CRAN Package Check Results for Package plmDE

Last updated on 2018-06-17 19:49:52 CEST.

Check Details

Version: 1.0
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘R.oo’ ‘limma’ ‘splines’
     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-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     head.DEresults head.plmDE hist.DEresults info.plmDE
     plmDEmodel.default plot.DEresults
    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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.0
Check: R code for possible problems
Result: NOTE
    fitBspline: no visible global function definition for ‘median’
    fitBspline: no visible global function definition for ‘quantile’
    fitGAPLM: no visible global function definition for ‘poisson’
    fitGAPLM: no visible global function definition for ‘quantile’
    fitGAPLM: no visible global function definition for ‘anova’
    fitGAPLM: no visible global function definition for ‘as.formula’
    fitGAPLM: no visible global function definition for ‘glm’
    fitGAPLM: no visible global function definition for ‘pf’
    fitGAPLM: no visible global function definition for ‘lm’
    fitGAPLM: no visible global function definition for ‘p.adjust’
    head.DEresults: no visible global function definition for ‘head’
    head.plmDE: no visible global function definition for ‘head’
    hist.DEresults: no visible global function definition for ‘hist’
    hist.DEresults: no visible global function definition for ‘colors’
    hist.DEresults: no visible global function definition for ‘box’
    limmaPLM: no visible global function definition for ‘quantile’
    plot.DEresults: no visible global function definition for ‘as.formula’
    plot.DEresults: no visible global function definition for ‘lm’
    plot.DEresults: no visible global function definition for ‘glm’
    plot.DEresults: no visible global function definition for ‘plot’
    plot.DEresults: no visible global function definition for ‘lines’
    plot.DEresults: no visible global function definition for ‘points’
    plot.DEresults: no visible global function definition for ‘predict’
    Undefined global functions or variables:
     anova as.formula box colors glm head hist lines lm median p.adjust pf
     plot points poisson predict quantile
    Consider adding
     importFrom("grDevices", "colors")
     importFrom("graphics", "box", "hist", "lines", "plot", "points")
     importFrom("stats", "anova", "as.formula", "glm", "lm", "median",
     "p.adjust", "pf", "poisson", "predict", "quantile")
     importFrom("utils", "head")
    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-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0
Check: Rd line widths
Result: NOTE
    Rd file 'info.plmDE.Rd':
     \examples lines wider than 100 characters:
     DataInfo = data.frame(sample = names(ExpressionData), group = c(rep("Control", 50), rep("Diseased", 50)), weight = abs(rnorm(100, 50, 2 ... [TRUNCATED]
    
    These lines will be truncated in the PDF 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-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0
Check: examples
Result: ERROR
    Running examples in ‘plmDE-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: fitGAPLM
    > ### Title: Fit a Generalized Additive Partially Linear Model on Gene
    > ### Expression Data
    > ### Aliases: fitGAPLM
    > ### Keywords: models regression
    >
    > ### ** Examples
    >
    > ## create an object of type \code{plmDE} containing disease with
    > ## "control" and "disease" and measures of weight and severity:
    > ExpressionData = as.data.frame(matrix(abs(rnorm(10000, 1, 1.5)), ncol = 100))
    > names(ExpressionData) = sapply(1:100, function(x) paste("Sample", x))
    > Genes = sapply(1:100, function(x) paste("Gene", x))
    > DataInfo = data.frame(sample = names(ExpressionData), group = c(rep("Control", 50),
    + rep("Diseased", 50)), weight = abs(rnorm(100, 50, 20)), severity = c(rep(0, 50),
    + abs(rnorm(50, 100, 20))))
    > plmDEobject = plmDEmodel(Genes, ExpressionData, DataInfo)
    Error in UseMethod("plmDEmodel") :
     no applicable method for 'plmDEmodel' applied to an object of class "character"
    Calls: plmDEmodel
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0
Check: DESCRIPTION meta-information
Result: ERROR
    dyld: Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib
     Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib
     Reason: no suitable image found. Did find:
     /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib: pread of first 4K failed: 0
     /Library/Frameworks/R.framework/Resources/lib/libgfortran.3.dylib: file too short
Flavor: r-release-osx-x86_64

Version: 1.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘edgeR’ ‘DESeq’
Flavor: r-oldrel-osx-x86_64