BioC 2.12: CHECK report for pRoloc on petty

Package: pRoloc

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pRoloc_1.0.1.tar.gz

StartedAt: 2013-10-08 23:31:57 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:45:57 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 840.2 seconds

RetCode: 0

Status:  OK

CheckDir: pRoloc.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/pRoloc.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 'pRoloc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pRoloc' version '1.0.1'
* 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 'pRoloc' can be installed ... [47s/48s] OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [100s/102s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 25.471  0.120  25.894
svmClassification       9.680  0.078   9.849
rfClassification        9.264  0.145   9.516
nnetClassification      8.822  0.057   9.124
nbClassification        7.614  0.060   7.761
ksvmClassification      6.910  0.145   7.124
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [271s/284s]
 [271s/284s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'pRoloc' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'alpha' when loading 'scales'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'alpha' when loading 'scales'
* DONE (pRoloc)

name	user	system	elapsed
GenRegRes-class	0.026	0.005	0.031
chi2-methods	0.035	0.009	0.045
empPvalues	0.408	0.019	0.428
exprsToRatios-methods	0.761	0.022	0.812
getMarkers	0.080	0.014	0.094
getStockcol	0.135	0.020	0.154
knnClassification	2.813	0.044	2.872
ksvmClassification	6.910	0.145	7.124
makeNaData	3.393	0.051	3.463
minClassScore	0.169	0.015	0.185
minMarkers	0.129	0.017	0.146
nbClassification	7.614	0.060	7.761
nnetClassification	8.822	0.057	9.124
perTurboClassification	25.471	0.120	25.894
phenoDisco	0.007	0.003	0.011
plot2D	0.124	0.016	0.141
plotDist	0.210	0.018	0.244
plsdaClassification	0.011	0.007	0.017
rfClassification	9.264	0.145	9.516
svmClassification	9.680	0.078	9.849