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BioC experimental data: CHECK report for TimerQuant on malbec2

This page was generated on 2017-10-18 15:09:45 -0400 (Wed, 18 Oct 2017).

Package 297/314HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimerQuant 1.6.0
Joseph Barry
Snapshot Date: 2017-10-18 09:00:07 -0400 (Wed, 18 Oct 2017)
URL: https://git.bioconductor.org/packages/TimerQuant
Branch: RELEASE_3_5
Last Commit: 90ab729
Last Changed Date: 2017-08-16 14:58:01 -0400 (Wed, 16 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: TimerQuant
Version: 1.6.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TimerQuant_1.6.0.tar.gz
StartedAt: 2017-10-18 11:15:24 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 11:15:52 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 28.4 seconds
RetCode: 0
Status:  OK 
CheckDir: TimerQuant.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TimerQuant_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/TimerQuant.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TimerQuant/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TimerQuant’ 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 ‘TimerQuant’ 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fitCV: no visible global function definition for ‘predict’
fitCV: no visible global function definition for ‘approxfun’
fitCV: no visible global function definition for ‘optimize’
genRatioHeatmap: no visible global function definition for ‘rainbow’
genTimeSteadyStateHeatmap: no visible global function definition for
  ‘rainbow’
plotPrimordiumProfile: no visible binding for global variable ‘median’
plotPrimordiumProfile: no visible binding for global variable ‘mad’
plotPrimordiumProfile: no visible global function definition for ‘par’
plotPrimordiumProfile: no visible global function definition for ‘plot’
plotPrimordiumProfile: no visible global function definition for ‘axis’
plotPrimordiumProfile: no visible global function definition for
  ‘points’
plotPrimordiumProfile: no visible global function definition for
  ‘polygon’
plotPrimordiumProfile: no visible global function definition for ‘rgb’
simulatedRatio: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approxfun axis mad median optimize par plot points polygon predict
  rainbow rgb rnorm
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "axis", "par", "plot", "points", "polygon")
  importFrom("stats", "approxfun", "mad", "median", "optimize",
             "predict", "rnorm")
to your NAMESPACE file.
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-data-experiment/meat/TimerQuant.Rcheck/00check.log’
for details.


TimerQuant.Rcheck/00install.out:

* installing *source* package ‘TimerQuant’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TimerQuant)

TimerQuant.Rcheck/TimerQuant-Ex.timings:

nameusersystemelapsed
fitCV0.0000.0000.001
genRatioHeatmap0.0000.0000.001
genTimeSteadyState000
getBreaks100.0000.0000.001
getSpacedSeq0.0040.0000.001
plotPrimordiumProfile000
ratioSteadyState0.0240.0040.028
ratioTimeDependent0.0760.0040.079
runShinyApps0.0000.0000.001
signal0.0160.0000.015
simulatedSignal0.0000.0000.001
x10.0200.0040.024