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 03:21:53 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:27:07 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 313.7 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 ... [51s/52s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ccEnrichResult-class 9.597  0.241   9.909
pvalueType           5.009  0.190   5.237
* 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	2.057	0.056	2.136
HyperGParamsCC-class	0.300	0.004	0.308
HyperGResultCC-class	0.008	0.006	0.013
breakEdges-methods	1.961	0.069	2.054
breakEdges	0.015	0.005	0.021
ccCompare	4.042	0.107	4.177
ccCompareCollection-class	0.004	0.006	0.010
ccCompareResult-class	0.005	0.005	0.009
ccData	0.997	0.040	1.052
ccEnrich	1.035	0.032	1.079
ccEnrichCollection-class	2.164	0.092	2.289
ccEnrichResult-class	9.597	0.241	9.909
ccGeneList-class	1.095	0.052	1.159
ccOptions-class	0.104	0.021	0.132
ccOutCyt-methods	0.032	0.008	0.041
ccSigList-class	0.004	0.006	0.009
cytOutData-methods	0.039	0.011	0.051
cytOutNodes-methods	0.034	0.009	0.044
hyperGTestCC	1.418	0.062	1.491
mergeLists-methods	1.446	0.069	1.554
mergedData-class	1.681	0.069	1.782
minCount	4.823	0.116	4.993
minNodes	0.003	0.005	0.009
pvalueType	5.009	0.190	5.237
show-methods	0.003	0.005	0.009