Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for cellGrowth on tokay2

This page was generated on 2017-10-18 14:21:46 -0400 (Wed, 18 Oct 2017).

Package 183/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellGrowth 1.20.0
Julien Gagneur
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/cellGrowth
Branch: RELEASE_3_5
Last Commit: 2c3f849
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellGrowth
Version: 1.20.0
Command: rm -rf cellGrowth.buildbin-libdir cellGrowth.Rcheck && mkdir cellGrowth.buildbin-libdir cellGrowth.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellGrowth.buildbin-libdir cellGrowth_1.20.0.tar.gz >cellGrowth.Rcheck\00install.out 2>&1 && cp cellGrowth.Rcheck\00install.out cellGrowth-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cellGrowth.buildbin-libdir --install="check:cellGrowth-install.out" --force-multiarch --no-vignettes --timings cellGrowth_1.20.0.tar.gz
StartedAt: 2017-10-17 22:35:36 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:36:53 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 77.5 seconds
RetCode: 0
Status:  OK  
CheckDir: cellGrowth.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cellGrowth.buildbin-libdir cellGrowth.Rcheck && mkdir cellGrowth.buildbin-libdir cellGrowth.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellGrowth.buildbin-libdir cellGrowth_1.20.0.tar.gz >cellGrowth.Rcheck\00install.out 2>&1 && cp cellGrowth.Rcheck\00install.out cellGrowth-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cellGrowth.buildbin-libdir --install="check:cellGrowth-install.out" --force-multiarch --no-vignettes --timings cellGrowth_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/cellGrowth.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.20.0'
* 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 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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 11.5   4.35   16.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
fitCellGrowths 10.57   4.14    14.8
* 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-3.5-bioc/meat/cellGrowth.Rcheck/00check.log'
for details.


cellGrowth.Rcheck/00install.out:


install for i386

* installing *source* package 'cellGrowth' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'cellGrowth' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellGrowth' as cellGrowth_1.20.0.zip
* DONE (cellGrowth)

cellGrowth.Rcheck/examples_i386/cellGrowth-Ex.timings:

nameusersystemelapsed
bandwidthCV2.200.002.21
baranyi000
fitCellGrowth0.080.000.08
fitCellGrowths11.50 4.3516.23
getRowColumn0.010.000.02
getWellIdsTecan0.380.030.41
gompertz0.010.000.01
guessCellGrowthParams0.030.000.03
logistic0.020.000.02
plot.cellGrowthFit0.340.030.37
plotPlate0.630.000.62
readGenios0.030.000.03
readYeastGrower0.530.010.55
rosso000
standardWellId000
wellDataFrame2.140.022.16

cellGrowth.Rcheck/examples_x64/cellGrowth-Ex.timings:

nameusersystemelapsed
bandwidthCV2.440.022.45
baranyi000
fitCellGrowth0.050.010.07
fitCellGrowths10.57 4.1414.80
getRowColumn000
getWellIdsTecan0.270.030.29
gompertz000
guessCellGrowthParams0.070.000.08
logistic0.020.000.02
plot.cellGrowthFit0.470.000.46
plotPlate0.730.000.74
readGenios0.030.000.03
readYeastGrower0.350.000.34
rosso000
standardWellId000
wellDataFrame1.930.001.94