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BioC 3.5: CHECK report for eegc on malbec2

This page was generated on 2017-10-18 14:18:00 -0400 (Wed, 18 Oct 2017).

Package 390/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eegc 1.2.0
Xiaoyuan Zhou
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/eegc
Branch: RELEASE_3_5
Last Commit: 8dae387
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: eegc
Version: 1.2.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings eegc_1.2.0.tar.gz
StartedAt: 2017-10-17 22:53:10 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:03:53 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 642.1 seconds
RetCode: 0
Status:  OK 
CheckDir: eegc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings eegc_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/eegc.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 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 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 ... 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* 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 or elapsed time > 5s
                  user system elapsed
functionEnrich 407.552  8.556 421.526
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/eegc.Rcheck/00check.log’
for details.


eegc.Rcheck/00install.out:

* installing *source* package ‘eegc’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (eegc)

eegc.Rcheck/eegc-Ex.timings:

nameusersystemelapsed
barplotEnrich0.0000.0000.001
categorizeGene0.0560.0040.082
densityPlot0.0040.0000.004
diffGene1.3480.0241.375
dotPercentage0.0000.0000.002
enrichment2.6520.0922.746
functionEnrich407.552 8.556421.526
grnPlot0.0000.0000.001
heatmapPlot1.0080.0001.024
markerScatter0.1880.0040.193
networkAnalyze0.1240.0000.126