Package: flowQ

Version: 1.14.1

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch flowQ_1.14.1.tar.gz

StartedAt: 2012-01-09 02:46:52 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 02:50:57 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 245.4 seconds

RetCode: 0

Status:  OK

CheckDir: flowQ.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/flowQ.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowQ' version '1.14.1'
* 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 whether package 'flowQ' 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 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 ... NOTE
evaluateProcess: multiple local function definitions for 'efun' with
  different formal arguments
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 for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 'flowQ' ...
** R
** data
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning: replacing previous import '.__C__character' when loading 'methods'

--------

for references have a look at
citation('robCompositions')    
--------

Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'IRanges' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'IRanges' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DataQualityAssessment.Rnw' 
   'Extending-flowQ.Rnw' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

--------

for references have a look at
citation('robCompositions')    
--------

Warning message:
replacing previous import '.__C__character' when loading 'methods' 

* DONE (flowQ)

name	user	system	elapsed
aggregatorList-class	0.01	0.00	0.01
binaryAggregator-class	0	0	0
discreteAggregator-class	0	0	0
evaluateProcess	0	0	0
factorAggregator-class	0	0	0
flowQ-package	0	0	0
numericAggregator-class	0.02	0.00	0.02
outlier-class	0	0	0
outlierResult-class	0	0	0
qaAggregator-class	0	0	0
qaGraph-class	0	0	0
qaGraphList-class	0	0	0
qaProcess-class	0	0	0
qaProcess.2DStatsPlot	6.72	0.08	12.76
qaProcess.BoundaryPlot	3.00	0.00	8.29
qaProcess.DensityPlot	6.98	0.08	13.85
qaProcess.ECDFPlot	7.13	0.09	13.44
qaProcess.KLDistPlot	5.37	0.09	11.06
qaProcess.cellnumber	0	0	0
qaProcess.marginevents	0	0	0
qaProcess.timeflow	0	0	0
qaProcess.timeline	0	0	0
qaProcessFrame-class	0	0	0
qaReport	0	0	0
rangeAggregator-class	0	0	0
stringAggregator-class	0	0	0
txtFormatQAObject	0.90	0.07	4.53
writeQAReport	0	0	0
writeQATextReport	0	0	0