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: 2013-03-24 08:53:37 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 08:58:05 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 268.3 seconds

RetCode: 0

Status:  OK

CheckDir: plateCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/plateCore.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-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 ... [12s/13s] 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 ... [134s/141s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
summaryStats-methods      15.646  0.154  16.017
applyControlGates-methods 15.297  0.145  15.839
mfiPlot-methods           15.135  0.148  15.813
on-methods                11.018  0.212  14.352
fpbind-methods             9.449  0.143   9.666
fixAutoFl-methods          7.451  0.143   7.638
compensate-methods         7.142  0.103   7.288
Subset-methods             5.730  0.139   6.283
plotPlate-methods          4.814  0.150   5.203
* 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	5.730	0.139	6.283
applyControlGates-methods	15.297	0.145	15.839
compensate-methods	7.142	0.103	7.288
compensationSet	0.425	0.044	0.500
densityplot-methods	1.845	0.042	1.912
fixAutoFl-methods	7.451	0.143	7.638
flowPlate-class	3.682	0.072	3.792
flowPlate-method	3.920	0.060	4.012
fpbind-methods	9.449	0.143	9.666
getGroups-methods	1.700	0.067	1.777
gutterPlot-methods	1.626	0.042	1.702
mfiPlot-methods	15.135	0.148	15.813
on-methods	11.018	0.212	14.352
panel.densityplot.flowPlate	2.031	0.056	2.506
panel.xyplot.flowPlate	1.768	0.052	2.268
plateCore-package	3.514	0.091	4.114
plateSet-methods	3.342	0.077	3.765
plotPlate-methods	4.814	0.150	5.203
prepanel.densityplot.flowPlate	1.831	0.042	1.924
prepanel.xyplot.flowPlate	1.946	0.050	2.021
setControlGates-methods	3.505	0.074	3.622
summaryStats-methods	15.646	0.154	16.017
wellAnnotation-methods	1.588	0.064	1.660
xyplot-methods	1.759	0.059	1.821