Package: pRoloc

Version: 0.99.17

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pRoloc_0.99.17.tar.gz

StartedAt: 2013-03-25 04:09:22 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:20:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 671.5 seconds

RetCode: 0

Status:  OK

CheckDir: pRoloc.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'pRoloc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pRoloc' version '0.99.17'
* 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 ... [34s/35s] 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 ... [96s/96s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 24.077  0.068  24.149
rfClassification        9.764  0.525  10.301
nnetClassification      9.907  0.057   9.967
nbClassification        7.499  0.062   7.562
svmClassification       7.473  0.058   7.537
ksvmClassification      6.778  0.137   6.919
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [209s/209s]
 [209s/209s] 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	0.336	0.010	0.346
chi2-methods	0.033	0.016	0.051
empPvalues	0.452	0.025	0.478
exprsToRatios-methods	0.726	0.033	0.769
getMarkers	0.082	0.014	0.096
getStockcol	0.161	0.035	0.195
knnClassification	2.262	0.054	2.323
ksvmClassification	6.778	0.137	6.919
makeNaData	3.343	0.056	3.399
minClassScore	0.169	0.021	0.190
minMarkers	0.146	0.017	0.165
nbClassification	7.499	0.062	7.562
nnetClassification	9.907	0.057	9.967
perTurboClassification	24.077	0.068	24.149
phenoDisco	0.009	0.007	0.016
plot2D	0.102	0.022	0.126
plotDist	0.175	0.017	0.193
plsdaClassification	0.019	0.012	0.031
rfClassification	9.764	0.525	10.301
svmClassification	7.473	0.058	7.537