BioC 2.12: CHECK report for cellGrowth on petty

Package: cellGrowth

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellGrowth_1.4.0.tar.gz

StartedAt: 2013-10-08 21:50:52 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:52:50 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 118.2 seconds

RetCode: 0

Status:  OK

CheckDir: cellGrowth.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cellGrowth.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cellGrowth/DESCRIPTION' ... OK
* this is package 'cellGrowth' version '1.4.0'
* 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 ... [79s/87s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fitCellGrowths 56.374  3.412  66.839
wellDataFrame   5.760  0.096   6.259
bandwidthCV     5.412  0.084   6.126
* 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
** testing if installed package can be loaded
* DONE (cellGrowth)

name	user	system	elapsed
bandwidthCV	5.412	0.084	6.126
baranyi	0.023	0.001	0.026
fitCellGrowth	0.193	0.007	0.222
fitCellGrowths	56.374	3.412	66.839
getRowColumn	0.017	0.000	0.018
getWellIdsTecan	1.258	0.039	1.300
gompertz	0.024	0.002	0.027
guessCellGrowthParams	0.082	0.003	0.086
logistic	0.024	0.001	0.027
plot.cellGrowthFit	1.247	0.039	1.288
plotPlate	2.066	0.030	2.114
readGenios	0.083	0.005	0.089
readYeastGrower	1.277	0.039	1.330
rosso	0.018	0.002	0.020
standardWellId	0.007	0.001	0.007
wellDataFrame	5.760	0.096	6.259