Package: pRoloc

Version: 0.99.16

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pRoloc_0.99.16.tar.gz

StartedAt: 2013-03-24 08:58:38 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:10:23 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 705.2 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 3.0.0 beta (2013-03-21 r62346)
* 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 '0.99.16'
* 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 ... [41s/44s] 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 ... [83s/84s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 20.068  0.138  20.382
rfClassification        8.354  0.242   8.809
nnetClassification      8.157  0.053   8.495
svmClassification       7.790  0.112   7.941
nbClassification        5.750  0.058   6.066
ksvmClassification      5.376  0.125   5.585
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [222s/223s]
 [222s/224s] 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
   'pRoloc-tutorial.Rnw' 
processing file: pRoloc-tutorial.Rnw
output file: /Users/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/pRoloc/doc/pRoloc-tutorial.R
** testing if installed package can be loaded
Warning: replacing previous import 'alpha' when loading 'scales'
* DONE (pRoloc)

name	user	system	elapsed
GenRegRes-class	0.498	0.007	0.505
chi2-methods	0.032	0.010	0.041
empPvalues	0.324	0.026	0.351
exprsToRatios-methods	0.579	0.021	0.617
getMarkers	0.068	0.017	0.091
getStockcol	0.120	0.018	0.138
knnClassification	1.741	0.038	1.790
ksvmClassification	5.376	0.125	5.585
makeNaData	2.528	0.033	2.597
minClassScore	0.130	0.015	0.146
minMarkers	0.108	0.010	0.118
nbClassification	5.750	0.058	6.066
nnetClassification	8.157	0.053	8.495
perTurboClassification	20.068	0.138	20.382
phenoDisco	0.020	0.006	0.027
plot2D	0.110	0.020	0.158
plotDist	0.184	0.016	0.237
plsdaClassification	0.016	0.006	0.024
rfClassification	8.354	0.242	8.809
svmClassification	7.790	0.112	7.941