BioC 3.3: CHECK report for categoryCompare on morelia

Package: categoryCompare

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings categoryCompare_1.15.0.tar.gz

StartedAt: 2015-10-22 04:11:35 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 04:13:58 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 143.0 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings categoryCompare_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/categoryCompare.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.15.0’
* 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 ... [11s/11s] 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
.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’
.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] 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.

* 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)

name	user	system	elapsed
GENccEnrichResult-class	0.587	0.021	0.609
HyperGParamsCC-class	0.200	0.001	0.200
HyperGResultCC-class	0.001	0.000	0.002
breakEdges-methods	0.562	0.013	0.575
breakEdges	0.001	0.000	0.000
ccCompare	0.497	0.013	0.510
ccCompareCollection-class	0.000	0.000	0.001
ccCompareResult-class	0.001	0.000	0.001
ccData	0.489	0.012	0.501
ccEnrich	0.699	0.010	0.709
ccEnrichCollection-class	1.632	0.037	1.669
ccEnrichResult-class	2.671	0.030	2.701
ccGeneList-class	0.569	0.012	0.582
ccOptions-class	0.019	0.001	0.019
ccOutCyt-methods	0	0	0
ccSigList-class	0.002	0.000	0.002
cytOutData-methods	0.001	0.001	0.002
cytOutNodes-methods	0.001	0.000	0.002
hyperGTestCC	0.878	0.024	0.902
mergeLists-methods	0.836	0.020	0.859
mergedData-class	0.688	0.018	0.706
minCount	1.870	0.033	1.905
minNodes	0	0	0
pvalueType	1.831	0.030	1.863
show-methods	0.001	0.000	0.000