BioC 2.13: CHECK report for plateCore on perceval

Package: plateCore

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch plateCore_1.20.0.tar.gz

StartedAt: 2014-04-05 03:24:16 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:28:26 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 250.2 seconds

RetCode: 0

Status:  OK

CheckDir: plateCore.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/plateCore.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [13s/16s] 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 sizes of PDF files under ‘inst/doc’ ... 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 ... [114s/121s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
summaryStats-methods      13.032  0.099  13.359
mfiPlot-methods           12.934  0.116  13.536
applyControlGates-methods 11.826  0.087  12.015
on-methods                 8.881  0.126  11.773
fpbind-methods             8.892  0.100   9.420
Subset-methods             6.279  0.132   6.648
fixAutoFl-methods          6.085  0.069   6.441
compensate-methods         5.327  0.044   5.492
* 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
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/plateCore.Rcheck/00check.log’
for details.

* installing *source* package ‘plateCore’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (plateCore)

name	user	system	elapsed
Subset-methods	6.279	0.132	6.648
applyControlGates-methods	11.826	0.087	12.015
compensate-methods	5.327	0.044	5.492
compensationSet	0.168	0.025	0.198
densityplot-methods	1.447	0.038	1.556
fixAutoFl-methods	6.085	0.069	6.441
flowPlate-class	3.137	0.052	3.295
flowPlate-method	3.456	0.048	3.653
fpbind-methods	8.892	0.100	9.420
getGroups-methods	1.562	0.051	1.706
gutterPlot-methods	1.277	0.041	1.376
mfiPlot-methods	12.934	0.116	13.536
on-methods	8.881	0.126	11.773
panel.densityplot.flowPlate	1.718	0.045	1.849
panel.xyplot.flowPlate	1.640	0.037	1.716
plateCore-package	3.264	0.060	3.467
plateSet-methods	2.847	0.053	2.996
plotPlate-methods	3.886	0.078	4.125
prepanel.densityplot.flowPlate	1.696	0.037	1.820
prepanel.xyplot.flowPlate	1.394	0.033	1.501
setControlGates-methods	3.064	0.043	3.237
summaryStats-methods	13.032	0.099	13.359
wellAnnotation-methods	1.301	0.036	1.486
xyplot-methods	1.417	0.032	1.460