Package: plateCore

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch plateCore_1.17.0.tar.gz

StartedAt: 2013-03-25 04:04:56 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:08:53 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 237.3 seconds

RetCode: 0

Status:  OK

CheckDir: plateCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/plateCore.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 ... [9s/9s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [118s/118s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
mfiPlot-methods           14.407  0.269  14.680
applyControlGates-methods 12.956  0.301  13.267
on-methods                12.845  0.360  13.495
summaryStats-methods      12.282  0.287  12.576
fpbind-methods             6.899  0.449   7.363
Subset-methods             5.481  0.251   5.747
fixAutoFl-methods          5.115  0.464   5.588
compensate-methods         4.793  0.331   5.132
* 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
  '/Users/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	5.481	0.251	5.747
applyControlGates-methods	12.956	0.301	13.267
compensate-methods	4.793	0.331	5.132
compensationSet	0.229	0.028	0.258
densityplot-methods	1.451	0.080	1.533
fixAutoFl-methods	5.115	0.464	5.588
flowPlate-class	2.823	0.188	3.019
flowPlate-method	2.831	0.189	3.024
fpbind-methods	6.899	0.449	7.363
getGroups-methods	1.638	0.083	1.722
gutterPlot-methods	1.308	0.096	1.408
mfiPlot-methods	14.407	0.269	14.680
on-methods	12.845	0.360	13.495
panel.densityplot.flowPlate	1.892	0.108	2.005
panel.xyplot.flowPlate	1.659	0.099	1.762
plateCore-package	3.181	0.204	3.397
plateSet-methods	2.747	0.186	2.936
plotPlate-methods	4.050	0.301	4.367
prepanel.densityplot.flowPlate	1.636	0.092	1.732
prepanel.xyplot.flowPlate	1.699	0.096	1.800
setControlGates-methods	3.441	0.222	3.671
summaryStats-methods	12.282	0.287	12.576
wellAnnotation-methods	1.291	0.083	1.378
xyplot-methods	1.430	0.082	1.516