BioC 2.12: CHECK report for flowQ on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/flowQ.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowQ’ version ‘1.20.0’
* 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 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 ... [33s/33s] 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 ... NOTE
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 ... [98s/100s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qaProcess.2DStatsPlot  19.369  2.004  21.482
qaProcess.ECDFPlot     15.494  1.196  17.120
qaProcess.DensityPlot  14.156  1.284  15.525
qaProcess.KLDistPlot   11.992  1.280  13.378
qaProcess.BoundaryPlot  8.081  1.040   9.324
txtFormatQAObject       5.196  1.460   7.067
* 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 4 notes.
See
  ‘/home/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: 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
** testing if installed package can be loaded
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	0.604	0.036	0.639
binaryAggregator-class	0.008	0.000	0.011
discreteAggregator-class	0.012	0.000	0.012
evaluateProcess	0.012	0.000	0.011
factorAggregator-class	0.008	0.000	0.012
flowQ-package	0.008	0.000	0.008
numericAggregator-class	0.016	0.000	0.015
outlier-class	0.008	0.000	0.009
outlierResult-class	0.008	0.000	0.008
qaAggregator-class	0.012	0.000	0.013
qaGraph-class	0.004	0.004	0.011
qaGraphList-class	0.012	0.000	0.009
qaProcess-class	0.012	0.000	0.009
qaProcess.2DStatsPlot	19.369	2.004	21.482
qaProcess.BoundaryPlot	8.081	1.040	9.324
qaProcess.DensityPlot	14.156	1.284	15.525
qaProcess.ECDFPlot	15.494	1.196	17.120
qaProcess.KLDistPlot	11.992	1.280	13.378
qaProcess.cellnumber	0.016	0.004	0.021
qaProcess.marginevents	0.016	0.004	0.020
qaProcess.timeflow	0.012	0.008	0.020
qaProcess.timeline	0.016	0.004	0.019
qaProcessFrame-class	0.012	0.000	0.009
qaReport	0.024	0.000	0.022
rangeAggregator-class	0.016	0.008	0.022
stringAggregator-class	0.024	0.004	0.025
txtFormatQAObject	5.196	1.460	7.067
writeQAReport	0.024	0.000	0.024
writeQATextReport	0.012	0.000	0.012

BioC 2.12: CHECK report for flowQ on george2

Summary

Command output