Package: categoryCompare

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch categoryCompare_1.1.0.tar.gz

StartedAt: 2012-06-20 22:32:46 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 22:38:11 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 324.8 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/categoryCompare.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.1.0'
* 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 whether package 'categoryCompare' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'categoryCompare' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'categoryCompare_vignette.Rnw' 
** testing if installed package can be loaded

* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	1.377	0.043	1.431
HyperGParamsCC-class	0.003	0.000	0.003
HyperGResultCC-class	0.001	0.000	0.002
breakEdges-methods	2.238	0.056	2.305
breakEdges	0.000	0.000	0.001
ccCompare	2.653	0.072	2.755
ccCompareCollection-class	0.001	0.000	0.002
ccCompareResult-class	0.001	0.001	0.001
ccData	1.547	0.037	1.593
ccEnrich	1.342	0.039	1.385
ccEnrichCollection-class	2.937	0.109	3.074
ccEnrichResult-class	6.985	0.230	7.277
ccGeneList-class	1.411	0.039	1.464
ccOptions-class	0.038	0.002	0.052
ccOutCyt-methods	0.000	0.001	0.001
ccSigList-class	0.000	0.000	0.001
cytOutData-methods	0.000	0.001	0.000
cytOutNodes-methods	0.001	0.000	0.001
hyperGTestCC	1.826	0.064	1.915
mergeLists-methods	1.684	0.050	1.784
mergedData-class	1.567	0.044	1.620
minCount	4.959	0.173	5.162
minNodes	0	0	0
pvalueType	5.141	0.177	5.346
show-methods	0	0	0