CRAN Package Check Results for Package BayHap

Last updated on 2015-07-08 05:47:29.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.1 1.52 23.11 24.62 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.1 2.22 21.64 23.86 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.1 43.77 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.1 42.03 NOTE
r-devel-osx-x86_64-clang 1.0.1 33.18 NOTE
r-devel-windows-ix86+x86_64 1.0.1 7.00 45.00 52.00 NOTE
r-patched-linux-x86_64 1.0.1 1.98 22.07 24.05 NOTE
r-patched-solaris-sparc 1.0.1 275.00 NOTE
r-patched-solaris-x86 1.0.1 61.70 NOTE
r-release-linux-x86_64 1.0.1 1.96 22.12 24.08 NOTE
r-release-osx-x86_64-mavericks 1.0.1 NOTE
r-release-windows-ix86+x86_64 1.0.1 8.00 49.00 57.00 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
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
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