Package: cellGrowth

Version: 1.26.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellGrowth.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cellGrowth_1.26.1.tar.gz

StartedAt: 2019-04-13 01:02:48 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 01:05:01 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 133.1 seconds

RetCode: 0

Status:  OK

CheckDir: cellGrowth.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellGrowth.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cellGrowth_1.26.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/cellGrowth.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
fitCellGrowths 10.3   4.43   17.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
fitCellGrowths 11.31   4.61   18.85
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/cellGrowth.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/cellGrowth_1.26.1.tar.gz && rm -rf cellGrowth.buildbin-libdir && mkdir cellGrowth.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellGrowth.buildbin-libdir cellGrowth_1.26.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL cellGrowth_1.26.1.zip && rm cellGrowth_1.26.1.tar.gz cellGrowth_1.26.1.zip
###
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install for i386

* installing *source* package 'cellGrowth' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cellGrowth'
    finding HTML links ... done
    bandwidthCV                             html  
    baranyi                                 html  
    fitCellGrowth                           html  
    fitCellGrowths                          html  
    getRowColumn                            html  
    getWellIdsTecan                         html  
    gompertz                                html  
    guessCellGrowthParams                   html  
    logistic                                html  
    plot.cellGrowthFit                      html  
    plot.well                               html  
    plotPlate                               html  
    readGenios                              html  
    readYeastGrower                         html  
    rosso                                   html  
    standardWellId                          html  
    wellDataFrame                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cellGrowth' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellGrowth' as cellGrowth_1.26.1.zip
* DONE (cellGrowth)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'cellGrowth' successfully unpacked and MD5 sums checked
In R CMD INSTALL