BioC 2.13: CHECK report for flowQ on perceval

Package: flowQ

Version: 1.22.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowQ_1.22.4.tar.gz

StartedAt: 2014-04-05 01:17:29 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:22:56 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 327.1 seconds

RetCode: 0

Status:  OK

CheckDir: flowQ.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/flowQ.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.22.4’
* 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 ... [24s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘flowViz’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘IRanges’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘bioDist’ ‘flowViz’ ‘lattice’ ‘latticeExtra’ ‘mvoutlier’ ‘outliers’
  ‘parody’ ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ‘:::’ calls:
  ‘flowCore:::copyFlowSet’ ‘flowCore:::findTimeChannel’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [75s/77s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qaProcess.2DStatsPlot  14.366  1.453  16.165
qaProcess.ECDFPlot     11.157  0.980  12.405
qaProcess.DensityPlot  10.517  0.799  11.566
qaProcess.KLDistPlot   10.129  1.004  11.328
qaProcess.BoundaryPlot  6.550  0.694   7.423
txtFormatQAObject       4.080  0.877   5.176
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
** 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
* DONE (flowQ)

name	user	system	elapsed
aggregatorList-class	0.010	0.003	0.013
binaryAggregator-class	0.010	0.002	0.012
discreteAggregator-class	0.010	0.004	0.013
evaluateProcess	0.010	0.003	0.014
factorAggregator-class	0.018	0.004	0.022
flowQ-package	0.015	0.004	0.019
numericAggregator-class	0.026	0.005	0.031
outlier-class	0.007	0.002	0.009
outlierResult-class	0.007	0.002	0.010
qaAggregator-class	0.008	0.002	0.009
qaGraph-class	0.007	0.003	0.011
qaGraphList-class	0.010	0.003	0.012
qaProcess-class	0.014	0.004	0.018
qaProcess.2DStatsPlot	14.366	1.453	16.165
qaProcess.BoundaryPlot	6.550	0.694	7.423
qaProcess.DensityPlot	10.517	0.799	11.566
qaProcess.ECDFPlot	11.157	0.980	12.405
qaProcess.KLDistPlot	10.129	1.004	11.328
qaProcess.cellnumber	0.003	0.004	0.007
qaProcess.marginevents	0.009	0.007	0.017
qaProcess.timeflow	0.011	0.007	0.017
qaProcess.timeline	0.011	0.007	0.018
qaProcessFrame-class	0.004	0.004	0.007
qaReport	0.009	0.006	0.015
rangeAggregator-class	0.009	0.005	0.015
stringAggregator-class	0.011	0.005	0.015
txtFormatQAObject	4.080	0.877	5.176
writeQAReport	0.020	0.014	0.034
writeQATextReport	0.010	0.008	0.018