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CHECK report for TimerQuant on riesling1

This page was generated on 2021-01-14 15:59:12 -0500 (Thu, 14 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: 2021-01-14 09:00:13 -0500 (Thu, 14 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: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TimerQuant.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TimerQuant_1.21.0.tar.gz
StartedAt: 2021-01-14 11:45:10 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:45:49 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 38.1 seconds
RetCode: 0
Status:  OK  
CheckDir: TimerQuant.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TimerQuant.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TimerQuant_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/TimerQuant.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/TimerQuant.Rcheck/00check.log'
for details.



Installation output

TimerQuant.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/TimerQuant_1.21.0.tar.gz && rm -rf TimerQuant.buildbin-libdir && mkdir TimerQuant.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TimerQuant.buildbin-libdir TimerQuant_1.21.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TimerQuant_1.21.0.zip && rm TimerQuant_1.21.0.tar.gz TimerQuant_1.21.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  384k  100  384k    0     0  26.8M      0 --:--:-- --:--:-- --:--:-- 26.8M

install for i386

* installing *source* package 'TimerQuant' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TimerQuant'
    finding HTML links ... done
    FRETdata                                html  
REDIRECT:topic	 FRETdata -> FRETdata.html [ SUCCESS ]
    fitCV                                   html  
REDIRECT:topic	 fitCV -> fitCV.html [ SUCCESS ]
    genRatioHeatmap                         html  
REDIRECT:topic	 genRatioHeatmap -> genRatioHeatmap.html [ SUCCESS ]
    genTimeSteadyState                      html  
REDIRECT:topic	 genTimeSteadyStateHeatmap -> genTimeSteadyState.html [ SUCCESS ]
REDIRECT:file	 genTimeSteadyState.html -> genTimeSteadyState.html [ SUCCESS ]
    getBreaks10                             html  
REDIRECT:topic	 getBreaks10 -> getBreaks10.html [ SUCCESS ]
    getSpacedSeq                            html  
REDIRECT:topic	 getSpacedSeq -> getSpacedSeq.html [ SUCCESS ]
    maturationData                          html  
REDIRECT:topic	 maturationData -> maturationData.html [ SUCCESS ]
    plotPrimordiumProfile                   html  
REDIRECT:topic	 plotPrimordiumProfile -> plotPrimordiumProfile.html [ SUCCESS ]
    profileGradients                        html  
REDIRECT:topic	 profileGradients -> profileGradients.html [ SUCCESS ]
    ratioSteadyState                        html  
REDIRECT:topic	 ratioSteadyState -> ratioSteadyState.html [ SUCCESS ]
    ratioTimeDependent                      html  
REDIRECT:topic	 ratioTimeDependent -> ratioTimeDependent.html [ SUCCESS ]
    runShinyApps                            html  
REDIRECT:topic	 runShinyApps -> runShinyApps.html [ SUCCESS ]
REDIRECT:topic	 runChooseFP2App -> runShinyApps.html [ SUCCESS ]
REDIRECT:topic	 runTimerModellingApp -> runShinyApps.html [ SUCCESS ]
    signal                                  html  
REDIRECT:topic	 signal -> signal.html [ SUCCESS ]
    simulatedSignal                         html  
REDIRECT:topic	 simulatedSignal -> simulatedSignal.html [ SUCCESS ]
REDIRECT:topic	 simulatedSignalN -> simulatedSignal.html [ SUCCESS ]
REDIRECT:topic	 simulatedRatio -> simulatedSignal.html [ SUCCESS ]
    x1                                      html  
REDIRECT:topic	 tss -> x1.html [ SUCCESS ]
REDIRECT:topic	 x0ss -> x1.html [ SUCCESS ]
REDIRECT:topic	 x1 -> x1.html [ SUCCESS ]
REDIRECT:topic	 x1ss -> x1.html [ SUCCESS ]
REDIRECT:topic	 x1fretFP1 -> x1.html [ SUCCESS ]
REDIRECT:topic	 x1fretFP1ss -> x1.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'TimerQuant' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TimerQuant' as TimerQuant_1.21.0.zip
* DONE (TimerQuant)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'TimerQuant' successfully unpacked and MD5 sums checked

Tests output


Example timings

TimerQuant.Rcheck/examples_i386/TimerQuant-Ex.timings

nameusersystemelapsed
fitCV000
genRatioHeatmap000
genTimeSteadyState000
getBreaks10000
getSpacedSeq000
plotPrimordiumProfile000
ratioSteadyState0.030.000.03
ratioTimeDependent0.030.000.03
runShinyApps000
signal000
simulatedSignal000
x10.040.000.03

TimerQuant.Rcheck/examples_x64/TimerQuant-Ex.timings

nameusersystemelapsed
fitCV000
genRatioHeatmap000
genTimeSteadyState000
getBreaks10000
getSpacedSeq000
plotPrimordiumProfile000
ratioSteadyState0.030.000.03
ratioTimeDependent0.030.000.05
runShinyApps000
signal000
simulatedSignal000
x10.020.000.02