BioC 2.12: CHECK report for flowQ on pelham

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowQ.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowQ' version '1.19.5'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'flowQ' can be installed ... [27s/29s] 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 ... WARNING
Found a .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.

In addition to the above warning(s), found the following notes:

evaluateProcess: multiple local function definitions for 'efun' with
  different formal arguments
* 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 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 ... [89s/92s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qaProcess.2DStatsPlot  18.038  1.516  20.271
qaProcess.ECDFPlot     13.189  0.961  14.400
qaProcess.DensityPlot  13.081  0.916  14.156
qaProcess.KLDistPlot   11.212  0.903  12.609
qaProcess.BoundaryPlot  8.308  0.741   9.193
txtFormatQAObject       5.099  0.800   6.482
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/flowQ.Rcheck/00check.log'
for details.

* installing *source* package 'flowQ' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import 'plot' when loading 'graphics'
Warning: replacing previous import 'sort' when loading 'flowCore'
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 in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import 'plot' when loading 'graphics'
Warning: replacing previous import 'sort' when loading 'flowCore'
Warning: replacing previous import 'as' when loading 'methods'
* DONE (flowQ)

name	user	system	elapsed
aggregatorList-class	0.016	0.003	0.020
binaryAggregator-class	0.018	0.004	0.022
discreteAggregator-class	0.012	0.002	0.014
evaluateProcess	0.014	0.001	0.015
factorAggregator-class	0.014	0.003	0.017
flowQ-package	0.011	0.003	0.013
numericAggregator-class	0.012	0.003	0.016
outlier-class	0.013	0.003	0.017
outlierResult-class	0.013	0.002	0.015
qaAggregator-class	0.011	0.002	0.013
qaGraph-class	0.011	0.000	0.012
qaGraphList-class	0.014	0.004	0.018
qaProcess-class	0.012	0.002	0.015
qaProcess.2DStatsPlot	18.038	1.516	20.271
qaProcess.BoundaryPlot	8.308	0.741	9.193
qaProcess.DensityPlot	13.081	0.916	14.156
qaProcess.ECDFPlot	13.189	0.961	14.400
qaProcess.KLDistPlot	11.212	0.903	12.609
qaProcess.cellnumber	0.389	0.008	0.398
qaProcess.marginevents	0.008	0.007	0.015
qaProcess.timeflow	0.008	0.007	0.014
qaProcess.timeline	0.007	0.008	0.015
qaProcessFrame-class	0.003	0.005	0.012
qaReport	0.004	0.006	0.010
rangeAggregator-class	0.004	0.004	0.007
stringAggregator-class	0.009	0.005	0.014
txtFormatQAObject	5.099	0.800	6.482
writeQAReport	0.014	0.008	0.022
writeQATextReport	0.015	0.006	0.021

Summary

Command output