Package: phenoDist

Version: 1.1.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch phenoDist_1.1.0.tar.gz

StartedAt: 2011-06-02 15:16:44 -0700 (Thu, 02 Jun 2011)

EndedAt: 2011-06-02 15:23:14 -0700 (Thu, 02 Jun 2011)

EllapsedTime: 389.9 seconds

RetCode: 0

Status:  OK

CheckDir: phenoDist.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/phenoDist.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phenoDist/DESCRIPTION' ... OK
* this is package 'phenoDist' version '1.1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'phenoDist' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 examples ... 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 'phenoDist' ...
** R
** inst
** preparing package for lazy loading
Loading required package: EBImage
Loading required package: abind
Loading required package: cellHTS2
Loading required package: RColorBrewer
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object(s) are masked from 'package:EBImage':

    channel, combine

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
Loading required package: akima
Loading required package: lattice
locfit 1.5-6 	 2010-01-20 
Loading required package: grid
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
Loading required package: class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'phenoDist.Rnw' 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)

* DONE (phenoDist)

name	user	system	elapsed
PDMByFactorAnalysis	3.99	0.01	55.67
PDMByKS	11.58	0.27	136.20
PDMBySvmAccuracy	14.17	0.06	14.29
PDMBySvmWeightVector	21.42	0.03	21.53
PDMByWellAvg	2.42	0.03	4.56
clusterDist	0.53	0.00	0.53
ctlSeparatn	0	0	0
distToNeg	12.96	0.00	13.00
enrichAnalysis	0	0	0
repCorr	0	0	0
repDistRank	0	0	0