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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:eegc.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings eegc_1.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/eegc.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'eegc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eegc' version '1.21.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'eegc' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  10.5Mb
* checking package directory ... OK
* checking 'build' 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 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 ... NOTE
categorizeGene : <anonymous>: no visible global function definition for
  'quantile'
densityPlot: no visible binding for global variable 'density'
densityPlot: no visible global function definition for 'lines'
densityPlot: no visible global function definition for 'axis'
densityPlot: no visible global function definition for 'adjustcolor'
densityPlot: no visible global function definition for 'legend'
densityPlot : <anonymous>: no visible global function definition for
  'quantile'
densityPlot: no visible global function definition for 'text'
densityPlot: no visible global function definition for 'dev.copy2pdf'
diffGene: no visible global function definition for 'model.matrix'
diffGene: no visible binding for global variable 'treat'
diffGene: no visible binding for global variable 'control'
diffGene: no visible global function definition for 'results'
diffGene: no visible global function definition for 'p.adjust'
dotPercentage: no visible global function definition for 'lines'
dotPercentage: no visible global function definition for 'axis'
dotPercentage: no visible global function definition for 'text'
dotPercentage: no visible global function definition for 'par'
enrichment : enrichment : <anonymous>: no visible global function
  definition for 'phyper'
enrichment : enrichment: no visible global function definition for
  'p.adjust'
grnPlot: no visible global function definition for 'title'
grnPlot: no visible global function definition for 'legend'
markerScatter: no visible global function definition for
  'colorRampPalette'
markerScatter: no visible global function definition for 'points'
markerScatter: no visible global function definition for 'lm'
markerScatter: no visible global function definition for 'abline'
markerScatter: no visible global function definition for 'text'
markerScatter: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline adjustcolor axis colorRampPalette control density dev.copy2pdf
  legend lines lm model.matrix p.adjust par phyper points quantile
  results text title treat
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette",
             "dev.copy2pdf")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points", "text", "title")
  importFrom("stats", "density", "lm", "model.matrix", "p.adjust",
             "phyper", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'barplotEnrich.Rd':
  '[DOSE]{barplot.enrichResult}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
  LazyData DB of 10.5 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
functionEnrich 190.02  24.46  218.72
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/eegc.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL eegc
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'eegc' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'eegc'
    finding HTML links ... done
    SandlerFPKM                             html  
    barplotEnrich                           html  
    cate.gene                               html  
    cate.ratio                              html  
    categorizeGene                          html  
    densityPlot                             html  
    diffGene                                html  
    diffgene.genes                          html  
    dotPercentage                           html  
    eegc                                    html  
    enrichment                              html  
    expr.filter                             html  
    functionEnrich                          html  
    goenrich                                html  
    grnPlot                                 html  
    heatmapPlot                             html  
    human.gene                              html  
    human.grn                               html  
    human.tf                                html  
    markerScatter                           html  
    markers                                 html  
    mouse.gene                              html  
    mouse.grn                               html  
    mouse.tf                                html  
    networkAnalyze                          html  
    tissueGenes                             html  
    tissueGroup                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (eegc)
Making 'packages.html' ... done