CRAN Package Check Results for Package AFLPsim

Last updated on 2015-08-05 03:47:53.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3-4 4.69 58.74 63.44 ERROR
r-devel-linux-x86_64-debian-gcc 0.3-4 4.58 58.25 62.83 ERROR
r-devel-linux-x86_64-fedora-clang 0.3-4 136.65 ERROR
r-devel-linux-x86_64-fedora-gcc 0.3-4 123.27 ERROR
r-devel-osx-x86_64-clang 0.3-4 115.02 ERROR
r-devel-windows-ix86+x86_64 0.3-4 26.00 102.00 128.00 ERROR
r-patched-linux-x86_64 0.3-4 4.96 58.06 63.02 ERROR
r-patched-solaris-sparc 0.3-4 789.00 ERROR
r-patched-solaris-x86 0.3-4 184.10 ERROR
r-release-linux-x86_64 0.3-4 4.70 58.74 63.44 ERROR
r-release-osx-x86_64-mavericks 0.3-4 OK
r-release-windows-ix86+x86_64 0.3-4 24.00 96.00 120.00 ERROR
r-oldrel-windows-ix86+x86_64 0.3-4 31.00 171.00 202.00 ERROR

Check Details

Version: 0.3-4
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.demosimhybrid plot.hybridsim
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.3-4
Check: R code for possible problems
Result: NOTE
    bayescan: no visible global function definition for ‘read.table’
    demosimhybrid: no visible global function definition for
     ‘capture.output’
    gscan : p.L: no visible global function definition for ‘qbeta’
    gscan : p.U: no visible global function definition for ‘qbeta’
    gscan : zbinomial: no visible global function definition for
     ‘binom.test’
    gscan: no visible global function definition for ‘p.adjust’
    gscan: no visible global function definition for ‘binom.test’
    hybridize: no visible global function definition for ‘rbinom’
    hybridsim: no visible global function definition for ‘rbeta’
    hybridsim: no visible global function definition for ‘rbinom’
    plot.demosimhybrid: no visible global function definition for ‘layout’
    plot.demosimhybrid: no visible global function definition for ‘par’
    plot.demosimhybrid: no visible global function definition for ‘legend’
    plot.demosimhybrid: no visible global function definition for ‘barplot’
    plot.hybridsim: no visible global function definition for ‘persp’
    plot.hybridsim: no visible global function definition for ‘points’
    plot.hybridsim: no visible global function definition for ‘trans3d’
    plot.hybridsim: no visible global function definition for ‘segments’
    sim2genind: possible error in df2genind(X, pop = pop, missing = NA,
     ploidy = 2, type = "PA"): unused argument (missing = NA)
    Undefined global functions or variables:
     barplot binom.test capture.output layout legend p.adjust par persp
     points qbeta rbeta rbinom read.table segments trans3d
    Consider adding
     importFrom("grDevices", "trans3d")
     importFrom("graphics", "barplot", "layout", "legend", "par", "persp",
     "points", "segments")
     importFrom("stats", "binom.test", "p.adjust", "qbeta", "rbeta",
     "rbinom")
     importFrom("utils", "capture.output", "read.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

Version: 0.3-4
Check: examples
Result: ERROR
    Running examples in ‘AFLPsim-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: sim2genind
    > ### Title: Converting a hybridsim object to a genind object
    > ### Aliases: sim2genind
    > ### Keywords: hybridization simulation
    >
    > ### ** Examples
    >
    > ## simulate F1 hybrids
    > F1hybrids<-hybridsim(Nmarker=100,Na=100,Nb=100,Nf1=30, type="neutral", hybrid="F1")
    ########Neutral hybridization########>
    > ## convert to genind object
    > F1gen<-sim2genind(F1hybrids)
    Error in df2genind(X, pop = pop, missing = NA, ploidy = 2, type = "PA") :
     unused argument (missing = NA)
    Calls: sim2genind -> df2genind
    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

Version: 0.3-4
Check: R code for possible problems
Result: NOTE
    sim2genind: possible error in df2genind(X, pop = pop, missing = NA,
     ploidy = 2, type = "PA"): unused argument (missing = NA)
Flavors: r-devel-osx-x86_64-clang, 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

Version: 0.3-4
Check: R code for possible problems
Result: NOTE
    bayescan: no visible global function definition for 'shortPathName'
    bayescan: no visible global function definition for 'read.table'
    demosimhybrid: no visible global function definition for
     'capture.output'
    gscan : p.L: no visible global function definition for 'qbeta'
    gscan : p.U: no visible global function definition for 'qbeta'
    gscan : zbinomial: no visible global function definition for
     'binom.test'
    gscan: no visible global function definition for 'p.adjust'
    gscan: no visible global function definition for 'binom.test'
    hybridize: no visible global function definition for 'rbinom'
    hybridsim: no visible global function definition for 'rbeta'
    hybridsim: no visible global function definition for 'rbinom'
    plot.demosimhybrid: no visible global function definition for 'layout'
    plot.demosimhybrid: no visible global function definition for 'par'
    plot.demosimhybrid: no visible global function definition for 'legend'
    plot.demosimhybrid: no visible global function definition for 'barplot'
    plot.hybridsim: no visible global function definition for 'persp'
    plot.hybridsim: no visible global function definition for 'points'
    plot.hybridsim: no visible global function definition for 'trans3d'
    plot.hybridsim: no visible global function definition for 'segments'
    sim2genind: possible error in df2genind(X, pop = pop, missing = NA,
     ploidy = 2, type = "PA"): unused argument (missing = NA)
    Undefined global functions or variables:
     barplot binom.test capture.output layout legend p.adjust par persp
     points qbeta rbeta rbinom read.table segments shortPathName trans3d
    Consider adding
     importFrom("grDevices", "trans3d")
     importFrom("graphics", "barplot", "layout", "legend", "par", "persp",
     "points", "segments")
     importFrom("stats", "binom.test", "p.adjust", "qbeta", "rbeta",
     "rbinom")
     importFrom("utils", "capture.output", "read.table", "shortPathName")
    to your NAMESPACE.
Flavor: r-devel-windows-ix86+x86_64