BioC 2.12: CHECK report for categoryCompare on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/categoryCompare.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.4.0'
* 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 ... [29s/30s] WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
See '/Users/biocbuild/bbs-2.12-bioc/meat/categoryCompare.Rcheck/00install.out' for details.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [59s/59s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ccEnrichResult-class 8.664  0.227   8.942
pvalueType           6.763  0.213   7.004
minCount             6.391  0.166   6.573
* 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

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/categoryCompare.Rcheck/00check.log'
for details.

* 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
Warning: package 'KEGG.db' was built under R version 3.1.0
** 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	2.283	0.051	2.370
HyperGParamsCC-class	0.323	0.002	0.325
HyperGResultCC-class	0.008	0.005	0.013
breakEdges-methods	2.153	0.070	2.227
breakEdges	0.007	0.002	0.010
ccCompare	4.300	0.077	4.411
ccCompareCollection-class	0.003	0.004	0.007
ccCompareResult-class	0.009	0.005	0.016
ccData	1.275	0.048	1.371
ccEnrich	1.315	0.036	1.353
ccEnrichCollection-class	3.266	0.114	3.427
ccEnrichResult-class	8.664	0.227	8.942
ccGeneList-class	1.895	0.057	1.957
ccOptions-class	0.065	0.020	0.085
ccOutCyt-methods	0.004	0.005	0.009
ccSigList-class	0.016	0.007	0.022
cytOutData-methods	0.005	0.008	0.012
cytOutNodes-methods	0.018	0.010	0.028
hyperGTestCC	1.658	0.068	1.728
mergeLists-methods	1.628	0.053	1.686
mergedData-class	1.416	0.045	1.463
minCount	6.391	0.166	6.573
minNodes	0.095	0.015	0.110
pvalueType	6.763	0.213	7.004
show-methods	0.003	0.005	0.008

BioC 2.12: CHECK report for categoryCompare on petty

Summary

Command output