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CHECK report for eegc on tokay2

This page was generated on 2018-10-17 08:42:47 -0400 (Wed, 17 Oct 2018).

Package 435/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eegc 1.6.1
Xiaoyuan Zhou
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/eegc
Branch: RELEASE_3_7
Last Commit: 2e661ec
Last Changed Date: 2018-05-17 13:00:28 -0400 (Thu, 17 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ TIMEOUT ] OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: eegc
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eegc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings eegc_1.6.1.tar.gz
StartedAt: 2018-10-17 01:45:58 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:26:04 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 2406.2 seconds
RetCode: None
Status:  TIMEOUT  
CheckDir: eegc.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eegc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings eegc_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/eegc.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.1'
* 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 whether package 'eegc' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/barplotEnrich.Rd:29: missing file link 'barplot.enrichResult'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/functionEnrich.Rd:17: file link 'org.Hs.eg.db' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/grnPlot.Rd:33: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/grnPlot.Rd:36: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/grnPlot.Rd:38: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/grnPlot.Rd:42: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/eegc.Rcheck/00install.out' for details.
* 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
* 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 '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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
functionEnrich 969.97  81.29 1054.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
functionEnrich 927.08  22.39 1034.31
heatmapPlot      0.72   0.00   27.47
* checking for unstated dependencies in vignettes ...

Installation output

eegc.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/eegc_1.6.1.tar.gz && rm -rf eegc.buildbin-libdir && mkdir eegc.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=eegc.buildbin-libdir eegc_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL eegc_1.6.1.zip && rm eegc_1.6.1.tar.gz eegc_1.6.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 9085k  100 9085k    0     0  55.4M      0 --:--:-- --:--:-- --:--:-- 57.9M

install for i386

* installing *source* package 'eegc' ...
** 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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/barplotEnrich.Rd:29: missing file link 'barplot.enrichResult'
    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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/functionEnrich.Rd:17: file link 'org.Hs.eg.db' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
    goenrich                                html  
    grnPlot                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/grnPlot.Rd:33: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/grnPlot.Rd:36: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/grnPlot.Rd:38: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKaPcNJ/R.INSTALL17c862006f62/eegc/man/grnPlot.Rd:42: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
    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
In R CMD INSTALL

install for x64

* installing *source* package 'eegc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'eegc' as eegc_1.6.1.zip
* DONE (eegc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'eegc' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

eegc.Rcheck/examples_i386/eegc-Ex.timings

nameusersystemelapsed
barplotEnrich000
categorizeGene0.280.010.30
densityPlot0.030.000.03
diffGene1.030.081.11
dotPercentage0.000.020.02
enrichment3.360.043.40
functionEnrich 969.97 81.291054.99
grnPlot000
heatmapPlot0.440.010.45
markerScatter0.310.000.31
networkAnalyze0.170.000.18

eegc.Rcheck/examples_x64/eegc-Ex.timings

nameusersystemelapsed
barplotEnrich000
categorizeGene0.080.030.10
densityPlot0.000.020.02
diffGene101
dotPercentage0.000.020.02
enrichment1.840.141.98
functionEnrich 927.08 22.391034.31
grnPlot000
heatmapPlot 0.72 0.0027.47
markerScatter0.250.030.28
networkAnalyze0.130.000.12