Package: flowQ

Version: 1.19.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowQ_1.19.5.tar.gz

StartedAt: 2013-03-25 02:27:11 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:33:09 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 357.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowQ.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowQ.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowQ' version '1.19.5'
* 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 ... [23s/24s] 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
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.

In addition to the above warning(s), found the following notes:

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 ... [90s/89s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qaProcess.2DStatsPlot  16.554  3.388  18.992
qaProcess.ECDFPlot     12.377  2.510  14.929
qaProcess.DensityPlot  11.720  2.387  14.528
qaProcess.KLDistPlot   11.230  2.281  13.239
qaProcess.BoundaryPlot  7.102  1.723   8.522
txtFormatQAObject       5.739  1.534   7.247
* 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 3 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: 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
   'DataQualityAssessment.Rnw' 
   'Extending-flowQ.Rnw' 
** 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	0.012	0.006	0.018
binaryAggregator-class	0.011	0.007	0.018
discreteAggregator-class	0.007	0.006	0.013
evaluateProcess	0.007	0.006	0.013
factorAggregator-class	0.010	0.005	0.016
flowQ-package	0.007	0.005	0.013
numericAggregator-class	0.009	0.007	0.017
outlier-class	0.009	0.007	0.016
outlierResult-class	0.006	0.005	0.012
qaAggregator-class	0.007	0.006	0.012
qaGraph-class	0.007	0.005	0.011
qaGraphList-class	0.007	0.005	0.012
qaProcess-class	0.007	0.006	0.013
qaProcess.2DStatsPlot	16.554	3.388	18.992
qaProcess.BoundaryPlot	7.102	1.723	8.522
qaProcess.DensityPlot	11.720	2.387	14.528
qaProcess.ECDFPlot	12.377	2.510	14.929
qaProcess.KLDistPlot	11.230	2.281	13.239
qaProcess.cellnumber	0.003	0.006	0.008
qaProcess.marginevents	0.003	0.008	0.014
qaProcess.timeflow	0.003	0.006	0.009
qaProcess.timeline	0.003	0.006	0.009
qaProcessFrame-class	0.003	0.005	0.007
qaReport	0.005	0.010	0.015
rangeAggregator-class	0.005	0.008	0.014
stringAggregator-class	0.006	0.007	0.013
txtFormatQAObject	5.739	1.534	7.247
writeQAReport	0.008	0.009	0.017
writeQATextReport	0.008	0.009	0.016