BioC 3.5: CHECK report for categoryCompare on malbec2

Package: categoryCompare

Version: 1.20.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings categoryCompare_1.20.0.tar.gz

StartedAt: 2017-10-17 21:47:18 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:49:54 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 155.9 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings categoryCompare_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/categoryCompare.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘categoryCompare/DESCRIPTION’ ... OK
* this is package ‘categoryCompare’ version ‘1.20.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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’
.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-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	0.560	0.000	0.561
HyperGParamsCC-class	0.000	0.000	0.002
HyperGResultCC-class	0.000	0.000	0.001
breakEdges-methods	0.980	0.008	0.990
breakEdges	0.000	0.000	0.001
ccCompare	0.556	0.008	0.564
ccCompareCollection-class	0.000	0.000	0.001
ccCompareResult-class	0.000	0.000	0.002
ccData	0.564	0.000	0.567
ccEnrich	0.984	0.000	0.982
ccEnrichCollection-class	2.016	0.016	2.040
ccEnrichResult-class	2.448	0.020	2.469
ccGeneList-class	0.624	0.008	0.632
ccOptions-class	0.04	0.00	0.04
ccOutCyt-methods	0.000	0.000	0.001
ccSigList-class	0	0	0
cytOutData-methods	0.000	0.000	0.001
cytOutNodes-methods	0.000	0.000	0.001
hyperGTestCC	0.808	0.016	0.823
mergeLists-methods	1.032	0.016	1.050
mergedData-class	0.764	0.000	0.764
minCount	1.580	0.008	1.590
minNodes	0.000	0.000	0.001
pvalueType	1.864	0.004	1.871
show-methods	0	0	0