Package: flowQ

Version: 1.19.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings flowQ_1.19.0.tar.gz

StartedAt: 2013-01-16 02:29:26 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:34:11 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 285.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowQ.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/flowQ.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.19.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowQ’ can be installed ... 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
evaluateProcess: multiple local function definitions for ‘efun’ with
  different formal arguments

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.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qaProcess.2DStatsPlot  13.421  1.248  13.582
qaProcess.ECDFPlot     10.540  0.820  10.965
qaProcess.DensityPlot  10.017  0.848  10.494
qaProcess.KLDistPlot    8.740  0.908   9.251
qaProcess.BoundaryPlot  6.056  0.856   6.541
txtFormatQAObject       4.701  0.992   5.188
* 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 2 notes.
See
  ‘/loc/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 ‘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: replacing previous import ‘sort’ when loading ‘flowCore’
Warning: replacing previous import ‘as’ when loading ‘methods’

* DONE (flowQ)

name	user	system	elapsed
aggregatorList-class	0.044	0.004	0.047
binaryAggregator-class	0.036	0.000	0.037
discreteAggregator-class	0.04	0.00	0.04
evaluateProcess	0.032	0.000	0.033
factorAggregator-class	0.032	0.000	0.033
flowQ-package	0.016	0.000	0.019
numericAggregator-class	0.036	0.000	0.038
outlier-class	0.02	0.00	0.02
outlierResult-class	0.036	0.000	0.033
qaAggregator-class	0.020	0.000	0.018
qaGraph-class	0.032	0.000	0.034
qaGraphList-class	0.016	0.000	0.019
qaProcess-class	0.392	0.000	0.391
qaProcess.2DStatsPlot	13.421	1.248	13.582
qaProcess.BoundaryPlot	6.056	0.856	6.541
qaProcess.DensityPlot	10.017	0.848	10.494
qaProcess.ECDFPlot	10.540	0.820	10.965
qaProcess.KLDistPlot	8.740	0.908	9.251
qaProcess.cellnumber	0.012	0.000	0.011
qaProcess.marginevents	0.016	0.000	0.018
qaProcess.timeflow	0.012	0.000	0.011
qaProcess.timeline	0.008	0.012	0.022
qaProcessFrame-class	0.004	0.000	0.004
qaReport	0.012	0.000	0.012
rangeAggregator-class	0.012	0.000	0.010
stringAggregator-class	0.012	0.000	0.012
txtFormatQAObject	4.701	0.992	5.188
writeQAReport	0.012	0.000	0.014
writeQATextReport	0.016	0.000	0.016