CRAN Package Check Results for Package PopGenome

Last updated on 2016-12-04 12:47:59.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1.6 12.88 79.79 92.67 NOTE
r-devel-linux-x86_64-debian-gcc 2.1.6 12.86 76.15 89.01 NOTE
r-devel-linux-x86_64-fedora-clang 2.1.6 176.12 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 2.1.6 151.28 NOTE
r-devel-macos-x86_64-clang 2.1.6 128.41 NOTE
r-devel-windows-ix86+x86_64 2.1.6 111.00 163.00 274.00 WARN
r-patched-linux-x86_64 2.1.6 11.67 76.46 88.14 NOTE
r-patched-solaris-sparc 2.1.6 839.90 NOTE
r-patched-solaris-x86 2.1.6 154.80 NOTE
r-release-linux-x86_64 2.1.6 11.73 74.83 86.55 NOTE
r-release-osx-x86_64-mavericks 2.1.6 NOTE
r-release-windows-ix86+x86_64 2.1.6 181.00 129.00 310.00 NOTE
r-oldrel-windows-ix86+x86_64 2.1.6 91.00 149.00 240.00 OK

Check Details

Version: 2.1.6
Check: R code for possible problems
Result: NOTE
    BayeScanR: no visible global function definition for ‘rnorm’
    MK: no visible global function definition for ‘combn’
    MS: no visible global function definition for ‘var’
    MS: no visible binding for global variable ‘var’
    PopGplot: no visible global function definition for ‘rainbow’
    PopGplot: no visible global function definition for ‘loess’
    PopGplot: no visible global function definition for ‘plot’
    PopGplot: no visible global function definition for ‘predict’
    PopGplot: no visible global function definition for ‘lines’
    Whop_readVCF: no visible global function definition for ‘read.table’
    calc_average_nuc_diversity_between_per_site: no visible global function
     definition for ‘combn’
    calc_diversities: no visible global function definition for ‘combn’
    calc_hwhafsth: no visible global function definition for ‘combn’
    calc_hwhafsth_FAST: no visible global function definition for ‘combn’
    calc_pi: no visible global function definition for ‘combn’
    calc_quantile: no visible global function definition for ‘quantile’
    coalsim: no visible global function definition for ‘var’
    coalsim: no visible binding for global variable ‘var’
    fstcalc: no visible global function definition for ‘combn’
    get.feature.names: no visible global function definition for
     ‘read.table’
    get_gff_info: no visible global function definition for ‘read.table’
    get_ref_alleles: no visible global function definition for ‘read.table’
    gffRead: no visible global function definition for ‘read.table’
    gtest: no visible global function definition for ‘pchisq’
    hudsonkaplan85rm: no visible global function definition for ‘combn’
    intern.calc.R2 : <anonymous>: no visible global function definition for
     ‘fisher.test’
    jump_model_codominant: no visible global function definition for
     ‘rnorm’
    jump_model_codominant: no visible global function definition for
     ‘runif’
    linkdisequ: no visible global function definition for ‘combn’
    mismatch: no visible global function definition for ‘combn’
    my_rdirichlet: no visible global function definition for ‘rgamma’
    pair_linkdisequ_FAST : <anonymous>: no visible global function
     definition for ‘fisher.test’
    permute: no visible global function definition for ‘combn’
    plot_avg_cs: no visible global function definition for ‘plot’
    plot_avg_cs: no visible global function definition for ‘density’
    plot_avg_cs: no visible global function definition for ‘abline’
    readData: no visible global function definition for ‘combn’
    readSNP: no visible global function definition for ‘read.table’
    readVCF: no visible global function definition for ‘read.table’
    readVCFchunk: no visible global function definition for ‘read.table’
    readVCFchunkHap: no visible global function definition for ‘read.table’
    readVCFchunk_tet: no visible global function definition for
     ‘read.table’
    readVCFchunk_tri: no visible global function definition for
     ‘read.table’
    set_gff_info: no visible global function definition for ‘read.table’
    snn: no visible global function definition for ‘combn’
    split_data_into_GFF_attributes: no visible global function definition
     for ‘read.table’
    update_d_alphaco_i: no visible global function definition for ‘rnorm’
    update_d_alphaco_i: no visible global function definition for ‘runif’
    update_d_betaco: no visible global function definition for ‘rnorm’
    update_d_betaco: no visible global function definition for ‘runif’
    update_freq_codominant: no visible global function definition for
     ‘runif’
    F_ST.stats.2,GENOME: no visible global function definition for ‘combn’
    F_ST.stats,GENOME: no visible global function definition for ‘combn’
    MKT,GENOME: no visible global function definition for ‘combn’
    MKT,GENOME : <anonymous>: no visible global function definition for
     ‘fisher.test’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘colors’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘plot’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘axis’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘abline’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘points’
    SNPFST,GENOME: no visible global function definition for ‘combn’
    diversity.stats,GENOME: no visible global function definition for
     ‘combn’
    mult.linkage.stats,GENOME: no visible global function definition for
     ‘combn’
    popFSTN,GENOME: no visible global function definition for ‘combn’
    Undefined global functions or variables:
     abline axis colors combn density fisher.test lines loess pchisq plot
     points predict quantile rainbow read.table rgamma rnorm runif var
    Consider adding
     importFrom("grDevices", "colors", "rainbow")
     importFrom("graphics", "abline", "axis", "lines", "plot", "points")
     importFrom("stats", "density", "fisher.test", "loess", "pchisq",
     "predict", "quantile", "rgamma", "rnorm", "runif", "var")
     importFrom("utils", "combn", "read.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-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: 2.1.6
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    BayeScanR: no visible global function definition for ‘rnorm’
    MK: no visible global function definition for ‘combn’
    MS: no visible global function definition for ‘var’
    MS: no visible binding for global variable ‘var’
    PopGplot: no visible global function definition for ‘rainbow’
    PopGplot: no visible global function definition for ‘loess’
    PopGplot: no visible global function definition for ‘plot’
    PopGplot: no visible global function definition for ‘predict’
    PopGplot: no visible global function definition for ‘lines’
    Whop_readVCF: no visible global function definition for ‘read.table’
    calc_average_nuc_diversity_between_per_site: no visible global function
     definition for ‘combn’
    calc_diversities: no visible global function definition for ‘combn’
    calc_hwhafsth: no visible global function definition for ‘combn’
    calc_hwhafsth_FAST: no visible global function definition for ‘combn’
    calc_pi: no visible global function definition for ‘combn’
    calc_quantile: no visible global function definition for ‘quantile’
    coalsim: no visible global function definition for ‘var’
    coalsim: no visible binding for global variable ‘var’
    fstcalc: no visible global function definition for ‘combn’
    get.feature.names: no visible global function definition for
     ‘read.table’
    get_gff_info: no visible global function definition for ‘read.table’
    get_ref_alleles: no visible global function definition for ‘read.table’
    gffRead: no visible global function definition for ‘read.table’
    gtest: no visible global function definition for ‘pchisq’
    hudsonkaplan85rm: no visible global function definition for ‘combn’
    intern.calc.R2 : <anonymous>: no visible global function definition for
     ‘fisher.test’
    jump_model_codominant: no visible global function definition for
     ‘rnorm’
    jump_model_codominant: no visible global function definition for
     ‘runif’
    linkdisequ: no visible global function definition for ‘combn’
    mismatch: no visible global function definition for ‘combn’
    my_rdirichlet: no visible global function definition for ‘rgamma’
    pair_linkdisequ_FAST : <anonymous>: no visible global function
     definition for ‘fisher.test’
    permute: no visible global function definition for ‘combn’
    plot_avg_cs: no visible global function definition for ‘plot’
    plot_avg_cs: no visible global function definition for ‘density’
    plot_avg_cs: no visible global function definition for ‘abline’
    readData: no visible global function definition for ‘combn’
    readSNP: no visible global function definition for ‘read.table’
    readVCF: no visible global function definition for ‘read.table’
    readVCFchunk: no visible global function definition for ‘read.table’
    readVCFchunkHap: no visible global function definition for ‘read.table’
    readVCFchunk_tet: no visible global function definition for
     ‘read.table’
    readVCFchunk_tri: no visible global function definition for
     ‘read.table’
    set_gff_info: no visible global function definition for ‘read.table’
    snn: no visible global function definition for ‘combn’
    split_data_into_GFF_attributes: no visible global function definition
     for ‘read.table’
    update_d_alphaco_i: no visible global function definition for ‘rnorm’
    update_d_alphaco_i: no visible global function definition for ‘runif’
    update_d_betaco: no visible global function definition for ‘rnorm’
    update_d_betaco: no visible global function definition for ‘runif’
    update_freq_codominant: no visible global function definition for
     ‘runif’
    F_ST.stats.2,GENOME: no visible global function definition for ‘combn’
    F_ST.stats,GENOME: no visible global function definition for ‘combn’
    MKT,GENOME: no visible global function definition for ‘combn’
    MKT,GENOME : <anonymous>: no visible global function definition for
     ‘fisher.test’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘colors’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘plot’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘axis’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘abline’
    PG_plot.biallelic.matrix,GENOME: no visible global function definition
     for ‘points’
    SNPFST,GENOME: no visible global function definition for ‘combn’
    diversity.stats,GENOME: no visible global function definition for
     ‘combn’
    mult.linkage.stats,GENOME: no visible global function definition for
     ‘combn’
    popFSTN,GENOME: no visible global function definition for ‘combn’
    Undefined global functions or variables:
     abline axis colors combn density fisher.test lines loess pchisq plot
     points predict quantile rainbow read.table rgamma rnorm runif var
    Consider adding
     importFrom("grDevices", "colors", "rainbow")
     importFrom("graphics", "abline", "axis", "lines", "plot", "points")
     importFrom("stats", "density", "fisher.test", "loess", "pchisq",
     "predict", "quantile", "rgamma", "rnorm", "runif", "var")
     importFrom("utils", "combn", "read.table")
    to your NAMESPACE file.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.1.6
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     tabix/knetfile.c:434:5: warning: ISO C does not support the 'I64' ms_printf length modifier [-Wformat=]
Flavor: r-devel-windows-ix86+x86_64