• using R version 2.8.0 Under development (unstable) (2008-07-01 r46019)
  • using session charset: UTF-8
  • checking for file 'Geneland/DESCRIPTION' ... OK
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  • this is package 'Geneland' version '2.0.12'
  • checking package dependencies ... OK
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  • checking if this is a source package ... OK
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  • checking whether package 'Geneland' can be installed ... WARNING
    Found the following significant warnings:
    Warning: Deleted feature: End expression in DO loop at (1) must be integer
    See http://www.r-project.org/nosvn/R.check/r-devel-linux-ix86/Geneland-00install.html for details.
  • checking package directory ... OK
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  • checking for portable file names ... OK
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  • checking for sufficient/correct file permissions ... OK
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  • checking DESCRIPTION meta-information ... OK
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  • checking top-level files ... OK
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  • checking index information ... OK
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  • checking package subdirectories ... OK
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  • checking R files for non-ASCII characters ... OK
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  • checking R files for syntax errors ... OK
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  • checking whether the package can be loaded ... OK
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  • checking whether the package can be loaded with stated dependencies ... OK
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  • checking for unstated dependencies in R code ... OK
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  • checking S3 generic/method consistency ... OK
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  • checking replacement functions ... OK
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  • checking foreign function calls ... OK
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  • checking R code for possible problems ... NOTE
    Geneland.GUI : run : RunmcmcFmodel: no visible binding for '<<-'
    assignment to ‘probs’
    Geneland.GUI : run : RunmcmcFmodel: no visible binding for '<<-'
    assignment to ‘pops’
    Geneland.GUI : run : RunmcmcFmodel : Sort: no visible binding for
    global variable ‘probs’
    Geneland.GUI : run : RunmcmcFmodel : Sort: no visible binding for
    global variable ‘pops’
    Geneland.GUI : run : RunmcmcFmodel : Reburn: no visible binding for
    '<<-' assignment to ‘probs’
    Geneland.GUI : run : RunmcmcFmodel : Reburn: no visible binding for
    '<<-' assignment to ‘pops’
    Geneland.GUI : run : RunmcmcFmodel : Reburn: no visible binding for
    global variable ‘pops’
    Geneland.GUI : run : RunmcmcFmodel : Reburn: no visible binding for
    global variable ‘probs’
    Geneland.GUI : run : RunmcmcFmodel: no visible binding for global
    variable ‘pops’
    Geneland.GUI : run : RunmcmcFmodel: no visible binding for global
    variable ‘probs’
  • checking Rd files ... OK
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  • checking Rd cross-references ... OK
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  • checking for missing documentation entries ... OK
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  • checking for code/documentation mismatches ... OK
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  • checking Rd \usage sections ... OK
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  • checking line endings in C/C++/Fortran sources/headers ... OK
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  • checking line endings in Makefiles ... OK
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  • checking for portable use of $BLAS_LIBS ... OK
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  • creating Geneland-Ex.R ... OK
    •
  • checking examples ... ERROR
    Running examples in 'Geneland-Ex.R' failed.
    The error most likely occurred in:

    > ### * simdata
    >
    > flush(stderr()); flush(stdout())
    >
    > ### Name: simdata
    > ### Title: Simulation of georeferenced genotypes under an IBD + barrier
    > ### model
    > ### Aliases: simdata
    >
    >
    > ### ** Examples
    >
    > dataset <- simdata(nindiv=100,
    + number.nuclei=10,
    + allele.numbers=rep(5,3),
    + model="stable",
    + IBD=TRUE,
    + alpha=1,
    + beta=1,
    + gamma=1,
    + npop=3,
    + give.tess.grid=TRUE,
    + give.freq.grid=TRUE,
    + npix=c(10,10),
    + comp.Fst=TRUE,
    + comp.Dsigma2=TRUE,
    + comp.diff=TRUE,
    + width=0.1,
    + plot.pairs.borders=TRUE)
    [1] "Calling GaussRF"
    *********************************************
    [1] "End of GaussRF"
    [1] "data arranged"
    [1] "freq. stored"
    [1] "genotyped sampled"
    [1] "Computing Fstat"
    [1] "End of call to Fstat"
    [1] "Computing IBD index Dsigma^2"
    [1] "End of computation of IBD index Dsigma^2"
    Error in get(getOption("device")) : invalid first argument
    Calls: simdata -> get
    Execution halted