Package: categoryCompare

Version: 1.3.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings categoryCompare_1.3.0.tar.gz

StartedAt: 2013-03-25 00:34:05 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:40:18 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 372.5 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/categoryCompare.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [29s/30s] 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 ... [62s/64s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ccEnrichResult-class 10.669  0.076  11.280
pvalueType            8.420  0.104   8.576
minCount              7.661  0.092   8.182
ccCompare             5.340  0.052   5.432
* 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	2.352	0.048	2.582
HyperGParamsCC-class	0.56	0.00	0.56
HyperGResultCC-class	0.012	0.004	0.016
breakEdges-methods	2.013	0.036	2.139
breakEdges	0.012	0.000	0.014
ccCompare	5.340	0.052	5.432
ccCompareCollection-class	0.008	0.000	0.007
ccCompareResult-class	0.008	0.000	0.007
ccData	0.764	0.012	0.776
ccEnrich	0.808	0.016	0.824
ccEnrichCollection-class	2.796	0.056	2.853
ccEnrichResult-class	10.669	0.076	11.280
ccGeneList-class	1.056	0.032	1.089
ccOptions-class	0.256	0.004	0.263
ccOutCyt-methods	0.060	0.004	0.066
ccSigList-class	0.068	0.000	0.074
cytOutData-methods	0.124	0.000	0.122
cytOutNodes-methods	0.064	0.000	0.065
hyperGTestCC	2.020	0.040	2.134
mergeLists-methods	1.144	0.032	1.174
mergedData-class	0.892	0.016	0.909
minCount	7.661	0.092	8.182
minNodes	0.000	0.008	0.010
pvalueType	8.420	0.104	8.576
show-methods	0.000	0.008	0.009