Package: categoryCompare

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch categoryCompare_1.2.0.tar.gz

StartedAt: 2013-03-24 22:51:46 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:55:52 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 246.9 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 2.15.3 (2013-03-01)
* 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 '1.2.0'
* 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ccEnrichResult-class 5.869  0.209   6.204
pvalueType           4.782  0.167   5.364
* 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) :
  A specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'IRanges' 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) :
  A specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class

* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	0.935	0.043	0.985
HyperGParamsCC-class	0.002	0.000	0.002
HyperGResultCC-class	0.000	0.001	0.001
breakEdges-methods	1.780	0.052	1.842
breakEdges	0	0	0
ccCompare	2.255	0.066	2.332
ccCompareCollection-class	0.000	0.000	0.001
ccCompareResult-class	0.001	0.000	0.000
ccData	1.159	0.036	1.208
ccEnrich	0.916	0.033	0.974
ccEnrichCollection-class	2.437	0.094	2.551
ccEnrichResult-class	5.869	0.209	6.204
ccGeneList-class	1.028	0.039	1.093
ccOptions-class	0.027	0.002	0.028
ccOutCyt-methods	0	0	0
ccSigList-class	0.001	0.000	0.001
cytOutData-methods	0	0	0
cytOutNodes-methods	0	0	0
hyperGTestCC	1.230	0.070	1.332
mergeLists-methods	1.107	0.056	1.205
mergedData-class	1.056	0.052	1.167
minCount	3.853	0.157	4.148
minNodes	0.000	0.000	0.001
pvalueType	4.782	0.167	5.364
show-methods	0	0	0