BioC 3.3: CHECK report for categoryCompare on moscato2

Package: categoryCompare

Version: 1.16.2

Command: rm -rf categoryCompare.buildbin-libdir categoryCompare.Rcheck && mkdir categoryCompare.buildbin-libdir categoryCompare.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.16.2.tar.gz >categoryCompare.Rcheck\00install.out 2>&1 && cp categoryCompare.Rcheck\00install.out categoryCompare-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.16.2.tar.gz

StartedAt: 2016-06-26 01:39:18 -0700 (Sun, 26 Jun 2016)

EndedAt: 2016-06-26 01:44:49 -0700 (Sun, 26 Jun 2016)

EllapsedTime: 331.1 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf categoryCompare.buildbin-libdir categoryCompare.Rcheck && mkdir categoryCompare.buildbin-libdir categoryCompare.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.16.2.tar.gz >categoryCompare.Rcheck\00install.out 2>&1 && cp categoryCompare.Rcheck\00install.out categoryCompare-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.16.2.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/categoryCompare.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ccEnrichResult-class 5.82      0    5.81
** running examples for arch 'x64' ... 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
  'E:/biocbld/bbs-3.3-bioc/meat/categoryCompare.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'categoryCompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'categoryCompare' as categoryCompare_1.16.2.zip
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	0.79	0.02	0.82
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0	0	0
breakEdges-methods	0.83	0.01	0.84
breakEdges	0	0	0
ccCompare	1.23	0.00	1.23
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	1.30	0.02	1.31
ccEnrich	0.95	0.04	1.00
ccEnrichCollection-class	2.98	0.05	3.03
ccEnrichResult-class	5.82	0.00	5.81
ccGeneList-class	1.26	0.00	1.27
ccOptions-class	0.03	0.00	0.03
ccOutCyt-methods	0	0	0
ccSigList-class	0	0	0
cytOutData-methods	0	0	0
cytOutNodes-methods	0	0	0
hyperGTestCC	1.57	0.08	1.65
mergeLists-methods	1.20	0.01	1.22
mergedData-class	1.50	0.02	1.51
minCount	4.84	0.03	4.87
minNodes	0	0	0
pvalueType	3.07	0.00	3.07
show-methods	0	0	0

name	user	system	elapsed
GENccEnrichResult-class	1.01	0.03	1.05
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0	0	0
breakEdges-methods	1.23	0.00	1.23
breakEdges	0	0	0
ccCompare	0.81	0.00	0.81
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	0.86	0.00	0.85
ccEnrich	1.23	0.01	1.25
ccEnrichCollection-class	2.78	0.03	2.81
ccEnrichResult-class	4.29	0.04	4.32
ccGeneList-class	0.98	0.01	1.00
ccOptions-class	0.04	0.00	0.03
ccOutCyt-methods	0	0	0
ccSigList-class	0	0	0
cytOutData-methods	0	0	0
cytOutNodes-methods	0	0	0
hyperGTestCC	1.40	0.05	1.45
mergeLists-methods	1.22	0.05	1.26
mergedData-class	1.53	0.00	1.53
minCount	3.83	0.00	3.84
minNodes	0	0	0
pvalueType	3.45	0.00	3.45
show-methods	0	0	0