BioC 2.14: CHECK report for categoryCompare on moscato2

Package: categoryCompare

Version: 1.8.0

Command: rm -rf categoryCompare.buildbin-libdir && mkdir categoryCompare.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.8.0.tar.gz >categoryCompare-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.8.0.tar.gz

StartedAt: 2014-10-07 23:26:36 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:32:10 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 333.9 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 && mkdir categoryCompare.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.8.0.tar.gz >categoryCompare-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.8.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/categoryCompare.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'categoryCompare/DESCRIPTION' ... OK
* this is package 'categoryCompare' version '1.8.0'
* 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 ... OK
* 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 ... NOTE
  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.
* 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' ... [33s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ccEnrichResult-class 5.36   0.07    5.45
* 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

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.14-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_1.8.0.zip
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	0.73	0.01	0.75
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0	0	0
breakEdges-methods	1.43	0.02	1.45
breakEdges	0	0	0
ccCompare	1.06	0.00	1.06
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	0.75	0.00	0.75
ccEnrich	0.76	0.00	0.76
ccEnrichCollection-class	2.70	0.01	2.72
ccEnrichResult-class	4.62	0.07	4.68
ccGeneList-class	0.81	0.01	0.83
ccOptions-class	0.03	0.00	0.03
ccOutCyt-methods	0	0	0
ccSigList-class	0	0	0
cytOutData-methods	0.02	0.00	0.01
cytOutNodes-methods	0	0	0
hyperGTestCC	1.04	0.00	1.05
mergeLists-methods	1.00	0.03	1.03
mergedData-class	0.89	0.00	0.89
minCount	3.31	0.00	3.33
minNodes	0	0	0
pvalueType	2.89	0.05	2.94
show-methods	0	0	0

name	user	system	elapsed
GENccEnrichResult-class	0.89	0.00	0.88
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0	0	0
breakEdges-methods	0.94	0.04	0.98
breakEdges	0	0	0
ccCompare	0.89	0.00	0.89
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	0.59	0.05	0.64
ccEnrich	0.64	0.00	0.64
ccEnrichCollection-class	3.33	0.05	3.37
ccEnrichResult-class	5.36	0.07	5.45
ccGeneList-class	1.45	0.03	1.48
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	0.89	0.06	0.96
mergeLists-methods	0.80	0.02	0.82
mergedData-class	0.81	0.00	0.81
minCount	3.63	0.01	3.65
minNodes	0	0	0
pvalueType	2.61	0.02	2.62
show-methods	0	0	0