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This page was generated on 2023-04-11 14:50:27 -0400 (Tue, 11 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TimerQuant on nebbiolo2


To the developers/maintainers of the TimerQuant package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 393/416HostnameOS / ArchINSTALLBUILDCHECK
TimerQuant 1.28.0  (landing page)
Joseph Barry
Snapshot Date: 2023-04-11 07:30:01 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/TimerQuant
git_branch: RELEASE_3_16
git_last_commit: 2cf29e4
git_last_commit_date: 2022-11-01 11:08:18 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TimerQuant
Version: 1.28.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TimerQuant.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TimerQuant_1.28.0.tar.gz
StartedAt: 2023-04-11 12:24:51 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 12:26:06 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 74.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TimerQuant.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TimerQuant.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TimerQuant_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/TimerQuant.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘TimerQuant/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TimerQuant’ version ‘1.28.0’
* 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 ‘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 ...
  ‘genPaperFigures.Rnw’... OK
  ‘mathematicalDerivations.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-data-experiment/meat/TimerQuant.Rcheck/00check.log’
for details.



Installation output

TimerQuant.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TimerQuant
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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
genTimeSteadyState000
getBreaks100.0010.0000.000
getSpacedSeq0.0010.0000.001
plotPrimordiumProfile000
ratioSteadyState0.0230.0000.022
ratioTimeDependent0.0320.0000.033
runShinyApps000
signal0.0000.0000.001
simulatedSignal000
x10.0170.0000.018