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CHECK report for eegc on merida1

This page was generated on 2019-04-16 11:59:53 -0400 (Tue, 16 Apr 2019).

Package 459/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eegc 1.8.1
Xiaoyuan Zhou
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/eegc
Branch: RELEASE_3_8
Last Commit: 33d0080
Last Changed Date: 2018-12-21 14:44:48 -0400 (Fri, 21 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: eegc
Version: 1.8.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:eegc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings eegc_1.8.1.tar.gz
StartedAt: 2019-04-15 23:43:12 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-16 00:04:44 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 1292.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: eegc.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:eegc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings eegc_1.8.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/eegc.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eegc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eegc’ version ‘1.8.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘eegc’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.1Mb
  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 ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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 plot points quantile
  results text title treat
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette",
             "dev.copy2pdf")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system  elapsed
functionEnrich 932.019 94.639 1045.964
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocStyle’
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/eegc.Rcheck/00check.log’
for details.



Installation output

eegc.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL eegc
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘eegc’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘eegc.Rnw’ 
** testing if installed package can be loaded
* DONE (eegc)

Tests output


Example timings

eegc.Rcheck/eegc-Ex.timings

nameusersystemelapsed
barplotEnrich000
categorizeGene0.080.010.09
densityPlot0.0030.0010.004
diffGene1.0170.0511.076
dotPercentage0.0020.0010.003
enrichment2.7030.1212.838
functionEnrich 932.019 94.6391045.964
grnPlot0.0000.0000.001
heatmapPlot0.4080.0110.434
markerScatter0.3760.0100.428
networkAnalyze0.4170.0210.443