CRAN Package Check Results for Package HIest

Last updated on 2017-11-17 21:49:33.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0 0.74 21.62 22.35 NOTE
r-devel-linux-x86_64-debian-gcc 2.0 0.80 21.56 22.36 NOTE
r-devel-linux-x86_64-fedora-clang 2.0 38.71 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0 37.97 NOTE
r-devel-windows-ix86+x86_64 2.0 5.00 70.00 75.00 NOTE
r-patched-linux-x86_64 2.0 0.82 21.37 22.19 NOTE
r-patched-solaris-x86 2.0 47.60 NOTE
r-release-linux-x86_64 2.0 0.78 21.47 22.26 NOTE
r-release-windows-ix86+x86_64 2.0 3.00 73.00 76.00 NOTE
r-release-osx-x86_64 2.0 NOTE
r-oldrel-windows-ix86+x86_64 2.0 4.00 52.00 56.00 NOTE
r-oldrel-osx-x86_64 2.0 NOTE

Check Details

Version: 2.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘nnet’ ‘stats’
     Please remove these calls from your code.
    Package in Depends field not imported from: ‘nnet’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 2.0
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following functions:
     ‘spatial.AD’ ‘spatial.HZ’
    Found the platform-specific device:
     ‘quartz’
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    Cline.fit: no visible global function definition for ‘aggregate’
    Cline.fit: no visible global function definition for ‘na.omit’
    Cline.fit: no visible global function definition for ‘mahalanobis’
    Cline.fit: no visible global function definition for ‘cov’
    Cline.fit: no visible global function definition for ‘pchisq’
    Cline.plot : Beta.p: no visible global function definition for ‘pbeta’
    Cline.plot: no visible global function definition for ‘par’
    Cline.plot: no visible global function definition for ‘plot’
    Cline.plot: no visible global function definition for ‘lines’
    Cline.plot: no visible global function definition for ‘qchisq’
    HIest : HIproposal: no visible global function definition for
     ‘rmultinom’
    HIest: no visible global function definition for ‘optim’
    HIest: no visible global function definition for ‘runif’
    gcline.fn: no visible global function definition for ‘glm’
    gcline.fn: no visible global function definition for ‘logLik’
    gcline.fn: no visible global function definition for ‘multinom’
    gcline.fn : LL.fn: no visible global function definition for ‘dbinom’
    gcline.fn : GR: no visible global function definition for ‘rlnorm’
    gcline.fn : GR: no visible global function definition for ‘rnorm’
    gcline.fn : LL.fn: no visible global function definition for ‘pbeta’
    gcline.fn: no visible global function definition for ‘optim’
    gcline.fn: no visible global function definition for ‘runif’
    longX2: no visible global function definition for ‘pchisq’
    spatial.AD : rbnorm: no visible global function definition for ‘rnorm’
    spatial.AD: no visible global function definition for ‘dist’
    spatial.AD: no visible global function definition for ‘dnorm’
    spatial.AD: no visible global function definition for ‘rpois’
    spatial.AD: no visible global function definition for ‘runif’
    spatial.AD: no visible global function definition for ‘rbinom’
    spatial.AD: no visible global function definition for ‘quartz’
    spatial.AD: no visible global function definition for ‘plot’
    spatial.HZ : rbnorm: no visible global function definition for ‘rnorm’
    spatial.HZ: no visible global function definition for ‘dist’
    spatial.HZ: no visible global function definition for ‘dnorm’
    spatial.HZ: no visible global function definition for ‘rpois’
    spatial.HZ: no visible global function definition for ‘rbinom’
    spatial.HZ: no visible global function definition for ‘quartz’
    spatial.HZ: no visible global function definition for ‘plot’
    threeway : GR: no visible global function definition for ‘rmultinom’
    threeway: no visible global function definition for ‘runif’
    threeway: no visible global function definition for ‘optim’
    Undefined global functions or variables:
     aggregate cov dbinom dist dnorm glm lines logLik mahalanobis multinom
     na.omit optim par pbeta pchisq plot qchisq quartz rbinom rlnorm
     rmultinom rnorm rpois runif
    Consider adding
     importFrom("grDevices", "quartz")
     importFrom("graphics", "lines", "par", "plot")
     importFrom("stats", "aggregate", "cov", "dbinom", "dist", "dnorm",
     "glm", "logLik", "mahalanobis", "na.omit", "optim", "pbeta",
     "pchisq", "qchisq", "rbinom", "rlnorm", "rmultinom",
     "rnorm", "rpois", "runif")
    to your NAMESPACE file.
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-x86, r-release-linux-x86_64

Version: 2.0
Check: Rd line widths
Result: NOTE
    Rd file 'HItest3.Rd':
     \examples lines wider than 100 characters:
     # individuals will have nonzero contributions from each of the
    
    Rd file 'spatial.AD.Rd':
     \examples lines wider than 100 characters:
     # simulate secondary contact by sorting aling the x dimension and assigning parental genotypes on each side of the centerline:
     # selection, inlcuding heterozygote disadvantage at locus 2 and a DM incompatibility between 3 and 4:
     G10 <- spatial.AD(minX,minY,maxX,maxY,XY,Genotypes,beta,sel,mid,h,DM,sigmac,R,M,gens=10,immigrants=TRUE)
    
    Rd file 'spatial.HZ.Rd':
     \examples lines wider than 100 characters:
     # simulate secondary contact by sorting aling the x dimension and assigning parental genotypes on each side of the centerline:
     # selection, inlcuding heterozygote disadvantage at locus 2 and a DM incompatibility between 3 and 4:
     G10 <- spatial.HZ(minX,minY,maxX,maxY,XY,Genotypes,beta,sel,mid,h,DM,sigmad,sigmac,sigmam,R,M,gens=10,immigrants=TRUE)
    
    Rd file 'thirdclass.Rd':
     \examples lines wider than 100 characters:
     # individuals will have nonzero contributions from each of the
    
    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: 2.0
Check: R code for possible problems
Result: NOTE
    Cline.fit: no visible global function definition for 'aggregate'
    Cline.fit: no visible global function definition for 'na.omit'
    Cline.fit: no visible global function definition for 'mahalanobis'
    Cline.fit: no visible global function definition for 'cov'
    Cline.fit: no visible global function definition for 'pchisq'
    Cline.plot : Beta.p: no visible global function definition for 'pbeta'
    Cline.plot: no visible global function definition for 'par'
    Cline.plot: no visible global function definition for 'plot'
    Cline.plot: no visible global function definition for 'lines'
    Cline.plot: no visible global function definition for 'qchisq'
    HIest : HIproposal: no visible global function definition for
     'rmultinom'
    HIest: no visible global function definition for 'optim'
    HIest: no visible global function definition for 'runif'
    gcline.fn: no visible global function definition for 'glm'
    gcline.fn: no visible global function definition for 'logLik'
    gcline.fn: no visible global function definition for 'multinom'
    gcline.fn : LL.fn: no visible global function definition for 'dbinom'
    gcline.fn : GR: no visible global function definition for 'rlnorm'
    gcline.fn : GR: no visible global function definition for 'rnorm'
    gcline.fn : LL.fn: no visible global function definition for 'pbeta'
    gcline.fn: no visible global function definition for 'optim'
    gcline.fn: no visible global function definition for 'runif'
    longX2: no visible global function definition for 'pchisq'
    spatial.AD : rbnorm: no visible global function definition for 'rnorm'
    spatial.AD: no visible global function definition for 'dist'
    spatial.AD: no visible global function definition for 'dnorm'
    spatial.AD: no visible global function definition for 'rpois'
    spatial.AD: no visible global function definition for 'runif'
    spatial.AD: no visible global function definition for 'rbinom'
    spatial.AD: no visible global function definition for 'plot'
    spatial.HZ : rbnorm: no visible global function definition for 'rnorm'
    spatial.HZ: no visible global function definition for 'dist'
    spatial.HZ: no visible global function definition for 'dnorm'
    spatial.HZ: no visible global function definition for 'rpois'
    spatial.HZ: no visible global function definition for 'rbinom'
    spatial.HZ: no visible global function definition for 'plot'
    threeway : GR: no visible global function definition for 'rmultinom'
    threeway: no visible global function definition for 'runif'
    threeway: no visible global function definition for 'optim'
    Undefined global functions or variables:
     aggregate cov dbinom dist dnorm glm lines logLik mahalanobis multinom
     na.omit optim par pbeta pchisq plot qchisq rbinom rlnorm rmultinom
     rnorm rpois runif
    Consider adding
     importFrom("graphics", "lines", "par", "plot")
     importFrom("stats", "aggregate", "cov", "dbinom", "dist", "dnorm",
     "glm", "logLik", "mahalanobis", "na.omit", "optim", "pbeta",
     "pchisq", "qchisq", "rbinom", "rlnorm", "rmultinom",
     "rnorm", "rpois", "runif")
    to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0
Check: R code for possible problems
Result: NOTE
    Cline.fit: no visible global function definition for ‘aggregate’
    Cline.fit: no visible global function definition for ‘na.omit’
    Cline.fit: no visible global function definition for ‘mahalanobis’
    Cline.fit: no visible global function definition for ‘cov’
    Cline.fit: no visible global function definition for ‘pchisq’
    Cline.plot : Beta.p: no visible global function definition for ‘pbeta’
    Cline.plot: no visible global function definition for ‘par’
    Cline.plot: no visible global function definition for ‘plot’
    Cline.plot: no visible global function definition for ‘lines’
    Cline.plot: no visible global function definition for ‘qchisq’
    HIest : HIproposal: no visible global function definition for
     ‘rmultinom’
    HIest: no visible global function definition for ‘optim’
    HIest: no visible global function definition for ‘runif’
    gcline.fn: no visible global function definition for ‘glm’
    gcline.fn: no visible global function definition for ‘logLik’
    gcline.fn: no visible global function definition for ‘multinom’
    gcline.fn : LL.fn: no visible global function definition for ‘dbinom’
    gcline.fn : GR: no visible global function definition for ‘rlnorm’
    gcline.fn : GR: no visible global function definition for ‘rnorm’
    gcline.fn : LL.fn: no visible global function definition for ‘pbeta’
    gcline.fn: no visible global function definition for ‘optim’
    gcline.fn: no visible global function definition for ‘runif’
    longX2: no visible global function definition for ‘pchisq’
    spatial.AD : rbnorm: no visible global function definition for ‘rnorm’
    spatial.AD: no visible global function definition for ‘dist’
    spatial.AD: no visible global function definition for ‘dnorm’
    spatial.AD: no visible global function definition for ‘rpois’
    spatial.AD: no visible global function definition for ‘runif’
    spatial.AD: no visible global function definition for ‘rbinom’
    spatial.AD: no visible global function definition for ‘quartz’
    spatial.AD: no visible global function definition for ‘plot’
    spatial.HZ : rbnorm: no visible global function definition for ‘rnorm’
    spatial.HZ: no visible global function definition for ‘dist’
    spatial.HZ: no visible global function definition for ‘dnorm’
    spatial.HZ: no visible global function definition for ‘rpois’
    spatial.HZ: no visible global function definition for ‘rbinom’
    spatial.HZ: no visible global function definition for ‘quartz’
    spatial.HZ: no visible global function definition for ‘plot’
    threeway : GR: no visible global function definition for ‘rmultinom’
    threeway: no visible global function definition for ‘runif’
    threeway: no visible global function definition for ‘optim’
    Undefined global functions or variables:
     aggregate cov dbinom dist dnorm glm lines logLik mahalanobis multinom
     na.omit optim par pbeta pchisq plot qchisq quartz rbinom rlnorm
     rmultinom rnorm rpois runif
    Consider adding
     importFrom("grDevices", "quartz")
     importFrom("graphics", "lines", "par", "plot")
     importFrom("stats", "aggregate", "cov", "dbinom", "dist", "dnorm",
     "glm", "logLik", "mahalanobis", "na.omit", "optim", "pbeta",
     "pchisq", "qchisq", "rbinom", "rlnorm", "rmultinom",
     "rnorm", "rpois", "runif")
    to your NAMESPACE file.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64