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CHECK report for cellGrowth on merida2

This page was generated on 2019-04-09 13:26:59 -0400 (Tue, 09 Apr 2019).

Package 223/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellGrowth 1.27.1
Julien Gagneur
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/cellGrowth
Branch: master
Last Commit: e46d29a
Last Changed Date: 2019-01-04 13:24:39 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

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

Command output

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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.



Installation output

cellGrowth.Rcheck/00install.out

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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)

Tests output


Example timings

cellGrowth.Rcheck/cellGrowth-Ex.timings

nameusersystemelapsed
bandwidthCV1.7850.0481.844
baranyi0.0070.0000.008
fitCellGrowth0.0750.0040.081
fitCellGrowths26.897 3.74833.346
getRowColumn0.0010.0000.001
getWellIdsTecan0.1290.0160.145
gompertz0.0070.0010.007
guessCellGrowthParams0.0240.0020.026
logistic0.0070.0010.008
plot.cellGrowthFit0.1570.0230.181
plotPlate0.9860.0231.018
readGenios0.0220.0020.024
readYeastGrower0.1590.0220.186
rosso0.0040.0000.005
standardWellId000
wellDataFrame2.0480.0942.174