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BioC 2.13: CHECK report for cellGrowth on perceval

This page was generated on 2014-04-05 09:52:49 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellGrowth_1.6.0.tar.gz
StartedAt: 2014-04-05 00:02:33 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:03:53 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 80.4 seconds
RetCode: 0
Status:  OK 
CheckDir: cellGrowth.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/cellGrowth.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* 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 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 ‘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
* 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 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 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 ... [54s/56s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
fitCellGrowths 36.74  3.684  43.104
* 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 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
bandwidthCV2.8330.0292.862
baranyi0.0160.0010.018
fitCellGrowth0.1850.0040.189
fitCellGrowths36.740 3.68443.104
getRowColumn0.0110.0000.012
getWellIdsTecan0.8510.0290.904
gompertz0.0270.0010.030
guessCellGrowthParams0.0640.0050.073
logistic0.0230.0020.027
plot.cellGrowthFit0.8820.0340.948
plotPlate1.4590.0331.600
readGenios0.0570.0050.062
readYeastGrower0.8530.0230.878
rosso0.0120.0020.015
standardWellId0.0030.0000.003
wellDataFrame4.4990.0814.581