CRAN Package Check Results for Package CoxBoost

Last updated on 2020-11-11 10:49:13 CET.

Check Details

Version: 1.4
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.4
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     'changeLog'
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: 1.4
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     'parallel' 'snowfall'
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     'Matrix' 'prodlim'
     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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.4
Check: foreign function calls
Result: NOTE
    Calls with DUP:
     .C("find_best01", x.double.vec, as.integer(n), as.integer(p),
     uncens.C, as.integer(length(uncens)), as.double(actual.beta),
     as.double(actual.risk.score), as.double(actual.linear.predictor),
     weight.double.vec, max.nz.vec, max.1.vec, as.double(weightmat.times.risk),
     as.double(weightmat.times.risk.sum), as.double(penalty),
     warncount = integer(1), min.index = integer(1), min.deviance = double(1),
     min.beta.delta = double(1), score.vec = double(p), DUP = FALSE,
     NAOK = TRUE)
     .C("find_best", x.double.vec, as.integer(n), as.integer(p), uncens.C,
     as.integer(length(uncens)), as.double(actual.beta), as.double(actual.risk.score),
     as.double(actual.linear.predictor), weight.double.vec, max.nz.vec,
     max.1.vec, as.double(weightmat.times.risk), as.double(weightmat.times.risk.sum),
     as.double(penalty), as.integer(criterion == "pscore" || criterion ==
     "hpscore"), warncount = integer(1), min.index = integer(1),
     min.deviance = double(1), min.beta.delta = double(1), score.vec = double(p),
     DUP = FALSE, NAOK = TRUE)
     .C("find_best_candidate", x.double.vec, as.integer(n), as.integer(p),
     uncens.C, as.integer(length(uncens)), as.double(actual.beta),
     as.double(actual.risk.score), as.double(actual.linear.predictor),
     weight.double.vec, max.nz.vec, max.1.vec, as.double(weightmat.times.risk),
     as.double(weightmat.times.risk.sum), as.double(penalty),
     as.integer(criterion == "pscore" || criterion == "hpscore"),
     as.integer(presel.index - 1), as.integer(length(presel.index)),
     warncount = integer(1), min.index = integer(1), min.deviance = double(1),
     min.beta.delta = double(1), score.vec = double(p), DUP = FALSE,
     NAOK = TRUE)
     .C("find_best_candidate", x.double.vec, as.integer(n), as.integer(p),
     uncens.C, as.integer(length(uncens)), as.double(actual.beta),
     as.double(actual.risk.score), as.double(actual.linear.predictor),
     weight.double.vec, max.nz.vec, max.1.vec, as.double(weightmat.times.risk),
     as.double(weightmat.times.risk.sum), as.double(penalty),
     as.integer(criterion == "pscore"), as.integer(new.candidates -
     1), as.integer(length(new.candidates)), warncount = integer(1),
     min.index = integer(1), min.deviance = double(1), min.beta.delta = double(1),
     score.vec = double(p), DUP = FALSE, NAOK = TRUE)
     .C("get_I_vec", as.double(x[subset.time.order, pen.index[I.index]]),
     as.integer(n), as.integer(length(I.index)), as.integer(length(uncens)),
     as.double(weightmat.times.risk), as.double(weightmat.times.risk.sum),
     I.vec = double(length(I.index)), 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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.4
Check: R code for possible problems
Result: NOTE
    CoxBoost: no visible global function definition for 'Matrix'
    CoxBoost: no visible binding for global variable 'sd'
    CoxBoost: no visible global function definition for 'predict'
    cv.CoxBoost : eval.fold: no visible global function definition for
     'predict'
    cv.CoxBoost: no visible global function definition for 'mclapply'
    cv.CoxBoost: no visible binding for global variable 'sd'
    estimPVal: no visible global function definition for 'mclapply'
    iCoxBoost: no visible global function definition for 'terms'
    iCoxBoost: no visible global function definition for 'model.response'
    iCoxBoost: no visible global function definition for 'model.frame'
    iCoxBoost: no visible global function definition for 'model.matrix'
    iCoxBoost: no visible global function definition for 'Matrix'
    plot.CoxBoost: no visible global function definition for 'lines'
    plot.CoxBoost: no visible global function definition for 'text'
    predict.iCoxBoost: no visible global function definition for
     'model.response'
    predict.iCoxBoost: no visible global function definition for
     'model.frame'
    predict.iCoxBoost: no visible global function definition for
     'model.matrix'
    Undefined global functions or variables:
     Matrix lines mclapply model.frame model.matrix model.response predict
     sd terms text
    Consider adding
     importFrom("graphics", "lines", "text")
     importFrom("stats", "model.frame", "model.matrix", "model.response",
     "predict", "sd", "terms")
    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-macos-x86_64, r-release-windows-ix86+x86_64

Version: 1.4
Check: compiled code
Result: NOTE
    File ‘CoxBoost/libs/CoxBoost.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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.4
Check: R code for possible problems
Result: NOTE
    CoxBoost: no visible global function definition for ‘Matrix’
    CoxBoost: no visible binding for global variable ‘sd’
    CoxBoost: no visible global function definition for ‘predict’
    cv.CoxBoost : eval.fold: no visible global function definition for
     ‘predict’
    cv.CoxBoost: no visible global function definition for ‘mclapply’
    cv.CoxBoost: no visible binding for global variable ‘sd’
    estimPVal: no visible global function definition for ‘mclapply’
    iCoxBoost: no visible global function definition for ‘terms’
    iCoxBoost: no visible global function definition for ‘model.response’
    iCoxBoost: no visible global function definition for ‘model.frame’
    iCoxBoost: no visible global function definition for ‘model.matrix’
    iCoxBoost: no visible global function definition for ‘Matrix’
    plot.CoxBoost: no visible global function definition for ‘plot’
    plot.CoxBoost: no visible global function definition for ‘lines’
    plot.CoxBoost: no visible global function definition for ‘text’
    predict.iCoxBoost: no visible global function definition for
     ‘model.response’
    predict.iCoxBoost: no visible global function definition for
     ‘model.frame’
    predict.iCoxBoost: no visible global function definition for
     ‘model.matrix’
    Undefined global functions or variables:
     Matrix lines mclapply model.frame model.matrix model.response plot
     predict sd terms text
    Consider adding
     importFrom("graphics", "lines", "plot", "text")
     importFrom("stats", "model.frame", "model.matrix", "model.response",
     "predict", "sd", "terms")
    to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64