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CHECK report for TimerQuant on malbec2

This page was generated on 2021-01-18 15:58:41 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE TimerQuant PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 365/385HostnameOS / ArchINSTALLBUILDCHECK
TimerQuant 1.21.0
Joseph Barry
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/TimerQuant
Branch: master
Last Commit: 6d51284
Last Changed Date: 2020-10-27 10:14:37 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: TimerQuant
Version: 1.21.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TimerQuant.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TimerQuant_1.21.0.tar.gz
StartedAt: 2021-01-18 12:52:43 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 12:53:18 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 34.7 seconds
RetCode: 0
Status:  OK 
CheckDir: TimerQuant.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TimerQuant.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TimerQuant_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/TimerQuant.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘1.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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 ‘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 points polygon predict rainbow
  rgb rnorm
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "axis", "par", "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 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/TimerQuant.Rcheck/00check.log’
for details.



Installation output

TimerQuant.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL TimerQuant
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘TimerQuant’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TimerQuant)

Tests output


Example timings

TimerQuant.Rcheck/TimerQuant-Ex.timings

nameusersystemelapsed
fitCV000
genRatioHeatmap000
genTimeSteadyState0.0000.0000.001
getBreaks10000
getSpacedSeq0.0010.0000.001
plotPrimordiumProfile000
ratioSteadyState0.0310.0040.035
ratioTimeDependent0.0540.0000.053
runShinyApps0.0010.0000.000
signal000
simulatedSignal000
x10.0230.0000.023