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BioC 3.2: CHECK report for cellGrowth on zin1

This page was generated on 2015-08-24 10:48:39 -0700 (Mon, 24 Aug 2015).

Package 144/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellGrowth 1.13.0
Julien Gagneur
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cellGrowth
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellGrowth
Version: 1.13.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cellGrowth_1.13.0.tar.gz
StartedAt: 2015-08-23 22:18:33 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 22:19:04 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 31.0 seconds
RetCode: 0
Status:  OK 
CheckDir: cellGrowth.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cellGrowth_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/cellGrowth.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellGrowth/DESCRIPTION’ ... OK
* this is package ‘cellGrowth’ version ‘1.13.0’
* 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 ... [1s/1s] 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 ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fitCellGrowths 13.532  0.108  13.654
* 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
  ‘/home/biocbuild/bbs-3.2-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
bandwidthCV1.8810.0151.923
baranyi0.0080.0000.008
fitCellGrowth0.0530.0000.053
fitCellGrowths13.532 0.10813.654
getRowColumn0.0020.0000.001
getWellIdsTecan0.1990.0040.203
gompertz0.0030.0040.007
guessCellGrowthParams0.0250.0000.026
logistic0.0060.0000.006
plot.cellGrowthFit0.2030.0000.203
plotPlate0.7240.0000.727
readGenios0.0260.0000.026
readYeastGrower0.2310.0000.231
rosso0.0050.0000.005
standardWellId000
wellDataFrame1.8020.0281.828