• using R version 4.0.0 (2020-04-24)
• using platform: x86_64-apple-darwin17.0 (64-bit)
• using session charset: UTF-8
• checking for file ‘GWAF/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘GWAF’ version ‘2.2’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘GWAF’ can be installed ... [13s/17s] WARNING
  Found the following significant warnings:
    Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
  See https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64/GWAF-00install.html for details.
  Information on the location(s) of code generating the ‘Note’s can be
  obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
  to ‘yes’.
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [13s/17s] NOTE
  GWplot: no visible global function definition for ‘bitmap’
  GWplot: no visible global function definition for ‘par’
  GWplot: no visible global function definition for ‘write.table’
  GWplot: no visible binding for global variable ‘median’
  GWplot: no visible global function definition for ‘axis’
  GWplot: no visible global function definition for ‘points’
  GWplot: no visible global function definition for ‘abline’
  GWplot: no visible global function definition for ‘dev.off’
  auto: no visible global function definition for ‘read.table’
  geepack.lgst: no visible global function definition for ‘na.omit’
  geepack.lgst : cor.snp: no visible global function definition for ‘sd’
  geepack.lgst : cor.snp: no visible global function definition for ‘cor’
  geepack.lgst: no visible global function definition for ‘fisher.test’
  geepack.lgst: no visible global function definition for ‘chisq.test’
  geepack.lgst: no visible global function definition for ‘as.formula’
  geepack.lgst: no visible global function definition for ‘glm’
  geepack.lgst: no visible binding for global variable ‘na.omit’
  geepack.lgst: no visible global function definition for ‘pchisq’
  geepack.lgst.batch : read.in.data: no visible global function
    definition for ‘read.table’
  geepack.lgst.batch: no visible global function definition for ‘na.omit’
  geepack.lgst.batch: no visible global function definition for ‘var’
  geepack.lgst.batch: no visible binding for global variable ‘var’
  geepack.lgst.batch: no visible global function definition for ‘cor’
  geepack.lgst.batch: no visible global function definition for
    ‘write.table’
  geepack.lgst.batch.imputed : read.in.data: no visible global function
    definition for ‘read.table’
  geepack.lgst.batch.imputed: no visible global function definition for
    ‘na.omit’
  geepack.lgst.batch.imputed: no visible global function definition for
    ‘var’
  geepack.lgst.batch.imputed: no visible binding for global variable
    ‘var’
  geepack.lgst.batch.imputed: no visible global function definition for
    ‘cor’
  geepack.lgst.batch.imputed: no visible global function definition for
    ‘write.table’
  geepack.lgst.imputed: no visible global function definition for
    ‘na.omit’
  geepack.lgst.imputed : cor.snp: no visible global function definition
    for ‘sd’
  geepack.lgst.imputed : cor.snp: no visible global function definition
    for ‘cor’
  geepack.lgst.imputed: no visible global function definition for
    ‘chisq.test’
  geepack.lgst.imputed: no visible global function definition for
    ‘as.formula’
  geepack.lgst.imputed: no visible global function definition for ‘glm’
  geepack.lgst.imputed: no visible binding for global variable ‘na.omit’
  geepack.lgst.imputed: no visible global function definition for
    ‘pchisq’
  geepack.lgst.int: no visible global function definition for ‘na.omit’
  geepack.lgst.int : cor.snp: no visible global function definition for
    ‘sd’
  geepack.lgst.int : cor.snp: no visible global function definition for
    ‘cor’
  geepack.lgst.int: no visible global function definition for ‘cor’
  geepack.lgst.int: no visible global function definition for
    ‘chisq.test’
  geepack.lgst.int: no visible global function definition for ‘glm’
  geepack.lgst.int: no visible global function definition for ‘pchisq’
  geepack.lgst.int.batch : read.in.data: no visible global function
    definition for ‘read.table’
  geepack.lgst.int.batch: no visible global function definition for
    ‘na.omit’
  geepack.lgst.int.batch: no visible global function definition for ‘var’
  geepack.lgst.int.batch: no visible binding for global variable ‘var’
  geepack.lgst.int.batch: no visible global function definition for ‘cor’
  geepack.lgst.int.batch: no visible global function definition for
    ‘write.table’
  geepack.lgst.int.batch.imputed : read.in.data: no visible global
    function definition for ‘read.table’
  geepack.lgst.int.batch.imputed: no visible global function definition
    for ‘na.omit’
  geepack.lgst.int.batch.imputed: no visible global function definition
    for ‘var’
  geepack.lgst.int.batch.imputed: no visible binding for global variable
    ‘var’
  geepack.lgst.int.batch.imputed: no visible global function definition
    for ‘cor’
  geepack.lgst.int.batch.imputed: no visible global function definition
    for ‘write.table’
  geepack.lgst.int.imputed: no visible global function definition for
    ‘var’
  geepack.lgst.int.imputed: no visible binding for global variable ‘var’
  geepack.lgst.int.imputed: no visible global function definition for
    ‘na.omit’
  geepack.lgst.int.imputed : cor.snp: no visible global function
    definition for ‘sd’
  geepack.lgst.int.imputed : cor.snp: no visible global function
    definition for ‘cor’
  geepack.lgst.int.imputed: no visible global function definition for
    ‘cor’
  geepack.lgst.int.imputed: no visible global function definition for
    ‘glm’
  geepack.lgst.int.imputed: no visible global function definition for
    ‘pchisq’
  geepack.quant.batch : cor.snp: no visible global function definition
    for ‘sd’
  geepack.quant.batch : cor.snp: no visible global function definition
    for ‘cor’
  geepack.quant.batch : read.in.data: no visible global function
    definition for ‘read.table’
  geepack.quant.batch: no visible global function definition for
    ‘na.omit’
  geepack.quant.batch: no visible global function definition for ‘var’
  geepack.quant.batch: no visible binding for global variable ‘var’
  geepack.quant.batch: no visible global function definition for ‘cor’
  geepack.quant.batch: no visible global function definition for ‘pchisq’
  geepack.quant.batch: no visible global function definition for
    ‘write.table’
  geepack.quant.batch.imputed : cor.snp: no visible global function
    definition for ‘sd’
  geepack.quant.batch.imputed : cor.snp: no visible global function
    definition for ‘cor’
  geepack.quant.batch.imputed : read.in.data: no visible global function
    definition for ‘read.table’
  geepack.quant.batch.imputed: no visible global function definition for
    ‘na.omit’
  geepack.quant.batch.imputed: no visible global function definition for
    ‘var’
  geepack.quant.batch.imputed: no visible binding for global variable
    ‘var’
  geepack.quant.batch.imputed: no visible global function definition for
    ‘cor’
  geepack.quant.batch.imputed: no visible global function definition for
    ‘pchisq’
  geepack.quant.batch.imputed: no visible global function definition for
    ‘write.table’
  geepack.quant.int.batch : cor.snp: no visible global function
    definition for ‘sd’
  geepack.quant.int.batch : cor.snp: no visible global function
    definition for ‘cor’
  geepack.quant.int.batch : read.in.data: no visible global function
    definition for ‘read.table’
  geepack.quant.int.batch: no visible global function definition for
    ‘na.omit’
  geepack.quant.int.batch: no visible global function definition for
    ‘pchisq’
  geepack.quant.int.batch: no visible global function definition for
    ‘write.table’
  geepack.quant.int.batch.imputed : cor.snp: no visible global function
    definition for ‘sd’
  geepack.quant.int.batch.imputed : cor.snp: no visible global function
    definition for ‘cor’
  geepack.quant.int.batch.imputed : read.in.data: no visible global
    function definition for ‘read.table’
  geepack.quant.int.batch.imputed: no visible global function definition
    for ‘na.omit’
  geepack.quant.int.batch.imputed: no visible global function definition
    for ‘pchisq’
  geepack.quant.int.batch.imputed: no visible global function definition
    for ‘write.table’
  glmm.lgst: no visible global function definition for ‘na.omit’
  glmm.lgst : cor.snp: no visible global function definition for ‘sd’
  glmm.lgst : cor.snp: no visible global function definition for ‘cor’
  glmm.lgst: no visible global function definition for ‘fisher.test’
  glmm.lgst: possible error in lmer(phen1 ~ x.snp + x.covar + (1 |
    famid), family = "binomial"): unused argument (family = "binomial")
  glmm.lgst: possible error in lmer(phen1 ~ x.snp + (1 | famid), family =
    "binomial"): unused argument (family = "binomial")
  glmm.lgst: no visible global function definition for ‘chisq.test’
  glmm.lgst: no visible global function definition for ‘coef’
  glmm.lgst: no visible global function definition for ‘pchisq’
  glmm.lgst: no visible global function definition for ‘vcov’
  glmm.lgst.batch : read.in.data: no visible global function definition
    for ‘read.table’
  glmm.lgst.batch: no visible global function definition for ‘na.omit’
  glmm.lgst.batch: no visible global function definition for ‘var’
  glmm.lgst.batch: no visible binding for global variable ‘var’
  glmm.lgst.batch: no visible global function definition for ‘cor’
  glmm.lgst.batch: no visible global function definition for
    ‘write.table’
  lmeVpack.batch.imputed : cor.snp: no visible global function definition
    for ‘sd’
  lmeVpack.batch.imputed : cor.snp: no visible global function definition
    for ‘cor’
  lmeVpack.batch.imputed : read.in.data: no visible global function
    definition for ‘read.table’
  lmeVpack.batch.imputed: no visible global function definition for
    ‘na.omit’
  lmeVpack.batch.imputed: no visible global function definition for ‘var’
  lmeVpack.batch.imputed: no visible binding for global variable ‘var’
  lmeVpack.batch.imputed: no visible global function definition for ‘cor’
  lmeVpack.batch.imputed: no visible binding for global variable
    ‘na.omit’
  lmeVpack.batch.imputed: no visible global function definition for
    ‘pchisq’
  lmeVpack.batch.imputed: no visible global function definition for
    ‘write.table’
  lmepack.batch : cor.snp: no visible global function definition for ‘sd’
  lmepack.batch : cor.snp: no visible global function definition for
    ‘cor’
  lmepack.batch : read.in.data: no visible global function definition for
    ‘read.table’
  lmepack.batch: no visible global function definition for ‘na.omit’
  lmepack.batch: no visible global function definition for ‘var’
  lmepack.batch: no visible binding for global variable ‘var’
  lmepack.batch: no visible global function definition for ‘cor’
  lmepack.batch: no visible binding for global variable ‘na.omit’
  lmepack.batch: no visible global function definition for ‘pchisq’
  lmepack.batch: no visible global function definition for ‘write.table’
  lmepack.batch.imputed : cor.snp: no visible global function definition
    for ‘sd’
  lmepack.batch.imputed : cor.snp: no visible global function definition
    for ‘cor’
  lmepack.batch.imputed : read.in.data: no visible global function
    definition for ‘read.table’
  lmepack.batch.imputed: no visible global function definition for
    ‘na.omit’
  lmepack.batch.imputed: no visible global function definition for ‘var’
  lmepack.batch.imputed: no visible binding for global variable ‘var’
  lmepack.batch.imputed: no visible global function definition for ‘cor’
  lmepack.batch.imputed: no visible binding for global variable ‘na.omit’
  lmepack.batch.imputed: no visible global function definition for
    ‘pchisq’
  lmepack.batch.imputed: no visible global function definition for
    ‘write.table’
  lmepack.int.batch : cor.snp: no visible global function definition for
    ‘sd’
  lmepack.int.batch : cor.snp: no visible global function definition for
    ‘cor’
  lmepack.int.batch : read.in.data: no visible global function definition
    for ‘read.table’
  lmepack.int.batch: no visible global function definition for ‘na.omit’
  lmepack.int.batch: no visible binding for global variable ‘na.omit’
  lmepack.int.batch: no visible global function definition for ‘pchisq’
  lmepack.int.batch: no visible global function definition for
    ‘write.table’
  lmepack.int.batch.imputed : cor.snp: no visible global function
    definition for ‘sd’
  lmepack.int.batch.imputed : cor.snp: no visible global function
    definition for ‘cor’
  lmepack.int.batch.imputed : read.in.data: no visible global function
    definition for ‘read.table’
  lmepack.int.batch.imputed: no visible global function definition for
    ‘na.omit’
  lmepack.int.batch.imputed: no visible binding for global variable
    ‘na.omit’
  lmepack.int.batch.imputed: no visible global function definition for
    ‘pchisq’
  lmepack.int.batch.imputed: no visible global function definition for
    ‘write.table’
  qq: no visible global function definition for ‘bitmap’
  qq: no visible global function definition for ‘na.omit’
  qq: no visible global function definition for ‘median’
  qq: no visible global function definition for ‘qchisq’
  qq: no visible global function definition for ‘par’
  qq: no visible global function definition for ‘qqplot’
  qq: no visible global function definition for ‘abline’
  qq: no visible global function definition for ‘text’
  qq: no visible global function definition for ‘dev.off’
  Undefined global functions or variables:
    abline as.formula axis bitmap chisq.test coef cor dev.off fisher.test
    glm median na.omit par pchisq points qchisq qqplot read.table sd text
    var vcov write.table
  Consider adding
    importFrom("grDevices", "bitmap", "dev.off")
    importFrom("graphics", "abline", "axis", "par", "points", "text")
    importFrom("stats", "as.formula", "chisq.test", "coef", "cor",
               "fisher.test", "glm", "median", "na.omit", "pchisq",
               "qchisq", "qqplot", "sd", "var", "vcov")
    importFrom("utils", "read.table", "write.table")
  to your NAMESPACE file.
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [3s/4s] OK
• checking PDF version of manual ... OK
• DONE
  Status: 1 WARNING, 1 NOTE