Package: flowQ

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowQ_1.20.0.tar.gz

StartedAt: 2013-05-01 05:20:35 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:26:42 -0700 (Wed, 01 May 2013)

EllapsedTime: 367.1 seconds

RetCode: 0

Status:  OK

CheckDir: flowQ.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowQ.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* 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 '1.20.0'
* 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 ... [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 ... 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 ... [89s/93s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qaProcess.2DStatsPlot  17.663  1.558  20.327
qaProcess.DensityPlot  12.988  0.942  14.398
qaProcess.ECDFPlot     12.875  0.972  14.157
qaProcess.KLDistPlot   11.381  0.990  13.631
qaProcess.BoundaryPlot  8.640  0.757   9.579
txtFormatQAObject       5.521  0.810   6.901
* 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
  '/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
** 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	0.021	0.004	0.025
binaryAggregator-class	0.012	0.003	0.014
discreteAggregator-class	0.008	0.002	0.009
evaluateProcess	0.012	0.002	0.013
factorAggregator-class	0.012	0.002	0.014
flowQ-package	0.008	0.001	0.011
numericAggregator-class	0.012	0.001	0.014
outlier-class	0.011	0.002	0.014
outlierResult-class	0.007	0.002	0.009
qaAggregator-class	0.013	0.002	0.014
qaGraph-class	0.014	0.001	0.014
qaGraphList-class	0.009	0.004	0.012
qaProcess-class	0.013	0.002	0.016
qaProcess.2DStatsPlot	17.663	1.558	20.327
qaProcess.BoundaryPlot	8.640	0.757	9.579
qaProcess.DensityPlot	12.988	0.942	14.398
qaProcess.ECDFPlot	12.875	0.972	14.157
qaProcess.KLDistPlot	11.381	0.990	13.631
qaProcess.cellnumber	0.008	0.005	0.013
qaProcess.marginevents	0.008	0.005	0.013
qaProcess.timeflow	0.015	0.006	0.022
qaProcess.timeline	0.010	0.005	0.016
qaProcessFrame-class	0.024	0.008	0.032
qaReport	0.009	0.006	0.015
rangeAggregator-class	0.004	0.005	0.008
stringAggregator-class	0.004	0.006	0.010
txtFormatQAObject	5.521	0.810	6.901
writeQAReport	0.011	0.008	0.019
writeQATextReport	0.009	0.007	0.015