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: 2013-03-24 03:15:21 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 03:20:36 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 314.4 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/categoryCompare.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-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 ... [26s/27s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [52s/52s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ccEnrichResult-class 9.651  0.246   9.991
minCount             5.076  0.158   5.291
pvalueType           4.932  0.196   5.155
* 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	2.233	0.057	2.308
HyperGParamsCC-class	0.349	0.003	0.352
HyperGResultCC-class	0.008	0.006	0.015
breakEdges-methods	1.778	0.073	1.857
breakEdges	0.012	0.004	0.016
ccCompare	4.121	0.097	4.230
ccCompareCollection-class	0.003	0.006	0.009
ccCompareResult-class	0.004	0.003	0.007
ccData	0.926	0.037	0.965
ccEnrich	1.007	0.035	1.051
ccEnrichCollection-class	2.149	0.110	2.264
ccEnrichResult-class	9.651	0.246	9.991
ccGeneList-class	1.019	0.045	1.068
ccOptions-class	0.103	0.021	0.124
ccOutCyt-methods	0.033	0.007	0.042
ccSigList-class	0.003	0.005	0.008
cytOutData-methods	0.034	0.009	0.043
cytOutNodes-methods	0.034	0.008	0.041
hyperGTestCC	1.368	0.054	1.423
mergeLists-methods	1.432	0.070	1.526
mergedData-class	1.703	0.068	1.776
minCount	5.076	0.158	5.291
minNodes	0.004	0.005	0.009
pvalueType	4.932	0.196	5.155
show-methods	0.003	0.005	0.009