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BioC 2.13: CHECK report for cellGrowth on moscato1

This page was generated on 2014-04-05 09:50:45 -0700 (Sat, 05 Apr 2014).

Package 114/750HostnameOS / ArchBUILDCHECKBUILD BIN
cellGrowth 1.6.0
Julien Gagneur
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/cellGrowth
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: cellGrowth
Version: 1.6.0
Command: rm -rf cellGrowth.buildbin-libdir && mkdir cellGrowth.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellGrowth.buildbin-libdir cellGrowth_1.6.0.tar.gz >cellGrowth-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=cellGrowth.buildbin-libdir --install="check:cellGrowth-install.out" --force-multiarch --no-vignettes --timings cellGrowth_1.6.0.tar.gz && mv cellGrowth.buildbin-libdir/* cellGrowth.Rcheck/ && rmdir cellGrowth.buildbin-libdir
StartedAt: 2014-04-05 02:47:53 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:49:45 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 112.2 seconds
RetCode: 0
Status:  OK  
CheckDir: cellGrowth.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/cellGrowth.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellGrowth/DESCRIPTION' ... OK
* this is package 'cellGrowth' version '1.6.0'
* 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
* 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.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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'
wellDataFrame: no visible binding for global variable 'use'
* 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 the 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'cellGrowth.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [34s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
fitCellGrowths 12.51   3.58   24.39
** running examples for arch 'x64' ... [43s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
fitCellGrowths 17.14   5.35      30
* 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-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_1.6.0.zip
* DONE (cellGrowth)

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

nameusersystemelapsed
bandwidthCV2.660.012.67
baranyi0.010.000.01
fitCellGrowth0.10.00.1
fitCellGrowths12.51 3.5824.39
getRowColumn0.020.000.01
getWellIdsTecan0.500.010.52
gompertz0.010.000.01
guessCellGrowthParams0.030.000.03
logistic0.010.000.01
plot.cellGrowthFit0.500.020.52
plotPlate0.980.001.31
readGenios0.050.000.04
readYeastGrower0.470.070.55
rosso0.010.000.02
standardWellId0.020.000.01
wellDataFrame2.610.002.61

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

nameusersystemelapsed
bandwidthCV3.790.033.83
baranyi0.000.010.02
fitCellGrowth0.140.000.14
fitCellGrowths17.14 5.3530.00
getRowColumn000
getWellIdsTecan0.470.040.50
gompertz0.010.000.02
guessCellGrowthParams0.050.000.05
logistic0.010.000.02
plot.cellGrowthFit0.650.020.67
plotPlate1.780.011.84
readGenios0.070.000.06
readYeastGrower0.710.020.74
rosso0.010.000.02
standardWellId000
wellDataFrame4.040.054.09