BioC 2.12: CHECK report for flowQ on moscato2

Package: flowQ

Version: 1.19.0

Command: rm -rf flowQ.buildbin-libdir && mkdir flowQ.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowQ.buildbin-libdir flowQ_1.19.0.tar.gz >flowQ-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=flowQ.buildbin-libdir --install="check:flowQ-install.out" --force-multiarch --no-vignettes --timings flowQ_1.19.0.tar.gz && mv flowQ.buildbin-libdir/* flowQ.Rcheck/ && rmdir flowQ.buildbin-libdir

StartedAt: 2013-01-02 01:29:32 -0800 (Wed, 02 Jan 2013)

EndedAt: 2013-01-02 01:35:27 -0800 (Wed, 02 Jan 2013)

EllapsedTime: 354.7 seconds

RetCode: 0

Status: OK

CheckDir: flowQ.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/flowQ.Rcheck'
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
qaProcess.DensityPlot  5.68   0.10   11.17
qaProcess.2DStatsPlot  5.49   0.04   11.22
qaProcess.ECDFPlot     5.49   0.01   11.42
qaProcess.KLDistPlot   4.81   0.05   12.04
qaProcess.BoundaryPlot 3.26   0.00    8.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
qaProcess.ECDFPlot     6.30   0.06   12.53
qaProcess.DensityPlot  5.98   0.06   10.72
qaProcess.2DStatsPlot  5.95   0.08   11.81
qaProcess.KLDistPlot   5.01   0.03   11.37
qaProcess.BoundaryPlot 2.82   0.03    9.03
* 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/flowQ.Rcheck/00check.log'
for details.


install for i386

* 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'

install for x64

* installing *source* package 'flowQ' ...
** testing if installed package can be loaded
Warning: replacing previous import 'sort' when loading 'flowCore'
Warning: replacing previous import 'as' when loading 'methods'
* MD5 sums
packaged installation of 'flowQ' as flowQ_1.19.0.zip

* DONE (flowQ)

Summary

Command output