BioC 3.2: CHECK report for categoryCompare on windows1.bioconductor.org

Package: categoryCompare

Version: 1.14.0

Command: rm -rf categoryCompare.buildbin-libdir categoryCompare.Rcheck && mkdir categoryCompare.buildbin-libdir categoryCompare.Rcheck && C:\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 && C:\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: 2015-10-27 00:21:42 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 00:25:20 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 217.7 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 && C:\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  && C:\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 'C:/biocbld/bbs-3.2-bioc/meat/categoryCompare.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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' ... [21s] OK
** running examples for arch 'x64' ... [20s] 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
  'C:/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_1.14.0.zip
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	0.60	0.00	0.61
HyperGParamsCC-class	0.00	0.01	0.02
HyperGResultCC-class	0	0	0
breakEdges-methods	1.16	0.00	1.15
breakEdges	0	0	0
ccCompare	0.58	0.00	0.58
ccCompareCollection-class	0	0	0
ccCompareResult-class	0.00	0.02	0.02
ccData	0.58	0.01	0.59
ccEnrich	0.59	0.00	0.59
ccEnrichCollection-class	1.97	0.00	1.97
ccEnrichResult-class	2.81	0.00	2.81
ccGeneList-class	0.64	0.00	0.64
ccOptions-class	0.01	0.00	0.02
ccOutCyt-methods	0	0	0
ccSigList-class	0	0	0
cytOutData-methods	0.02	0.00	0.01
cytOutNodes-methods	0	0	0
hyperGTestCC	0.81	0.04	0.85
mergeLists-methods	0.86	0.06	0.92
mergedData-class	0.89	0.01	0.90
minCount	2.46	0.05	2.50
minNodes	0	0	0
pvalueType	2.06	0.00	2.07
show-methods	0	0	0

name	user	system	elapsed
GENccEnrichResult-class	0.79	0.00	0.80
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0	0	0
breakEdges-methods	0.80	0.00	0.79
breakEdges	0	0	0
ccCompare	0.5	0.0	0.5
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	0.53	0.00	0.53
ccEnrich	0.75	0.00	0.75
ccEnrichCollection-class	1.89	0.03	1.93
ccEnrichResult-class	2.5	0.0	2.5
ccGeneList-class	0.52	0.02	0.53
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	0.88	0.00	0.88
mergeLists-methods	0.95	0.00	0.95
mergedData-class	0.64	0.00	0.64
minCount	1.66	0.00	1.66
minNodes	0	0	0
pvalueType	2.12	0.00	2.12
show-methods	0	0	0