CRAN Package Check Results for Package strum

Last updated on 2020-03-03 15:50:05 CET.

Check Details

Version: 0.6.2
Check: R code for possible problems
Result: NOTE
    .computeBivariateLL: no visible global function definition for 'optim'
    .computeUnivariateLL: no visible global function definition for 'lm'
    .computeUnivariateLL: no visible global function definition for 'coef'
    .computeUnivariateLL: no visible global function definition for 'optim'
    .estimateThetaParameter: no visible global function definition for
     'optim'
    .estimateThetaParameter : <anonymous>: no visible global function
     definition for 'rnorm'
    .estimateThetaParameter : <anonymous>: no visible global function
     definition for 'optim'
    .findMissing: no visible global function definition for
     'complete.cases'
    .generateStartValue : <anonymous>: no visible global function
     definition for 'rnorm'
    .generateStartValue: no visible global function definition for 'rbinom'
    .generateStartValue: no visible global function definition for 'rnorm'
    .getAnalysisX : <anonymous>: no visible global function definition for
     'model.matrix'
    .getPhi : <anonymous>: no visible global function definition for
     'read.table'
    .getTheoCorrectT: no visible global function definition for 'rchisq'
    .getTheoCorrectT: no visible global function definition for 'qchisq'
    .rdirichlet: no visible global function definition for 'rgamma'
    .simulateHaplotypes: no visible global function definition for 'rpois'
    .simulateHaplotypes: no visible global function definition for 'runif'
    .simulateVC : <anonymous>: no visible global function definition for
     'rnorm'
    .simulateVC: no visible global function definition for 'rnorm'
    .testModel: no visible global function definition for 'qnorm'
    .testModel: no visible global function definition for 'pnorm'
    .testModel: no visible global function definition for 'pchisq'
    importHapmapData: no visible global function definition for
     'download.file'
    importHapmapData: no visible global function definition for
     'read.table'
    show,strumData: no visible global function definition for 'head'
    show,strumIBD: no visible global function definition for 'head'
    show,strumMarker: no visible global function definition for 'head'
    Undefined global functions or variables:
     coef complete.cases download.file head lm model.matrix optim pchisq
     pnorm qchisq qnorm rbinom rchisq read.table rgamma rnorm rpois runif
    Consider adding
     importFrom("stats", "coef", "complete.cases", "lm", "model.matrix",
     "optim", "pchisq", "pnorm", "qchisq", "qnorm", "rbinom",
     "rchisq", "rgamma", "rnorm", "rpois", "runif")
     importFrom("utils", "download.file", "head", "read.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-devel-windows-ix86+x86_64-gcc8, 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: 0.6.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
     computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
     computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.6.2
Check: installed package size
Result: NOTE
     installed size is 5.6Mb
     sub-directories of 1Mb or more:
     libs 3.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64

Version: 0.6.2
Check: compiled code
Result: NOTE
    File ‘strum/libs/strum.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