CRAN Package Check Results for Package GWAF

Last updated on 2020-05-06 06:48:24 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.2	17.10	121.99	139.09	WARN
r-devel-linux-x86_64-debian-gcc	2.2	14.08	91.68	105.76	WARN
r-devel-linux-x86_64-fedora-clang	2.2			166.06	WARN
r-devel-linux-x86_64-fedora-gcc	2.2			164.13	WARN
r-devel-windows-ix86+x86_64	2.2	45.00	173.00	218.00	WARN
r-patched-linux-x86_64	2.2	19.18	115.65	134.83	WARN
r-patched-solaris-x86	2.2			217.40	WARN
r-release-linux-x86_64	2.2	16.48	118.94	135.42	WARN
r-release-osx-x86_64	2.2				WARN
r-release-windows-ix86+x86_64	2.2	52.00	189.00	241.00	WARN
r-oldrel-osx-x86_64	2.2				NOTE
r-oldrel-windows-ix86+x86_64	2.2	25.00	150.00	175.00	WARN

Check Details

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GWAF.Rcheck/00install.out' 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'.
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.2
Check: R code for possible problems
Result: 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.
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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-release-windows-ix86+x86_64

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GWAF.Rcheck/00install.out’ 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’.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See ‘/data/gannet/ripley/R/packages/tests-clang/GWAF.Rcheck/00install.out’ 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’.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See ‘/data/gannet/ripley/R/packages/tests-devel/GWAF.Rcheck/00install.out’ 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’.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See 'd:/Rcompile/CRANpkg/local/4.1/GWAF.Rcheck/00install.out' 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'.
Flavor: r-devel-windows-ix86+x86_64

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GWAF.Rcheck/00install.out’ 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’.
Flavor: r-patched-linux-x86_64

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See ‘/home/ripley/R/packages/tests32/GWAF.Rcheck/00install.out’ 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’.
Flavor: r-patched-solaris-x86

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/GWAF.Rcheck/00install.out’ 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’.
Flavor: r-release-linux-x86_64

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/GWAF.Rcheck/00install.out’ 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’.
Flavor: r-release-osx-x86_64

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See 'd:/Rcompile/CRANpkg/local/4.0/GWAF.Rcheck/00install.out' 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'.
Flavor: r-release-windows-ix86+x86_64

Version: 2.2
Check: R code for possible problems
Result: 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 ‘plot’
    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: 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 plot points qchisq qqplot read.table sd
     text var vcov write.table
    Consider adding
     importFrom("grDevices", "bitmap", "dev.off")
     importFrom("graphics", "abline", "axis", "par", "plot", "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.
Flavor: r-oldrel-osx-x86_64

Version: 2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial")
    See 'd:/Rcompile/CRANpkg/local/3.6/GWAF.Rcheck/00install.out' 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'.
Flavor: r-oldrel-windows-ix86+x86_64

Version: 2.2
Check: R code for possible problems
Result: 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 'plot'
    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 plot points qchisq qqplot read.table sd
     text var vcov write.table
    Consider adding
     importFrom("grDevices", "bitmap", "dev.off")
     importFrom("graphics", "abline", "axis", "par", "plot", "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.
Flavor: r-oldrel-windows-ix86+x86_64