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BioC 2.12: CHECK report for cellGrowth on petty

This page was generated on 2013-10-09 09:40:09 -0700 (Wed, 09 Oct 2013).

Package 103/671HostnameOS / ArchBUILDCHECKBUILD BIN
cellGrowth 1.4.0
Julien Gagneur
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/cellGrowth
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: cellGrowth
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellGrowth_1.4.0.tar.gz
StartedAt: 2013-10-08 21:50:52 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:52:50 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 118.2 seconds
RetCode: 0
Status:  OK 
CheckDir: cellGrowth.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cellGrowth.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cellGrowth/DESCRIPTION' ... OK
* this is package 'cellGrowth' version '1.4.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'cellGrowth' can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'cellGrowth-platePlotex.pdf' from 335Kb to 37Kb
     compacted 'cellGrowth-welldatex.pdf' from 1177Kb to 115Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... OK
* checking examples ... [79s/87s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fitCellGrowths 56.374  3.412  66.839
wellDataFrame   5.760  0.096   6.259
bandwidthCV     5.412  0.084   6.126
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/cellGrowth.Rcheck/00check.log'
for details.

cellGrowth.Rcheck/00install.out:

* 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
* DONE (cellGrowth)

cellGrowth.Rcheck/cellGrowth-Ex.timings:

nameusersystemelapsed
bandwidthCV5.4120.0846.126
baranyi0.0230.0010.026
fitCellGrowth0.1930.0070.222
fitCellGrowths56.374 3.41266.839
getRowColumn0.0170.0000.018
getWellIdsTecan1.2580.0391.300
gompertz0.0240.0020.027
guessCellGrowthParams0.0820.0030.086
logistic0.0240.0010.027
plot.cellGrowthFit1.2470.0391.288
plotPlate2.0660.0302.114
readGenios0.0830.0050.089
readYeastGrower1.2770.0391.330
rosso0.0180.0020.020
standardWellId0.0070.0010.007
wellDataFrame5.7600.0966.259