Back to Multiple platform build/check report for BioC 3.6
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for categoryCompare on veracruz1

This page was generated on 2018-04-12 13:35:34 -0400 (Thu, 12 Apr 2018).

Package 185/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.22.0
Robert M. Flight
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/categoryCompare
Branch: RELEASE_3_6
Last Commit: 13312c6
Last Changed Date: 2017-10-30 12:39:40 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: categoryCompare
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings categoryCompare_1.22.0.tar.gz
StartedAt: 2018-04-12 01:21:00 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:23:38 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 157.9 seconds
RetCode: 0
Status:  OK 
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings categoryCompare_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/categoryCompare.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.22.0’
* 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 loading without being on the library search path ... 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
.annotateOutData: no visible global function definition for
  ‘write.table’
.ccCompare: no visible global function definition for ‘new’
.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’
.ccCompareGO: no visible global function definition for ‘new’
.ccCompareGeneric: no visible global function definition for ‘new’
.ccCompareKEGG: no visible global function definition for ‘getGeneric’
.ccCompareKEGG: no visible binding for global variable
  ‘KEGGPATHID2NAME’
.ccCompareKEGG: no visible global function definition for ‘new’
.colorData: no visible global function definition for ‘colors’
.compData: no visible global function definition for ‘combn’
.cwReload: possible error in existing.CytoscapeWindow(windowName,
  rpcPort = rpcPort, host = host, copy.graph.from.cytoscape.to.R =
  FALSE): unused argument (rpcPort = rpcPort)
.extractRes: no visible global function definition for ‘getGeneric’
.getDesc : <anonymous>: no visible global function definition for
  ‘Term’
.goEnrich: no visible global function definition for ‘new’
.headerOutData: no visible global function definition for ‘write.table’
.initGraphAtts: no visible global function definition for ‘as’
.keggEnrich: no visible global function definition for ‘new’
.mergeLists: no visible global function definition for ‘new’
createGraph: no visible global function definition for ‘new’
createGraph2: no visible global function definition for ‘new’
hyperGTestCC: no visible global function definition for
  ‘.valueClassTest’
hyperGTestCat: no visible global function definition for ‘new’
[,GENccEnrichResult-ANY-ANY-ANY: no visible global function definition
  for ‘new’
[,ccEnrichResult-ANY-ANY-ANY: no visible global function definition for
  ‘new’
ccEnrich,ccGeneList: no visible global function definition for ‘new’
initialize,ccGeneList: no visible global function definition for
  ‘callNextMethod’
initialize,ccOptions: no visible global function definition for
  ‘callNextMethod’
show,HyperGResultCC: no visible global function definition for
  ‘description’
show,ccCompareCollection: no visible global function definition for
  ‘show’
show,ccCompareResult: no visible global function definition for ‘show’
show,ccEnrichCollection: no visible global function definition for
  ‘show’
show,ccEnrichResult: no visible global function definition for ‘show’
Undefined global functions or variables:
  .valueClassTest GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM
  KEGGPATHID2NAME Term as callNextMethod colors combn description
  getGeneric new show write.table
Consider adding
  importFrom("grDevices", "colors")
  importFrom("methods", ".valueClassTest", "as", "callNextMethod",
             "getGeneric", "new", "show")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... 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-3.6-bioc/meat/categoryCompare.Rcheck/00check.log’
for details.



Installation output

categoryCompare.Rcheck/00install.out

* installing *source* package ‘categoryCompare’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (categoryCompare)

Tests output


Example timings

categoryCompare.Rcheck/categoryCompare-Ex.timings

nameusersystemelapsed
GENccEnrichResult-class0.8760.0160.899
HyperGParamsCC-class0.0030.0000.003
HyperGResultCC-class0.0020.0000.003
breakEdges-methods0.9030.0190.938
ccCompare0.6420.0140.665
ccCompareCollection-class0.0010.0000.001
ccCompareResult-class0.0020.0000.001
ccData0.6190.0140.652
ccEnrich0.8990.0100.919
ccEnrichCollection-class1.7920.0331.854
ccEnrichResult-class2.4560.0282.511
ccGeneList-class0.5790.0080.599
ccOptions-class0.0400.0010.042
ccOutCyt-methods0.0010.0010.001
ccSigList-class0.0010.0000.002
cytOutData-methods0.0010.0000.001
cytOutNodes-methods0.0010.0010.001
hyperGTestCC0.8730.0140.897
mergeLists-methods1.1380.0581.211
mergedData-class0.6260.0160.645
minCount1.2730.0281.318
minNodes0.0010.0000.001
pvalueType1.3280.0281.386
show-methods000