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: 2016-04-20 23:59:29 -0700 (Wed, 20 Apr 2016)

EndedAt: 2016-04-21 00:02:38 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 189.2 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 version 3.3.0 beta (2016-04-06 r70435)
* 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 ... [15s/16s] 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 ... [24s/27s] 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
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)

name	user	system	elapsed
GENccEnrichResult-class	0.829	0.025	0.857
HyperGParamsCC-class	0.002	0.000	0.003
HyperGResultCC-class	0.001	0.001	0.002
breakEdges-methods	0.647	0.017	0.681
breakEdges	0.000	0.000	0.001
ccCompare	0.730	0.013	0.757
ccCompareCollection-class	0.001	0.000	0.004
ccCompareResult-class	0.001	0.000	0.002
ccData	0.725	0.011	0.737
ccEnrich	0.970	0.012	1.144
ccEnrichCollection-class	1.714	0.034	1.751
ccEnrichResult-class	2.641	0.031	2.688
ccGeneList-class	0.805	0.010	0.818
ccOptions-class	0.023	0.001	0.023
ccOutCyt-methods	0.001	0.000	0.001
ccSigList-class	0.001	0.001	0.001
cytOutData-methods	0.001	0.000	0.098
cytOutNodes-methods	0.001	0.000	0.002
hyperGTestCC	1.104	0.018	1.127
mergeLists-methods	1.069	0.020	1.092
mergedData-class	0.967	0.013	1.003
minCount	2.553	0.049	2.610
minNodes	0.001	0.000	0.001
pvalueType	2.075	0.026	2.106
show-methods	0.000	0.000	0.001