Multiple platform build/check report for BioC 3.9 - CHECK report for categoryCompare on merida2

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/categoryCompare.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘categoryCompare’ ...
** 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
* DONE (categoryCompare)

Tests output

Example timings

name	user	system	elapsed
GENccEnrichResult-class	0.823	0.022	0.850
HyperGParamsCC-class	0.002	0.000	0.002
HyperGResultCC-class	0.001	0.000	0.001
breakEdges-methods	0.956	0.024	0.994
ccCompare	0.785	0.018	0.806
ccCompareCollection-class	0.001	0.000	0.001
ccCompareResult-class	0.001	0.000	0.001
ccData	1.172	0.017	1.192
ccEnrich	0.809	0.018	0.832
ccEnrichCollection-class	1.448	0.046	1.501
ccEnrichResult-class	3.241	0.047	3.296
ccGeneList-class	0.914	0.012	0.930
ccOptions-class	0.018	0.002	0.019
ccOutCyt-methods	0.000	0.000	0.001
ccSigList-class	0.001	0.000	0.001
cytOutData-methods	0.001	0.000	0.000
cytOutNodes-methods	0.001	0.000	0.001
hyperGTestCC	1.131	0.021	1.164
mergeLists-methods	1.201	0.023	1.228
mergedData-class	1.047	0.022	1.074
minCount	2.821	0.060	2.914
minNodes	0	0	0
pvalueType	2.002	0.037	2.056
show-methods	0.001	0.000	0.000

CHECK report for categoryCompare on merida2

Summary

Command output

Installation output

Tests output

Example timings