BioC 2.12: CHECK report for pRoloc on george2

Package: pRoloc

Version: 1.0.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings pRoloc_1.0.1.tar.gz

StartedAt: 2013-10-09 04:10:43 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:24:06 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 802.7 seconds

RetCode: 0

Status:  OK

CheckDir: pRoloc.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [49s/50s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [93s/93s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 22.197  0.024  22.239
rfClassification        9.433  0.068   9.505
svmClassification       8.048  0.040   8.092
nnetClassification      7.381  0.012   7.398
ksvmClassification      6.985  0.044   7.211
nbClassification        6.296  0.016   6.316
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [231s/234s]
 [232s/234s] 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	0.836	0.012	0.848
chi2-methods	0.064	0.004	0.067
empPvalues	0.276	0.028	0.306
exprsToRatios-methods	0.584	0.008	0.605
getMarkers	0.064	0.000	0.065
getStockcol	0.156	0.016	0.173
knnClassification	2.932	0.020	2.959
ksvmClassification	6.985	0.044	7.211
makeNaData	2.728	0.020	2.752
minClassScore	0.152	0.008	0.160
minMarkers	0.136	0.000	0.137
nbClassification	6.296	0.016	6.316
nnetClassification	7.381	0.012	7.398
perTurboClassification	22.197	0.024	22.239
phenoDisco	0.020	0.008	0.026
plot2D	0.124	0.004	0.129
plotDist	0.176	0.012	0.198
plsdaClassification	0.024	0.000	0.025
rfClassification	9.433	0.068	9.505
svmClassification	8.048	0.040	8.092