BioC 2.14: CHECK report for categoryCompare on petty

Package: categoryCompare

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch categoryCompare_1.8.0.tar.gz

StartedAt: 2014-10-07 21:05:18 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:13:18 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 479.1 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

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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-darwin10.8.0 (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 ... [39s/41s] 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 ... [54s/56s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ccEnrichResult-class 5.801  0.057   5.984
minCount             5.343  0.069   5.466
pvalueType           4.917  0.056   5.200
* 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	1.643	0.046	1.696
HyperGParamsCC-class	0.004	0.001	0.004
HyperGResultCC-class	0.004	0.000	0.004
breakEdges-methods	1.909	0.029	2.038
breakEdges	0.001	0.000	0.002
ccCompare	1.689	0.021	1.954
ccCompareCollection-class	0.002	0.000	0.003
ccCompareResult-class	0.002	0.001	0.003
ccData	1.293	0.024	1.392
ccEnrich	1.740	0.020	1.836
ccEnrichCollection-class	4.739	0.077	4.903
ccEnrichResult-class	5.801	0.057	5.984
ccGeneList-class	1.802	0.026	1.849
ccOptions-class	0.052	0.001	0.054
ccOutCyt-methods	0.001	0.000	0.002
ccSigList-class	0.002	0.000	0.002
cytOutData-methods	0.002	0.000	0.002
cytOutNodes-methods	0.002	0.000	0.002
hyperGTestCC	1.745	0.039	1.810
mergeLists-methods	1.664	0.037	1.766
mergedData-class	1.425	0.027	1.482
minCount	5.343	0.069	5.466
minNodes	0.002	0.000	0.002
pvalueType	4.917	0.056	5.200
show-methods	0.001	0.000	0.001