CRAN Package Check Results for Package reGenotyper

Last updated on 2019-12-21 10:47:57 CET.

Check Details

Version: 1.2.0
Check: R code for possible problems
Result: NOTE
    .area.my: no visible global function definition for 'density'
    optimalGT : <anonymous>: no visible global function definition for
     'median'
    optimalGT: no visible global function definition for 'png'
    optimalGT: no visible global function definition for 'dev.off'
    permutation: no visible global function definition for 'flush.console'
    plot.wls: no visible global function definition for 'par'
    plot.wls: no visible global function definition for 'plot'
    plot.wls: no visible global function definition for 'text'
    plot.wls: no visible global function definition for 'abline'
    reGenotyper: no visible global function definition for 'flush.console'
    reGenotyper: no visible binding for global variable 'var'
    reGenotyper: no visible global function definition for 'plot'
    Undefined global functions or variables:
     abline density dev.off flush.console median par plot png text var
    Consider adding
     importFrom("grDevices", "dev.off", "png")
     importFrom("graphics", "abline", "par", "plot", "text")
     importFrom("stats", "density", "median", "var")
     importFrom("utils", "flush.console")
    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-devel-windows-ix86+x86_64-gcc8, 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: 1.2.0
Check: examples
Result: ERROR
    Running examples in 'reGenotyper-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: reGenotyper
    > ### Title: Detecting mislabeled samples, recovering the optimal genotypes
    > ### for genetical genomics experiments
    > ### Aliases: reGenotyper
    > ### Keywords: method
    >
    > ### ** Examples
    >
    > library(reGenotyper)
    > #load example genotype and phenotype data
    > data(genotype)
    > data(phenotype)
    > ### For this test dataset 5 permutations is enough. In real case at least few hundreds
    > ### of permutations are needed.
    > wlsObject <- reGenotyper(phenotype, genotype, fileName = "test", thres = 0.9, optGT = TRUE,
    + optGTplot = FALSE, optGT.thres = 0, permu = TRUE, n.permu = 5, wls.score.permu = NULL,
    + process = TRUE, t.thres = 1.5, GT.ref=NULL)
    STEP 1: Checking arguments...
     There were two possible gentoypes: 1 and 2 in input genotypes, which have been coded as 0,1 in reGenotyper
    
    STEP 2: Computing QTL profiles using original genotype data...
    Error in CreateFromMatrix(mat) : class(mat) == "matrix" are not all TRUE
    Calls: reGenotyper ... initialize -> <Anonymous> -> CreateFromMatrix -> stopifnot
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.2.0
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     ‘delta_t_mat_allmk_list_test.Rdata’ ‘gt_opt_test.Rdata’
     ‘t_mat0_test.Rdata’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc