Package: cellGrowth

Version: 1.27.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellGrowth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellGrowth_1.27.1.tar.gz

StartedAt: 2019-04-08 23:43:39 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:44:44 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 65.9 seconds

RetCode: 0

Status:  OK

CheckDir: cellGrowth.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellGrowth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellGrowth_1.27.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cellGrowth.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellGrowth/DESCRIPTION’ ... OK
* this is package ‘cellGrowth’ version ‘1.27.1’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘locfit’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.cellGrowthFit plot.well
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bandwidthCV : cvpred_mu : <anonymous>: no visible global function
  definition for ‘predict’
bandwidthCV : err2_mustd_well: no visible binding for global variable
  ‘sd’
fitCellGrowth: no visible global function definition for ‘nls’
fitCellGrowth: no visible global function definition for ‘as.formula’
fitCellGrowth: no visible global function definition for ‘predict’
fitCellGrowth: no visible global function definition for ‘locfit’
fitCellGrowths: no visible global function definition for ‘png’
fitCellGrowths: no visible global function definition for ‘plot’
fitCellGrowths: no visible global function definition for ‘dev.off’
plot.cellGrowthFit: no visible global function definition for ‘plot’
plot.cellGrowthFit: no visible global function definition for ‘lines’
plot.cellGrowthFit: no visible global function definition for ‘predict’
plot.cellGrowthFit: no visible global function definition for ‘abline’
plot.cellGrowthFit: no visible global function definition for ‘legend’
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’
readGenios: no visible global function definition for ‘read.delim’
readYeastGrower: no visible global function definition for ‘read.delim’
wellDataFrame: no visible global function definition for ‘read.delim’
wellDataFrame: no visible binding for global variable ‘use’
Undefined global functions or variables:
  abline as.formula dev.off legend lines locfit nls plot png predict
  read.delim sd trellis.par.get use
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "as.formula", "nls", "predict", "sd")
  importFrom("utils", "read.delim")
to your NAMESPACE file.
* 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 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fitCellGrowths 26.897  3.748  33.346
* 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
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/cellGrowth.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cellGrowth
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘cellGrowth’ ...
** R
** inst
** byte-compile and prepare 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	1.785	0.048	1.844
baranyi	0.007	0.000	0.008
fitCellGrowth	0.075	0.004	0.081
fitCellGrowths	26.897	3.748	33.346
getRowColumn	0.001	0.000	0.001
getWellIdsTecan	0.129	0.016	0.145
gompertz	0.007	0.001	0.007
guessCellGrowthParams	0.024	0.002	0.026
logistic	0.007	0.001	0.008
plot.cellGrowthFit	0.157	0.023	0.181
plotPlate	0.986	0.023	1.018
readGenios	0.022	0.002	0.024
readYeastGrower	0.159	0.022	0.186
rosso	0.004	0.000	0.005
standardWellId	0	0	0
wellDataFrame	2.048	0.094	2.174