BioC 2.14: CHECK report for categoryCompare on zin2

* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/categoryCompare.Rcheck’
* using R version 3.1.0 (2014-04-10)
* 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 ‘1.8.0’
* 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 ... [18s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... NOTE
  Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/categoryCompare.Rcheck/00check.log’
for details.

* installing *source* package ‘categoryCompare’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: 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
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	0.804	0.008	0.813
HyperGParamsCC-class	0.000	0.004	0.001
HyperGResultCC-class	0.000	0.000	0.001
breakEdges-methods	0.924	0.008	0.933
breakEdges	0	0	0
ccCompare	0.808	0.004	0.813
ccCompareCollection-class	0.000	0.000	0.001
ccCompareResult-class	0	0	0
ccData	0.824	0.000	0.827
ccEnrich	0.568	0.008	0.574
ccEnrichCollection-class	2.492	0.028	2.524
ccEnrichResult-class	3.021	0.016	3.050
ccGeneList-class	0.848	0.008	0.860
ccOptions-class	0.024	0.000	0.023
ccOutCyt-methods	0	0	0
ccSigList-class	0.000	0.000	0.001
cytOutData-methods	0	0	0
cytOutNodes-methods	0	0	0
hyperGTestCC	0.736	0.016	0.755
mergeLists-methods	0.736	0.016	0.752
mergedData-class	0.736	0.008	0.742
minCount	2.892	0.020	2.916
minNodes	0	0	0
pvalueType	2.480	0.008	2.488
show-methods	0	0	0

BioC 2.14: CHECK report for categoryCompare on zin2

Summary

Command output