CRAN Package Check Results for Package BayHap

Last updated on 2015-08-31 16:51:38.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.1 1.49 22.08 23.57 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.1 1.84 21.70 23.54 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.1 45.25 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.1 43.06 NOTE
r-devel-osx-x86_64-clang 1.0.1 33.77 NOTE
r-devel-windows-ix86+x86_64 1.0.1 6.00 54.00 60.00 NOTE
r-patched-linux-x86_64 1.0.1 2.00 22.94 24.94 NOTE
r-patched-solaris-sparc 1.0.1 289.40 NOTE
r-patched-solaris-x86 1.0.1 63.70 NOTE
r-release-linux-x86_64 1.0.1 2.04 22.38 24.42 NOTE
r-release-osx-x86_64-mavericks 1.0.1 NOTE
r-release-windows-ix86+x86_64 1.0.1 12.00 67.00 79.00 NOTE
r-oldrel-windows-ix86+x86_64 1.0.1 8.00 57.00 65.00 NOTE

Check Details

Version: 1.0.1
Check: dependencies in R code
Result: NOTE
    Unexported object imported by a ':::' call: ‘boa:::boa.getparms’
     See the note in ?`:::` about the use of this operator.
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-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.1
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following functions:
     ‘plotACF’ ‘plotDensity’ ‘plotRmean’ ‘plotTrace’
    Found the platform-specific device:
     ‘x11’
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    bayhapReg: no visible global function definition for ‘terms’
    bayhapReg: no visible global function definition for ‘model.response’
    bayhapReg: no visible global function definition for ‘model.frame’
    bayhapReg: no visible global function definition for ‘var’
    boa.plot.acf.ad: no visible global function definition for ‘acf’
    boa.plot.acf.ad: no visible global function definition for ‘plot’
    boa.plot.acf.ad: no visible global function definition for ‘abline’
    boa.plot.acf.ad: no visible global function definition for ‘par’
    boa.plot.acf.ad: no visible global function definition for ‘legend’
    correl: no visible global function definition for ‘cor’
    genotype: no visible global function definition for ‘na.omit’
    haplo.prior: no visible global function definition for ‘qnorm’
    import: no visible global function definition for ‘read.table’
    plotACF: no visible global function definition for ‘x11’
    plotACF: no visible global function definition for ‘par’
    plotDensity: no visible global function definition for ‘x11’
    plotDensity: no visible global function definition for ‘par’
    plotRmean: no visible global function definition for ‘x11’
    plotRmean: no visible global function definition for ‘par’
    plotTrace: no visible global function definition for ‘x11’
    plotTrace: no visible global function definition for ‘par’
    print.freq: no visible binding for global variable ‘sd’
    print.freq: no visible binding for global variable ‘quantile’
    print.reg: no visible global function definition for ‘sd’
    print.reg: no visible binding for global variable ‘quantile’
    print.reg: no visible global function definition for ‘quantile’
    Undefined global functions or variables:
     abline acf cor legend model.frame model.response na.omit par plot
     qnorm quantile read.table sd terms var x11
    Consider adding
     importFrom("grDevices", "x11")
     importFrom("graphics", "abline", "legend", "par", "plot")
     importFrom("stats", "acf", "cor", "model.frame", "model.response",
     "na.omit", "qnorm", "quantile", "sd", "terms", "var")
     importFrom("utils", "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: 1.0.1
Check: Rd line widths
Result: NOTE
    Rd file 'BayHap-internal.Rd':
     \usage lines wider than 90 characters:
     expectedGenotypes(x, alleles = allele.names(x), ploidy = 2, sort = TRUE, haplotype = FALSE)
    
    These lines will be truncated in the PDF 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-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0.1
Check: compiled code
Result: NOTE
    File ‘BayHap/libs/BayHap.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Object: ‘mcmc.o’
     Found ‘srand’, possibly from ‘srand’ (C)
     Object: ‘mcmc.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See ‘Writing portable packages’ 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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.0.1
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following functions:
     ‘plotACF’ ‘plotDensity’ ‘plotRmean’ ‘plotTrace’
    Found the platform-specific device:
     ‘x11’
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
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

Version: 1.0.1
Check: compiled code
Result: NOTE
    File ‘BayHap/libs/BayHap.so’:
     Found ‘_rand’, possibly from ‘rand’ (C)
     Object: ‘mcmc.o’
     Found ‘_srand’, possibly from ‘srand’ (C)
     Object: ‘mcmc.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-osx-x86_64-clang, r-release-osx-x86_64-mavericks

Version: 1.0.1
Check: R code for possible problems
Result: NOTE
    bayhapReg: no visible global function definition for 'terms'
    bayhapReg: no visible global function definition for 'model.response'
    bayhapReg: no visible global function definition for 'model.frame'
    bayhapReg: no visible global function definition for 'var'
    boa.plot.acf.ad: no visible global function definition for 'acf'
    boa.plot.acf.ad: no visible global function definition for 'plot'
    boa.plot.acf.ad: no visible global function definition for 'abline'
    boa.plot.acf.ad: no visible global function definition for 'par'
    boa.plot.acf.ad: no visible global function definition for 'legend'
    correl: no visible global function definition for 'cor'
    genotype: no visible global function definition for 'na.omit'
    haplo.prior: no visible global function definition for 'qnorm'
    import: no visible global function definition for 'read.table'
    plotACF: no visible global function definition for 'x11'
    plotACF: no visible global function definition for 'par'
    plotDensity: no visible global function definition for 'x11'
    plotDensity: no visible global function definition for 'par'
    plotRmean: no visible global function definition for 'x11'
    plotRmean: no visible global function definition for 'par'
    plotTrace: no visible global function definition for 'x11'
    plotTrace: no visible global function definition for 'par'
    print.freq: no visible binding for global variable 'sd'
    print.freq: no visible binding for global variable 'quantile'
    print.reg: no visible global function definition for 'sd'
    print.reg: no visible binding for global variable 'quantile'
    print.reg: no visible global function definition for 'quantile'
    Undefined global functions or variables:
     abline acf cor legend model.frame model.response na.omit par plot
     qnorm quantile read.table sd terms var x11
    Consider adding
     importFrom("grDevices", "x11")
     importFrom("graphics", "abline", "legend", "par", "plot")
     importFrom("stats", "acf", "cor", "model.frame", "model.response",
     "na.omit", "qnorm", "quantile", "sd", "terms", "var")
     importFrom("utils", "read.table")
    to your NAMESPACE.
Flavor: r-devel-windows-ix86+x86_64

Version: 1.0.1
Check: compiled code
Result: NOTE
    File 'BayHap/libs/i386/BayHap.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'mcmc.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'mcmc.o'
    File 'BayHap/libs/x64/BayHap.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'mcmc.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'mcmc.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64