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BioC 3.3: CHECK report for categoryCompare on oaxaca

This page was generated on 2016-10-13 12:58:19 -0700 (Thu, 13 Oct 2016).

Package 152/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.16.2
Robert M. Flight
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/categoryCompare
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: categoryCompare
Version: 1.16.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings categoryCompare_1.16.2.tar.gz
StartedAt: 2016-10-12 23:54:46 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:57:48 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 181.7 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_1.16.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/categoryCompare.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘categoryCompare/DESCRIPTION’ ... OK
* this is package ‘categoryCompare’ version ‘1.16.2’
* 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’
.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’
.colorData: no visible global function definition for ‘colors’
.compData: no visible global function definition for ‘combn’
.getDesc : <anonymous>: no visible global function definition for
  ‘Term’
.headerOutData: no visible global function definition for ‘write.table’
show,HyperGResultCC: no visible global function definition for
  ‘description’
Undefined global functions or variables:
  GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM KEGGPATHID2NAME Term
  colors combn description write.table
Consider adding
  importFrom("grDevices", "colors")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file.
* 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-3.3-bioc/meat/categoryCompare.Rcheck/00check.log’
for details.


categoryCompare.Rcheck/00install.out:

* installing *source* package ‘categoryCompare’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘categoryCompare’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (categoryCompare)

categoryCompare.Rcheck/categoryCompare-Ex.timings:

nameusersystemelapsed
GENccEnrichResult-class1.0180.0261.046
HyperGParamsCC-class0.0010.0000.002
HyperGResultCC-class0.0010.0000.002
breakEdges-methods1.0110.0221.034
breakEdges0.0010.0000.001
ccCompare1.0330.0181.053
ccCompareCollection-class0.0010.0010.001
ccCompareResult-class0.0010.0000.001
ccData0.7360.0140.750
ccEnrich0.7020.0150.718
ccEnrichCollection-class1.9500.0401.993
ccEnrichResult-class2.7310.0392.774
ccGeneList-class0.8390.0150.855
ccOptions-class0.0250.0010.027
ccOutCyt-methods0.0010.0000.001
ccSigList-class0.0010.0000.001
cytOutData-methods0.0010.0000.001
cytOutNodes-methods0.0010.0010.001
hyperGTestCC1.1020.0261.129
mergeLists-methods1.1320.0231.156
mergedData-class1.0230.0181.043
minCount2.7320.0492.789
minNodes0.0010.0010.001
pvalueType2.0820.0372.122
show-methods0.0000.0010.001