Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-17 15:06:04 -0400 (Fri, 17 Sep 2021).

CHECK results for eegc on tokay2

To the developers/maintainers of the eegc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/eegc.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 558/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eegc 1.18.0  (landing page)
Xiaoyuan Zhou
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/eegc
git_branch: RELEASE_3_13
git_last_commit: d0acc6a
git_last_commit_date: 2021-05-19 12:22:38 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: eegc
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eegc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings eegc_1.18.0.tar.gz
StartedAt: 2021-09-16 22:42:54 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 22:56:04 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 790.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: eegc.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eegc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings eegc_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/eegc.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.18.0'
* 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 11.3Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ยง1.1.6 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
functionEnrich 223.03   7.31  235.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
functionEnrich 231.58   3.96  240.65
* 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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/eegc.Rcheck/00check.log'
for details.



Installation output

eegc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/eegc_1.18.0.tar.gz && rm -rf eegc.buildbin-libdir && mkdir eegc.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=eegc.buildbin-libdir eegc_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL eegc_1.18.0.zip && rm eegc_1.18.0.tar.gz eegc_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 9087k    0 13287    0     0   122k      0  0:01:13 --:--:--  0:01:13  122k
 43 9087k   43 3979k    0     0  3736k      0  0:00:02  0:00:01  0:00:01 3736k
100 9087k  100 9087k    0     0  4577k      0  0:00:01  0:00:01 --:--:-- 4577k

install for i386

* 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
   'eegc.Rnw' 
** 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

install for x64

* installing *source* package 'eegc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'eegc' as eegc_1.18.0.zip
* DONE (eegc)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'eegc' successfully unpacked and MD5 sums checked

Tests output


Example timings

eegc.Rcheck/examples_i386/eegc-Ex.timings

nameusersystemelapsed
barplotEnrich000
categorizeGene0.080.050.13
densityPlot000
diffGene0.480.060.55
dotPercentage000
enrichment2.090.082.17
functionEnrich223.03 7.31235.25
grnPlot000
heatmapPlot0.310.000.31
markerScatter0.240.000.23
networkAnalyze0.130.000.13

eegc.Rcheck/examples_x64/eegc-Ex.timings

nameusersystemelapsed
barplotEnrich000
categorizeGene0.060.000.07
densityPlot0.010.000.01
diffGene1.040.001.03
dotPercentage000
enrichment2.370.082.46
functionEnrich231.58 3.96240.65
grnPlot000
heatmapPlot0.340.000.36
markerScatter0.350.000.35
networkAnalyze0.140.000.14