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Package 214/631HostnameOS / ArchBUILDCHECKBUILD BIN
flowQ 1.19.0
Mike Jiang
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowQ
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  ERROR  skipped  skipped 
petty Mac OS X Leopard (10.5.8) / i386  ERROR  skipped  skipped 

Summary

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

Command output

* 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.

flowQ.Rcheck/00install.out:

* 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)

flowQ.Rcheck/flowQ-Ex.timings:

nameusersystemelapsed
aggregatorList-class0.0440.0040.047
binaryAggregator-class0.0360.0000.037
discreteAggregator-class0.040.000.04
evaluateProcess0.0320.0000.033
factorAggregator-class0.0320.0000.033
flowQ-package0.0160.0000.019
numericAggregator-class0.0360.0000.038
outlier-class0.020.000.02
outlierResult-class0.0360.0000.033
qaAggregator-class0.0200.0000.018
qaGraph-class0.0320.0000.034
qaGraphList-class0.0160.0000.019
qaProcess-class0.3920.0000.391
qaProcess.2DStatsPlot13.421 1.24813.582
qaProcess.BoundaryPlot6.0560.8566.541
qaProcess.DensityPlot10.017 0.84810.494
qaProcess.ECDFPlot10.540 0.82010.965
qaProcess.KLDistPlot8.7400.9089.251
qaProcess.cellnumber0.0120.0000.011
qaProcess.marginevents0.0160.0000.018
qaProcess.timeflow0.0120.0000.011
qaProcess.timeline0.0080.0120.022
qaProcessFrame-class0.0040.0000.004
qaReport0.0120.0000.012
rangeAggregator-class0.0120.0000.010
stringAggregator-class0.0120.0000.012
txtFormatQAObject4.7010.9925.188
writeQAReport0.0120.0000.014
writeQATextReport0.0160.0000.016