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: 2013-01-16 01:15:46 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:20:01 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 255.0 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/categoryCompare.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ccEnrichResult-class 9.072  0.016   9.086
pvalueType           5.308  0.032   5.341
* 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	1.740	0.028	1.776
HyperGParamsCC-class	0.356	0.000	0.353
HyperGResultCC-class	0.004	0.004	0.007
breakEdges-methods	1.360	0.028	1.387
breakEdges	0.008	0.004	0.011
ccCompare	3.761	0.028	3.797
ccCompareCollection-class	0.004	0.000	0.005
ccCompareResult-class	0.008	0.000	0.006
ccData	0.624	0.012	0.638
ccEnrich	0.648	0.024	0.671
ccEnrichCollection-class	1.740	0.040	1.783
ccEnrichResult-class	9.072	0.016	9.086
ccGeneList-class	0.784	0.032	0.814
ccOptions-class	0.168	0.000	0.169
ccOutCyt-methods	0.052	0.000	0.050
ccSigList-class	0.052	0.000	0.050
cytOutData-methods	0.100	0.000	0.102
cytOutNodes-methods	0.048	0.004	0.054
hyperGTestCC	1.052	0.028	1.084
mergeLists-methods	1.453	0.028	1.480
mergedData-class	0.732	0.008	0.742
minCount	4.712	0.044	4.765
minNodes	0.072	0.000	0.073
pvalueType	5.308	0.032	5.341
show-methods	0.072	0.004	0.074