Package: cellGrowth

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellGrowth_1.3.0.tar.gz

StartedAt: 2013-03-25 01:35:58 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:37:17 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 79.4 seconds

RetCode: 0

Status:  OK

CheckDir: cellGrowth.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cellGrowth.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 'cellGrowth/DESCRIPTION' ... OK
* this is package 'cellGrowth' version '1.3.0'
* 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 'cellGrowth' can be installed ... [2s/2s] 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
plotPlate : strip.plate: no visible global function definition for
  'trellis.par.get'
plotPlate : strip.plate.left: no visible global function definition for
  'trellis.par.get'
wellDataFrame: no visible binding for global variable 'use'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.cellGrowthFit':
  'plot.cellGrowthFit'

S3 methods shown with full name in documentation object 'plot.well':
  'plot.well'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'cellGrowth-platePlotex.pdf' from 335Kb to 37Kb
     compacted 'cellGrowth-welldatex.pdf' from 1177Kb to 115Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... OK
* checking examples ... [49s/49s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fitCellGrowths 34.885  2.031  37.631
* 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 were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/cellGrowth.Rcheck/00check.log'
for details.

* installing *source* package 'cellGrowth' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'cellGrowth.Rnw' 
** testing if installed package can be loaded
* DONE (cellGrowth)

name	user	system	elapsed
bandwidthCV	3.346	0.107	3.454
baranyi	0.021	0.008	0.029
fitCellGrowth	0.165	0.024	0.191
fitCellGrowths	34.885	2.031	37.631
getRowColumn	0.011	0.005	0.017
getWellIdsTecan	0.435	0.040	0.479
gompertz	0.017	0.008	0.025
guessCellGrowthParams	0.048	0.018	0.066
logistic	0.015	0.008	0.024
plot.cellGrowthFit	0.275	0.034	0.313
plotPlate	1.283	0.053	1.337
readGenios	0.052	0.015	0.068
readYeastGrower	0.285	0.034	0.320
rosso	0.059	0.012	0.072
standardWellId	0.009	0.006	0.015
wellDataFrame	3.922	0.290	4.223