CRAN Package Check Results for Package soil.spec

Last updated on 2016-10-24 23:48:34.

Check Details

Version: 2.1.4
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘chemometrics’ ‘spatstat’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
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-macos-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.1.4
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.Spectra plot.ken.sto plot.trans predict.SpectraPoints
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
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-macos-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 2.1.4
Check: R code for possible problems
Result: NOTE
    .read.opus: no visible global function definition for ‘mtext’
    fit.SpectraModel: no visible binding for global variable ‘na.omit’
    fit.SpectraModel: no visible global function definition for ‘coef’
    fit.SpectraModel: no visible global function definition for
     ‘as.formula’
    ken.sto: no visible global function definition for ‘dist’
    ken.sto: no visible global function definition for ‘dev.new’
    ken.sto: no visible global function definition for ‘par’
    ken.sto: no visible global function definition for ‘points’
    plot.Spectra: no visible global function definition for ‘par’
    plot.Spectra: no visible global function definition for ‘na.omit’
    plot.Spectra: no visible global function definition for ‘axis’
    plot.Spectra: no visible global function definition for ‘lines’
    plot.Spectra: no visible global function definition for ‘box’
    plot.Spectra: no visible global function definition for ‘mtext’
    plot.ken.sto: no visible global function definition for ‘dev.new’
    plot.ken.sto: no visible global function definition for ‘par’
    plot.ken.sto: no visible global function definition for ‘points’
    plot.trans: no visible global function definition for ‘dev.new’
    plot.trans: no visible global function definition for ‘par’
    plot.trans: no visible global function definition for ‘lines’
    predict.SpectraPoints: no visible global function definition for ‘qt’
    read.spc: no visible global function definition for ‘lines’
    read.spc: no visible global function definition for ‘graphics.off’
    read.spc: no visible global function definition for ‘abline’
    trans: no visible global function definition for ‘sortedXyData’
    trans: no visible global function definition for ‘chull’
    trans: no visible global function definition for ‘approx’
    trans: no visible global function definition for ‘dev.new’
    trans: no visible global function definition for ‘par’
    trans: no visible global function definition for ‘lines’
    validate.SpectraPoints: no visible global function definition for
     ‘quantile’
    fit,formula-SpectraPoints-data.frame: no visible binding for global
     variable ‘na.omit’
    fit,formula-SpectraPoints-data.frame: no visible global function
     definition for ‘coef’
    fit,formula-SpectraPoints-data.frame: no visible global function
     definition for ‘as.formula’
    plot,Spectra-ANY: no visible global function definition for ‘par’
    plot,Spectra-ANY: no visible global function definition for ‘na.omit’
    plot,Spectra-ANY: no visible global function definition for ‘axis’
    plot,Spectra-ANY: no visible global function definition for ‘lines’
    plot,Spectra-ANY: no visible global function definition for ‘box’
    plot,Spectra-ANY: no visible global function definition for ‘mtext’
    predict,SpectraPoints: no visible global function definition for ‘qt’
    read.opus,character: no visible global function definition for ‘mtext’
    validate,SpectraPoints: no visible global function definition for
     ‘quantile’
    Undefined global functions or variables:
     abline approx as.formula axis box chull coef dev.new dist
     graphics.off lines mtext na.omit par points qt quantile sortedXyData
    Consider adding
     importFrom("grDevices", "chull", "dev.new", "graphics.off")
     importFrom("graphics", "abline", "axis", "box", "lines", "mtext",
     "par", "points")
     importFrom("stats", "approx", "as.formula", "coef", "dist", "na.omit",
     "qt", "quantile", "sortedXyData")
    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-macos-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 2.1.4
Check: examples
Result: ERROR
    Running examples in ‘soil.spec-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: read.opus-method
    > ### Title: Reads binary OPUS files containing spectroscopy
    > ### Aliases: read.opus read.opus,character-method read.opus,list-method
    > ### Keywords: methods
    >
    > ### ** Examples
    >
    > ## Original binary Opus files:
    > pth = system.file(package = "soil.spec")
    > lst <- as.list(list.files(path=pth, pattern="*.0$", full.names=TRUE))
    > file.info(lst[[1]])
     size isdir mode
    /home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 167196 FALSE 644
     mtime
    /home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 2016-06-13 03:26:01
     ctime
    /home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 2016-06-13 03:27:24
     atime uid gid
    /home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 2016-06-13 23:14:43 501 1
     uname grname
    /home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 ripley other
    > xx <- read.opus(lst)
    Error in seq.default(lxv, fxv, (fxv - lxv)/(NPT1 - 1)) :
     wrong sign in 'by' argument
    Calls: read.opus ... read.opus -> lapply -> FUN -> rev -> seq -> seq.default
    Execution halted
Flavor: r-patched-solaris-sparc