ‘read.table’
    read.Structure: no visible global function definition for ‘read.table’
    write.GeneMapper: no visible global function definition for
     ‘write.table’
    write.SPAGeDi: no visible global function definition for ‘write.table’
    write.Structure: no visible global function definition for
     ‘write.table’
    write.freq.SPAGeDi: no visible global function definition for
     ‘write.table’
    editGenotypes,genambig: no visible global function definition for
     ‘edit’
    editGenotypes,genbinary: no visible global function definition for
     ‘edit’
    estimatePloidy,genambig: no visible global function definition for
     ‘edit’
    estimatePloidy,genbinary: no visible global function definition for
     ‘edit’
    Undefined global functions or variables:
     as.dist combn cutree edit fisher.test hclust kmeans read.table stack
     write.table
    Consider adding
     importFrom("stats", "as.dist", "cutree", "fisher.test", "hclust",
     "kmeans")
     importFrom("utils", "combn", "edit", "read.table", "stack",
     "write.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 1.4-0
Check: examples
Result: ERROR
    Running examples in ‘polysat-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: gendata.to.genind
    > ### Title: Convert Data to genind Format
    > ### Aliases: gendata.to.genind
    > ### Keywords: manip
    >
    > ### ** Examples
    >
    > # create a "genambig" object
    > mydata <- new("genambig", samples=c("a","b","c","d"), loci=c("e","f"))
    > PopNames(mydata) <- c("G","H")
    > PopInfo(mydata) <- c(1,1,2,2)
    > mydata <- reformatPloidies(mydata, output="one")
    > Ploidies(mydata) <- 3
    > Genotypes(mydata, loci="e") <- list(c(100),c(100,102),
    + c(98,102,104),c(102,106))
    > Genotypes(mydata, loci="f") <- list(c(200,202,204),Missing(mydata),
    + c(210,212),c(204,210,214))
    >
    > # convert to "genind"
    > mydata2 <- gendata.to.genind(mydata)
    > mydata2@tab
     e-98 e-100 e-102 e-104 e-106 f-200 f-202 f-204 f-210 f-212 f-214
    a 0 1 0 0 0 1 1 1 0 0 0
    b 0 1 1 0 0 NA NA NA NA NA NA
    c 1 0 1 1 0 0 0 0 1 1 0
    d 0 0 1 0 1 0 0 1 1 0 1
    > mydata2@loc.names
    Error: no slot of name "loc.names" for this object of class "genind"
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64