BioC 2.12: CHECK report for plateCore on george2

Package: plateCore

Version: 1.18.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings plateCore_1.18.0.tar.gz

StartedAt: 2013-10-09 04:03:15 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:08:03 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 287.3 seconds

RetCode: 0

Status:  OK

CheckDir: plateCore.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/plateCore.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plateCore/DESCRIPTION’ ... OK
* this is package ‘plateCore’ version ‘1.18.0’
* 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 ‘plateCore’ can be installed ... [14s/14s] 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 ... NOTE
panel.xyplot.flowPlate: warning in filterBoundary(filter =
  filter[[nm]], parameters = c(channel.x.name, channel.y.name), frame =
  frames[[nm]]): partial argument match of 'filter' to 'filter.object'
* checking Rd files ... OK
* 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’ ... OK
* checking examples ... [143s/144s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
summaryStats-methods      16.817  0.008  16.848
applyControlGates-methods 16.181  0.008  16.352
mfiPlot-methods           16.077  0.028  16.290
on-methods                11.781  0.076  11.858
fpbind-methods            10.821  0.024  10.854
compensate-methods         7.525  0.020   7.552
fixAutoFl-methods          7.408  0.028   7.441
Subset-methods             7.296  0.100   7.400
* 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/plateCore.Rcheck/00check.log’
for details.

* installing *source* package ‘plateCore’ ...
** 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 (plateCore)

name	user	system	elapsed
Subset-methods	7.296	0.100	7.400
applyControlGates-methods	16.181	0.008	16.352
compensate-methods	7.525	0.020	7.552
compensationSet	0.516	0.028	0.544
densityplot-methods	1.848	0.012	1.863
fixAutoFl-methods	7.408	0.028	7.441
flowPlate-class	3.965	0.024	3.991
flowPlate-method	3.772	0.016	3.791
fpbind-methods	10.821	0.024	10.854
getGroups-methods	1.580	0.008	1.588
gutterPlot-methods	1.860	0.008	1.964
mfiPlot-methods	16.077	0.028	16.290
on-methods	11.781	0.076	11.858
panel.densityplot.flowPlate	2.812	0.016	2.828
panel.xyplot.flowPlate	1.724	0.016	1.741
plateCore-package	3.824	0.004	3.826
plateSet-methods	3.792	0.032	3.824
plotPlate-methods	4.709	0.044	4.754
prepanel.densityplot.flowPlate	2.320	0.004	2.325
prepanel.xyplot.flowPlate	1.788	0.016	1.808
setControlGates-methods	4.044	0.048	4.287
summaryStats-methods	16.817	0.008	16.848
wellAnnotation-methods	1.648	0.004	1.650
xyplot-methods	1.840	0.004	1.843