BioC 2.12: CHECK report for flowQ on petty

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: 2013-10-08 22:22:34 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:29:18 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 403.4 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 3.0.1 (2013-05-16)
* 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 ... [29s/30s] 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 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 ... [100s/102s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qaProcess.2DStatsPlot  20.338  1.299  22.167
qaProcess.ECDFPlot     15.530  0.810  16.622
qaProcess.DensityPlot  14.887  0.760  15.919
qaProcess.KLDistPlot   13.602  0.850  14.845
qaProcess.BoundaryPlot  9.646  0.626  10.460
txtFormatQAObject       5.722  0.808   6.676
* 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, onlyNULL) :
  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, onlyNULL) :
  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	0.304	0.004	0.311
binaryAggregator-class	0.007	0.001	0.008
discreteAggregator-class	0.011	0.002	0.013
evaluateProcess	0.011	0.002	0.013
factorAggregator-class	0.009	0.001	0.010
flowQ-package	0.009	0.001	0.009
numericAggregator-class	0.011	0.001	0.012
outlier-class	0.010	0.000	0.011
outlierResult-class	0.005	0.001	0.008
qaAggregator-class	0.012	0.003	0.015
qaGraph-class	0.006	0.002	0.009
qaGraphList-class	0.011	0.003	0.014
qaProcess-class	0.006	0.001	0.008
qaProcess.2DStatsPlot	20.338	1.299	22.167
qaProcess.BoundaryPlot	9.646	0.626	10.460
qaProcess.DensityPlot	14.887	0.760	15.919
qaProcess.ECDFPlot	15.530	0.810	16.622
qaProcess.KLDistPlot	13.602	0.850	14.845
qaProcess.cellnumber	0.009	0.005	0.014
qaProcess.marginevents	0.008	0.004	0.012
qaProcess.timeflow	0.008	0.004	0.012
qaProcess.timeline	0.008	0.004	0.013
qaProcessFrame-class	0.009	0.004	0.012
qaReport	0.012	0.005	0.017
rangeAggregator-class	0.008	0.004	0.011
stringAggregator-class	0.004	0.006	0.009
txtFormatQAObject	5.722	0.808	6.676
writeQAReport	0.008	0.005	0.014
writeQATextReport	0.008	0.004	0.013