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: 2013-01-16 05:20:14 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:23:37 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 203.9 seconds

RetCode: 0

Status:  OK

CheckDir: plateCore.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/plateCore.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
mfiPlot-methods           12.596  0.008  12.603
summaryStats-methods      12.369  0.008  12.386
applyControlGates-methods 12.205  0.016  12.224
on-methods                 9.697  0.020   9.719
fpbind-methods             7.685  0.024   7.709
Subset-methods             5.696  0.064   5.766
fixAutoFl-methods          5.377  0.016   5.399
compensate-methods         5.332  0.028   5.360
* 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
  ‘/loc/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	5.696	0.064	5.766
applyControlGates-methods	12.205	0.016	12.224
compensate-methods	5.332	0.028	5.360
compensationSet	0.168	0.012	0.181
densityplot-methods	1.412	0.012	1.425
fixAutoFl-methods	5.377	0.016	5.399
flowPlate-class	3.052	0.012	3.062
flowPlate-method	2.896	0.020	2.921
fpbind-methods	7.685	0.024	7.709
getGroups-methods	1.436	0.004	1.441
gutterPlot-methods	1.280	0.008	1.287
mfiPlot-methods	12.596	0.008	12.603
on-methods	9.697	0.020	9.719
panel.densityplot.flowPlate	1.884	0.012	1.897
panel.xyplot.flowPlate	1.660	0.008	1.669
plateCore-package	2.820	0.012	2.833
plateSet-methods	2.665	0.020	2.684
plotPlate-methods	3.496	0.000	3.497
prepanel.densityplot.flowPlate	1.564	0.008	1.577
prepanel.xyplot.flowPlate	1.224	0.000	1.227
setControlGates-methods	2.856	0.004	2.863
summaryStats-methods	12.369	0.008	12.386
wellAnnotation-methods	1.272	0.004	1.276
xyplot-methods	1.652	0.008	1.661