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CHECK report for sojourner on merida1

This page was generated on 2020-04-15 12:49:53 -0400 (Wed, 15 Apr 2020).

Package 1629/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sojourner 1.0.2
Sojourner Developer
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/sojourner
Branch: RELEASE_3_10
Last Commit: 2c59633
Last Changed Date: 2020-04-05 19:54:57 -0400 (Sun, 05 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: sojourner
Version: 1.0.2
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_1.0.2.tar.gz
StartedAt: 2020-04-15 05:50:17 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:01:54 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 696.7 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_1.0.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/sojourner.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sojourner/DESCRIPTION’ ... OK
* this is package ‘sojourner’ version ‘1.0.2’
* 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 or elapsed time > 5s
                                    user system elapsed
plotLocalizations_Density-methods 54.501  0.383  56.169
plotTrackOverlay_Dcoef-methods    44.980  0.135  45.884
fitNormDistr-methods              38.313  0.299  39.078
plotTrack-methods                 20.091  0.415  21.056
maskTracks-methods                17.853  0.423  18.743
selComponentTracks-methods        16.715  0.183  17.056
Dcoef-methods                     15.887  0.237  16.249
plotIndividualTracks-methods      14.609  0.186  15.055
fitCDF-methods                    13.780  0.556  14.464
getCI-methods                     13.151  0.089  13.404
fitRT-methods                      6.007  0.773   5.643
compare_RT_CDF-methods             5.009  0.453 124.451
combineTrackll-methods             5.047  0.092 127.487
* 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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Wed Apr 15 06:01:46 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 
  9.579   0.522  10.228 

Example timings

sojourner.Rcheck/sojourner-Ex.timings

nameusersystemelapsed
Dcoef-methods15.887 0.23716.249
bootstrap-methods3.2190.0293.302
combineTrackll-methods 5.047 0.092127.487
compareFolder-methods0.1950.0120.207
compare_RT_CDF-methods 5.009 0.453124.451
createTrackll-methods0.2280.2810.073
densityMaskTracks-methods3.1360.5543.068
dispVariance-methods1.5310.0181.589
displacementCDF-methods3.2140.0993.374
dwellTime-methods0.5900.0070.600
exportTrackll-methods0.1120.0150.130
filterTrack-methods0.1320.0070.144
fitCDF-methods13.780 0.55614.464
fitNormDistr-methods38.313 0.29939.078
fitRT-methods6.0070.7735.643
getCI-methods13.151 0.08913.404
hmmTrackll-methods0.9290.0150.948
linkSkippedFrames-methods0.2010.0110.215
maskTracks-methods17.853 0.42318.743
mergeTracks-methods0.0720.0060.079
msd-methods4.0760.0404.230
plotIndividualTracks-methods14.609 0.18615.055
plotLocalizations_Density-methods54.501 0.38356.169
plotTrack-methods20.091 0.41521.056
plotTrackOverlay_Dcoef-methods44.980 0.13545.884
selComponentTracks-methods16.715 0.18317.056
sojournerGUI-methods000
squareDisp-methods0.2360.0110.251