BioC 2.13: CHECK report for categoryCompare on moscato1

Package: categoryCompare

Version: 1.6.0

Command: rm -rf categoryCompare.buildbin-libdir && mkdir categoryCompare.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.6.0.tar.gz >categoryCompare-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.6.0.tar.gz && mv categoryCompare.buildbin-libdir/* categoryCompare.Rcheck/ && rmdir categoryCompare.buildbin-libdir

StartedAt: 2014-04-05 02:47:38 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:54:00 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 381.6 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/categoryCompare.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.6.0'
* 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
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'categoryCompare_vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [37s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ccEnrichResult-class 5.87   0.04    5.89
** running examples for arch 'x64' ... [37s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ccEnrichResult-class 5.76   0.05     5.8
* 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 were 2 notes.
See
  'D:/biocbld/bbs-2.13-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_1.6.0.zip
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	0.98	0.02	1.00
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0.02	0.00	0.02
breakEdges-methods	1.01	0.01	1.02
breakEdges	0	0	0
ccCompare	1.62	0.02	1.64
ccCompareCollection-class	0	0	0
ccCompareResult-class	0	0	0
ccData	1.12	0.01	1.14
ccEnrich	1.12	0.00	1.12
ccEnrichCollection-class	2.20	0.01	2.22
ccEnrichResult-class	5.87	0.04	5.89
ccGeneList-class	0.92	0.00	0.92
ccOptions-class	0.05	0.00	0.04
ccOutCyt-methods	0	0	0
ccSigList-class	0	0	0
cytOutData-methods	0.02	0.00	0.01
cytOutNodes-methods	0.01	0.00	0.02
hyperGTestCC	1.06	0.00	1.06
mergeLists-methods	1.01	0.00	1.02
mergedData-class	0.88	0.01	0.89
minCount	3.45	0.02	3.47
minNodes	0.01	0.00	0.01
pvalueType	4.65	0.01	4.67
show-methods	0.02	0.00	0.01

name	user	system	elapsed
GENccEnrichResult-class	0.92	0.00	0.92
HyperGParamsCC-class	0	0	0
HyperGResultCC-class	0	0	0
breakEdges-methods	1.41	0.00	1.40
breakEdges	0	0	0
ccCompare	2.70	0.02	2.71
ccCompareCollection-class	0.01	0.00	0.01
ccCompareResult-class	0	0	0
ccData	0.64	0.00	0.64
ccEnrich	0.66	0.00	0.66
ccEnrichCollection-class	1.87	0.00	1.87
ccEnrichResult-class	5.76	0.05	5.80
ccGeneList-class	0.70	0.01	0.72
ccOptions-class	0.05	0.00	0.05
ccOutCyt-methods	0.01	0.00	0.01
ccSigList-class	0.02	0.00	0.02
cytOutData-methods	0.01	0.00	0.01
cytOutNodes-methods	0	0	0
hyperGTestCC	0.87	0.00	0.87
mergeLists-methods	0.84	0.00	0.84
mergedData-class	0.69	0.00	0.69
minCount	3.41	0.06	3.48
minNodes	0.05	0.00	0.04
pvalueType	3.85	0.04	3.89
show-methods	0	0	0