BioC 3.2: CHECK report for categoryCompare on moscato1

Package: categoryCompare

Version: 1.14.0

Command: rm -rf categoryCompare.buildbin-libdir categoryCompare.Rcheck && mkdir categoryCompare.buildbin-libdir categoryCompare.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.14.0.tar.gz >categoryCompare.Rcheck\00install.out 2>&1 && cp categoryCompare.Rcheck\00install.out categoryCompare-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.14.0.tar.gz

StartedAt: 2016-04-23 00:22:58 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:28:28 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 330.5 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.14.0.tar.gz >categoryCompare.Rcheck\00install.out 2>&1 && cp categoryCompare.Rcheck\00install.out categoryCompare-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.14.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/categoryCompare.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.14.0'
* 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 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
.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'
* 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' ... [31s] OK
** running examples for arch 'x64' ... [29s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/categoryCompare.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'categoryCompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'categoryCompare' as categoryCompare_1.14.0.zip
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	0.93	0.02	0.95
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0	0	0
breakEdges-methods	1.19	0.01	1.20
breakEdges	0	0	0
ccCompare	0.75	0.00	0.75
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	1.25	0.00	1.25
ccEnrich	1.08	0.01	1.09
ccEnrichCollection-class	2.96	0.00	2.98
ccEnrichResult-class	4.24	0.06	4.30
ccGeneList-class	0.94	0.00	0.94
ccOptions-class	0.02	0.00	0.02
ccOutCyt-methods	0	0	0
ccSigList-class	0	0	0
cytOutData-methods	0	0	0
cytOutNodes-methods	0	0	0
hyperGTestCC	1.25	0.02	1.27
mergeLists-methods	1.50	0.02	1.51
mergedData-class	1.00	0.01	1.01
minCount	2.79	0.02	2.81
minNodes	0	0	0
pvalueType	2.96	0.01	2.98
show-methods	0	0	0

name	user	system	elapsed
GENccEnrichResult-class	1.38	0.00	1.37
HyperGParamsCC-class	0.01	0.00	0.02
HyperGResultCC-class	0	0	0
breakEdges-methods	1.75	0.00	1.74
breakEdges	0	0	0
ccCompare	0.83	0.05	0.88
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	0.82	0.00	0.83
ccEnrich	1.14	0.02	1.16
ccEnrichCollection-class	2.48	0.00	2.48
ccEnrichResult-class	3.28	0.00	3.27
ccGeneList-class	0.92	0.03	0.95
ccOptions-class	0.01	0.00	0.07
ccOutCyt-methods	0	0	0
ccSigList-class	0	0	0
cytOutData-methods	0	0	0
cytOutNodes-methods	0.02	0.00	0.01
hyperGTestCC	1.67	0.05	1.72
mergeLists-methods	1.42	0.00	1.42
mergedData-class	0.84	0.00	0.84
minCount	2.18	0.00	2.18
minNodes	0	0	0
pvalueType	2.91	0.01	2.92
show-methods	0	0	0