CRAN Package Check Results for Package RMark

Last updated on 2015-07-07 15:46:46.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1.13 4.12 60.40 64.52 NOTE --install=fake
r-devel-linux-x86_64-debian-gcc 2.1.13 4.01 58.76 62.77 NOTE --install=fake
r-devel-linux-x86_64-fedora-clang 2.1.13 130.59 NOTE
r-devel-linux-x86_64-fedora-gcc 2.1.13 124.64 NOTE
r-devel-windows-ix86+x86_64 2.1.13 18.00 104.00 122.00 NOTE
r-patched-linux-x86_64 2.1.13 4.01 63.02 67.02 OK --install=fake
r-release-linux-x86_64 2.1.13 4.52 60.17 64.69 OK --install=fake
r-release-osx-x86_64-mavericks 2.1.13 ERROR
r-release-windows-ix86+x86_64 2.1.13 19.00 94.00 113.00 OK
r-oldrel-windows-ix86+x86_64 2.1.13 17.00 112.00 129.00 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
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
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