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BioC 3.1: CHECK report for cellGrowth on petty

This page was generated on 2015-10-09 09:35:01 -0700 (Fri, 09 Oct 2015).

Package 139/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellGrowth 1.12.0
Julien Gagneur
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cellGrowth
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellGrowth
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellGrowth_1.12.0.tar.gz
StartedAt: 2015-10-08 21:55:46 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 21:57:24 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 97.9 seconds
RetCode: 0
Status:  OK 
CheckDir: cellGrowth.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellGrowth_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/cellGrowth.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.12.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/71s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fitCellGrowths 49.694  3.381  58.715
* 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
  ‘/Users/biocbuild/bbs-3.1-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
bandwidthCV2.8580.0352.893
baranyi0.0070.0010.007
fitCellGrowth0.0710.0030.075
fitCellGrowths49.694 3.38158.715
getRowColumn0.0020.0010.003
getWellIdsTecan1.1050.0291.136
gompertz0.0130.0020.015
guessCellGrowthParams0.0470.0020.050
logistic0.0120.0020.016
plot.cellGrowthFit1.0630.0271.092
plotPlate1.4630.0141.478
readGenios0.0560.0030.061
readYeastGrower1.060.031.09
rosso0.0070.0010.008
standardWellId0.0010.0010.001
wellDataFrame3.1700.0693.339