BioC 2.14: CHECK report for categoryCompare on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch categoryCompare_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/categoryCompare.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ... [23s/23s] 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/32s] 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
  ‘/Users/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	0.995	0.018	1.014
HyperGParamsCC-class	0.002	0.000	0.002
HyperGResultCC-class	0.002	0.000	0.002
breakEdges-methods	1.167	0.020	1.188
breakEdges	0.001	0.000	0.001
ccCompare	0.977	0.013	0.989
ccCompareCollection-class	0.001	0.000	0.001
ccCompareResult-class	0.000	0.000	0.001
ccData	0.750	0.013	0.762
ccEnrich	0.842	0.010	0.852
ccEnrichCollection-class	3.180	0.046	3.227
ccEnrichResult-class	3.217	0.034	3.253
ccGeneList-class	1.124	0.012	1.137
ccOptions-class	0.026	0.000	0.027
ccOutCyt-methods	0.001	0.000	0.000
ccSigList-class	0.001	0.000	0.002
cytOutData-methods	0.001	0.000	0.001
cytOutNodes-methods	0.001	0.000	0.001
hyperGTestCC	1.059	0.024	1.084
mergeLists-methods	1.027	0.021	1.050
mergedData-class	0.953	0.021	0.976
minCount	3.070	0.034	3.106
minNodes	0.001	0.000	0.000
pvalueType	2.509	0.029	2.544
show-methods	0.001	0.000	0.001

BioC 2.14: CHECK report for categoryCompare on morelia

Summary

Command output