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BioC 3.0: CHECK report for cellGrowth on moscato1

This page was generated on 2015-04-10 09:47:52 -0700 (Fri, 10 Apr 2015).

Package 129/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellGrowth 1.10.0
Julien Gagneur
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/cellGrowth
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: cellGrowth
Version: 1.10.0
Command: rm -rf cellGrowth.buildbin-libdir cellGrowth.Rcheck && mkdir cellGrowth.buildbin-libdir cellGrowth.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellGrowth.buildbin-libdir cellGrowth_1.10.0.tar.gz >cellGrowth.Rcheck\00install.out 2>&1 && cp cellGrowth.Rcheck\00install.out cellGrowth-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=cellGrowth.buildbin-libdir --install="check:cellGrowth-install.out" --force-multiarch --no-vignettes --timings cellGrowth_1.10.0.tar.gz
StartedAt: 2015-04-09 23:24:54 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:26:58 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 124.2 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 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellGrowth.buildbin-libdir cellGrowth_1.10.0.tar.gz >cellGrowth.Rcheck\00install.out 2>&1 && cp cellGrowth.Rcheck\00install.out cellGrowth-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=cellGrowth.buildbin-libdir --install="check:cellGrowth-install.out" --force-multiarch --no-vignettes --timings cellGrowth_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/cellGrowth.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.10.0'
* 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
fitCellGrowth: no visible global function definition for 'locfit'
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 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' ... [41s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
fitCellGrowths 13.85   3.82   28.45
** running examples for arch 'x64' ... [44s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
fitCellGrowths 13.64   4.11   33.56
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-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_1.10.0.zip
* DONE (cellGrowth)

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

nameusersystemelapsed
bandwidthCV3.570.033.61
baranyi0.020.000.01
fitCellGrowth0.110.020.13
fitCellGrowths13.85 3.8228.45
getRowColumn000
getWellIdsTecan0.580.000.58
gompertz0.010.000.01
guessCellGrowthParams0.050.000.05
logistic0.020.000.02
plot.cellGrowthFit0.620.020.64
plotPlate1.010.001.02
readGenios0.060.000.06
readYeastGrower0.550.011.61
rosso0.010.000.01
standardWellId000
wellDataFrame2.590.032.62

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

nameusersystemelapsed
bandwidthCV4.060.004.06
baranyi0.010.000.01
fitCellGrowth0.080.000.08
fitCellGrowths13.64 4.1133.56
getRowColumn000
getWellIdsTecan0.400.010.42
gompertz0.020.000.01
guessCellGrowthParams0.050.000.05
logistic0.010.000.02
plot.cellGrowthFit0.440.000.43
plotPlate1.140.001.14
readGenios0.030.000.03
readYeastGrower0.390.050.44
rosso0.010.000.02
standardWellId000
wellDataFrame2.970.012.98