BioC 2.13: CHECK report for flowQ on zin1

Package: flowQ

Version: 1.22.4

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings flowQ_1.22.4.tar.gz

StartedAt: 2014-04-05 01:10:14 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:13:21 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 186.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowQ.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/flowQ.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.22.4’
* 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 ... [14s/14s] 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:
  ‘RColorBrewer’ ‘bioDist’ ‘flowViz’ ‘lattice’ ‘latticeExtra’
  ‘mvoutlier’ ‘outliers’ ‘parody’
  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 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 ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qaProcess.2DStatsPlot  9.828  0.660  10.372
qaProcess.ECDFPlot     7.088  0.392   7.511
qaProcess.DensityPlot  6.961  0.412   7.378
qaProcess.KLDistPlot   6.736  0.440   7.246
qaProcess.BoundaryPlot 4.800  0.412   5.341
* 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
  ‘/home/biocbuild/bbs-2.13-bioc/meat/flowQ.Rcheck/00check.log’
for details.

* installing *source* package ‘flowQ’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowQ)

name	user	system	elapsed
aggregatorList-class	0.004	0.000	0.004
binaryAggregator-class	0.004	0.000	0.004
discreteAggregator-class	0.004	0.000	0.004
evaluateProcess	0.004	0.000	0.003
factorAggregator-class	0.004	0.000	0.004
flowQ-package	0.000	0.000	0.003
numericAggregator-class	0.004	0.004	0.005
outlier-class	0.000	0.000	0.002
outlierResult-class	0.000	0.000	0.002
qaAggregator-class	0.000	0.000	0.002
qaGraph-class	0.000	0.000	0.003
qaGraphList-class	0.008	0.000	0.005
qaProcess-class	0.004	0.000	0.004
qaProcess.2DStatsPlot	9.828	0.660	10.372
qaProcess.BoundaryPlot	4.800	0.412	5.341
qaProcess.DensityPlot	6.961	0.412	7.378
qaProcess.ECDFPlot	7.088	0.392	7.511
qaProcess.KLDistPlot	6.736	0.440	7.246
qaProcess.cellnumber	0.000	0.000	0.003
qaProcess.marginevents	0.000	0.000	0.001
qaProcess.timeflow	0.004	0.000	0.004
qaProcess.timeline	0.004	0.000	0.003
qaProcessFrame-class	0.004	0.000	0.003
qaReport	0.004	0.000	0.003
rangeAggregator-class	0.004	0.000	0.004
stringAggregator-class	0.004	0.000	0.003
txtFormatQAObject	3.261	0.488	3.752
writeQAReport	0.004	0.000	0.004
writeQATextReport	0.004	0.000	0.004