CRAN Package Check Results for Package SimPhe

Last updated on 2020-08-07 01:50:00 CEST.

Check Details

Version: 0.2.0
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'simu.pheno' 'usedpars.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: 0.2.0
Check: examples
Result: ERROR
    Running examples in 'SimPhe-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: sim.phe
    > ### Title: Simulation for phenotypes (SimPhe main process)
    > ### Aliases: sim.phe
    >
    > ### ** Examples
    >
    > #### file path of example
    > # simulation parameters:
    > fpar.path <- system.file("extdata", "simupars.txt", package="SimPhe")
    >
    > # genotype file: rows are individuals and columns are SNPs
    > fgeno.path <- system.file("extdata", "10SNP.txt", package="SimPhe")
    >
    >
    > #### instead of a parameter file, prepared list like genepars also works
    > genepars
    $P1mean
     mean
    1 10
    
    $P1main
     SNP additive dominance
    1 SNP01 4.0 2.0
    2 SNP02 2.5 1.5
    3 SNP03 5.5 1.8
    4 SNP04 -2.5 1.0
    5 SNP05 8.5 9.8
    6 SNP06 8.7 8.4
    
    $P1epistasis
     SNPA SNPB additive_additive additive_dominance dominance_additive
    1 SNP01 SNP02 10.0 2.0 2.8
    2 SNP03 SNP04 8.0 3.0 3.5
    3 SNP05 SNP06 20.5 20.6 20.4
     dominance_dominance
    1 1.8
    2 2.5
    3 10.2
    
    $P1heritability
     heritability
    1 0.6
    
    $P2mean
     mean
    1 20
    
    $P2main
     SNP additive dominance
    1 SNP01 8.0 2.0
    2 SNP02 4.5 1.8
    3 SNP03 6.5 1.5
    4 SNP04 -3.5 -1.2
    5 SNP07 10.4 8.6
    6 SNP08 12.3 11.9
    
    $P2epistasis
     SNPA SNPB additive_additive additive_dominance dominance_additive
    1 SNP01 SNP02 15.0 4.0 3.0
    2 SNP03 SNP04 12.0 5.0 3.5
    3 SNP07 SNP08 21.5 20.9 20.5
     dominance_dominance
    1 2.0
    2 2.5
    3 20.3
    
    >
    >
    > #### simulate phenotype(s)
    > phe <- sim.phe(sim.pars = fpar.path, fgeno = fgeno.path, ftype = "snp.head", fwrite = FALSE)
    Warning in readLines(file.new) :
     line 1 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 2 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 3 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 4 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 5 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 6 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 7 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 8 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 9 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 10 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 11 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 12 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 13 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 14 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 15 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 16 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 17 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 18 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 19 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 20 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 21 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 22 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 23 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 24 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 25 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 26 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 27 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 28 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 29 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 30 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 31 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 32 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 33 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 34 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 35 appears to contain an embedded nul
    Warning in readLines(file.new) :
     line 36 appears to contain an embedded nul
    Error in matrix(unlist(sapply(regmatches(x, gregexpr(pattern, x)), function(e) regmatches(e, :
     'data' must be of a vector type, was 'NULL'
    Calls: sim.phe -> read.simu.pars -> regextract -> matrix
    Execution halted
Flavor: r-release-windows-ix86+x86_64