CRAN Package Check Results for Package chipPCR

Last updated on 2017-02-28 08:47:56.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0.8-10 4.82 103.25 108.08 NOTE
r-devel-linux-x86_64-debian-gcc 0.0.8-10 4.91 101.12 106.03 NOTE
r-devel-linux-x86_64-fedora-clang 0.0.8-10 224.14 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 0.0.8-10 215.90 NOTE --no-stop-on-test-error
r-devel-macos-x86_64-clang 0.0.8-10 165.58 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 0.0.8-10 27.00 318.00 345.00 NOTE
r-patched-linux-x86_64 0.0.8-10 5.08 95.44 100.52 NOTE
r-patched-solaris-sparc 0.0.8-10 1147.70 NOTE
r-patched-solaris-x86 0.0.8-10 220.50 NOTE
r-release-linux-x86_64 0.0.8-10 4.86 94.13 98.99 NOTE
r-release-osx-x86_64-mavericks 0.0.8-10 NOTE
r-release-windows-ix86+x86_64 0.0.8-10 19.00 189.00 208.00 ERROR
r-oldrel-windows-ix86+x86_64 0.0.8-10 15.00 208.00 223.00 ERROR

Check Details

Version: 0.0.8-10
Check: R code for possible problems
Result: NOTE
    AmpSim: no visible global function definition for ‘sd’
    AmpSim: no visible global function definition for ‘rnorm’
    RGt: no visible global function definition for ‘na.omit’
    RGt : <anonymous>: no visible global function definition for ‘lm’
    amptester: no visible global function definition for ‘shapiro.test’
    amptester : <anonymous>: no visible global function definition for ‘lm’
    amptester : <anonymous>: no visible global function definition for
     ‘cor’
    amptester : <anonymous>: no visible global function definition for
     ‘rstudent’
    amptester: no visible global function definition for ‘na.omit’
    amptester: no visible global function definition for ‘median’
    amptester: no visible global function definition for ‘mad’
    amptester: no visible global function definition for ‘rnorm’
    amptester: no visible global function definition for ‘wilcox.test’
    amptester: no visible global function definition for ‘head’
    amptester: no visible global function definition for ‘tail’
    amptester : pco: no visible global function definition for ‘predict’
    amptester : pco: no visible global function definition for
     ‘smooth.spline’
    amptester: no visible global function definition for ‘coef’
    amptester: no visible global function definition for ‘lm’
    lm.coefs : lm.fit : <anonymous>: no visible global function definition
     for ‘lm’
    normalizer : <anonymous>: no visible global function definition for
     ‘quantile’
    normalizer : <anonymous>: no visible global function definition for
     ‘sd’
    plotCurves: no visible global function definition for ‘matplot’
    plotCurves: no visible global function definition for ‘par’
    plotCurves: no visible global function definition for ‘layout’
    plotCurves : <anonymous>: no visible global function definition for
     ‘rect’
    plotCurves : <anonymous>: no visible global function definition for
     ‘par’
    plotCurves : <anonymous>: no visible global function definition for
     ‘text’
    plotCurves : <anonymous>: no visible global function definition for
     ‘rug’
    plotCurves : <anonymous>: no visible global function definition for
     ‘axis’
    plotCurves : <anonymous>: no visible global function definition for
     ‘lines’
    rtg.test : <anonymous>: no visible global function definition for ‘lm’
    rtg.test : <anonymous>: no visible global function definition for ‘cor’
    rtg.test : <anonymous>: no visible global function definition for
     ‘rstudent’
    th.cyc: no visible global function definition for ‘quantile’
    th.cyc: no visible global function definition for ‘mad’
    th.est: no visible global function definition for ‘tail’
    th.est: no visible global function definition for ‘head’
    th.est: no visible global function definition for ‘lm’
    plot,amptest-ANY: no visible global function definition for ‘head’
    plot,amptest-ANY: no visible global function definition for ‘tail’
    plot,amptest-ANY: no visible global function definition for ‘median’
    plot,amptest-ANY: no visible global function definition for ‘mad’
    plot,amptest-ANY: no visible global function definition for
     ‘shapiro.test’
    plot,amptest-ANY: no visible global function definition for
     ‘wilcox.test’
    plot,amptest-ANY: no visible global function definition for ‘layout’
    plot,amptest-ANY: no visible global function definition for ‘abline’
    plot,amptest-ANY: no visible global function definition for ‘text’
    plot,amptest-ANY: no visible global function definition for ‘arrows’
    plot,amptest-ANY: no visible global function definition for ‘mtext’
    plot,amptest-ANY: no visible global function definition for ‘axis’
    plot,bg-ANY: no visible global function definition for ‘abline’
    plot,bg-ANY: no visible global function definition for ‘text’
    plot,der-ANY: no visible global function definition for ‘points’
    plot,eff-ANY: no visible global function definition for ‘predict.lm’
    plot,eff-ANY: no visible global function definition for ‘polygon’
    plot,eff-ANY: no visible global function definition for ‘adjustcolor’
    plot,eff-ANY: no visible global function definition for ‘arrows’
    plot,eff-ANY: no visible global function definition for ‘abline’
    plot,eff-ANY: no visible global function definition for ‘legend’
    plot,refMFI-ANY: no visible global function definition for ‘par’
    plot,refMFI-ANY: no visible global function definition for ‘layout’
    plot,refMFI-ANY: no visible global function definition for ‘arrows’
    plot,refMFI-ANY: no visible global function definition for ‘mtext’
    plot,refMFI-ANY: no visible global function definition for ‘abline’
    plot,refMFI-refMFI: no visible global function definition for ‘par’
    plot,refMFI-refMFI: no visible global function definition for ‘layout’
    plot,refMFI-refMFI: no visible global function definition for ‘points’
    plot,refMFI-refMFI: no visible global function definition for
     ‘adjustcolor’
    plot,refMFI-refMFI: no visible global function definition for ‘arrows’
    plot,refMFI-refMFI: no visible global function definition for ‘mtext’
    plot,refMFI-refMFI: no visible global function definition for ‘abline’
    plot,refMFI-refMFI: no visible global function definition for ‘legend’
    plot,refMFI-refMFI: no visible global function definition for ‘lines’
    qqline,refMFI: no visible binding for global variable ‘qnorm’
    Undefined global functions or variables:
     abline adjustcolor arrows axis coef cor head layout legend lines lm
     mad matplot median mtext na.omit par points polygon predict
     predict.lm qnorm quantile rect rnorm rstudent rug sd shapiro.test
     smooth.spline tail text wilcox.test
    Consider adding
     importFrom("grDevices", "adjustcolor")
     importFrom("graphics", "abline", "arrows", "axis", "layout", "legend",
     "lines", "matplot", "mtext", "par", "points", "polygon",
     "rect", "rug", "text")
     importFrom("stats", "coef", "cor", "lm", "mad", "median", "na.omit",
     "predict", "predict.lm", "qnorm", "quantile", "rnorm",
     "rstudent", "sd", "shapiro.test", "smooth.spline",
     "wilcox.test")
     importFrom("utils", "head", "tail")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, 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: 0.0.8-10
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    AmpSim: no visible global function definition for ‘sd’
    AmpSim: no visible global function definition for ‘rnorm’
    RGt: no visible global function definition for ‘na.omit’
    RGt : <anonymous>: no visible global function definition for ‘lm’
    amptester: no visible global function definition for ‘shapiro.test’
    amptester : <anonymous>: no visible global function definition for ‘lm’
    amptester : <anonymous>: no visible global function definition for
     ‘cor’
    amptester : <anonymous>: no visible global function definition for
     ‘rstudent’
    amptester: no visible global function definition for ‘na.omit’
    amptester: no visible global function definition for ‘median’
    amptester: no visible global function definition for ‘mad’
    amptester: no visible global function definition for ‘rnorm’
    amptester: no visible global function definition for ‘wilcox.test’
    amptester: no visible global function definition for ‘head’
    amptester: no visible global function definition for ‘tail’
    amptester : pco: no visible global function definition for ‘predict’
    amptester : pco: no visible global function definition for
     ‘smooth.spline’
    amptester: no visible global function definition for ‘coef’
    amptester: no visible global function definition for ‘lm’
    lm.coefs : lm.fit : <anonymous>: no visible global function definition
     for ‘lm’
    normalizer : <anonymous>: no visible global function definition for
     ‘quantile’
    normalizer : <anonymous>: no visible global function definition for
     ‘sd’
    plotCurves: no visible global function definition for ‘matplot’
    plotCurves: no visible global function definition for ‘par’
    plotCurves: no visible global function definition for ‘layout’
    plotCurves : <anonymous>: no visible global function definition for
     ‘rect’
    plotCurves : <anonymous>: no visible global function definition for
     ‘par’
    plotCurves : <anonymous>: no visible global function definition for
     ‘text’
    plotCurves : <anonymous>: no visible global function definition for
     ‘rug’
    plotCurves : <anonymous>: no visible global function definition for
     ‘axis’
    plotCurves : <anonymous>: no visible global function definition for
     ‘lines’
    rtg.test : <anonymous>: no visible global function definition for ‘lm’
    rtg.test : <anonymous>: no visible global function definition for ‘cor’
    rtg.test : <anonymous>: no visible global function definition for
     ‘rstudent’
    th.cyc: no visible global function definition for ‘quantile’
    th.cyc: no visible global function definition for ‘mad’
    th.est: no visible global function definition for ‘tail’
    th.est: no visible global function definition for ‘head’
    th.est: no visible global function definition for ‘lm’
    plot,amptest-ANY: no visible global function definition for ‘head’
    plot,amptest-ANY: no visible global function definition for ‘tail’
    plot,amptest-ANY: no visible global function definition for ‘median’
    plot,amptest-ANY: no visible global function definition for ‘mad’
    plot,amptest-ANY: no visible global function definition for
     ‘shapiro.test’
    plot,amptest-ANY: no visible global function definition for
     ‘wilcox.test’
    plot,amptest-ANY: no visible global function definition for ‘layout’
    plot,amptest-ANY: no visible global function definition for ‘abline’
    plot,amptest-ANY: no visible global function definition for ‘text’
    plot,amptest-ANY: no visible global function definition for ‘arrows’
    plot,amptest-ANY: no visible global function definition for ‘mtext’
    plot,amptest-ANY: no visible global function definition for ‘axis’
    plot,bg-ANY: no visible global function definition for ‘abline’
    plot,bg-ANY: no visible global function definition for ‘text’
    plot,der-ANY: no visible global function definition for ‘points’
    plot,eff-ANY: no visible global function definition for ‘predict.lm’
    plot,eff-ANY: no visible global function definition for ‘polygon’
    plot,eff-ANY: no visible global function definition for ‘adjustcolor’
    plot,eff-ANY: no visible global function definition for ‘arrows’
    plot,eff-ANY: no visible global function definition for ‘abline’
    plot,eff-ANY: no visible global function definition for ‘legend’
    plot,refMFI-ANY: no visible global function definition for ‘par’
    plot,refMFI-ANY: no visible global function definition for ‘layout’
    plot,refMFI-ANY: no visible global function definition for ‘arrows’
    plot,refMFI-ANY: no visible global function definition for ‘mtext’
    plot,refMFI-ANY: no visible global function definition for ‘abline’
    plot,refMFI-refMFI: no visible global function definition for ‘par’
    plot,refMFI-refMFI: no visible global function definition for ‘layout’
    plot,refMFI-refMFI: no visible global function definition for ‘points’
    plot,refMFI-refMFI: no visible global function definition for
     ‘adjustcolor’
    plot,refMFI-refMFI: no visible global function definition for ‘arrows’
    plot,refMFI-refMFI: no visible global function definition for ‘mtext’
    plot,refMFI-refMFI: no visible global function definition for ‘abline’
    plot,refMFI-refMFI: no visible global function definition for ‘legend’
    plot,refMFI-refMFI: no visible global function definition for ‘lines’
    qqline,refMFI: no visible binding for global variable ‘qnorm’
    Undefined global functions or variables:
     abline adjustcolor arrows axis coef cor head layout legend lines lm
     mad matplot median mtext na.omit par points polygon predict
     predict.lm qnorm quantile rect rnorm rstudent rug sd shapiro.test
     smooth.spline tail text wilcox.test
    Consider adding
     importFrom("grDevices", "adjustcolor")
     importFrom("graphics", "abline", "arrows", "axis", "layout", "legend",
     "lines", "matplot", "mtext", "par", "points", "polygon",
     "rect", "rug", "text")
     importFrom("stats", "coef", "cor", "lm", "mad", "median", "na.omit",
     "predict", "predict.lm", "qnorm", "quantile", "rnorm",
     "rstudent", "sd", "shapiro.test", "smooth.spline",
     "wilcox.test")
     importFrom("utils", "head", "tail")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 0.0.8-10
Check: examples
Result: ERROR
    Running examples in 'chipPCR-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: amptest
    > ### Title: Class '"amptest"'
    > ### Aliases: amptest amptest-class summary.amptest summary,amptest-method
    > ### show.amptest show,amptest-method plot.amptest plot,amptest-method
    > ### plot,amptest,ANY-method
    > ### Keywords: classes
    >
    > ### ** Examples
    >
    > # Compare a positive and a negative amplification reaction.
    > # First simulate positive reaction (fluo.pos) and than the
    > # negative reaction (fluo.neg).
    > # Simulation of an amplifiaction curve with some noise and a high signal.
    >
    > fluo.pos <- AmpSim(cyc = 1:40, noise = TRUE)[, 2]
    > ampt.pos <- amptester(fluo.pos, manual = TRUE, background = c(0, 15),
    + noiselevel = 0.15)
    Error in validObject(.Object) :
     invalid class "amptest" object: superclass "Mnumeric" not defined in the environment of the object's class
    Calls: amptester -> new -> initialize -> initialize -> validObject
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.0.8-10
Check: examples
Result: ERROR
    Running examples in 'chipPCR-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: amptest
    > ### Title: Class '"amptest"'
    > ### Aliases: amptest amptest-class summary.amptest summary,amptest-method
    > ### show.amptest show,amptest-method plot.amptest plot,amptest-method
    > ### plot,amptest,ANY-method
    > ### Keywords: classes
    >
    > ### ** Examples
    >
    > # Compare a positive and a negative amplification reaction.
    > # First simulate positive reaction (fluo.pos) and than the
    > # negative reaction (fluo.neg).
    > # Simulation of an amplifiaction curve with some noise and a high signal.
    >
    > fluo.pos <- AmpSim(cyc = 1:40, noise = TRUE)[, 2]
    > ampt.pos <- amptester(fluo.pos, manual = TRUE, background = c(0, 15),
    + noiselevel = 0.15)
    Error in validObject(.Object) :
     invalid class "amptest" object: superclass "replValueSp" not defined in the environment of the object's class
    Calls: amptester -> new -> initialize -> initialize -> validObject
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64