CRAN Package Check Results for Package RMark

Last updated on 2015-09-02 06:48:12.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1.13 4.01 58.28 62.29 NOTE --install=fake
r-devel-linux-x86_64-debian-gcc 2.1.13 4.34 58.05 62.39 NOTE --install=fake
r-devel-linux-x86_64-fedora-clang 2.1.13 130.39 NOTE
r-devel-linux-x86_64-fedora-gcc 2.1.13 121.95 NOTE
r-devel-windows-ix86+x86_64 2.1.13 18.00 108.00 126.00 NOTE
r-patched-linux-x86_64 2.1.13 4.14 60.87 65.01 OK --install=fake
r-release-linux-x86_64 2.1.13 4.12 62.25 66.38 OK --install=fake
r-release-osx-x86_64-mavericks 2.1.13 ERROR
r-release-windows-ix86+x86_64 2.1.13 20.00 101.00 121.00 OK
r-oldrel-windows-ix86+x86_64 2.1.13 26.00 166.00 192.00 OK

Check Details

Version: 2.1.13
Flags: --install=fake
Check: R code for possible problems
Result: NOTE
    convert.inp: no visible global function definition for ‘read.table’
    deltamethod.special: no visible global function definition for
     ‘as.formula’
    export.chdata: no visible global function definition for ‘write.table’
    extract.mark.output: no visible global function definition for
     ‘type.convert’
    extract.mark.output: no visible global function definition for
     ‘read.fwf’
    import.chdata: no visible global function definition for ‘read.table’
    logitCI: no visible global function definition for ‘plogis’
    make.mark.model : simplify.pim.structure: no visible global function
     definition for ‘write.table’
    make.mark.model: no visible global function definition for ‘terms’
    make.mark.model: no visible global function definition for
     ‘write.table’
    make.mark.model: no visible global function definition for
     ‘model.matrix’
    make.mark.model: no visible global function definition for ‘formula’
    make.time.factor: no visible global function definition for
     ‘model.matrix’
    mata.wald: no visible global function definition for ‘uniroot’
    model.average.marklist: no visible global function definition for
     ‘qnorm’
    process.data: no visible global function definition for ‘median’
    release.gof: no visible global function definition for ‘type.convert’
    setup.model: no visible global function definition for ‘read.delim’
    setup.parameters: no visible global function definition for
     ‘read.delim’
    setup.parameters: no visible global function definition for
     ‘as.formula’
    summary.mark: no visible global function definition for ‘coef’
    tailarea.t: no visible global function definition for ‘pt’
    tailarea.z: no visible global function definition for ‘pnorm’
    var.components: no visible global function definition for ‘optimize’
    var.components: no visible global function definition for ‘uniroot’
    var.components : mom.sigCI: no visible global function definition for
     ‘qchisq’
    var.components: no visible global function definition for ‘qnorm’
    var.components.reml: no visible global function definition for
     ‘optimize’
    var.components.reml: no visible global function definition for ‘optim’
    Undefined global functions or variables:
     as.formula coef formula median model.matrix optim optimize plogis
     pnorm pt qchisq qnorm read.delim read.fwf read.table terms
     type.convert uniroot write.table
    Consider adding
     importFrom("stats", "as.formula", "coef", "formula", "median",
     "model.matrix", "optim", "optimize", "plogis", "pnorm",
     "pt", "qchisq", "qnorm", "terms", "uniroot")
     importFrom("utils", "read.delim", "read.fwf", "read.table",
     "type.convert", "write.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.1.13
Check: R code for possible problems
Result: NOTE
    convert.inp: no visible global function definition for ‘read.table’
    deltamethod.special: no visible global function definition for
     ‘as.formula’
    export.chdata: no visible global function definition for ‘write.table’
    extract.mark.output: no visible global function definition for
     ‘type.convert’
    extract.mark.output: no visible global function definition for
     ‘read.fwf’
    import.chdata: no visible global function definition for ‘read.table’
    logitCI: no visible global function definition for ‘plogis’
    make.mark.model : simplify.pim.structure: no visible global function
     definition for ‘write.table’
    make.mark.model: no visible global function definition for ‘terms’
    make.mark.model: no visible global function definition for
     ‘write.table’
    make.mark.model: no visible global function definition for
     ‘model.matrix’
    make.mark.model: no visible global function definition for ‘formula’
    make.time.factor: no visible global function definition for
     ‘model.matrix’
    mata.wald: no visible global function definition for ‘uniroot’
    model.average.marklist: no visible global function definition for
     ‘qnorm’
    process.data: no visible global function definition for ‘median’
    release.gof: no visible global function definition for ‘type.convert’
    setup.model: no visible global function definition for ‘read.delim’
    setup.parameters: no visible global function definition for
     ‘read.delim’
    setup.parameters: no visible global function definition for
     ‘as.formula’
    summary.mark: no visible global function definition for ‘coef’
    tailarea.t: no visible global function definition for ‘pt’
    tailarea.z: no visible global function definition for ‘pnorm’
    var.components: no visible global function definition for ‘optimize’
    var.components: no visible global function definition for ‘uniroot’
    var.components : mom.sigCI: no visible global function definition for
     ‘qchisq’
    var.components: no visible global function definition for ‘qnorm’
    var.components.reml: no visible global function definition for
     ‘optimize’
    var.components.reml: no visible global function definition for ‘optim’
    Undefined global functions or variables:
     as.formula coef formula median model.matrix optim optimize plogis
     pnorm pt qchisq qnorm read.delim read.fwf read.table terms
     type.convert uniroot write.table
    Consider adding
     importFrom("stats", "as.formula", "coef", "formula", "median",
     "model.matrix", "optim", "optimize", "plogis", "pnorm",
     "pt", "qchisq", "qnorm", "terms", "uniroot")
     importFrom("utils", "read.delim", "read.fwf", "read.table",
     "type.convert", "write.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 2.1.13
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: Software mark not found in path.
Flavor: r-release-osx-x86_64-mavericks

Version: 2.1.13
Check: examples
Result: ERROR
    Running examples in ‘RMark-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: Blackduck
    > ### Title: Black duck known fate data
    > ### Aliases: Blackduck
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > data(Blackduck)
    > # Change BirdAge to numeric; starting with version 1.6.3 factor variables are
    > # no longer allowed. They can work as in this example but they can be misleading
    > # and fail if the levels are non-numeric. The real parameters will remain
    > # unchanged but the betas will be different.
    > Blackduck$BirdAge=as.numeric(Blackduck$BirdAge)-1
    > run.Blackduck=function()
    + {
    + #
    + # Process data
    + #
    + bduck.processed=process.data(Blackduck,model="Known")
    + #
    + # Create default design data
    + #
    + bduck.ddl=make.design.data(bduck.processed)
    + #
    + # Add occasion specific data min < 0; I have no idea what it is
    + #
    + bduck.ddl$S$min=c(4,6,7,7,7,6,5,5)
    + #
    + # Define range of models for S
    + #
    + S.dot=list(formula=~1)
    + S.time=list(formula=~time)
    + S.min=list(formula=~min)
    + S.BirdAge=list(formula=~BirdAge)
    + #
    + # Note that in the following model in the MARK example, the covariates
    + # have been standardized. That means that the beta parameters will be different
    + # for BirdAge, Weight and their interaction but the likelihood and real parameter
    + # estimates are the same.
    + #
    + S.BirdAgexWeight.min=list(formula=~min+BirdAge*Weight)
    + S.BirdAge.Weight=list(formula=~BirdAge+Weight)
    + #
    + # Create model list and run assortment of models
    + #
    + model.list=create.model.list("Known")
    + bduck.results=mark.wrapper(model.list,data=bduck.processed,ddl=bduck.ddl,
    + invisible=FALSE,threads=1)
    +
    + #
    + # Return model table and list of models
    + #
    + return(bduck.results)
    + }
    > bduck.results=run.Blackduck()
    
    S.BirdAge
    
    sh: mark: command not found
    Error in run.mark.model(model, invisible = invisible, adjust = adjust, :
    
    Output file does not exist. Unable to find or run mark.exe
    
    
    S.BirdAge.Weight
    
    sh: mark: command not found
    Error in run.mark.model(model, invisible = invisible, adjust = adjust, :
    
    Output file does not exist. Unable to find or run mark.exe
    
    
    S.BirdAgexWeight.min
    
    sh: mark: command not found
    Error in run.mark.model(model, invisible = invisible, adjust = adjust, :
    
    Output file does not exist. Unable to find or run mark.exe
    
    
    S.dot
    
    sh: mark: command not found
    Error in run.mark.model(model, invisible = invisible, adjust = adjust, :
    
    Output file does not exist. Unable to find or run mark.exe
    
    
    S.min
    
    sh: mark: command not found
    Error in run.mark.model(model, invisible = invisible, adjust = adjust, :
    
    Output file does not exist. Unable to find or run mark.exe
    
    
    S.time
    
    sh: mark: command not found
    Error in run.mark.model(model, invisible = invisible, adjust = adjust, :
    
    Output file does not exist. Unable to find or run mark.exe
    
    
    No mark models found
    
    Error in collect.models() :
    Calls: run.Blackduck -> mark.wrapper -> collect.models
    Execution halted
Flavor: r-release-osx-x86_64-mavericks