BioC 3.2: CHECK report for categoryCompare on moscato1

Package: categoryCompare

Version: 1.13.0

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_1.13.0.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_1.13.0.tar.gz

StartedAt: 2015-08-20 02:17:58 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 02:24:15 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 377.8 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_1.13.0.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_1.13.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-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 '1.13.0'
* 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' ... [36s] OK
** running examples for arch 'x64' ... [35s] 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
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
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
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_1.13.0.zip
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	1.14	0.00	1.14
HyperGParamsCC-class	0.02	0.00	0.01
HyperGResultCC-class	0	0	0
breakEdges-methods	1.20	0.01	1.22
breakEdges	0	0	0
ccCompare	0.98	0.00	0.99
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	1.04	0.00	1.05
ccEnrich	1.33	0.03	1.36
ccEnrichCollection-class	2.73	0.02	2.75
ccEnrichResult-class	4.92	0.01	4.94
ccGeneList-class	1.24	0.03	1.27
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	1.61	0.03	1.90
mergeLists-methods	1.77	0.03	1.81
mergedData-class	1.50	0.02	1.51
minCount	3.78	0.05	3.82
minNodes	0	0	0
pvalueType	4.43	0.01	4.45
show-methods	0	0	0

name	user	system	elapsed
GENccEnrichResult-class	1.29	0.03	1.32
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0.02	0.00	0.02
breakEdges-methods	0.98	0.00	0.98
breakEdges	0	0	0
ccCompare	0.92	0.03	0.95
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	1.01	0.00	1.01
ccEnrich	1.33	0.00	1.33
ccEnrichCollection-class	2.82	0.05	2.87
ccEnrichResult-class	4.34	0.00	4.34
ccGeneList-class	1.31	0.00	1.31
ccOptions-class	0.03	0.00	0.09
ccOutCyt-methods	0	0	0
ccSigList-class	0	0	0
cytOutData-methods	0	0	0
cytOutNodes-methods	0	0	0
hyperGTestCC	1.32	0.03	1.35
mergeLists-methods	1.22	0.05	1.26
mergedData-class	1.2	0.0	1.2
minCount	3.23	0.04	3.28
minNodes	0	0	0
pvalueType	3.75	0.03	3.77
show-methods	0	0	0