Package: plateCore

Version: 1.17.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings plateCore_1.17.0.tar.gz

StartedAt: 2013-03-25 03:48:39 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:53:40 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 300.5 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 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.17.0’
* 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/20s] 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 ... [148s/152s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
summaryStats-methods      18.185  0.072  18.392
applyControlGates-methods 17.289  0.008  17.389
mfiPlot-methods           16.789  0.052  18.278
on-methods                11.561  0.036  11.713
fpbind-methods            11.289  0.068  11.428
compensate-methods         8.009  0.052   8.060
Subset-methods             7.804  0.092   7.968
fixAutoFl-methods          6.504  0.028   6.560
plotPlate-methods          4.925  0.008   5.318
* 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
   ‘plateCoreVig.Rnw’ 
** testing if installed package can be loaded
* DONE (plateCore)

name	user	system	elapsed
Subset-methods	7.804	0.092	7.968
applyControlGates-methods	17.289	0.008	17.389
compensate-methods	8.009	0.052	8.060
compensationSet	0.480	0.024	0.501
densityplot-methods	1.752	0.024	1.775
fixAutoFl-methods	6.504	0.028	6.560
flowPlate-class	4.233	0.008	4.300
flowPlate-method	4.612	0.020	4.870
fpbind-methods	11.289	0.068	11.428
getGroups-methods	1.912	0.016	1.958
gutterPlot-methods	1.680	0.020	1.716
mfiPlot-methods	16.789	0.052	18.278
on-methods	11.561	0.036	11.713
panel.densityplot.flowPlate	2.192	0.032	2.228
panel.xyplot.flowPlate	1.940	0.008	1.994
plateCore-package	3.884	0.008	4.418
plateSet-methods	3.792	0.012	3.902
plotPlate-methods	4.925	0.008	5.318
prepanel.densityplot.flowPlate	2.140	0.016	2.196
prepanel.xyplot.flowPlate	1.780	0.020	1.809
setControlGates-methods	4.548	0.016	4.635
summaryStats-methods	18.185	0.072	18.392
wellAnnotation-methods	1.697	0.016	1.792
xyplot-methods	2.240	0.000	2.351