CRAN Package Check Results for Maintainer ‘Stephanie Kovalchik <s.a.kovalchik at gmail.com>’

Last updated on 2019-11-18 20:47:59 CET.

Package ERROR NOTE OK
anoint 12
blm 12
ipdmeta 12
RISmed 2 4 6

Package anoint

Current CRAN status: NOTE: 12

Version: 1.4
Check: whether the namespace can be loaded with stated dependencies
Result: NOTE
    Warning: no function found corresponding to methods exports from 'anoint' for: 'show'
    
    A namespace must be able to be loaded with just the base namespace
    loaded: otherwise if the namespace gets loaded by a saved object, the
    session will be unable to start.
    
    Probably some imports need to be declared in the 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, r-oldrel-osx-x86_64

Package blm

Current CRAN status: NOTE: 12

Version: 2013.2.4.4
Check: R code for possible problems
Result: NOTE
    EO: no visible global function definition for 'qnorm'
    LRT: no visible global function definition for 'pchisq'
    LRT.blm: no visible global function definition for 'terms'
    LRT.blm: no visible global function definition for 'update'
    LRT.lexpit: no visible global function definition for 'terms'
    LRT.lexpit: no visible global function definition for 'update'
    LRT.lexpit: no visible global function definition for 'glm'
    blm: no visible binding for global variable 'na.omit'
    blm: no visible global function definition for 'model.frame'
    blm: no visible global function definition for 'model.matrix'
    blm: no visible global function definition for 'terms'
    blm.cohort: no visible binding for global variable 'na.omit'
    blm.cohort : blm.cohort.optim: no visible global function definition
     for 'constrOptim'
    blm.cohort: no visible global function definition for 'model.frame'
    blm.cohort: no visible global function definition for 'model.matrix'
    blm.leverage: no visible global function definition for 'model.matrix'
    blm.optim: no visible global function definition for 'constrOptim'
    crude.risk: no visible binding for global variable 'na.omit'
    crude.risk : risk: no visible global function definition for 'quantile'
    crude.risk : covariate: no visible global function definition for
     'quantile'
    gof: no visible global function definition for 'quantile'
    gof: no visible global function definition for 'pchisq'
    gof: no visible global function definition for 'pf'
    gof.pearson: no visible global function definition for 'model.matrix'
    gof.pearson: no visible global function definition for 'pchisq'
    influence.blm: no visible global function definition for 'binomial'
    influence.blm: no visible global function definition for 'make.link'
    influence.blm: no visible global function definition for 'lm.influence'
    influence.lexpit: no visible global function definition for
     'lm.influence'
    lexpit: no visible binding for global variable 'na.omit'
    lexpit: no visible global function definition for 'model.frame'
    lexpit: no visible global function definition for 'model.matrix'
    lexpit: no visible global function definition for 'terms'
    lexpit: no visible binding for global variable 'glm'
    lexpit.leverage: no visible global function definition for
     'model.matrix'
    predict.se.blm: no visible global function definition for
     'model.matrix'
    predict.se.blm: no visible global function definition for 'update'
    predict.se.blm: no visible global function definition for 'terms'
    risk.exposure.plot: no visible global function definition for
     'scatter.smooth'
    stage1.optim: no visible global function definition for 'constrOptim'
    stage2.optim: no visible global function definition for 'nlm'
    tapply.risk: no visible global function definition for 'model.frame'
    vcov.blm.big: no visible global function definition for 'binomial'
    vcov.blm.big: no visible global function definition for 'make.link'
    vcov.lexpit.big: no visible global function definition for 'binomial'
    vcov.lexpit.big: no visible global function definition for 'make.link'
    which.at.boundary: no visible global function definition for
     'model.matrix'
    confint,blm: no visible global function definition for 'qnorm'
    confint,lexpit: no visible global function definition for 'qnorm'
    predict,blm: no visible global function definition for 'model.matrix'
    predict,blm: no visible global function definition for 'update'
    predict,blm: no visible global function definition for 'terms'
    predict,lexpit: no visible global function definition for
     'model.matrix'
    predict,lexpit: no visible global function definition for 'update'
    predict,lexpit: no visible global function definition for 'terms'
    summary,blm : <anonymous>: no visible global function definition for
     'pt'
    summary,blm: no visible global function definition for 'printCoefmat'
    summary,lexpit : <anonymous>: no visible global function definition for
     'pt'
    summary,lexpit: no visible global function definition for
     'printCoefmat'
    Undefined global functions or variables:
     binomial constrOptim glm lm.influence make.link model.frame
     model.matrix na.omit nlm pchisq pf printCoefmat pt qnorm quantile
     scatter.smooth terms update
    Consider adding
     importFrom("stats", "binomial", "constrOptim", "glm", "lm.influence",
     "make.link", "model.frame", "model.matrix", "na.omit",
     "nlm", "pchisq", "pf", "printCoefmat", "pt", "qnorm",
     "quantile", "scatter.smooth", "terms", "update")
    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, r-oldrel-osx-x86_64

Package ipdmeta

Current CRAN status: NOTE: 12

Version: 2.4
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     'beta'
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: 2.4
Check: whether the namespace can be loaded with stated dependencies
Result: NOTE
    Warning: no function found corresponding to methods exports from 'ipdmeta' for: 'show'
    
    A namespace must be able to be loaded with just the base namespace
    loaded: otherwise if the namespace gets loaded by a saved object, the
    session will be unable to start.
    
    Probably some imports need to be declared in the 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, r-oldrel-osx-x86_64

Version: 2.4
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: 'methods'
     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, r-oldrel-osx-x86_64

Version: 2.4
Check: R code for possible problems
Result: NOTE
    ipd.meta.power.base.function : power: no visible global function
     definition for 'qnorm'
    ipd.meta.power.base.function : power: no visible global function
     definition for 'pnorm'
    ipd.meta.power.base.function: no visible global function definition for
     'qnorm'
    ipdlme.hetero: no visible global function definition for 'new'
    ipdlme.homo: no visible global function definition for 'new'
    plot_ipdlme: no visible global function definition for 'par'
    plot_ipdlme: no visible global function definition for 'abline'
    plot_ipdlme: no visible global function definition for 'axis'
    plot_ipdlme: no visible global function definition for 'segments'
    confint,ipdlme: no visible global function definition for 'qt'
    plot,ipdlme: no visible global function definition for 'par'
    plot,ipdlme: no visible global function definition for 'abline'
    plot,ipdlme: no visible global function definition for 'axis'
    plot,ipdlme: no visible global function definition for 'segments'
    summary,ipdlme: no visible global function definition for 'pt'
    Undefined global functions or variables:
     abline axis new par pnorm pt qnorm qt segments
    Consider adding
     importFrom("graphics", "abline", "axis", "par", "segments")
     importFrom("methods", "new")
     importFrom("stats", "pnorm", "pt", "qnorm", "qt")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
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

Package RISmed

Current CRAN status: ERROR: 2, NOTE: 4, OK: 6

Version: 2.1.7
Check: data for non-ASCII characters
Result: NOTE
     Note: found 12 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 2.1.7
Check: examples
Result: ERROR
    Running examples in ‘RISmed-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: Cited
    > ### Title: Number of citations
    > ### Aliases: Cited
    >
    > ### ** Examples
    >
    > res <- EUtilsSummary("myeloma[ti]", mindate = "2002/01/01", maxdate = "2002/02/01", retmax = 5)
    > Cited(res)
    Warning in readLines(the_url) :
     cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor': HTTP status was '429 Unknown Error'
    Error in readLines(the_url) :
     cannot open the connection to 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor'
    Calls: Cited -> Cited -> sapply -> lapply -> FUN -> readLines
    Execution halted
Flavor: r-release-osx-x86_64

Version: 2.1.7
Check: examples
Result: ERROR
    Running examples in 'RISmed-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: Cited
    > ### Title: Number of citations
    > ### Aliases: Cited
    >
    > ### ** Examples
    >
    > res <- EUtilsSummary("myeloma[ti]", mindate = "2002/01/01", maxdate = "2002/02/01", retmax = 5)
    > Cited(res)
    Warning in readLines(the_url) :
     cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor': HTTP status was '429 Too Many Requests'
    Error in readLines(the_url) : cannot open the connection
    Calls: Cited -> Cited -> sapply -> lapply -> FUN -> readLines
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64