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CHECK report for sojourner on merida1

This page was generated on 2021-05-06 12:36:53 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the sojourner package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1750/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sojourner 1.4.2  (landing page)
Sojourner Developer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/sojourner
Branch: RELEASE_3_12
Last Commit: 8242813
Last Changed Date: 2021-03-27 23:05:09 -0400 (Sat, 27 Mar 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: sojourner
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sojourner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sojourner_1.4.2.tar.gz
StartedAt: 2021-05-06 06:27:05 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:39:03 -0400 (Thu, 06 May 2021)
EllapsedTime: 718.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sojourner.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sojourner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sojourner_1.4.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/sojourner.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sojourner/DESCRIPTION’ ... OK
* this is package ‘sojourner’ version ‘1.4.2’
* package encoding: UTF-8
* 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 ‘sojourner’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
plotLocalizations_Density-methods 50.326  0.268  50.659
plotTrackOverlay_Dcoef-methods    39.104  0.159  39.408
fitNormDistr-methods              35.288  0.194  35.531
Dcoef-methods                     14.353  0.107  14.483
maskTracks-methods                13.918  0.252  14.199
plotIndividual_Tracks-methods     11.047  0.240  11.299
plotTrack-methods                  6.120  0.175   6.318
fitRT-methods                      5.218  0.063   5.290
combineTrackll-methods             4.591  0.046 138.488
compare_RT_CDF-methods             4.276  0.102 141.354
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: OK


Installation output

sojourner.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sojourner
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘sojourner’ ...
** using staged installation
** R
** 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 (sojourner)

Tests output

sojourner.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("sojourner")

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.
applying filter, min 5   max Inf 

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.
applying filter, min 5   max Inf 
applying filter, min 7   max Inf 

 45 	tracks length > & =	 1
 45 	tracks length > & =	 2
 45 	tracks length > & =	 3
 45 	tracks length > & =	 4
 45 	tracks length > & =	 5
 45 	tracks length > & =	 6

...

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.
applying trimmer, min 1   max 20 


RUNIT TEST PROTOCOL -- Thu May  6 06:38:55 2021 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sojourner RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 12.878   0.490  13.365 

Example timings

sojourner.Rcheck/sojourner-Ex.timings

nameusersystemelapsed
Dcoef-methods14.353 0.10714.483
combineTrackll-methods 4.591 0.046138.488
compareFolder-methods0.2260.0270.254
compare_RT_CDF-methods 4.276 0.102141.354
createTrackll-methods0.0510.0050.057
dispVariance-methods1.4580.0261.486
displacementCDF-methods2.7130.1122.863
dwellTime-methods0.4580.0250.509
exportTrackll-methods0.1120.0160.130
filterTrack-methods0.0980.0050.104
fitNormDistr-methods35.288 0.19435.531
fitRT-methods5.2180.0635.290
linkSkippedFrames-methods0.2080.0130.221
maskTracks-methods13.918 0.25214.199
mergeTracks-methods0.0670.0070.075
msd-methods4.8910.0414.975
plotIndividual_Tracks-methods11.047 0.24011.299
plotLocalizations_Density-methods50.326 0.26850.659
plotTrack-methods6.1200.1756.318
plotTrackOverlay_Dcoef-methods39.104 0.15939.408
sojournerGUI-methods000
squareDisp-methods0.2560.0140.271