BioC 2.13: CHECK report for plateCore on zin1

Package: plateCore

Version: 1.20.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings plateCore_1.20.0.tar.gz

StartedAt: 2014-04-05 03:06:44 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:09:06 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 142.1 seconds

RetCode: 0

Status:  OK

CheckDir: plateCore.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/plateCore.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.20.0’
* 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 ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’ ‘lattice’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘flowViz’ ‘latticeExtra’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘plateCoreVig.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [77s/77s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
summaryStats-methods      9.396  0.004   9.423
mfiPlot-methods           8.972  0.004   8.991
applyControlGates-methods 8.960  0.004   8.981
on-methods                6.249  0.020   6.341
fpbind-methods            5.445  0.032   5.486
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	3.280	0.028	3.313
applyControlGates-methods	8.960	0.004	8.981
compensate-methods	3.641	0.024	3.671
compensationSet	0.168	0.000	0.166
densityplot-methods	1.068	0.012	1.082
fixAutoFl-methods	4.076	0.020	4.107
flowPlate-class	2.352	0.000	2.353
flowPlate-method	2.208	0.004	2.219
fpbind-methods	5.445	0.032	5.486
getGroups-methods	1.072	0.004	1.074
gutterPlot-methods	1.052	0.004	1.055
mfiPlot-methods	8.972	0.004	8.991
on-methods	6.249	0.020	6.341
panel.densityplot.flowPlate	1.400	0.012	1.414
panel.xyplot.flowPlate	1.064	0.008	1.073
plateCore-package	2.052	0.004	2.092
plateSet-methods	2.072	0.008	2.086
plotPlate-methods	2.624	0.012	2.643
prepanel.densityplot.flowPlate	1.220	0.004	1.224
prepanel.xyplot.flowPlate	1.024	0.008	1.034
setControlGates-methods	2.157	0.004	2.162
summaryStats-methods	9.396	0.004	9.423
wellAnnotation-methods	0.888	0.004	0.895
xyplot-methods	1.068	0.000	1.105