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CHECK report for categoryCompare on machv2

This page was generated on 2020-10-17 11:58:10 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE categoryCompare PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 236/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.32.0
Robert M. Flight
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/categoryCompare
Branch: RELEASE_3_11
Last Commit: 0ee538e
Last Changed Date: 2020-04-27 14:29:40 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: categoryCompare
Version: 1.32.0
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_1.32.0.tar.gz
StartedAt: 2020-10-16 23:24:55 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:29:06 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 251.5 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_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/categoryCompare.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘categoryCompare/DESCRIPTION’ ... OK
* this is package ‘categoryCompare’ version ‘1.32.0’
* 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-3.11-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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-class0.8280.0200.848
HyperGParamsCC-class0.0020.0010.003
HyperGResultCC-class0.0020.0010.003
breakEdges-methods0.9010.0130.914
ccCompare0.9030.0070.910
ccCompareCollection-class0.0010.0000.001
ccCompareResult-class0.0010.0000.000
ccData1.3660.0061.383
ccEnrich0.9450.0050.950
ccEnrichCollection-class1.8850.0591.946
ccEnrichResult-class3.5330.0683.609
ccGeneList-class0.9580.0060.965
ccOptions-class0.0220.0020.024
ccOutCyt-methods0.0000.0010.001
ccSigList-class0.0010.0010.002
cytOutData-methods0.0000.0010.001
cytOutNodes-methods0.0010.0000.001
hyperGTestCC1.2770.0181.295
mergeLists-methods1.3600.0161.378
mergedData-class1.2370.0121.250
minCount2.8940.0352.931
minNodes0.0000.0010.000
pvalueType2.4580.0432.502
show-methods000