Package: flowQ

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowQ_1.18.0.tar.gz

StartedAt: 2013-03-24 23:29:42 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:34:40 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 298.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowQ.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/flowQ.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowQ' version '1.18.0'
* 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 for sufficient/correct file permissions ... 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 ... NOTE
evaluateProcess: multiple local function definitions for 'efun' with
  different formal arguments
Found .Internal call in the following function:
  'sysFun'
with calls to .Internal functions
  'system'

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following directories should probably not be installed:
  'images'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qaProcess.2DStatsPlot  11.543  3.766  15.438
qaProcess.DensityPlot   9.463  2.685  12.601
qaProcess.ECDFPlot      9.188  2.838  12.239
qaProcess.KLDistPlot    8.853  2.371  11.443
qaProcess.BoundaryPlot  5.441  1.879   7.707
* 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

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/flowQ.Rcheck/00check.log'
for details.

* installing *source* package 'flowQ' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'plot' when loading 'graphics'
Warning: replacing previous import 'as' when loading 'methods'
** help
*** installing help indices
** building package indices
** installing vignettes
   'DataQualityAssessment.Rnw' 
   'Extending-flowQ.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'plot' when loading 'graphics'
Warning: replacing previous import 'as' when loading 'methods'

* DONE (flowQ)

name	user	system	elapsed
aggregatorList-class	0.028	0.003	0.032
binaryAggregator-class	0.001	0.000	0.001
discreteAggregator-class	0.000	0.001	0.001
evaluateProcess	0	0	0
factorAggregator-class	0.001	0.000	0.001
flowQ-package	0.000	0.001	0.000
numericAggregator-class	0.000	0.000	0.001
outlier-class	0	0	0
outlierResult-class	0.000	0.000	0.001
qaAggregator-class	0.001	0.000	0.001
qaGraph-class	0	0	0
qaGraphList-class	0.001	0.000	0.001
qaProcess-class	0.000	0.000	0.001
qaProcess.2DStatsPlot	11.543	3.766	15.438
qaProcess.BoundaryPlot	5.441	1.879	7.707
qaProcess.DensityPlot	9.463	2.685	12.601
qaProcess.ECDFPlot	9.188	2.838	12.239
qaProcess.KLDistPlot	8.853	2.371	11.443
qaProcess.cellnumber	0	0	0
qaProcess.marginevents	0	0	0
qaProcess.timeflow	0	0	0
qaProcess.timeline	0.000	0.001	0.001
qaProcessFrame-class	0.000	0.000	0.001
qaReport	0	0	0
rangeAggregator-class	0.001	0.001	0.001
stringAggregator-class	0.001	0.001	0.001
txtFormatQAObject	2.916	1.821	4.896
writeQAReport	0.000	0.000	0.001
writeQATextReport	0.001	0.000	0.000