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CHECK report for categoryCompare on celaya2

This page was generated on 2019-04-09 13:04:50 -0400 (Tue, 09 Apr 2019).

Package 213/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.27.0
Robert M. Flight
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/categoryCompare
Branch: master
Last Commit: 344c525
Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: categoryCompare
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings categoryCompare_1.27.0.tar.gz
StartedAt: 2019-04-09 00:25:41 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:29:37 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 235.5 seconds
RetCode: 0
Status:  OK 
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings categoryCompare_1.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/categoryCompare.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘categoryCompare/DESCRIPTION’ ... OK
* this is package ‘categoryCompare’ version ‘1.27.0’
* 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 ‘categoryCompare’ can be installed ... OK
* checking installed package size ... OK
* 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
.ccCompareGO: no visible binding for global variable ‘GOBPPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOMFPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOCCPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOTERM’
.ccCompareGO: no visible binding for global variable ‘Term’
.ccCompareKEGG: no visible binding for global variable
  ‘KEGGPATHID2NAME’
.cytOutNodes: ... may be used in an incorrect context:
  exportImage(filename = fileName, type = "png", network = cwObj, ...)
.getDesc : <anonymous>: no visible global function definition for
  ‘Term’
show,HyperGResultCC: no visible global function definition for
  ‘description’
Undefined global functions or variables:
  GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM KEGGPATHID2NAME Term
  description
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/categoryCompare.Rcheck/00check.log’
for details.



Installation output

categoryCompare.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL categoryCompare
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘categoryCompare’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: ... may be used in an incorrect context 
** help
*** installing help indices
** 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 (categoryCompare)

Tests output


Example timings

categoryCompare.Rcheck/categoryCompare-Ex.timings

nameusersystemelapsed
GENccEnrichResult-class0.7530.0360.792
HyperGParamsCC-class0.0020.0000.002
HyperGResultCC-class0.0010.0000.002
breakEdges-methods0.9400.0370.981
ccCompare0.8480.0290.939
ccCompareCollection-class0.0010.0000.002
ccCompareResult-class0.0010.0000.002
ccData1.4100.0281.441
ccEnrich0.7250.0170.742
ccEnrichCollection-class1.6570.0781.738
ccEnrichResult-class3.6420.0913.736
ccGeneList-class0.9540.0210.977
ccOptions-class0.0230.0020.024
ccOutCyt-methods0.0000.0000.001
ccSigList-class0.0010.0000.001
cytOutData-methods0.0000.0000.001
cytOutNodes-methods0.0000.0000.001
hyperGTestCC1.3420.0401.383
mergeLists-methods1.4660.0401.511
mergedData-class1.1350.0331.170
minCount2.4700.0902.563
minNodes000
pvalueType2.5110.0782.660
show-methods0.0010.0000.001