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CHECK report for sojourner on malbec2

This page was generated on 2020-10-17 11:55:48 -0400 (Sat, 17 Oct 2020).

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 1697/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sojourner 1.2.1
Sojourner Developer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/sojourner
Branch: RELEASE_3_11
Last Commit: f0a6b71
Last Changed Date: 2020-05-29 20:21:02 -0400 (Fri, 29 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sojourner
Version: 1.2.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:sojourner.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings sojourner_1.2.1.tar.gz
StartedAt: 2020-10-17 05:40:13 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:48:50 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 517.4 seconds
RetCode: 0
Status:  OK 
CheckDir: sojourner.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:sojourner.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings sojourner_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/sojourner.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sojourner/DESCRIPTION’ ... OK
* this is package ‘sojourner’ version ‘1.2.1’
* 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 39.195  0.201  39.414
plotTrackOverlay_Dcoef-methods    35.021  0.181  35.246
fitNormDistr-methods              30.182  0.428  30.618
Dcoef-methods                     13.461  0.343  14.087
maskTracks-methods                13.529  0.259  14.286
plotIndividual_Tracks-methods     10.161  0.192  10.350
plotTrack-methods                  7.089  0.424   7.997
combineTrackll-methods             4.819  0.370 105.741
compare_RT_CDF-methods             4.729  0.283 108.417
* 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:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL sojourner
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Sat Oct 17 05:48:46 2020 
*********************************************** 
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 
  9.022   0.371   9.379 

Example timings

sojourner.Rcheck/sojourner-Ex.timings

nameusersystemelapsed
Dcoef-methods13.461 0.34314.087
combineTrackll-methods 4.819 0.370105.741
compareFolder-methods0.2460.0810.345
compare_RT_CDF-methods 4.729 0.283108.417
createTrackll-methods0.0620.0310.108
dispVariance-methods1.0120.0751.084
displacementCDF-methods1.9300.1722.116
dwellTime-methods0.6000.0980.717
exportTrackll-methods0.1330.1430.272
filterTrack-methods0.1320.0430.174
fitNormDistr-methods30.182 0.42830.618
fitRT-methods4.0110.1274.030
linkSkippedFrames-methods0.1970.1030.317
maskTracks-methods13.529 0.25914.286
mergeTracks-methods0.0510.0350.100
msd-methods3.1770.3873.597
plotIndividual_Tracks-methods10.161 0.19210.350
plotLocalizations_Density-methods39.195 0.20139.414
plotTrack-methods7.0890.4247.997
plotTrackOverlay_Dcoef-methods35.021 0.18135.246
sojournerGUI-methods000
squareDisp-methods0.1360.0920.225