CRAN Package Check Results for Package sidier

Last updated on 2016-12-03 05:47:27.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.0.1 2.16 51.28 53.44 NOTE
r-devel-linux-x86_64-debian-gcc 3.0.1 2.20 51.18 53.39 NOTE
r-devel-linux-x86_64-fedora-clang 3.0.1 100.20 NOTE
r-devel-linux-x86_64-fedora-gcc 3.0.1 98.84 NOTE
r-devel-macos-x86_64-clang 3.0.1 80.89 NOTE
r-devel-windows-ix86+x86_64 3.0.1 6.00 103.00 109.00 NOTE
r-patched-linux-x86_64 3.0.1 2.00 33.42 35.42 ERROR
r-patched-solaris-sparc 3.0.1 415.80 ERROR
r-patched-solaris-x86 3.0.1 88.10 ERROR
r-release-linux-x86_64 3.0.1 1.97 44.81 46.78 NOTE
r-release-osx-x86_64-mavericks 3.0.1 NOTE
r-release-windows-ix86+x86_64 3.0.1 12.00 126.00 138.00 NOTE
r-oldrel-windows-ix86+x86_64 3.0.1 11.00 82.00 93.00 OK

Check Details

Version: 3.0.1
Check: R code for possible problems
Result: NOTE
    BARRIEL: no visible global function definition for ‘write.table’
    FIFTH: no visible global function definition for ‘write.table’
    FindHaplo: no visible global function definition for ‘write.table’
    HapPerPop: no visible global function definition for ‘read.table’
    HapPerPop: no visible global function definition for ‘write.table’
    MCIC: no visible global function definition for ‘write.table’
    NINA.thr: no visible global function definition for ‘pdf’
    NINA.thr: no visible global function definition for ‘dev.off’
    NINA.thr: no visible global function definition for ‘write.table’
    SIC: no visible global function definition for ‘write.table’
    distance.comb: no visible global function definition for ‘write.table’
    double.plot: no visible global function definition for ‘layout’
    double.plot: no visible global function definition for ‘mtext’
    mergeNodes: no visible global function definition for ‘write.table’
    mutation.network: no visible global function definition for
     ‘write.table’
    mutation.network: no visible global function definition for ‘png’
    mutation.network: no visible global function definition for ‘dev.off’
    mutation.network: no visible global function definition for ‘plot’
    mutation.network: no visible global function definition for ‘mtext’
    mutation.network: no visible global function definition for ‘segments’
    mutation.network: no visible global function definition for ‘lines’
    mutation.network: no visible global function definition for ‘points’
    mutation.network: no visible global function definition for ‘text’
    nt.gap.comb: no visible global function definition for ‘write.table’
    perc.thr: no visible global function definition for ‘pdf’
    perc.thr: no visible global function definition for ‘dev.off’
    perc.thr: no visible global function definition for ‘plot’
    perc.thr: no visible global function definition for ‘points’
    perc.thr: no visible global function definition for ‘write.table’
    pie.network: no visible global function definition for ‘write.table’
    pie.network: no visible global function definition for ‘mtext’
    pie.network: no visible global function definition for ‘par’
    pie.network: no visible global function definition for ‘text’
    pie.network: no visible global function definition for ‘lines’
    pie.network: no visible global function definition for ‘colors’
    pie.network: no visible global function definition for ‘points’
    pie.network: no visible global function definition for ‘pie’
    pop.dist: no visible global function definition for ‘read.table’
    pop.dist: no visible global function definition for ‘write.table’
    simplify.network: no visible global function definition for ‘plot’
    simplify.network: no visible global function definition for ‘lines’
    simplify.network: no visible global function definition for ‘points’
    simplify.network: no visible global function definition for ‘text’
    simplify.network: no visible global function definition for ‘as.dist’
    simuEvolution: no visible global function definition for ‘write.table’
    single.network: no visible global function definition for ‘write.table’
    single.network: no visible global function definition for ‘pdf’
    single.network: no visible global function definition for ‘dev.off’
    spatial.plot: no visible global function definition for ‘write.table’
    spatial.plot: no visible global function definition for ‘plot’
    spatial.plot: no visible global function definition for ‘segments’
    spatial.plot: no visible global function definition for ‘text’
    spatial.plot: no visible global function definition for ‘dev.new’
    zero.thr: no visible global function definition for ‘write.table’
    zero.thr: no visible global function definition for ‘pdf’
    zero.thr: no visible global function definition for ‘dev.off’
    Undefined global functions or variables:
     as.dist colors dev.new dev.off layout lines mtext par pdf pie plot
     png points read.table segments text write.table
    Consider adding
     importFrom("grDevices", "colors", "dev.new", "dev.off", "pdf", "png")
     importFrom("graphics", "layout", "lines", "mtext", "par", "pie",
     "plot", "points", "segments", "text")
     importFrom("stats", "as.dist")
     importFrom("utils", "read.table", "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-macos-x86_64-clang, 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: 3.0.1
Check: examples
Result: ERROR
    Running examples in ‘sidier-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: double.plot
    > ### Title: Haplotype and population networks including mutations and
    > ### haplotype frequencies.
    > ### Aliases: double.plot
    >
    > ### ** Examples
    >
    > cat(">Population1_sequence1",
    + "TTATAAAATCTA----TAGC",
    + ">Population1_sequence2",
    + "TAAT----TCTA----TAAC",
    + ">Population1_sequence3",
    + "TTATAAAAATTA----TAGC",
    + ">Population1_sequence4",
    + "TAAT----TCTA----TAAC",
    + ">Population2_sequence1",
    + "TTAT----TCGAGGGGTAGC",
    + ">Population2_sequence2",
    + "TAAT----TCTA----TAAC",
    + ">Population2_sequence3",
    + "TTATAAAA--------TAGC",
    + ">Population2_sequence4",
    + "TTAT----TCGAGGGGTAGC",
    + ">Population3_sequence1",
    + "TTAT----TCGA----TAGC",
    + ">Population3_sequence2",
    + "TTAT----TCGA----TAGC",
    + ">Population3_sequence3",
    + "TTAT----TCGA----TAGC",
    + ">Population3_sequence4",
    + "TTAT----TCGA----TAGC",
    + file = "ex2.fas", sep = "\n")
    > library(ape)
    > double.plot(align=read.dna(file="ex2.fas",format="fasta"))
    Warning in pie.network(align = align, indel.method = indel.method, substitution.model = substitution.model, :
     Population names defined by algorithm between character 1 and the first symbol '_' in sequences name.
    Error in rep(colnames(pop2)[which(pop2 != 0)], pop2[which(pop2 != 0)]) :
     invalid 'times' argument
    Calls: double.plot -> pie.network -> pop.dist
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 3.0.1
Check: examples
Result: ERROR
    Running examples in ‘sidier-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: double.plot
    > ### Title: Haplotype and population networks including mutations and
    > ### haplotype frequencies.
    > ### Aliases: double.plot
    >
    > ### ** Examples
    >
    > cat(">Population1_sequence1",
    + "TTATAAAATCTA----TAGC",
    + ">Population1_sequence2",
    + "TAAT----TCTA----TAAC",
    + ">Population1_sequence3",
    + "TTATAAAAATTA----TAGC",
    + ">Population1_sequence4",
    + "TAAT----TCTA----TAAC",
    + ">Population2_sequence1",
    + "TTAT----TCGAGGGGTAGC",
    + ">Population2_sequence2",
    + "TAAT----TCTA----TAAC",
    + ">Population2_sequence3",
    + "TTATAAAA--------TAGC",
    + ">Population2_sequence4",
    + "TTAT----TCGAGGGGTAGC",
    + ">Population3_sequence1",
    + "TTAT----TCGA----TAGC",
    + ">Population3_sequence2",
    + "TTAT----TCGA----TAGC",
    + ">Population3_sequence3",
    + "TTAT----TCGA----TAGC",
    + ">Population3_sequence4",
    + "TTAT----TCGA----TAGC",
    + file = "ex2.fas", sep = "\n")
    > library(ape)
    > double.plot(align=read.dna(file="ex2.fas",format="fasta"))
    Warning in pie.network(align = align, indel.method = indel.method, substitution.model = substitution.model, :
     Population names defined by algorithm between character 1 and the first symbol '_' in sequences name.
    Error in rep(colnames(pop2)[which(pop2 != 0)], pop2[which(pop2 != 0)]) :
     invalid 'times' argument
    Calls: double.plot -> pie.network -> pop.dist
    Execution halted
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86