Package: flowQ

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings flowQ_1.8.0.tar.gz

StartedAt: 2010-10-04 16:56:13 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 16:59:53 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 219.5 seconds

RetCode: 0

Status:  OK

CheckDir: flowQ.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/flowQ.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'flowQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowQ' version '1.8.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'flowQ' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... NOTE
evaluateProcess: multiple local function definitions for ‘efun’ with
  different formal arguments
normalizeSets : <anonymous>: no visible global function definition for
  ‘warpSet’
qaProcess.2DStatsPlot: no visible binding for global variable ‘Aliquot’
qaProcess.DensityPlot: no visible binding for global variable ‘Aliquot’
qaProcess.ECDFPlot: no visible binding for global variable ‘Aliquot’
* checking Rd files ... NOTE
prepare_Rd: normalizeSets.Rd:44-51: Dropping empty section \examples
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package ‘flowQ’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: flowCore
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)

Attaching package: 'flowCore'

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

    alias, filter

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: KernSmooth
Loading required package: tools

Attaching package: 'latticeExtra'

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

    ecdfplot

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Using ImageMagic library at /usr/local/lib/ImageMagick-6.3.3
(version 6.3.3)

* DONE (flowQ)

name	user	system	elapsed
aggregatorList-class	0.013	0.000	0.013
binaryAggregator-class	0.001	0.000	0.001
discreteAggregator-class	0.001	0.000	0.001
evaluateProcess	0.000	0.000	0.001
factorAggregator-class	0.002	0.000	0.002
flowQ-package	0.001	0.000	0.000
numericAggregator-class	0.002	0.000	0.002
outlier-class	0	0	0
outlierResult-class	0	0	0
qaAggregator-class	0.002	0.000	0.002
qaGraph-class	0.002	0.001	0.002
qaGraphList-class	0.002	0.000	0.002
qaProcess-class	0.001	0.001	0.002
qaProcess.2DStatsPlot	15.423	2.506	19.883
qaProcess.BoundaryPlot	7.198	1.256	10.784
qaProcess.DensityPlot	15.768	2.161	19.191
qaProcess.ECDFPlot	16.110	2.237	18.944
qaProcess.KLDistPlot	12.251	1.944	14.752
qaProcess.cellnumber	0.001	0.000	0.001
qaProcess.marginevents	0.000	0.000	0.001
qaProcess.timeflow	0.000	0.000	0.001
qaProcess.timeline	0.001	0.001	0.001
qaProcessFrame-class	0.002	0.001	0.002
qaReport	0.000	0.000	0.001
rangeAggregator-class	0.002	0.001	0.003
stringAggregator-class	0.001	0.000	0.002
txtFormatQAObject	4.231	1.233	5.647
writeQAReport	0.000	0.000	0.001
writeQATextReport	0.000	0.001	0.000