BioC 2.12: CHECK report for categoryCompare on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/categoryCompare.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.4.0’
* 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 ... [30s/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 ... [61s/61s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ccEnrichResult-class 9.261  0.060   9.332
pvalueType           8.460  0.068   8.529
minCount             7.749  0.048   7.827
ccCompare            5.516  0.052   5.619
* 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
** 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	2.508	0.028	2.539
HyperGParamsCC-class	0.645	0.004	0.649
HyperGResultCC-class	0.02	0.00	0.02
breakEdges-methods	2.084	0.060	2.143
breakEdges	0.008	0.008	0.016
ccCompare	5.516	0.052	5.619
ccCompareCollection-class	0.008	0.000	0.008
ccCompareResult-class	0.016	0.000	0.016
ccData	0.760	0.016	0.797
ccEnrich	0.816	0.028	0.844
ccEnrichCollection-class	2.884	0.092	2.978
ccEnrichResult-class	9.261	0.060	9.332
ccGeneList-class	1.700	0.032	1.734
ccOptions-class	0.068	0.000	0.071
ccOutCyt-methods	0.008	0.000	0.008
ccSigList-class	0.024	0.000	0.022
cytOutData-methods	0.008	0.004	0.010
cytOutNodes-methods	0.024	0.000	0.026
hyperGTestCC	1.048	0.032	1.081
mergeLists-methods	1.076	0.020	1.097
mergedData-class	0.896	0.048	0.943
minCount	7.749	0.048	7.827
minNodes	0.152	0.000	0.153
pvalueType	8.460	0.068	8.529
show-methods	0.000	0.008	0.010

BioC 2.12: CHECK report for categoryCompare on george2

Summary

Command output