CRAN Package Check Results for Package pbatR

Last updated on 2017-07-26 01:56:25.

Check Details

Version: 2.2-9
Check: DESCRIPTION meta-information
Result: NOTE
    Package listed in more than one of Depends, Imports, Suggests, Enhances:
     ‘tcltk’
    A package should be listed in only one of these fields.
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: 2.2-9
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘rootSolve’ which was already attached by Depends.
     Please remove these calls from your code.
    'library' or 'require' calls in package code:
     ‘kinship2’ ‘tcltk’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     ‘rootSolve’ ‘survival’
     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

Version: 2.2-9
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .C("powerR", as.integer(numOffspring), as.integer(numParents),
     as.integer(numFamilies), as.integer(additionalOffspringPhenos),
     as.integer(ascertainment), as.integer(modelGen), as.integer(modelTest),
     as.double(afreqMarker), as.double(penAA), as.double(penAB),
     as.double(penBB), as.double(heritability), as.double(contsAscertainmentLower),
     as.double(contsAscertainmentUpper), as.double(pDiseaseAlleleGivenMarkerAllele),
     as.double(afreqDSL), as.double(qnorm(1 - alpha/2)), as.double(offset),
     as.integer(numSim), as.integer(ITERATION_KILLER), result,
     DUP = FALSE)
    DUP is no longer supported and will be ignored.
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

Version: 2.2-9
Check: R code for possible problems
Result: NOTE
    c2bat: no visible global function definition for ‘read.table’
    getVersion: no visible global function definition for
     ‘installed.packages’
    loadPbatlog: no visible global function definition for ‘read.csv’
    loadPbatlog.bad: no visible global function definition for ‘read.table’
    loadPbatlogExtended: no visible global function definition for
     ‘read.csv’
    obfuscate: no visible global function definition for ‘runif’
    pbat.powerCmd: no visible global function definition for ‘qnorm’
    pbat.status: no visible global function definition for ‘tail’
    pbatGUI.mainForm : onPlot: no visible global function definition for
     ‘plot’
    pen_allelicOR: no visible global function definition for ‘optim’
    pen_ar: no visible global function definition for ‘optim’
    pen_or1: no visible global function definition for ‘multiroot’
    pen_or1: no visible global function definition for ‘runif’
    pen_or1_a: no visible global function definition for ‘optim’
    pen_or1_a: no visible global function definition for ‘runif’
    plot.pedigree : points.sym : circle: no visible global function
     definition for ‘par’
    plot.pedigree : points.sym : circle: no visible global function
     definition for ‘polygon’
    plot.pedigree : points.sym : square: no visible global function
     definition for ‘par’
    plot.pedigree : points.sym : square: no visible global function
     definition for ‘polygon’
    plot.pedigree : points.sym : diamond: no visible global function
     definition for ‘par’
    plot.pedigree : points.sym : diamond: no visible global function
     definition for ‘polygon’
    plot.pedigree : points.sym : triangle: no visible global function
     definition for ‘par’
    plot.pedigree : points.sym : triangle: no visible global function
     definition for ‘polygon’
    plot.pedigree : points.sym: no visible global function definition for
     ‘segments’
    plot.pedigree: no visible global function definition for
     ‘align.pedigree’
    plot.pedigree: no visible global function definition for ‘par’
    plot.pedigree: no visible global function definition for ‘plot’
    plot.pedigree: no visible global function definition for ‘text’
    plot.pedigree: no visible global function definition for ‘segments’
    plot.pedigree : arcconnect: no visible global function definition for
     ‘lines’
    plotPed: no visible global function definition for ‘pdf’
    plotPed: no visible global function definition for ‘pedigree’
    plotPed: no visible global function definition for ‘title’
    plotPed: no visible global function definition for ‘dev.off’
    read.badheader: no visible global function definition for ‘read.table’
    write.badheader: no visible global function definition for
     ‘write.table’
    write.pbat: no visible global function definition for ‘write.table’
    write.pbat.csv: no visible global function definition for ‘write.csv’
    write.pbat.csv: no visible global function definition for ‘write.table’
    Undefined global functions or variables:
     align.pedigree dev.off installed.packages lines multiroot optim par
     pdf pedigree plot polygon qnorm read.csv read.table runif segments
     tail text title write.csv write.table
    Consider adding
     importFrom("grDevices", "dev.off", "pdf")
     importFrom("graphics", "lines", "par", "plot", "polygon", "segments",
     "text", "title")
     importFrom("stats", "optim", "qnorm", "runif")
     importFrom("utils", "installed.packages", "read.csv", "read.table",
     "tail", "write.csv", "write.table")
    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-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

Version: 2.2-9
Check: compiled code
Result: NOTE
    File ‘pbatR/libs/pbatR.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: 2.2-9
Check: dependencies in R code
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rootSolve’ which was already attached by Depends.
     Please remove these calls from your code.
    'library' or 'require' calls in package code:
     ‘kinship2’ ‘tcltk’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     ‘rootSolve’ ‘survival’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavor: r-oldrel-osx-x86_64

Version: 2.2-9
Check: S3 generic/method consistency
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 2.2-9
Check: replacement functions
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavor: r-oldrel-osx-x86_64

Version: 2.2-9
Check: foreign function calls
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 keyCall with DUP:
     .C("powerR", as.integer(numOffspring), as.integer(numParents),
     as.integer(numFamilies), as.integer(additionalOffspringPhenos),
     as.integer(ascertainment), as.integer(modelGen), as.integer(modelTest),
     as.double(afreqMarker), as.double(penAA), as.double(penAB),
     as.double(penBB), as.double(heritability), as.double(contsAscertainmentLower),
     as.double(contsAscertainmentUpper), as.double(pDiseaseAlleleGivenMarkerAllele),
     as.double(afreqDSL), as.double(qnorm(1 - alpha/2)), as.double(offset),
     as.integer(numSim), as.integer(ITERATION_KILLER), result,
     DUP = FALSE)
    DUP is no longer supported and will be ignored.
Flavor: r-oldrel-osx-x86_64

Version: 2.2-9
Check: R code for possible problems
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 keyc2bat: no visible global function definition for ‘read.table’
    getVersion: no visible global function definition for
     ‘installed.packages’
    loadPbatlog: no visible global function definition for ‘read.csv’
    loadPbatlog.bad: no visible global function definition for ‘read.table’
    loadPbatlogExtended: no visible global function definition for
     ‘read.csv’
    obfuscate: no visible global function definition for ‘runif’
    pbat.powerCmd: no visible global function definition for ‘qnorm’
    pbat.status: no visible global function definition for ‘tail’
    pbatGUI.mainForm : onPlot: no visible global function definition for
     ‘plot’
    pen_allelicOR: no visible global function definition for ‘optim’
    pen_ar: no visible global function definition for ‘optim’
    pen_or1: no visible global function definition for ‘multiroot’
    pen_or1: no visible global function definition for ‘runif’
    pen_or1_a: no visible global function definition for ‘optim’
    pen_or1_a: no visible global function definition for ‘runif’
    plot.pedigree : points.sym : circle: no visible global function
     definition for ‘par’
    plot.pedigree : points.sym : circle: no visible global function
     definition for ‘polygon’
    plot.pedigree : points.sym : square: no visible global function
     definition for ‘par’
    plot.pedigree : points.sym : square: no visible global function
     definition for ‘polygon’
    plot.pedigree : points.sym : diamond: no visible global function
     definition for ‘par’
    plot.pedigree : points.sym : diamond: no visible global function
     definition for ‘polygon’
    plot.pedigree : points.sym : triangle: no visible global function
     definition for ‘par’
    plot.pedigree : points.sym : triangle: no visible global function
     definition for ‘polygon’
    plot.pedigree : points.sym: no visible global function definition for
     ‘segments’
    plot.pedigree: no visible global function definition for
     ‘align.pedigree’
    plot.pedigree: no visible global function definition for ‘par’
    plot.pedigree: no visible global function definition for ‘plot’
    plot.pedigree: no visible global function definition for ‘text’
    plot.pedigree: no visible global function definition for ‘segments’
    plot.pedigree : arcconnect: no visible global function definition for
     ‘lines’
    plotPed: no visible global function definition for ‘pdf’
    plotPed: no visible global function definition for ‘pedigree’
    plotPed: no visible global function definition for ‘title’
    plotPed: no visible global function definition for ‘dev.off’
    read.badheader: no visible global function definition for ‘read.table’
    write.badheader: no visible global function definition for
     ‘write.table’
    write.pbat: no visible global function definition for ‘write.table’
    write.pbat.csv: no visible global function definition for ‘write.csv’
    write.pbat.csv: no visible global function definition for ‘write.table’
    Undefined global functions or variables:
     align.pedigree dev.off installed.packages lines multiroot optim par
     pdf pedigree plot polygon qnorm read.csv read.table runif segments
     tail text title write.csv write.table
    Consider adding
     importFrom("grDevices", "dev.off", "pdf")
     importFrom("graphics", "lines", "par", "plot", "polygon", "segments",
     "text", "title")
     importFrom("stats", "optim", "qnorm", "runif")
     importFrom("utils", "installed.packages", "read.csv", "read.table",
     "tail", "write.csv", "write.table")
    to your NAMESPACE file.
Flavor: r-oldrel-osx-x86_64

Version: 2.2-9
Check: for missing documentation entries
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 2.2-9
Check: for code/documentation mismatches
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
Flavor: r-oldrel-osx-x86_64

Version: 2.2-9
Check: Rd \usage sections
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64