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CHECK report for cellGrowth on malbec1

This page was generated on 2019-04-16 11:49:33 -0400 (Tue, 16 Apr 2019).

Package 215/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellGrowth 1.26.1
Julien Gagneur
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/cellGrowth
Branch: RELEASE_3_8
Last Commit: b4320c2
Last Changed Date: 2019-01-04 13:24:42 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: 1.26.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:cellGrowth.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings cellGrowth_1.26.1.tar.gz
StartedAt: 2019-04-15 22:43:18 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:43:55 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 36.9 seconds
RetCode: 0
Status:  OK 
CheckDir: cellGrowth.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:cellGrowth.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings cellGrowth_1.26.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/cellGrowth.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellGrowth/DESCRIPTION’ ... OK
* this is package ‘cellGrowth’ version ‘1.26.1’
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fitCellGrowths 15.312  0.096  15.606
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/cellGrowth.Rcheck/00check.log’
for details.



Installation output

cellGrowth.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL cellGrowth
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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
bandwidthCV1.7640.0041.790
baranyi0.0040.0000.004
fitCellGrowth0.0880.0000.090
fitCellGrowths15.312 0.09615.606
getRowColumn0.0000.0000.001
getWellIdsTecan0.1120.0040.116
gompertz0.0080.0000.007
guessCellGrowthParams0.0160.0000.016
logistic0.0000.0040.005
plot.cellGrowthFit0.1000.0120.112
plotPlate0.9840.0000.987
readGenios0.0160.0040.019
readYeastGrower0.1080.0040.111
rosso0.0040.0000.004
standardWellId000
wellDataFrame1.7480.0201.773