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CHECK report for cellGrowth on merida1

This page was generated on 2020-04-15 12:37:40 -0400 (Wed, 15 Apr 2020).

Package 241/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellGrowth 1.30.0
Julien Gagneur
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/cellGrowth
Branch: RELEASE_3_10
Last Commit: 8775667
Last Changed Date: 2019-10-29 13:08:29 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cellGrowth
Version: 1.30.0
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_1.30.0.tar.gz
StartedAt: 2020-04-15 01:00:34 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:01:42 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 67.1 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_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/cellGrowth.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.30.0’
* 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 ... 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 27.848  3.759  34.495
* 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-3.10-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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cellGrowth)

Tests output


Example timings

cellGrowth.Rcheck/cellGrowth-Ex.timings

nameusersystemelapsed
bandwidthCV2.1350.0432.195
baranyi0.0070.0010.008
fitCellGrowth0.0770.0040.081
fitCellGrowths27.848 3.75934.495
getRowColumn0.0010.0010.002
getWellIdsTecan0.1460.0190.165
gompertz0.0070.0010.009
guessCellGrowthParams0.0310.0030.033
logistic0.0070.0010.008
plot.cellGrowthFit0.1550.0190.174
plotPlate1.1150.0251.149
readGenios0.0250.0030.028
readYeastGrower0.1530.0190.173
rosso0.0040.0010.004
standardWellId000
wellDataFrame2.0670.1032.228