CRAN Package Check Results for Package Bayesthresh

Last updated on 2018-05-24 06:46:34 CEST.

Check Details

Version: 2.0.1
Check: package dependencies
Result: NOTE
    Depends: includes the non-default packages:
     ‘lme4’ ‘MASS’ ‘VGAM’ ‘mvtnorm’ ‘matrixcalc’ ‘coda’
    Adding so many packages to the search path is excessive and importing
    selectively is preferable.
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: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0.1
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘MASS’ ‘VGAM’ ‘coda’ ‘lme4’ ‘matrixcalc’ ‘mvtnorm’
     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: 2.0.1
Check: R code for possible problems
Result: NOTE
    ACGaussian : <anonymous>: no visible global function definition for
     ‘qnorm’
    ACGaussian : <anonymous>: no visible global function definition for
     ‘pnorm’
    ACGaussian : <anonymous>: no visible global function definition for
     ‘runif’
    ACGaussian: no visible global function definition for ‘ginv’
    ACGaussian: no visible global function definition for ‘runif’
    ACGaussian: no visible global function definition for ‘rmvnorm’
    ACt: no visible global function definition for ‘qnorm’
    ACt: no visible global function definition for ‘pnorm’
    ACt: no visible global function definition for ‘runif’
    ACt: no visible global function definition for ‘ginv’
    ACt: no visible global function definition for ‘rmvnorm’
    ACt: no visible global function definition for ‘rpois’
    ACt: no visible global function definition for ‘dpois’
    Bayesthresh: no visible global function definition for ‘as.formula’
    Bayesthresh: no visible binding for global variable ‘contrasts’
    MCGaussian: no visible global function definition for ‘qnorm’
    MCGaussian: no visible global function definition for ‘pnorm’
    MCGaussian: no visible global function definition for ‘runif’
    MCGaussian: no visible global function definition for ‘ginv’
    MCGaussian: no visible global function definition for ‘rmvnorm’
    MCGaussian: no visible global function definition for ‘vec’
    MCGaussian: no visible global function definition for ‘sd’
    MCt: no visible global function definition for ‘qnorm’
    MCt: no visible global function definition for ‘pnorm’
    MCt: no visible global function definition for ‘runif’
    MCt: no visible global function definition for ‘ginv’
    MCt: no visible global function definition for ‘rmvnorm’
    MCt: no visible global function definition for ‘vec’
    MCt: no visible global function definition for ‘rpois’
    MCt: no visible global function definition for ‘dpois’
    MCt: no visible global function definition for ‘sd’
    NCGaussian: no visible global function definition for ‘qnorm’
    NCGaussian: no visible global function definition for ‘pnorm’
    NCGaussian: no visible global function definition for ‘runif’
    NCGaussian: no visible global function definition for ‘ginv’
    NCGaussian: no visible global function definition for ‘rmvnorm’
    NCGaussian: no visible global function definition for ‘rgamma’
    NCGaussian: no visible global function definition for ‘rdiric’
    NCt: no visible global function definition for ‘qnorm’
    NCt: no visible global function definition for ‘pnorm’
    NCt: no visible global function definition for ‘runif’
    NCt: no visible global function definition for ‘ginv’
    NCt: no visible global function definition for ‘rmvnorm’
    NCt: no visible global function definition for ‘rgamma’
    NCt: no visible global function definition for ‘rpois’
    NCt: no visible global function definition for ‘dpois’
    NCt: no visible global function definition for ‘rdiric’
    UniComp: no visible global function definition for ‘rgamma’
    VecFromNames: no visible global function definition for ‘as’
    coef.Bayesthresh: no visible global function definition for ‘mcmc’
    createCm: no visible global function definition for ‘is’
    createCm: no visible global function definition for ‘as’
    createCm: no visible global function definition for ‘new’
    isNested: no visible global function definition for ‘as’
    isNested: no visible global function definition for ‘new’
    lmerFactorList : <anonymous>: no visible global function definition for
     ‘as’
    lmerFactorList : <anonymous>: no visible global function definition for
     ‘validObject’
    lmerFactorList : <anonymous>: no visible global function definition for
     ‘model.matrix’
    lmerFactorList : <anonymous>: no visible binding for global variable
     ‘rBind’
    lmerFactorList : <anonymous>: no visible global function definition for
     ‘drop0’
    lmerFrames: no visible global function definition for ‘model.response’
    lmerFrames: no visible global function definition for ‘is.empty.model’
    lmerFrames: no visible global function definition for ‘model.matrix’
    lmerFrames: no visible global function definition for ‘model.weights’
    lmerFrames: no visible global function definition for ‘model.offset’
    mkZt: no visible binding for global variable ‘rBind’
    plot.random.effects: no visible global function definition for ‘gray’
    plot.random.effects: no visible global function definition for ‘plot’
    plot.random.effects: no visible global function definition for ‘axis’
    plot.random.effects: no visible global function definition for
     ‘segments’
    plot.random.effects: no visible global function definition for ‘box’
    plot.random.effects: no visible global function definition for ‘qnorm’
    predict.Bayesthresh: no visible global function definition for ‘coef’
    predict.Bayesthresh: no visible global function definition for ‘pnorm’
    predict.Bayesthresh: no visible global function definition for
     ‘rankMatrix’
    predict.Bayesthresh: no visible global function definition for ‘pt’
    random.effects: no visible global function definition for ‘coef’
    random.effects: no visible global function definition for ‘mcmc’
    Undefined global functions or variables:
     as as.formula axis box coef contrasts dpois drop0 ginv gray is
     is.empty.model mcmc model.matrix model.offset model.response
     model.weights new plot pnorm pt qnorm rBind rankMatrix rdiric rgamma
     rmvnorm rpois runif sd segments validObject vec
    Consider adding
     importFrom("grDevices", "gray")
     importFrom("graphics", "axis", "box", "plot", "segments")
     importFrom("methods", "as", "is", "new", "validObject")
     importFrom("stats", "as.formula", "coef", "contrasts", "dpois",
     "is.empty.model", "model.matrix", "model.offset",
     "model.response", "model.weights", "pnorm", "pt", "qnorm",
     "rgamma", "rpois", "runif", "sd")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
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: 2.0.1
Check: Rd line widths
Result: NOTE
    Rd file 'Bayesthresh.Rd':
     \examples lines wider than 100 characters:
     ... [TRUNCATED]
    
    Rd file 'MCMCsample.Rd':
     \examples lines wider than 100 characters:
     ... [TRUNCATED]
    
    Rd file 'coef.Bayesthresh.Rd':
     \examples lines wider than 100 characters:
     ... [TRUNCATED]
     ... [TRUNCATED]
    
    Rd file 'compVar.Rd':
     \examples lines wider than 100 characters:
     ... [TRUNCATED]
    
    Rd file 'plot.random.effects.Rd':
     \usage lines wider than 90 characters:
     xlim = NULL, ylim = NULL, pch=19, col.points='red', col.seg=gray(0.5), ...)
     \examples lines wider than 100 characters:
     ... [TRUNCATED]
    
    Rd file 'predict.Bayesthresh.Rd':
     \examples lines wider than 100 characters:
     ... [TRUNCATED]
    
    Rd file 'random.effects.Rd':
     \examples lines wider than 100 characters:
     ... [TRUNCATED]
    
    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: 2.0.1
Check: compiled code
Result: NOTE
    File ‘Bayesthresh/libs/Bayesthresh.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    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-release-linux-x86_64

Version: 2.0.1
Check: examples
Result: WARN
    Found the following significant warnings:
    
     Warning: 'rBind' is deprecated.
    Deprecated functions may be defunct as soon as of the next release of
    R.
    See ?Deprecated.
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, r-release-osx-x86_64

Version: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-clang/Bayesthresh.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-devel/Bayesthresh.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See 'd:/Rcompile/CRANpkg/local/3.6/Bayesthresh.Rcheck/00install.out' for details.
    Information on the location(s) of code generating the 'Note's can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to 'yes'.
Flavor: r-devel-windows-ix86+x86_64

Version: 2.0.1
Check: running examples for arch ‘i386’
Result: WARN
    Found the following significant warnings:
    
     Warning: 'rBind' is deprecated.
    Deprecated functions may be defunct as soon as of the next release of
    R.
    See ?Deprecated.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0.1
Check: running examples for arch ‘x64’
Result: WARN
    Found the following significant warnings:
    
     Warning: 'rBind' is deprecated.
    Deprecated functions may be defunct as soon as of the next release of
    R.
    See ?Deprecated.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-linux-x86_64

Version: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/ripley/R/packages/tests32/Bayesthresh.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-solaris-x86

Version: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-linux-x86_64

Version: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See 'd:/Rcompile/CRANpkg/local/3.5/Bayesthresh.Rcheck/00install.out' for details.
    Information on the location(s) of code generating the 'Note's can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to 'yes'.
Flavor: r-release-windows-ix86+x86_64

Version: 2.0.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Bayesthresh.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-osx-x86_64