BioC 2.13: CHECK report for categoryCompare on perceval

Package: categoryCompare

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch categoryCompare_1.6.0.tar.gz

StartedAt: 2014-04-05 00:01:31 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:07:46 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 375.5 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/categoryCompare.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.6.0’
* 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 ... [32s/32s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘categoryCompare_vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [53s/53s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ccEnrichResult-class 8.974  0.146   9.123
minCount             5.784  0.107   5.895
pvalueType           5.386  0.099   5.488
* 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 were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	1.292	0.047	1.340
HyperGParamsCC-class	0.01	0.01	0.02
HyperGResultCC-class	0.011	0.006	0.017
breakEdges-methods	2.068	0.056	2.136
breakEdges	0.007	0.003	0.010
ccCompare	4.539	0.081	4.641
ccCompareCollection-class	0.003	0.003	0.007
ccCompareResult-class	0.009	0.006	0.016
ccData	0.705	0.033	0.741
ccEnrich	0.712	0.040	0.752
ccEnrichCollection-class	1.777	0.076	1.856
ccEnrichResult-class	8.974	0.146	9.123
ccGeneList-class	0.834	0.050	0.885
ccOptions-class	0.122	0.020	0.141
ccOutCyt-methods	0.040	0.007	0.048
ccSigList-class	0.042	0.006	0.047
cytOutData-methods	0.056	0.011	0.067
cytOutNodes-methods	0.003	0.005	0.009
hyperGTestCC	1.146	0.060	1.206
mergeLists-methods	1.070	0.051	1.120
mergedData-class	0.942	0.041	0.983
minCount	5.784	0.107	5.895
minNodes	0.097	0.016	0.113
pvalueType	5.386	0.099	5.488
show-methods	0.002	0.004	0.006