Package: categoryCompare

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch categoryCompare_1.3.0.tar.gz

StartedAt: 2013-03-25 01:35:55 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:40:22 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 267.5 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/categoryCompare.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'categoryCompare/DESCRIPTION' ... OK
* this is package 'categoryCompare' version '1.3.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'categoryCompare' can be installed ... [22s/24s] OK
* checking installed package size ... OK
* checking package 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
* 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 for unstated 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
minCount             6.020  0.122   6.150
ccEnrichResult-class 5.339  0.169   5.523
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'categoryCompare' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices
** installing vignettes
   'categoryCompare_vignette.Rnw' 
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics' and is not turning on duplicate class definitions for this class
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	1.317	0.041	1.358
HyperGParamsCC-class	0.012	0.006	0.019
HyperGResultCC-class	0.012	0.009	0.021
breakEdges-methods	1.263	0.043	1.308
breakEdges	0.009	0.006	0.016
ccCompare	1.931	0.055	1.987
ccCompareCollection-class	0.003	0.004	0.080
ccCompareResult-class	0.003	0.005	0.008
ccData	0.943	0.027	0.973
ccEnrich	0.989	0.040	1.031
ccEnrichCollection-class	2.409	0.086	2.503
ccEnrichResult-class	5.339	0.169	5.523
ccGeneList-class	1.152	0.039	1.194
ccOptions-class	0.047	0.021	0.069
ccOutCyt-methods	0.012	0.010	0.022
ccSigList-class	0.011	0.007	0.018
cytOutData-methods	0.015	0.014	0.034
cytOutNodes-methods	0.013	0.012	0.026
hyperGTestCC	1.365	0.071	1.439
mergeLists-methods	1.735	0.070	1.811
mergedData-class	1.323	0.045	1.373
minCount	6.020	0.122	6.150
minNodes	0.065	0.012	0.077
pvalueType	4.805	0.153	4.975
show-methods	0.023	0.008	0.031