BioC 3.1: CHECK report for categoryCompare on moscato2

Package: categoryCompare

Version: 1.12.0

Command: rm -rf categoryCompare.buildbin-libdir categoryCompare.Rcheck && mkdir categoryCompare.buildbin-libdir categoryCompare.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.12.0.tar.gz >categoryCompare.Rcheck\00install.out 2>&1 && cp categoryCompare.Rcheck\00install.out categoryCompare-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.12.0.tar.gz

StartedAt: 2015-10-09 00:03:13 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:08:01 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 287.4 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-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.12.0.tar.gz >categoryCompare.Rcheck\00install.out 2>&1 && cp categoryCompare.Rcheck\00install.out categoryCompare-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.12.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/categoryCompare.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.12.0'
* 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' ... [28s] 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
  'E:/biocbld/bbs-3.1-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 'nchar' from package 'base' in package 'S4Vectors'
Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'categoryCompare' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'categoryCompare' as categoryCompare_1.12.0.zip
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	0.74	0.00	0.84
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0	0	0
breakEdges-methods	0.92	0.01	0.93
breakEdges	0	0	0
ccCompare	0.81	0.02	0.83
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	0.75	0.01	0.76
ccEnrich	0.78	0.00	0.78
ccEnrichCollection-class	2.31	0.02	2.33
ccEnrichResult-class	3.71	0.03	3.77
ccGeneList-class	0.8	0.0	0.8
ccOptions-class	0.01	0.00	0.01
ccOutCyt-methods	0	0	0
ccSigList-class	0	0	0
cytOutData-methods	0	0	0
cytOutNodes-methods	0	0	0
hyperGTestCC	1.11	0.01	1.13
mergeLists-methods	1.44	0.00	1.43
mergedData-class	1.63	0.04	1.65
minCount	3.68	0.03	3.71
minNodes	0	0	0
pvalueType	2.56	0.01	2.58
show-methods	0	0	0

name	user	system	elapsed
GENccEnrichResult-class	1.30	0.00	1.29
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0	0	0
breakEdges-methods	1.12	0.00	1.12
breakEdges	0	0	0
ccCompare	0.75	0.01	0.77
ccCompareCollection-class	0	0	0
ccCompareResult-class	0.00	0.02	0.01
ccData	0.67	0.00	0.67
ccEnrich	1.15	0.00	1.15
ccEnrichCollection-class	2.81	0.02	2.83
ccEnrichResult-class	3.79	0.01	3.80
ccGeneList-class	0.67	0.02	0.69
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	1.32	0.00	1.33
mergeLists-methods	1.06	0.03	1.09
mergedData-class	0.88	0.03	0.90
minCount	2.30	0.02	2.34
minNodes	0	0	0
pvalueType	2.75	0.04	2.79
show-methods	0	0	0