CRAN Package Check Results for Package RFLPtools

Last updated on 2020-10-23 01:49:03 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.6 4.06 54.21 58.27 NOTE
r-devel-linux-x86_64-debian-gcc 1.6 2.56 41.88 44.44 NOTE
r-devel-linux-x86_64-fedora-clang 1.6 82.67 NOTE
r-devel-linux-x86_64-fedora-gcc 1.6 72.26 NOTE
r-devel-windows-ix86+x86_64 1.6 7.00 83.00 90.00 NOTE
r-patched-linux-x86_64 1.6 3.49 51.71 55.20 NOTE
r-patched-solaris-x86 1.6 97.70 NOTE
r-release-linux-x86_64 1.6 3.18 51.40 54.58 NOTE
r-release-macos-x86_64 1.6 NOTE
r-release-windows-ix86+x86_64 1.6 7.00 84.00 91.00 NOTE
r-oldrel-macos-x86_64 1.6 ERROR
r-oldrel-windows-ix86+x86_64 1.6 5.00 82.00 87.00 NOTE

Check Details

Version: 1.6
Check: R code for possible problems
Result: NOTE
    RFLPdist: no visible binding for global variable 'dist'
    RFLPdist2: no visible binding for global variable 'dist'
    RFLPdist2 : dfun1: no visible global function definition for 'combn'
    RFLPdist2 : dfun2: no visible global function definition for 'combn'
    RFLPdist2ref: no visible binding for global variable 'dist'
    RFLPplot: no visible binding for global variable 'dist'
    RFLPplot: no visible global function definition for 'order.dendrogram'
    RFLPplot: no visible global function definition for 'as.dendrogram'
    RFLPplot: no visible global function definition for 'hclust'
    RFLPplot: no visible global function definition for 'par'
    RFLPplot: no visible global function definition for 'axis'
    RFLPplot: no visible global function definition for 'abline'
    RFLPplot: no visible global function definition for 'box'
    RFLPplot: no visible global function definition for 'title'
    RFLPplot: no visible global function definition for 'colorRampPalette'
    RFLPplot: no visible global function definition for 'matlines'
    RFLPrefplot: no visible binding for global variable 'dist'
    RFLPrefplot: no visible global function definition for 'par'
    RFLPrefplot: no visible global function definition for 'dev.new'
    RFLPrefplot: no visible global function definition for 'axis'
    RFLPrefplot: no visible global function definition for 'abline'
    RFLPrefplot: no visible global function definition for 'box'
    RFLPrefplot: no visible global function definition for 'title'
    RFLPrefplot: no visible global function definition for
     'colorRampPalette'
    RFLPrefplot: no visible global function definition for 'matlines'
    diffDist: no visible global function definition for 'dist'
    read.blast: no visible global function definition for 'read.table'
    read.rflp: no visible global function definition for 'read.delim'
    read.rflp : <anonymous>: no visible global function definition for
     'tail'
    sim2dist: no visible global function definition for 'as.dist'
    simulateRFLPdata: no visible global function definition for 'runif'
    write.hclust: no visible global function definition for 'cutree'
    write.hclust: no visible global function definition for 'write.table'
    Undefined global functions or variables:
     abline as.dendrogram as.dist axis box colorRampPalette combn cutree
     dev.new dist hclust matlines order.dendrogram par read.delim
     read.table runif tail title write.table
    Consider adding
     importFrom("grDevices", "colorRampPalette", "dev.new")
     importFrom("graphics", "abline", "axis", "box", "matlines", "par",
     "title")
     importFrom("stats", "as.dendrogram", "as.dist", "cutree", "dist",
     "hclust", "order.dendrogram", "runif")
     importFrom("utils", "combn", "read.delim", "read.table", "tail",
     "write.table")
    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-macos-x86_64, r-release-windows-ix86+x86_64

Version: 1.6
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'Test.txt'
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: 1.6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘MKmisc’
Flavor: r-oldrel-macos-x86_64

Version: 1.6
Check: R code for possible problems
Result: NOTE
    RFLPdist: no visible binding for global variable ‘dist’
    RFLPdist2: no visible binding for global variable ‘dist’
    RFLPdist2 : dfun1: no visible global function definition for ‘combn’
    RFLPdist2 : dfun2: no visible global function definition for ‘combn’
    RFLPdist2ref: no visible binding for global variable ‘dist’
    RFLPplot: no visible binding for global variable ‘dist’
    RFLPplot: no visible global function definition for ‘order.dendrogram’
    RFLPplot: no visible global function definition for ‘as.dendrogram’
    RFLPplot: no visible global function definition for ‘hclust’
    RFLPplot: no visible global function definition for ‘par’
    RFLPplot: no visible global function definition for ‘plot’
    RFLPplot: no visible global function definition for ‘axis’
    RFLPplot: no visible global function definition for ‘abline’
    RFLPplot: no visible global function definition for ‘box’
    RFLPplot: no visible global function definition for ‘title’
    RFLPplot: no visible global function definition for ‘colorRampPalette’
    RFLPplot: no visible global function definition for ‘matlines’
    RFLPrefplot: no visible binding for global variable ‘dist’
    RFLPrefplot: no visible global function definition for ‘par’
    RFLPrefplot: no visible global function definition for ‘dev.new’
    RFLPrefplot: no visible global function definition for ‘plot’
    RFLPrefplot: no visible global function definition for ‘axis’
    RFLPrefplot: no visible global function definition for ‘abline’
    RFLPrefplot: no visible global function definition for ‘box’
    RFLPrefplot: no visible global function definition for ‘title’
    RFLPrefplot: no visible global function definition for
     ‘colorRampPalette’
    RFLPrefplot: no visible global function definition for ‘matlines’
    diffDist: no visible global function definition for ‘dist’
    read.blast: no visible global function definition for ‘read.table’
    read.rflp: no visible global function definition for ‘read.delim’
    read.rflp : <anonymous>: no visible global function definition for
     ‘tail’
    sim2dist: no visible global function definition for ‘as.dist’
    simulateRFLPdata: no visible global function definition for ‘runif’
    write.hclust: no visible global function definition for ‘cutree’
    write.hclust: no visible global function definition for ‘write.table’
    Undefined global functions or variables:
     abline as.dendrogram as.dist axis box colorRampPalette combn cutree
     dev.new dist hclust matlines order.dendrogram par plot read.delim
     read.table runif tail title write.table
    Consider adding
     importFrom("grDevices", "colorRampPalette", "dev.new")
     importFrom("graphics", "abline", "axis", "box", "matlines", "par",
     "plot", "title")
     importFrom("stats", "as.dendrogram", "as.dist", "cutree", "dist",
     "hclust", "order.dendrogram", "runif")
     importFrom("utils", "combn", "read.delim", "read.table", "tail",
     "write.table")
    to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.6
Check: examples
Result: ERROR
    Running examples in ‘RFLPtools-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: RFLPtools-package
    > ### Title: Tools to analyse RFLP-data
    > ### Aliases: RFLPtools-package RFLPtools
    > ### Keywords: package multivariate cluster
    >
    > ### ** Examples
    >
    > data(RFLPdata)
    > res <- RFLPdist(RFLPdata)
    > plot(hclust(res[[1]]), main = "Euclidean distance")
    >
    > par(mfrow = c(1,2))
    > plot(hclust(RFLPdist(RFLPdata, nrBands = 3)), cex = 0.7)
    > RFLPplot(RFLPdata, nrBands = 3, mar.bottom = 6, cex.axis = 0.8)
    >
    > data(RFLPref)
    > RFLPrefplot(RFLPdata, RFLPref, nrBands = 6, cex.axis = 0.8)
    >
    >
    > library(MKmisc)
    Error in library(MKmisc) : there is no package called ‘MKmisc’
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 1.6
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘RFLPtools.Rnw’
     ...
     - attr(*, "Diag")= logi FALSE
     - attr(*, "Upper")= logi FALSE
     - attr(*, "method")= chr "maximum"
     - attr(*, "call")= language dist(x = x, method = "maximum")
    
    > library(MKmisc)
    
     When sourcing ‘RFLPtools.R’:
    Error: there is no package called ‘MKmisc’
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 1.6
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘RFLPtools.Rnw’ using Sweave
    Loading required package: RColorBrewer
    
    Error: processing vignette 'RFLPtools.Rnw' failed with diagnostics:
     chunk 5 (label = cor)
    Error in library(MKmisc) : there is no package called ‘MKmisc’
    
    --- failed re-building ‘RFLPtools.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘RFLPtools.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64